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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A nexus modeling framework for assessing water scarcity solutions
Kahil, Taher ; Albiac, Jose ; Fischer, Guenther ; Strokal, Maryna ; Tramberend, Sylvia ; Greve, Peter ; Tang, Ting ; Burek, Peter ; Burtscher, Robert ; Wada, Yoshihide - \ 2019
Current Opinion in Environmental Sustainability 40 (2019). - ISSN 1877-3435 - p. 72 - 80.

Water scarcity has become a crucial environmental issue worldwide. It has increased substantially in the last decades in many parts of the world, and it is expected to further exacerbate in the future driven by socio-economic and climatic changes. Several solution options could be implemented to address this growing water scarcity, including supply and demand-side management options that span the water, energy, and agricultural sectors. However, these options involve tradeoffs among various societal objectives, especially when the interactions between these objectives are not properly considered. This paper provides a review of the impending water scarcity challenges and suggests assessing water scarcity solution options using a nexus modeling framework that links well-established sectoral-oriented models.

The impacts of the eco-environmental policy on grassland degradation and livestock production in Inner Mongolia, China : An empirical analysis based on the simultaneous equation model
Liu, Min ; Dries, Liesbeth ; Huang, Jikun ; Min, Shi ; Tang, Jianjun - \ 2019
Land Use Policy 88 (2019). - ISSN 0264-8377
Eco-environmental program - Grassland condition - Livestock production - Pastoral area - Simultaneous equation model

Grassland degradation has been deteriorating while the demands for meat products have been surging in China over the past few decades, leading to multiple policy initiatives to balance the grassland ecosystem and livestock production of the pastoral areas. This paper investigates the impacts of a prevailing eco-environmental program, i.e. Subsidy and Incentive System for Grassland Conservation (SISGC), in the pastoral areas of Inner Mongolia, on grassland condition and livestock production. The Normalized Difference Vegetation Index (NDVI), measured with remote sensing technology, is used to quantify grassland condition. Our empirical analysis was based on the data of 52 counties across a 15-year timespan covering 10 years before the introduction of SISGC and 5 years after its implementation. Simultaneous equation models are employed to study the mutual relationship between grassland condition and livestock production. The results suggest that the SISGC has significantly improved grassland condition. The total livestock population, especially the sheep population, has decreased due to SISGC, but the large animal population has not been impacted. On the other hand, growing meat prices (market demands) have resulted in an increase in the population of sheep, large animals, and total livestock. Implications are that the SISGC has been successful in preventing grassland degradation by controlling the increase in livestock population of the pastoral areas. Other policy initiatives need to consider how to prevent grassland degradation not only by controlling the livestock population given the soaring meat demand by the Chinese population and to address the high level of poverty among pastoralists.

Increasing nitrogen export to sea: A scenario analysis for the Indus River
Wang, Mengru ; Tang, Ting ; Burek, P. ; Havlík, Petr ; Krisztin, Tamás ; Kroeze, Carolien ; Leclère, D. ; Strokal, Maryna ; Wada, Yoshihide ; Wang, Yaoping ; Langan, S. - \ 2019
Science of the Total Environment 694 (2019). - ISSN 0048-9697
Indus River - Nitrogen sources - Representative concentration pathways - River export of nitrogen (N) - Shared socio-economic pathways - Sub-basins

The Indus River Basin faces severe water quality degradation because of nutrient enrichment from human activities. Excessive nutrients in tributaries are transported to the river mouth, causing coastal eutrophication. This situation may worsen in the future because of population growth, economic development, and climate change. This study aims at a better understanding of the magnitude and sources of current (2010) and future (2050) river export of total dissolved nitrogen (TDN) by the Indus River at the sub-basin scale. To do this, we implemented the MARINA 1.0 model (Model to Assess River Inputs of Nutrients to seAs). The model inputs for human activities (e.g., agriculture, land use) were mainly from the GLOBIOM (Global Biosphere Management Model) and EPIC (Environmental Policy Integrated Model) models. Model inputs for hydrology were from the Community WATer Model (CWATM). For 2050, three scenarios combining Shared Socio-economic Pathways (SSPs 1, 2 and 3) and Representative Concentration Pathways (RCPs 2.6 and 6.0) were selected. A novelty of this study is the sub-basin analysis of future N export by the Indus River for SSPs and RCPs. Result shows that river export of TDN by the Indus River will increase by a factor of 1.6–2 between 2010 and 2050 under the three scenarios. >90% of the dissolved N exported by the Indus River is from midstream sub-basins. Human waste is expected to be the major source, and contributes by 66–70% to river export of TDN in 2050 depending on the scenarios. Another important source is agriculture, which contributes by 21–29% to dissolved inorganic N export in 2050. Thus a combined reduction in both diffuse and point sources in the midstream sub-basins can be effective to reduce coastal water pollution by nutrients at the river mouth of Indus.

Immunogenicity in Rabbits of Virus-Like Particles from a Contemporary Rabbit Haemorrhagic Disease Virus Type 2 (GI.2/RHDV2/b) Isolated in The Netherlands
Miao, Qiuhong ; Qi, Ruibing ; Veldkamp, Luut ; Ijzer, Jooske ; Kik, Marja L. ; Zhu, Jie ; Tang, Aoxing ; Dong, Dandan ; Shi, Yonghong ; Oers, Monique M. van; Liu, Guangqing ; Pijlman, Gorben P. - \ 2019
Viruses 11 (2019)6. - ISSN 1999-4915
baculovirus expression - immunogenicity - insect cells - Netherlands - rabbit haemorrhagic disease virus 2 (GI.2/RHDV2/b) - virus-like particles - VP60

Rabbit haemorrhagic disease virus (RHDV) type 2 (GI.2/RHDV2/b) is an emerging pathogen in wild rabbits and in domestic rabbits vaccinated against RHDV (GI.1). Here we report the genome sequence of a contemporary RHDV2 isolate from the Netherlands and investigate the immunogenicity of virus-like particles (VLPs) produced in insect cells. RHDV2 RNA was isolated from the liver of a naturally infected wild rabbit and the complete viral genome sequence was assembled from sequenced RT-PCR products. Phylogenetic analysis based on the VP60 capsid gene demonstrated that the RHDV2 NL2016 isolate clustered with other contemporary RHDV2 strains. The VP60 gene was cloned in a baculovirus expression vector to produce VLPs in Sf9 insect cells. Density-gradient purified RHDV2 VLPs were visualized by transmission electron microscopy as spherical particles of around 30 nm in diameter with a morphology resembling authentic RHDV. Immunization of rabbits with RHDV2 VLPs resulted in high production of serum antibodies against VP60, and the production of cytokines (IFN-γ and IL-4) was significantly elevated in the immunized rabbits compared to the control group. The results demonstrate that the recombinant RHDV2 VLPs are highly immunogenic and may find applications in serological detection assays and might be further developed as a vaccine candidate to protect domestic rabbits against RHDV2 infection.

Impact of desertification on soil and plant nutrient stoichiometry in a desert grassland
An, Hui ; Tang, Zhuangsheng ; Keesstra, Saskia ; Shangguan, Zhouping - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Grassland degradation resulting from desertification often alters the carbon (C), nitrogen (N) and phosphorus (P) cycles within grassland ecosystems. To estimate the effects of desertification on the C, N, and P concentrations and C:N:P stoichiometry of plants and soil, we examined C, N, and P concentrations in plant tissues (leaves, roots and litter) and soil across five degrees of desertification in the desert grassland of Ningxia, China (control, light, moderate, severe and very severe desertification stages). The C, N, and P concentrations and C:N:P stoichiometry of the leaves, roots and litter differed among the different desertification stages. Desertification resulted in opposing trends between the leaf N concentration and leaf C:N ratio. With the exception of the very severe desertification stage, the leaf N:P ratio decreased over the process of grassland desertification. The soil C, N, and P concentrations and soil N:P and C:P ratios decreased significantly along the grassland desertification gradient. In contrast, the soil C:N ratio remained relatively stable during desertification (10.85 to 11.48). The results indicate that desertification is unfavourable to C and N fixation and has a negative effect on the ecosystem structure and function of desert grassland.

sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Intercropping cereals with faba bean reduces plant disease incidence regardless of fertilizer input; a meta-analysis
Zhang, Chaochun ; Dong, Yan ; Tang, Li ; Zheng, Yi ; Makowski, David ; Yu, Yang ; Zhang, Fusuo ; Werf, Wopke van der - \ 2019
European Journal of Plant Pathology 154 (2019)4. - ISSN 0929-1873 - p. 931 - 942.
Disease control - Intercropping - Meta-analysis - Nutrient management

Ecological intensification of agriculture calls for ecological mechanisms to replace anthropogenic inputs. Cereal/legume intercropping increases yields due to species complementarities, it produces high protein food and feed, and it reduces the need for artificial N fertilizer because legumes fix N biologically. In addition, intercropping has the potential to suppress plant diseases, but its efficacy for disease suppression in cereal/legume mixtures has not been well characterized quantitatively. Here we conducted meta-analysis to quantify the disease suppressive effect of intercropping cereals with legumes at different levels of N fertilizer. Intercropping reduced disease incidence (measured by the odds ratio of disease occurrence) by 45% on average. This reduction was significant (P < 0.01) for four out of six studied pathogens: yellow rust (Puccinia striiformis f.sp. tritici) and mildew (Blumeria graminis) in wheat (Triticum aestivum), and chocolate spot (Botrytis fabae) and Fusarium wilt (Fusarium oxysporum) in faba bean (Vicia faba). Disease reduction was marginally significant for yellow rust in barley (Puccinia striiformis f.sp. hordei) (P < 0.10) and not significant for bean rust (Uromyces fabae). The reduction in disease incidence was greatest during the early stages of epidemics. N fertilizer strongly increased the incidence of powdery mildew of wheat, but it did not affect the incidence of the other diseases and it did not affect the effectiveness of intercropping as a management strategy for disease control. While nitrogen input increased powdery mildew incidence in both sole and intercropped wheat, the incidence was lower in the intercropped than sole wheat at all levels of N input. The disease suppressive effect of intercropping on wheat powdery mildew or any other disease was not affected by the amount of nitrogen fertilizer. The results show that intercropping has a substantial and consistent effect on disease incidence in cereal/faba bean mixtures across studies, but is not sufficient to provide complete disease control. Intercropping is therefore best used as a component in an integrated approach for managing plant diseases.

State-of-the-art global models underestimate impacts from climate extremes
Schewe, Jacob ; Gosling, Simon N. ; Reyer, Christopher ; Zhao, Fang ; Ciais, Philippe ; Elliott, Joshua ; Francois, Louis ; Huber, Veronika ; Lotze, Heike K. ; Seneviratne, Sonia I. ; Vliet, Michelle T.H. Van; Vautard, Robert ; Wada, Yoshihide ; Breuer, Lutz ; Büchner, Matthias ; Carozza, David A. ; Chang, Jinfeng ; Coll, Marta ; Deryng, Delphine ; Wit, Allard De; Eddy, Tyler D. ; Folberth, Christian ; Frieler, Katja ; Friend, Andrew D. ; Gerten, Dieter ; Gudmundsson, Lukas ; Hanasaki, Naota ; Ito, Akihiko ; Khabarov, Nikolay ; Kim, Hyungjun ; Lawrence, Peter ; Morfopoulos, Catherine ; Müller, Christoph ; Müller Schmied, Hannes ; Orth, René ; Ostberg, Sebastian ; Pokhrel, Yadu ; Pugh, Thomas A.M. ; Sakurai, Gen ; Satoh, Yusuke ; Schmid, Erwin ; Stacke, Tobias ; Steenbeek, Jeroen ; Steinkamp, Jörg ; Tang, Qiuhong ; Tian, Hanqin ; Tittensor, Derek P. ; Volkholz, Jan ; Wang, Xuhui ; Warszawski, Lila - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
Effects of DEM resolution on the accuracy of gully maps in loess hilly areas
Dai, Wen ; Yang, Xin ; Na, Jiaming ; Li, Jingwei ; Brus, Dick ; Xiong, Liyang ; Tang, Guoan ; Huang, Xiaoli - \ 2019
Catena 177 (2019). - ISSN 0341-8162 - p. 114 - 125.
Accuracy assessment - DEM resolution - Gully mapping - The Loess Plateau of China - Uncertainty

Gully maps are important prerequisites for the study of gully erosion and land degradation. Many digital elevation model (DEM)-based methods have been proposed to enable automated gully mapping. However, the accuracy of a gully map derived from a DEM is inevitably affected by the DEM resolution. This study investigates the effects of DEM resolution on the accuracy of gully maps. A series of DEMs with resolutions of 0.1–10 m is employed to map gully areas. The effects of DEM resolution on the error in the mapped gully area and on the position error are described by regression models. The results from two catchments in hilly areas of the Loess Plateau in China are as follows. DEMs with resolutions of 0.5–2 m are the most suitable for gully mapping. Very high-resolution DEMs increase local position errors and over-predict the extents of gullies, whereas DEMs with coarser resolutions cause the downward migration of mapped gully boundaries, resulting in the under-prediction of gully areas. However, the effects of DEM resolution on gully maps are not constant but vary in space. The spatial disparities of the resolution effects are related to the gully morphology. The resolution effects on the gully maps in V-shaped gullies are stronger than those in U-shaped gullies. The findings of this study can be used to select a suitable DEM resolution for gully mapping in loess hilly areas and contribute to understanding the characterization of gullies by using DEMs.

Exocyst subunit Sec6 is positioned by microtubule overlaps in the moss phragmoplast prior to cell plate membrane arrival
Tang, Han ; Keijzer, Jeroen de; Overdijk, Elysa J.R. ; Sweep, Els ; Steentjes, Maikel ; Vermeer, Joop E.M. ; Janson, Marcel E. ; Ketelaar, Tijs - \ 2019
Journal of Cell Science 132 (2019)3. - ISSN 0021-9533
Cell plate - Exocyst - MAP65 - Microtubule - Phragmoplast - Physcomitrella patens

During plant cytokinesis a radially expanding membrane-enclosed cell plate is formed from fusing vesicles that compartmentalizes the cell in two. How fusion is spatially restricted to the site of cell plate formation is unknown. Aggregation of cell-plate membrane starts near regions of microtubule overlap within the bipolar phragmoplast apparatus of the moss Physcomitrella patens Since vesicle fusion generally requires coordination of vesicle tethering and subsequent fusion activity, we analyzed the subcellular localization of several subunits of the exocyst, a tethering complex active during plant cytokinesis. We found that the exocyst complex subunit Sec6 but not the Sec3 or Sec5 subunits localized to microtubule overlap regions in advance of cell plate construction in moss. Moreover, Sec6 exhibited a conserved physical interaction with an ortholog of the Sec1/Munc18 protein KEULE, an important regulator for cell-plate membrane vesicle fusion in Arabidopsis Recruitment of the P. patens protein KEULE and vesicles to the early cell plate was delayed upon Sec6 gene silencing. Our findings, thus, suggest that vesicle-vesicle fusion is, in part, enabled by a pool of exocyst subunits at microtubule overlaps, which is recruited independently of vesicle delivery.

Modeling phosphorus in rivers at the global scale : recent successes, remaining challenges, and near-term opportunities
Harrison, John A. ; Beusen, Arthur H.W. ; Fink, Gabriel ; Tang, Ting ; Strokal, Maryna ; Bouwman, Alexander F. ; Metson, Geneviève S. ; Vilmin, Lauriane - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 68 - 77.

Understanding and mitigating the effects of phosphorus (P) overenrichment of waters globally, including the evaluation of the global Sustainability Development Goals, requires the use of global models. Such models quantitatively link land use, global population growth and climate to aquatic nutrient loading and biogeochemical cycling. Here we describe, compare, and contrast the existing global models capable of predicting P transport by rivers at a global scale. We highlight important insights gained from the development and application of these models, and identify important near-term opportunities for model improvements as well as additional insight to be gained through new model analysis.

Bridging global, basin and local-scale water quality modeling towards enhancing water quality management worldwide
Tang, Ting ; Strokal, Maryna ; Vliet, Michelle T.H. van; Seuntjens, Piet ; Burek, Peter ; Kroeze, Carolien ; Langan, Simon ; Wada, Yoshihide - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 39 - 48.

Global water quality (WQ) modeling is an emerging field. In this article, we identify the missing linkages between global and basin/local-scale WQ models, and discuss the possibilities to fill these gaps. We argue that WQ models need stronger linkages across spatial scales. This would help to identify effective scale-specific WQ management options and contribute to future development of global WQ models. Two directions are proposed to improve the linkages: nested multiscale WQ modeling towards enhanced water management, and development of next-generation global WQ models based-on basin/local-scale mechanistic understanding. We highlight the need for better collaboration among WQ modelers and policy-makers in order to deliver responsive water policies and management strategies across scales.

Global multi-pollutant modelling of water quality: scientific challenges and future directions
Strokal, M. ; Spanier, Emiel ; Kroeze, C. ; Koelmans, A.A. ; Florke, Martina ; Franssen, W.H.P. ; Hofstra, N. ; Langan, Simon ; Ting, Tang ; Vliet, M.T.H. van; Wada, Yoshihide ; Wang, M. ; Wijnen, Jikke van; Williams, R. - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 116 - 125.
Assessing global water quality issues requires a multi-pollutant modelling approach. We discuss scientific challenges and future directions for such modeling. Multi-pollutant river models need to integrate information on sources of pollutants such as plastic debris, nutrients, chemicals, pathogens, their effects and possible solutions. In this paper, we first explain what we consider multi-pollutant modelling. Second, we discuss scientific challenges in multi-pollutant modelling relating to consistent model inputs, modelling approaches and model evaluation. Next, we illustrate the potential of global multi-pollutant modelling for hotspot analyses. We show hotspots of river pollution with microplastics, nutrients, triclosan and Cryptosporidium in many sub-basins of Europe, North America and South Asia. Finally, we reflect on future directions for multi-pollutant modelling, and for linking model results to policy-making.
Assessment of the genetic and clinical determinants of fracture risk : Genome wide association and mendelian randomisation study
Trajanoska, Katerina ; Morris, John A. ; Oei, Ling ; Zheng, Hou Feng ; Evans, David M. ; Kiel, Douglas P. ; Ohlsson, Claes ; Richards, J.B. ; Rivadeneira, Fernando ; Forgett, V. ; Leong, A. ; Ahmad, O.S. ; Laurin, C. ; Mokry, L.E. ; Ross, S. ; Elks, C.E. ; Bowden, J. ; Warrington, N.M. ; Kleinman, A. ; Willems, S.M. ; Wright, D. ; Day, F.R. ; Murray, A. ; Ruth, K.S. ; Tsilidis, K.K. ; Ackert-Bicknell, C.L. ; Bassett, J.H.D. ; Eerden, B.C.J. van der; Gautvik, K. ; Reppe, S. ; Williams, G.R. ; Medina-Gómez, C. ; Estrada, K. ; Amin, N. ; Enneman, A.W. ; Li, G. ; Liu, C.T. ; Liu, Y. ; Xiao, S.M. ; Lee, S.H. ; Koh, J.M. ; Tang, N.L.S. ; Cummings, S.R. ; Brown, M. ; Groot, L. de; Jukema, J.W. ; Lips, P. ; Meurs, J.B.J. van; Smith, A.V. ; Tian, S. - \ 2018
BMJ: British Medical Journal 362 (2018). - ISSN 0959-8146

Objectives To identify the genetic determinants of fracture risk and assess the role of 15 clinical risk factors on osteoporotic fracture risk. Design Meta-analysis of genome wide association studies (GWAS) and a two-sample mendelian randomisation approach. Setting 25 cohorts from Europe, United States, east Asia, and Australia with genome wide genotyping and fracture data. Participants A discovery set of 37 857 fracture cases and 227 116 controls; with replication in up to 147 200 fracture cases and 150 085 controls. Fracture cases were defined as individuals (>18 years old) who had fractures at any skeletal site confirmed by medical, radiological, or questionnaire reports. Instrumental variable analyses were performed to estimate effects of 15 selected clinical risk factors for fracture in a two-sample mendelian randomisation framework, using the largest previously published GWAS meta-analysis of each risk factor. Results Of 15 fracture associated loci identified, all were also associated with bone mineral density and mapped to genes clustering in pathways known to be critical to bone biology (eg, SOST, WNT16, and ESR1) or novel pathways (FAM210A, GRB10, and ETS2). Mendelian randomisation analyses showed a clear effect of bone mineral density on fracture risk. One standard deviation decrease in genetically determined bone mineral density of the femoral neck was associated with a 55% increase in fracture risk (odds ratio 1.55 (95% confidence interval 1.48 to 1.63; P=1.5×10'68). Hand grip strength was inversely associated with fracture risk, but this result was not significant after multiple testing correction. The remaining clinical risk factors (including vitamin D levels) showed no evidence for an effect on fracture. Conclusions This large scale GWAS meta-analysis for fracture identified 15 genetic determinants of fracture, all of which also influenced bone mineral density. Among the clinical risk factors for fracture assessed, only bone mineral density showed a major causal effect on fracture. Genetic predisposition to lower levels of vitamin D and estimated calcium intake from dairy sources were not associated with fracture risk.

Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses
Edger, Patrick P. ; Hall, Jocelyn C. ; Harkess, Alex ; Tang, Michelle ; Mohammadin, S. ; Schranz, M.E. ; Xiong, Zhiyong ; Leebens-Mack, James ; Meyers, Blake C. ; Sytsma, Kenneth J. ; Koch, Marcus A. ; Al-Shehbaz, Ihsan A. ; Pires, J.C. - \ 2018
Glucosinolates - Phylogenetics - Plastomes - polyploidy - Whole Genome Duplications
PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS - Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At‐α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At‐β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS - We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole‐genome sequencing projects.
Nucleolin mediates the internalization of rabbit hemorrhagic disease virus through clathrin-dependent endocytosis
Zhu, Jie ; Miao, Qiuhong ; Tang, Jingyu ; Wang, Xiaoxue ; Dong, Dandan ; Liu, Teng ; Qi, Ruibin ; Yang, Zhibiao ; Liu, Guangqing - \ 2018
PLoS Pathogens 14 (2018)10. - ISSN 1553-7366

Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae family and a highly lethal pathogen in rabbits. Although the cell receptor of RHDV has been identified, the mechanism underlying RHDV internalization remains unknown. In this study, the entry and post-internalization of RHDV into host cells were investigated using several biochemical inhibitors and RNA interference. Our data demonstrate that rabbit nucleolin (NCL) plays a key role in RHDV internalization. Further study revealed that NCL specifically interacts with the RHDV capsid protein (VP60) through its N-terminal residues (aa 285-318), and the exact position of the VP60 protein for the interaction with NCL is located in a highly conserved region (472Asp-Val-Asn474; DVN motif). Following competitive blocking of the interaction between NCL and VP60 with an artificial DVN peptide (RRTGDVNAAAGSTNGTQ), the internalization efficiency of the virus was markedly reduced. Moreover, NCL also interacts with the C-terminal residues of clathrin light chain A, which is an important component in clathrin-dependent endocytosis. In addition, the results of animal experiments also demonstrated that artificial DVN peptides protected most rabbits from RHDV infection. These findings demonstrate that NCL is involved in RHDV internalization through clathrin-dependent endocytosis.

Phase II study of ERC1671 plus bevacizumab versus bevacizumab plus placebo in recurrent glioblastoma : interim results and correlations with CD4+ T-lymphocyte counts
Bota, Daniela A. ; Chung, Jinah ; Dandekar, Manisha ; Carrillo, Jose A. ; Kong, Xiao Tang ; Fu, Beverly D. ; Hsu, Frank Pk ; Schönthal, Axel H. ; Hofman, Florence M. ; Chen, Thomas C. ; Zidovetzki, Raphael ; Pretto, Chrystel ; Strik, Ankie ; Schijns, Virgil E.J.C. ; Stathopoulos, Apostolos - \ 2018
JAMA Oncology 7 (2018)3. - ISSN 2374-2437 - p. CNS22 - CNS22.
allogeneic - autologous - bevacizumab - CD4+ T lymphocyte - ERC1671 - GBM - GBM vaccine - glioma surgery - immunotherapy

AIM: ERC1671 is an allogeneic/autologous therapeutic glioblastoma (GBM) vaccine - composed of whole, inactivated tumor cells mixed with tumor cell lysates derived from the patient and three GBM donors.

METHODS: In this double-blinded, randomized, Phase II study bevacizumab-naive patients with recurrent GBM were randomized to receive either ERC1671 in combination with granulocyte-macrophage colony-stimulating factor (GM-CSF) (Leukine® or sargramostim) and cyclophosphamide plus bevacizumab, or placebo plus bevacizumab. Interim results: Median overall survival (OS) of patients treated with ERC1671 plus bevacizumab was 12 months. In the placebo plus bevacizumab group, median OS was 7.5 months. The maximal CD4+ T-lymphocyte count correlated with OS in the ERC1671 but not in the placebo group.

CONCLUSION: The addition of ERC1671/GM-CSF/cyclophosphamide to bevacizumab resulted in a clinically meaningful survival benefit with minimal additional toxicity.

A Mediterranean-like dietary pattern with Vitamin D3 (10 μg/d) supplements reduced the rate of bone loss in older Europeans with osteoporosis at baseline : Results of a 1-y randomized controlled trial
Jennings, Amy ; Cashman, Kevin D. ; Gillings, Rachel ; Cassidy, Aedin ; Tang, Jonathan ; Fraser, William ; Dowling, Kirsten G. ; Hull, George L.J. ; Berendsen, Agnes A.M. ; Groot, Lisette C.P.G.M. de; Pietruszka, Barbara ; Wierzbicka, Elzbieta ; Ostan, Rita ; Bazzocchi, Alberto ; Battista, Giuseppe ; Caumon, Elodie ; Meunier, Nathalie ; Malpuech-Brugère, Corinne ; Franceschi, Claudio ; Santoro, Aurelia ; Fairweather-Tait, Susan J. - \ 2018
American Journal of Clinical Nutrition 108 (2018)3. - ISSN 0002-9165 - p. 633 - 640.
bone - Mediterranean diet - older adults - Osteoporosis - Vitamin D supplementation

Background: The Mediterranean diet (MD) is widely recommended for the prevention of chronic disease, but evidence for a beneficial effect on bone health is lacking. Objective: The aim of this study was to examine the effect of a Mediterranean-like dietary pattern [NU-AGE (New Dietary Strategies Addressing the Specific Needs of the Elderly Population for Healthy Aging in Europe)] on indexes of inflammation with a number of secondary endpoints, including bone mineral density (BMD) and biomarkers of bone and collagen degradation in a 1-y multicenter randomized controlled trial (RCT; NU-AGE) in elderly Europeans. Design: An RCT was undertaken across 5 European centers. Subjects in the intervention group consumed the NU-AGE diet for 1 y by receiving individually tailored dietary advice, coupled with supplies of foods including whole-grain pasta, olive oil, and a vitamin D3 supplement (10 μg/d). Participants in the control group were provided with leaflets on healthy eating available in their country. Results: A total of 1294 participants (mean ± SD age: 70.9 ±4.0 y; 44% male) were recruited to the study and 1142 completed the 1-y trial. The Mediterranean-like dietary pattern had no effect on BMD (site-specific or whole-body); the inclusion of compliance to the intervention in the statistical model did not change the findings. There was also no effect of the intervention on the urinary biomarkers free pyridinoline or free deoxypyridinoline. Serum 25-hydroxyvitamin D significantly increased and parathyroid hormone decreased (P < 0.001) in the MD compared with the control group. Subgroup analysis of individuals with osteoporosis at baseline (site-specific BMD T-score ≤ -2.5 SDs) showed that the MD attenuated the expected decline in femoral neck BMD (n = 24 and 30 in MD and control groups, respectively; P = 0.04) but had no effect on lumbar spine or whole-body BMD. Conclusions: A 1-y intervention of the Mediterranean-like diet together with vitamin D3 supplements (10 μg/d) had no effect on BMD in the normal age-related range, but it significantly reduced the rate of loss of bone at the femoral neck in individuals with osteoporosis. The NU-AGE trial is registered at clinicaltrials.gov as NCT01754012.

Therapeutic immunization against glioblastoma
Schijns, Virgil E.J.C. ; Pretto, Chrystel ; Strik, Anna M. ; Gloudemans-Rijkers, Rianne ; Deviller, Laurent ; Pierre, Denis ; Chung, Jinah ; Dandekar, Manisha ; Carrillo, Jose A. ; Kong, Xiao Tang ; Fu, Beverly D. ; Hsu, Frank P.K. ; Hofman, Florence M. ; Chen, Thomas C. ; Zidovetzki, Raphael ; Bota, Daniela A. ; Stathopoulos, Apostolos - \ 2018
International Journal of Molecular Sciences 19 (2018)9. - ISSN 1661-6596
Allogenic - Autologous - Brain tumor - Glioma tumor - Immunotherapy - Therapeutic vaccine
Glioblastoma is the most common form of brain cancer in adults that produces severe damage to the brain leading to a very poor survival prognosis. The standard of care for glioblastoma is usually surgery, as well as radiotherapy followed by systemic temozolomide chemotherapy, resulting in a median survival time of about 12 to 15 months. Despite these therapeutic efforts, the tumor returns in the vast majority of patients. When relapsing, statistics suggest an imminent death dependent on the size of the tumor, the Karnofsky Performance Status, and the tumor localization. Following the standard of care, the administration of Bevacizumab, inhibiting the growth of the tumor vasculature, is an approved medicinal treatment option approved in the United States, but not in the European Union, as well as the recently approved alternating electric fields (AEFs) generator NovoTTF/Optune. However, it is clear that regardless of the current treatment regimens, glioma patients continue to have dismal prognosis and novel treatments are urgently needed. Here, we describe different approaches of recently developed therapeutic glioma brain cancer vaccines, which stimulate the patient’s immune system to recognize tumor-associated antigens (TAA) on cancer cells, aiming to instruct the immune system to eventually attack and destroy the brain tumor cells, with minimal bystander damage to normal brain cells. These distinct immunotherapies may target particular glioma TAAs which are molecularly defined, but they may also target broad patient-derived tumor antigen preparations intentionally evoking a very broad polyclonal antitumor immune stimulation.
Water-and nitrogen-use efficiencies of hemp (Cannabis sativa L.) based on whole-canopy measurements and modeling
Tang, Kailei ; Fracasso, Alessandra ; Struik, Paul C. ; Yin, Xinyou ; Amaducci, Stefano - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Cannabis sativa L. - Canopy gas exchange - Hemp - Nitrogen use efficiency - Water use efficiency

Interest in hemp (Cannabis sativa L.) as a crop for the biobased economy is growing worldwide because hemp produces a high and valuable biomass while requiring low inputs. To understand the physiological basis of hemp’s resource-use efficiency, canopy gas exchange was assessed using a chamber technique on canopies exposed to a range of nitrogen (N) and water levels. Since canopy transpiration and carbon assimilation were very sensitive to variations in microclimate among canopy chambers, observations were adjusted for microclimatic differences using a physiological canopy model, with leaf-level parameters estimated for hemp from our previous study. Canopy photosynthetic water-use efficiency (PWUEc), defined as the ratio of gross canopy photosynthesis to canopy transpiration, ranged from 4.0 mmol CO2 (mol H2 O)−1 to 7.5 mmol CO2 (mol H2 O)−1. Canopy photosynthetic nitrogen-use efficiency (PNUEc), the ratio of the gross canopy photosynthesis to canopy leaf-N content, ranged from 0.3mol CO2 d−1 (g N)−1 to 0.7mol CO2 d−1 (g N)−1. The effect of N-input levels on PWUEc and PNUEc was largely determined by the N effect on canopy size or leaf area index (LAI), whereas the effect of water-input levels differed between short-and long-term stresses. The effect of short-term water stress was reflected by stomatal regulation. The long-term stress increased leaf senescence, decreased LAI but retained total canopy N content; however, the increased average leaf-N could not compensate for the lost LAI, leading to a decreased PNUEc. Although hemp is known as a resource-use efficient crop, its final biomass yield and nitrogen use efficiency may be restricted by water limitation during growth. Our results also suggest that crop models should take stress-induced senescence into account in addition to stomatal effects if crops experience a prolonged water stress during growth.

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