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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    D5.5 Impacts of future scenarios on the resilience of farming systems across the EU assessed with quantitative and qualitative methods
    Accatino, F. ; Paas, W.H. ; Herrera, H. ; Appel, Franziska ; Pinsard, C. ; Shi, Y. ; Schutz, L. ; Kopainsky, B. ; Bańkowska, K. ; Bijttebier, J. ; Black, J. ; Gavrilescu, C. ; Krupin, V. ; Manevska-Tasevska, G. ; Ollendorf, F. ; Peneva, M. ; Rommel, J. ; San Martín, C. ; Severini, S. ; Soriano, B. ; Valchovska, S. ; Vigani, M. ; Wauters, E. ; Zawalińska, K. ; Zinnanti, C. ; Meuwissen, Miranda ; Reidsma, P. - \ 2020
    SURE Farm - 307 p.
    Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection
    Bellone, Rachel ; Lequime, Sebastian ; Jupille, Henri ; Göertz, Giel P. ; Aubry, Fabien ; Mousson, Laurence ; Piorkowski, Géraldine ; Yen, Pei Shi ; Gabiane, Gaelle ; Vazeille, Marie ; Sakuntabhai, Anavaj ; Pijlman, Gorben P. ; Lamballerie, Xavier de; Lambrechts, Louis ; Failloux, Anna Bella - \ 2020
    Scientific Reports 10 (2020). - ISSN 2045-2322

    In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3′UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.

    Modeling the Contribution of Crops to Nitrogen Pollution in the Yangtze River
    Chen, Xuanjing ; Strokal, Maryna ; Kroeze, Carolien ; Supit, Iwan ; Wang, Mengru ; Ma, Lin ; Chen, Xinping ; Shi, Xiaojun - \ 2020
    Environmental Science and Technology 54 (2020)19. - ISSN 0013-936X - p. 11929 - 11939.

    Agriculture contributes considerably to nitrogen (N) inputs to the world's rivers. In this study, we aim to improve our understanding of the contribution of different crops to N inputs to rivers. To this end, we developed a new model system by linking the MARINA 2.0 (Model to Assess River Input of Nutrient to seAs) and WOFOST (WOrld FOod STudy) models. We applied this linked model system to the Yangtze as an illustrative example. The N inputs to crops in the Yangtze River basin showed large spatial variability. Our results indicate that approximately 6,000 Gg of N entered all rivers of the Yangtze basin from crop production as dissolved inorganic N (DIN) in 2012. Half of this amount is from the production of single rice, wheat, and vegetables, where synthetic fertilizers were largely applied. In general, animal manure contributes 12% to total DIN inputs to rivers. Three-quarters of manure-related DIN in rivers are from vegetable, fruit, and potato production. The contributions of crops to river pollution differ among sub-basins. For example, potato is an important source of DIN in rivers of some upstream sub-basins. Our results may help to prioritize the dominant crop sources for management to mitigate N pollution in the future.

    Pinggu Agricultural Innovation Campus : master plan and design report
    Boone, P. ; Buuren, M. van; Hartgerink, G. ; Hu, X. - \ 2020
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 3038) - 99
    Beijing Municipal Government has developed an initiative to stimulate agricultural innovation in cooperation with Wageningen University & Research. One of the first results of this cooperative effort is the design of the Agricultural Innovation Campus (AIC) at Yukou Town in Pinggu District on the north-eastern border of Beijing. A master plan has been designed for the AIC that synthesizes regional and local characteristics (landscape, land use, cultural heritage) with existing planning policies and regulations. Chinese planning tradition has been combined with a typical Dutch landscape approach and theory to take the best of these ‘two worlds’. State-of-the-art knowledge and innovations are introduced in the design process where relevant and possible. The key aim of the master plan is the design of an interconnected blue/green framework (the Green Dragon) that envelops three building zones for the development of agricultural institutes, laboratories and other companies. The Green Dragon will connect the AIC with surrounding recreational, ecological and agricultural areas. The Green Dragon will also form an important landscape element that provides several ecosystem services for Yukou Town. These ecosystem services include recreational facilities and opportunities to collect and store water. The master plan includes a set of rules for the development of buildings within the AIC (the Quality Book). The master plan also contains detailed designs for roads and road verges and designs for several pocket parks (the Gardens of Life). Recommendations for the organization and management of the AIC complete the project.
    2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
    Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
    Archives of Virology 165 (2020). - ISSN 0304-8608 - p. 3023 - 3072.

    In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

    Assessing long-term spatial movement of wheat area across China
    Fan, Lingling ; Chen, Shi ; Liang, Shefang ; Sun, Xiao ; Chen, Hao ; You, Liangzhi ; Wu, Wenbin ; Sun, Jing ; Yang, Peng - \ 2020
    Agricultural Systems 185 (2020). - ISSN 0308-521X
    China - Climate change - Driving factors - Geographical centroid - Wheat area

    In the context of climate change, assessing spatiotemporal dynamics of crop production is becoming an important component of food security, which is one of the United Nations Sustainable Development Goals. Wheat is a major staple food that is grown worldwide. Although many studies have analyzed wheat production, spatial analyses, particularly geographical centroid (GC) studies, are rare. The GC studies are of important scientific value and policy implications. This study aims to estimate the GC movement of wheat area (including winter and spring wheat) from 1949 to 2014 in China (the largest wheat-producing country). A centroid model was adopted to measure GC movements, and then a regression analysis was conducted to understand the driving factors of wheat area changes (as area changes lead to GC movement). Then multiple scenario analyses were built to study GC movement driven by climatic factors alone. The net GC movements of winter and spring wheat area were estimated at 31 km northwestward and 692 km southwestward from 1949 to 2014, with both displaying a turning point in their movement routes around 1970s (the GC of winter wheat area moved 89 km before 1970s and 66 km after 1970s; while the GC of spring wheat area moved 89 km before 1970s and 799 km after 1970s); furthermore, the major driving factor of winter wheat GC movement is a socioeconomic factor (i.e., expanded irrigation area) while that of spring wheat GC movement is a climatic factor (i.e., temperature) among the factors considered in this study. Our “climate only” scenarios highlighted that the impact of temperature on GC movement of winter wheat is more significant than that of precipitation. We assessed the spatiotemporal movement of wheat area to better understand its production dynamics in response to climate change and human activities. This study provides scientific evidence for policymakers and related stakeholders in China and other countries regarding food production patterns and planting decisions.

    Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus
    Hou, Wei ; Liu, Fei ; Poel, W.H.M. van der; Hulst, M.M. - \ 2020
    BioRxiv - 26 p.
    The transcriptional response in Vero cells (ATCC® CCL-81) infected with the coronavirus Porcine Epidemic Diarrhea Virus (PEDV) was measured by RNAseq analysis 4 and 6 hours after infection. Differential expressed genes (DEGs) in PEDV infected cells were compared to DEGs responding in Vero cells infected with Mammalian Orthoreovirus (MRV). Functional analysis of MRV and PEDV DEGs showed that MRV increased the expression level of several cytokines and chemokines (e.g. IL6, CXCL10, IL1A, CXCL8 [alias IL8]) and antiviral genes (e.g. IFI44, IFIT1, MX1, OASL), whereas for PEDV no enhanced expression was observed for these “hallmark” antiviral and immune effector genes. Pathway and Gene Ontology “enrichment analysis” revealed that PEDV infection did not stimulate expression of genes able to activate an acquired immune response, whereas MRV did so within 6h. Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). PEDV also down-regulated expression of Ectodysplasin A, a cytokine of the TNF-family able to activate the canonical NFKB-pathway responsible for transcription of inflammatory genes like IL1B, TNF, CXCL8 and PTGS2. The only 2 cytokine genes found up-regulated by PEDV were Cardiotrophin-1, an IL6-type cytokine with pleiotropic functions on different tissues and types of cells, and Endothelin 2, a neuroactive peptide with vasoconstrictive properties. Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and “synaptic clefts” between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The information in this study describing a “very early” response of epithelial cells to an infection with a coronavirus may provide pharmacologists, immunological and medical specialists additional insights in the underlying mechanisms of coronavirus associated severe clinical symptoms including those induced by SARS-CoV-2. This may help them to fine-tune therapeutic treatments and apply specific approved drugs to treat COVID-19 patients.
    Spatiotemporal dynamics of the northern limit of winter wheat in China using MODIS time series images
    Chen, Shi ; Fan, Lingling ; Liang, Shefang ; Chen, Hao ; Sun, Xiao ; Hu, Yanan ; Liu, Zhenhuan ; Sun, Jing ; Yang, Peng - \ 2020
    Remote Sensing 12 (2020)15. - ISSN 2072-4292
    Crop mapping - MODIS EVI2 - Northern China - Northern limit of winter wheat - Time series classification

    Studying the spatiotemporal changes of the northern limit of winter wheat (NLWW) in China is important to ensure regional food security and deal with the effects of climate change. Previous studies mainly used climate indicators to analyze the variation of the potential NLWW in different historical periods, while little attention has been paid to the actual migrations and changes of the NLWW. The objectives of the present study were three-fold: (i) to map the spatial distribution of winter wheat in northern China in 2001, 2007, 2014 and 2019; (ii) to extract the actual NLWW; and (iii) to quantitatively explore the dynamics of the NLWW. First, we adopted the "combining variations before and after estimated heading dates" method to map the winter wheat in northern China based on time series MODIS EVI2 data. Second, we used the kernel density estimation algorithm to extract the actual NLWW in four historical periods. Finally, the fishnet method was utilized to quantitatively analyze the direction and distance of the spatiotemporal changes of the NLWW. The results demonstrated that the NLWW has exhibited a marked fluctuating trend of migration southward, with a 37-km shift in latitude over the past 20 years. The elevation limit of winter wheat planting was around 1600 m; however, the centroid of winter wheat planting has shifted slowly to lower elevations. There was a gap between the actual NLWW and the potential NLWW. The reason for this gap was that the actual NLWW moved southward under the interacting effects of human activities and climate change, while the potential NLWW moved northward due to climate change. The results of this study are of great scientific value in the formulation of winter wheat planting strategies in climate-sensitive areas to respond to climate change and ensure food security.

    Pantothenic acid requirement of male White Pekin ducks from hatch to 21 days of age
    Tang, J. ; Zhang, B. ; Xue, M. ; Shi, W.B. ; Wu, Y.B. ; Feng, Y.L. ; Huang, W. ; Zhou, Z.K. ; Xie, M. ; Hou, S.S. - \ 2020
    Animal Feed Science and Technology 269 (2020). - ISSN 0377-8401
    Duck - Growth performance - Pantothenic acid - Requirement

    An experiment was conducted to determine the effects of dietary pantothenic acid levels on growth performance, carcass traits, and pantothenic acid status of male White Pekin ducks from hatch to 21 days of age, and to evaluate the requirement of this B-vitamin for starter ducks. Different levels pantothenic acid (0, 2, 4, 6, 8, 10, and 20 mg/kg) were supplemented to corn-soy isolate protein basal diet to produce 7 dietary treatments with different analyzed total pantothenic acid levels (4.65, 6.80, 8.39, 9.98, 12.04, 13.70, and 22.50 mg/kg). A total of 448 one-day-old male White Pekin ducks were allotted to 7 dietary treatments with 8 replicate pens of 8 birds per pen. At 21 days of age, body weight, average daily weight gain (ADG), average daily feed intake (ADFI), gain to feed ratio (G/F), liver pantothenic acid content, as well as percentage yield of breast meat, leg meat, and abdominal fat were examined. The growth depression, exudate on eyelids, dermatosis, poor feathering, and 100 % of mortality were observed in the ducks fed the basal diet without pantothenic acid supplementation, and these adverse effects were ameliorated by pantothenic acid supplementation. The starter ducks on the diet containing 6.80 mg/kg of pantothenic acid had a lower parameter profile of body weight, ADG, ADFI, G/F, breast meat yield, abdominal fat yield, and liver pantothenic acid content compared to the birds fed the diets with higher levels of pantothenic acid (P < 0.05). And these criteria showed a linear or quadratic response to increasing dietary pantothenic acid levels (P < 0.05). The pantothenic acid requirements (based on dietary total pantothenic acid) of starter male White Pekin ducks for body weight, ADG, ADFI, G/F, and liver pantothenic acid content were 8.95, 8.95, 8.59, 9.56, and 10.22 mg/kg based on broken-line regression, while were 10.04, 10.05, 9.18, 11.01, and 11.24 mg/kg based on quadratic broken-line regression, respectively.

    Study on evaluation of regional cultivated land quality based on resource-asset-capital attributes and its spatial mechanism
    Shi, Yunyang ; Duan, Wenkai ; Fleskens, Luuk ; Li, Mu ; Hao, Jinmin - \ 2020
    Applied Geography 125 (2020). - ISSN 0143-6228
    Cultivated land quality evaluation (CQE) - Quzhou county - Resource-asset-capital attributes - Spatial mechanism - Spatial pattern

    In the context of rapid urbanization, changes in human demand and agricultural technology progress have deeply expanded the cultivated land attribute dimensions. Thus, evaluating the regional cultivated land quality with different attributes and studying its spatial mechanism is of great theoretical and practical significance. Based on the analytical framework of resource-asset-capital attributes of cultivated land quality, multi-source data were used to evaluate the quality indexes of 5332 cultivated land plots with different attributes in Quzhou county. Then, some spatial analysis models were applied to explore the spatial distribution features of these three quality attributes. The results showed that 1) in the analytical framework of resource-asset-capital attributes of regional cultivated land quality, the resource quality meant the natural production capacity of cultivated land. However, asset quality and capital quality indicate the ability of cultivated land to bring wealth, rights and surplus profits to humans. 2) Considerable gaps existed in the evaluation results of different quality attributes in Quzhou. The proportions of good, medium, and lower quality cultivated land in the total cultivated land area of resource quality was 40.35%, 23.78% and 35.87%, the proportions were 40.35%, 23.78% and 35.87% in the asset quality area and 30.87%, 28.48% and 40.65% in the capital quality area, respectively. 3) The spatial patterns of the three quality attributes all showed obvious positive autocorrelation, with numerical values of 0.705 3, 0.846 4 and. 0.969 0 in resource, asset and capital quality, respectively. The cultivated land quality in southwest Quzhou was relatively high, while that in central Quzhou was poor. 4) The distribution of cultivated land resource quality was more even than that of asset and capital quality, while the spatial structures of asset and capital quality have better stability and continuity than that of resource quality. According to the different quality attribute characteristics, various suggestions were provided to improve the efficiency of cultivated land quality construction and to promote sustainable development in Quzhou county.

    Acute porcine epidemic diarrhea virus infection reshapes the intestinal microbiota
    Yang, Shanshan ; Li, Yang ; Wang, Bin ; Yang, Ning ; Huang, Xin ; Chen, Qingbo ; Geng, Shuxian ; Zhou, Yawei ; Shi, Han ; Wang, Leyi ; Brugman, Sylvia ; Savelkoul, Huub ; Liu, Guangliang - \ 2020
    Virology 548 (2020). - ISSN 0042-6822 - p. 200 - 212.
    Intestinal microbiota - Pathogenicity - Porcine epidemic diarrhea virus

    The intestinal microbiota is crucial to intestinal homeostasis. Porcine epidemic diarrhea virus (PEDV) is high pathogenic to intestines, causing diarrhea, even death in piglets. To investigate the detailed relationship between PEDV infection and intestinal microbiota, the composition and distribution of intestinal microbiota from pigs were first analyzed using 16S rRNA sequencing technology. The results demonstrated that the composition and distribution of microbes in different intestinal segments were quite similar between 1-week-old and 2-week-old piglets but different from 4-week-old (weaned) piglets. Then piglets at different ages were inoculated with PEDV. The results showed that the 1-week-old piglets exhibited the most severe pathogenicity comparing to the other age groups. Further investigations indicated that Lactobacillus, Escherichia coli, and Lactococcus in the intestinal microbiota of piglets were significantly changed by PEDV infection. These results strengthen our understanding of viruses influencing intestinal microbes and remind us of the potential association between PEDV and intestinal microbes.

    Morphological and reproductive responses of coastal pioneer sedge vegetation to inundation intensity
    Li, Shi Hua ; Ge, Zhen Ming ; Tan, Li Shan ; Hu, Meng Yao ; Li, Ya Lei ; Li, Xiu Zhen ; Ysebaert, Tom - \ 2020
    Estuarine Coastal and Shelf Science 244 (2020). - ISSN 0272-7714
    Intraspecific traits - Inundation stresses - Phenotypic plasticity - Pioneer plant - Reproductive strategy - Salt marsh

    Coastal plants have unique adaptability to cope with strong hydrological stresses in tidal wetlands. A fundamental understanding of the establishment and maintenance of coastal plants is needed for conservation and restoration. In the Yangtze Estuary, the plasticity of the morphological and reproductive traits of a pioneer Scirpus species (sedge), in terms of phenotypic growth, biomass allocation, and sexual and asexual reproductive traits, was investigated with increasing flooding intensity (elevation gradient) in a tidal flat. The varying response extents (thresholds) of plant zonation and morphological and reproductive traits to multiscale environmental heterogeneity were also assessed. Our results showed that plant colonization and performance at coastal frontiers are sensitive to the microtopography of elevation and reflect the ecological adaptability at both the landscape and individual scales. Sedge species typically exhibit morphological and reproductive flexibility across the inundation intensity. The plants allocated more biomass to belowground tissues in response to decreasing elevation. The elevation thresholds for the yield of reproductive organs were higher (2.38–2.50 m based on the local Wusong datum) than those for morphology (2.05–2.14 m). The thresholds for the yield of asexual reproductive organs shifted to a lower elevation by approximately 0.15 m relative to that of the sexual reproductive organs. The increasing corm: spike ratios of plants with longer inundation durations also indicated this reproductive plasticity. This study revealed that the combination of morphological and reproductive responses of pioneer sedges contributed to survival and colonization at the foremost coastal flat. Our results are useful for developing restoration strategies for the native Scirpus species on China's coast.

    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    Effectiveness of re-vegetated forest and grassland on soil erosion control in the semi-arid Loess Plateau
    Liu, Yi Fan ; Liu, Yu ; Shi, Zhi Hua ; López-Vicente, Manuel ; Wu, Gao Lin - \ 2020
    Catena 195 (2020). - ISSN 0341-8162 - 6 p.
    Afforestation policy - Re-vegetation type - Runoff reduction benefit - Sediment reduction benefit - Understory grasses

    Afforestation reduces soil loss and minimizes landslide risk worldwide, but little is known on the effectiveness of afforestation policies to control soil erosion with different vegetation types in semi-arid areas. Understanding the effectiveness of distinct re-vegetation types under different physiographic conditions (slope gradient, percentage of vegetation cover and rainfall depth) is essential for better policy formulation. This study examines the benefits of soil erosion control in forests and grasslands using published data. This analysis proves that the benefits of vegetation restoration increase with increasing the vegetation cover and tend to be stable when the coverage exceeds 60%. The benefits on sediment yield reduction are more sensitive (vs. runoff reduction benefit) to rainfall intensity. Regarding slopes and soil erosion control, the highest efficiencies appear in forests on 20–25° slopes and in grasslands on 15–20° slopes. Grasslands can effectively reduce soil erosion, as well as forests with understory grasses. For long-term restoration, a 60% vegetation cover maximizes the benefits of reducing soil erosion and maintaining enough soil water supply that prevents possible soil drought. We propose that future afforestation policies should evaluate in advance the appropriate re-vegetation type; meanwhile, suitable vegetation coverage and local physiographic conditions should be considered. Importantly, promotion of grassland and preservation of forest understory grasses must be enforced in land use policies when considering afforestation to minimize soil erosion. We suggest further research to quantify the efficiency of understory vegetation on soil erosion control, which might provide scientific and practical guidance for afforestation policy in semi-arid areas.

    Replication Data for: The stove, dome, and umbrella effects of pollutant aerosol on the planetary boundary layer: a large-eddy simulation and observations in Beijing
    Ma, Yongjing ; Ye, Jianhuai ; Xin, Jinyuan ; Zhang, Wenyu ; Vila-Guerau de Arellano, Jordi ; Zhao, Dandan ; Dai, Lindong ; Ma, Yongxiang ; Wu, Xiaoyan ; Xia, Xiangao ; Tang, Guiqian ; Shen, Pengke ; Lei, Yali ; Martin, Scot T. - \ 2020
    Harvard University
    Dataset for campaign observations and LES input file for the reference case.
    Effect of dietary fiber fermentation on short-chain fatty acid production and microbial composition in vitro
    Bai, Yu ; Zhao, Jin Biao ; Tao, Shi Yu ; Zhou, Xing Jian ; Pi, Yu ; Gerrits, Walter J.J. ; Johnston, Lee J. ; Zhang, Shi Yi ; Yang, Hong Jian ; Liu, Ling ; Zhang, Shuai ; Wang, Jun Jun - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)11. - ISSN 0022-5142 - p. 4282 - 4291.
    fiber-rich co-products - gas production - in vitro fermentation - microbial community - short chain fatty acid

    BACKGROUND: The efficient utilization of fiber-rich co-products is important for optimizing feed resource utilization and animal health. This study was conducted to evaluate the fermentation characteristics of fiber-rich co-products, which had equal quantities of total dietary fiber (TDF), at different time points using batch in vitro methods. It considered their gas production, short-chain fatty acid (SCFA) production, and microbial composition. RESULTS: The fermentation of wheat bran (WB) and oat bran (OB) showed higher and faster (P < 0.05) gas and SCFA production than corn bran (CB), sugar beet pulp (SBP), and soybean hulls (SH). The α-diversity was higher in the CB, SBP, and SH groups than in the WB and OB groups (P < 0.05). At the phylum level, OB and WB fermentation showed lower (P < 0.05) relative abundance of Actinobacteria than the CB, SBP, and SH groups. At the genus level, OB and WB fermentation increased the Enterococcus population in comparison with the CB, SBP, and SH groups, whereas CB and SBP fermentation improved the relative abundance of the Christensenellaceae R-7 group more than the WB, OB, and SH groups (P < 0.05). CONCLUSION: Overall, WB and OB were rapidly fermented by fecal microbiota, in contrast with SBP, SH, and CB. Fermentation of different fiber-rich co-products with an equal TDF content gives different responses in terms of microbial composition and SCFA production due to variations in their physicochemical properties and molecular structure.

    Impacts of nitrogen fertilizer type and application rate on soil acidification rate under a wheat-maize double cropping system
    Hao, Tianxiang ; Zhu, Qichao ; Zeng, Mufan ; Shen, Jianbo ; Shi, Xiaojun ; Liu, Xuejun ; Zhang, Fusuo ; Vries, Wim de - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Ammonium chloride - Cropland - Soil acidification - Soil pH - Urea

    Nitrogen (N) fertilizer-induced soil acidification in Chinese croplands is well-known, but insight in the impacts of different N fertilizer management approaches (fertilizer type and rate) on soil acidification rates is very limited. Here, we conducted a field experiment on a moderate acid soil to quantify soil acidification rates in response to N fertilization by different fertilizer types and N rates through monitoring the fate of elements (mainly nutrients) related to H+ production and consumption. Two N fertilizer types (urea and NH4Cl) and three N rates (control, optimized and conventional, 0/120/240 kg N ha−1 for wheat, 0/160/320 kg N ha−1 for maize) were included. Nitrogen addition led to an average H+ production of 4.0, 8.7, 11.4, 29.7 and 52.6 keq ha−1 yr−1, respectively, for the control, optimized urea, conventional urea, optimized NH4Cl and conventional NH4Cl plots. This was accompanied with a decline in soil base saturation of 1–10% and in soil pH of 0.1–0.7 units in the topsoil (0–20 cm). Removal of base cations by crop harvesting and N transformations contributed ~70% and ~20% to the H+ production in the urea treated plots, being ~20% and ~75% in the NH4Cl treated plots, respectively. The large NH4+ input via fertilization in the NH4Cl treated plots strongly enhanced the H+ production induced by N transformations. The low contribution of N transformations to the H+ production in the urea treated plots was due to the limited NO3 leaching, induced by the high N losses to air caused by denitrification. Increased N addition by urea, however, strongly increased H+ production by enhanced plant uptake of base cations, mainly due to a large potassium uptake in straw. Our results highlight the important role of optimizing fertilizer form and N rate as well as straw return to the field in alleviating soil acidification.

    Evaluation of in vitro models of stem cell-derived cardiomyocytes to screen for potential cardiotoxicity of chemicals
    Shi, Miaoying ; Tien, Nguyen T. ; Haan, Laura de; Louisse, Jochem ; Rietjens, Ivonne M.C.M. ; Bouwmeester, Hans - \ 2020
    Toxicology in Vitro 67 (2020). - ISSN 0887-2333
    Cardiotoxicity - Clinical data - Human induced pluripotent stem cell-derived cardiomyocytes - Mouse embryonic stem cell-derived cardiomyocytes - Multi-electrode array

    Cardiotoxicity is an important toxicological endpoint for chemical and drug safety assessment. The present study aims to evaluate two stemcell-based in vitro models for cardiotoxicity screening of chemicals. Eleven model compounds were used to evaluate responses of mouse embryonic stem cell-derived cardiomyocytes (mESC-CMs) using beating arrest as a readout and the analysis of electrophysiological parameters measured with a multi-electrode array (MEA) platform of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Results revealed that the hiPSC-CM MEA assay responded to all compounds. The mESC-CM beating arrest assay was not responsive to potassium channel blockers and showed a lower sensitivity to sodium channel blockers and Na+/K+ ATPase inhibitors compared to the hiPSC-CM MEA assay. Calcium channel blockers and a β-adrenergic receptor agonist showed comparable potencies in both models. The in vitro response concentrations from hiPSC-CMs were highly concordant with human effective serum concentrations of potassium and sodium channel blockers. It is concluded that both in vitro models enable the cardiotoxicity screening with different applicability domains. The mESC-CM beating arrest assay may be used as a first step in a tiered approach while the hiPSC-CM MEA assay may be the best starting point for quantitative in vitro to in vivo extrapolations.

    Integrating in vitro data and physiologically based kinetic modeling-facilitated reverse dosimetry to predict human cardiotoxicity of methadone
    Shi, Miaoying ; Bouwmeester, Hans ; Rietjens, Ivonne M.C.M. ; Strikwold, Marije - \ 2020
    Archives of Toxicology 94 (2020). - ISSN 0340-5761 - p. 2809 - 2827.
    Cardiac electrophysiology - Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) - Methadone - Physiologically based kinetic (PBK) modeling - Quantitative in vitro to in vivo extrapolation (QIVIVE) - Reverse dosimetry

    Development of novel testing strategies to detect adverse human health effects is of interest to replace in vivo-based drug and chemical safety testing. The aim of the present study was to investigate whether physiologically based kinetic (PBK) modeling-facilitated conversion of in vitro toxicity data is an adequate approach to predict in vivo cardiotoxicity in humans. To enable evaluation of predictions made, methadone was selected as the model compound, being a compound for which data on both kinetics and cardiotoxicity in humans are available. A PBK model for methadone in humans was developed and evaluated against available kinetic data presenting an adequate match. Use of the developed PBK model to convert concentration–response curves for the effect of methadone on human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) in the so-called multi electrode array (MEA) assay resulted in predictions for in vivo dose–response curves for methadone-induced cardiotoxicity that matched the available in vivo data. The results also revealed differences in protein plasma binding of methadone to be a potential factor underlying variation between individuals with respect to sensitivity towards the cardiotoxic effects of methadone. The present study provides a proof-of-principle of using PBK modeling-based reverse dosimetry of in vitro data for the prediction of cardiotoxicity in humans, providing a novel testing strategy in cardiac safety studies.

    RIdeogram : Drawing SVG graphics to visualize and map genome-wide data on the idiograms
    Hao, Zhaodong ; Lv, Dekang ; Ge, Ying ; Shi, Jisen ; Weijers, Dolf ; Yu, Guangchuang ; Chen, Jinhui - \ 2020
    PeerJ Computer Science 6 (2020). - ISSN 2376-5992 - p. 1 - 11.
    Chromosome - Data visualization - Genome - Idiogram - R package

    Background. Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way to map and visualize the genome-wide information, such asGCcontent, gene and repeat density, DNA methylation distribution, genomic synteny, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly, or have limited application scenarios. As more and more non-model species are sequenced with chromosome-level assembly being available, tools that can generate idiograms for a broad range of species and be capable of visualizing more data types are needed to help better understanding fundamental genome characteristics. Results. The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. Conclusion. The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.

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