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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    Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history
    Schneijderberg, Martinus ; Cheng, Xu ; Franken, Carolien ; Hollander, Mattias de; Velzen, Robin van; Schmitz, Lucas ; Heinen, Robin ; Geurts, Rene ; Putten, Wim H. van der; Bezemer, Martijn T. ; Bisseling, Ton - \ 2020
    ISME Journal (2020). - ISSN 1751-7362

    As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species’ average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

    Intercomparison of Large-Eddy Simulations of the Antarctic Boundary Layer for Very Stable Stratification
    Couvreux, Fleur ; Bazile, Eric ; Rodier, Quentin ; Maronga, Björn ; Matheou, Georgios ; Chinita, Maria J. ; Edwards, John ; Stratum, Bart J.H. van; Heerwaarden, Chiel C. van; Huang, Jing ; Moene, Arnold F. ; Cheng, Anning ; Fuka, Vladimir ; Basu, Sukanta ; Bou-Zeid, Elie ; Canut, Guylaine ; Vignon, Etienne - \ 2020
    Boundary-Layer Meteorology 176 (2020)3. - ISSN 0006-8314 - p. 369 - 400.
    Antarctica - Dome C - Large-eddy simulation - Parametrization - Stable boundary layer - Subgrid turbulence parametrization

    In polar regions, where the boundary layer is often stably stratified, atmospheric models produce large biases depending on the boundary-layer parametrizations and the parametrization of the exchange of energy at the surface. This model intercomparison focuses on the very stable stratification encountered over the Antarctic Plateau in 2009. Here, we analyze results from 10 large-eddy-simulation (LES) codes for different spatial resolutions over 24 consecutive hours, and compare them with observations acquired at the Concordia Research Station during summer. This is a challenging exercise for such simulations since they need to reproduce both the 300-m-deep convective boundary layer and the very thin stable boundary layer characterized by a strong vertical temperature gradient (10 K difference over the lowest 20 m) when the sun is low over the horizon. A large variability in surface fluxes among the different models is highlighted. The LES models correctly reproduce the convective boundary layer in terms of mean profiles and turbulent characteristics but display more spread during stable conditions, which is largely reduced by increasing the horizontal and vertical resolutions in additional simulations focusing only on the stable period. This highlights the fact that very fine resolution is needed to represent such conditions. Complementary sensitivity studies are conducted regarding the roughness length, the subgrid-scale turbulence closure as well as the resolution and domain size. While we find little dependence on the surface-flux parametrization, the results indicate a pronounced sensitivity to both the roughness length and the turbulence closure.

    A systems analysis of microplastic pollution in Laizhou Bay, China
    Teng, Jia ; Zhao, Jianmin ; Zhang, C. ; Cheng, Bo ; Koelmans, A.A. ; Wu, Di ; Gao, Meng ; Sun, Xiyan ; Wang, Qing - \ 2020
    Science of the Total Environment 745 (2020). - ISSN 0048-9697
    Microplastic contamination is attracting increasing attention worldwide. In this study, the patterns of microplastic contamination in surface water and sediment from 58 sites, and living fish from 31 sites were investigated in a semi-closed bay (Laizhou Bay, China). Microplastics in Laizhou Bay were pervasively distributed, particularly in the form of fibers. Microplastic abundance exhibited no significant differences among regions in either surface waters or sediments, indicating multiple sources of microplastics pollution in the bay. Spatial hotspot (Getis-Ord Gi*) analysis demonstrated that microplastic pollution was mainly concentrated in the Laizhou-Weifang area, which in turn was mainly affected by ocean current dynamics. Although the spatial distribution of microplastics in sediments was different from surface water, it was also affected by geology, hydrogeology, and anthropogenic activities. The most common polymer in the surface waters was polyethylene terephthalate (PET), while cellophane (CP) was the most frequently observed polymer in sediment, suggesting different sinking behaviors of these microplastics. The proportion of low-density microplastics (PE and PP) in surface water was approximately 19.9%, but these microplastics accounted for only approximately 1.7% in the sediment, suggesting that low-density microplastic particles preferentially migrate to open sea. There were significant differences in shape, size and polymer type of the microplastics among surface water, sediment and biota (p < 0.05). Cluster analysis suggested that the Gudong, Yellow River Estuary and Laizhou-Weifang regions are three sources of microplastics, which might originate from river input, plastic recycling and marine raft aquaculture. Furthermore, microplastic particle diversity was greater in sediment at offshore sites, suggesting that these sites receive microplastics from multiple sources. Our results characterize the microplastic pollution pattern, clarify the possible transfer mechanisms between different environmental media, and will provide important information for risk evaluation and pollution control in this area.
    Increasing yield and nitrogen use efficiency of spring maize in Northeast China through ecological intensification management
    Xu, Rui ; Xu, Rui ; Xu, Xin Peng ; Hou, Yun Peng ; Zhang, Jia Jia ; Huang, Shao Hui ; Ding, Wen Cheng ; Liu, Ying Xia ; He, Ping - \ 2020
    Journal of Plant Nutrition and Fertilizers 26 (2020)3. - ISSN 1008-505X - p. 461 - 471.
    Ecological intensive nutrient management - Nitrogen balance - Nitrogen use efficiency - Spring maize

    [Objectives] In view of the problems in ecological environment and sustainable agricultural development caused by excessive and unreasonable fertilizer application in spring maize production in China, the effects of ecological intensive nutrient management on spring maize yield, nitrogen use efficiency and nitrogen balance in Northeast China were studied in order to make full use of resources, increase production efficiency and ensure national food security scientifically and rationally. [Methods] A long-term experiment was conducted from 2009 to 2017 in Gongzhuling City, Jilin Province. Two factors of split plot were designed in the experiment. The main plot was two fertilization managements: the ecological intensive nutrient management (EI) and farmer practice management (FP). The sub-plot was three N application methods, including no N application treatment (N0), N application in two of three years (N2/3) and in three years (N3/3). In EI treatment, P2O575 kg/hm2, K2O 90 kg/hm2, S 30 kg/hm2, Zn 5 kg/hm2and 1/4 of N (180 kg/hm2in 2009-2014, 200 kg/hm2in 2015-2017) applied as basal, 1/2 N top dressed at jointing stage and 1/4 N at tassel stage. In the treatment of FP, N 251 kg/hm2, P2O5145 kg/hm2and K2O 100 kg/hm2were applied once as basal. The yield, N uptake and accumulation of maize and the balance of soil N were investigated. [Results] In N0 treatment, the yield and N uptake showed a downward trend since 2010. In N2/3 treatment, the yield and N uptake decreased in the year without N application, and increased to the level of N3/3 treatment in the case of N application in the following year. In EI treatment, the average yield of N3/3 treatment was 11505 kg/hm2in 9 years, while that of FP treatment was significantly lower, which was 10764 kg/hm2. Compared with FP treatment, EI treatment significantly increased nitrogen agronomic efficiency (AEN), recovery efficiency (REN) and partial factor productivity (PFPN) by 47.4%, 39.6% and 43.8%, respectively. The residual N and apparent loss of N in EI treatment were 49.2% and 63.9% lower than those in FP treatment, respectively. [Conclusions] Ecological intensive nutrient management, including right fertilization rate and time, and suitable cultivar and plant density, is proved to be effective in increasing spring maize yield and N utilization, reducing residue and apparent loss of N in soil. The experiment also confirms that continuous appropriate N fertilizer application is essential for high and stable yield of maize in Northeast China.

    Protein A-mesoporous silica composites for chromatographic purification of immunoglobulin G
    Huang, Si ; Cheng, Si Yuan ; Zhang, Shu Yuan ; Yan, Yi Lun ; Cai, Song Liang ; Li, Xin Le ; Zheng, Sheng Run ; Fan, Jun ; Zhang, Wei Guang - \ 2020
    New Journal of Chemistry 44 (2020)19. - ISSN 1144-0546 - p. 7884 - 7890.

    The development of a robust and efficient stationary phase for chromatographic biopharmaceutical purification is of prime importance but remains challenging. Herein, we have developed a series of protein A-mesoporous silica composites for the first time by covalently coupling protein A with the tagged carbonyl imidazole moieties in the column, which constitutes a facile and efficient route for the preparation of protein A immunoaffinity materials. The resultant composites are employed as the stationary phase for chromatographic purification of immunoglobulin G (IgG). The effect of silica's pore size and coupled protein A on the antibody purification is systematically investigated. When the pore size of silica increased from 100 to 1000 Å, the amount of coupled protein A decreased, and the surface coverage on the silica significantly improved, accompanied by an increase in the amount of purified rabbit IgG. With an increasing coupled protein A, the surface coverage increased at first and decreased subsequently, which shows a similar trend to the amount of purified IgG and specific activity. When practically implemented for purifying several immunoglobulins that are central for commercial ELISA Kits, the protein A-mesoporous silica composite exhibited superior performance compared to the GE-Mabselcetxtra rProtein A column, particularly in the purification of immunoglobulin M (IgM), which cannot be realized by the GE-Mabselcetxtra rProtein A column. This study sheds new light on the rational development of protein-affinity chromatography for biopharmaceutical purification.

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

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

    In vivo analysis of formin dynamics in the moss P. patens reveals functional class diversification
    Gisbergen, Peter Van; Wu, Shu Zon ; Cheng, Xiaohang ; Pattavina, Kelli A. ; Bezanilla, Magdalena - \ 2020
    Journal of Cell Science 133 (2020)3. - ISSN 0021-9533
    Actin - Endocytosis - Exocytosis - Formin - Microtubule - Plant

    Formins are actin regulators critical for diverse processes across eukaryotes. With many formins in plants and animals, it has been challenging to determine formin function in vivo. We found that the phylogenetically distinct class I integral membrane formins (denoted For1) from the moss P. patens enrich at sites of membrane turnover, with For1D more tightly associated with the plasma membrane than For1A. To probe formin function, we generated formin-null lines with greatly reduced formin complexity. We found that For1A and For1D help to anchor actin near the cell apex, with For1A contributing to formation of cytosolic actin, while For1D contributes to plasma membrane-associated actin. At the cortex, For1A and For1D localized to motile puncta and differentially impacted actin dynamics. We found that class I cortical formin mobility depended on microtubules and only moderately on actin, whereas class II formin (denoted For2) mobility solely depended on actin. Moreover, cortical For2A tightly correlated with the puncta labeled by the endocytic membrane dye FM4-64, and null mutants in class I formins did not affect uptake of a similar dye, FM1-43, suggesting that class I and II formins are involved in distinct membrane trafficking pathways.

    Computer-assisted terrain sketch mapping that considers the geomorphological features in a loess landform
    Cheng, Yihan ; Yang, Xin ; Liu, Hailong ; Li, Min ; Rossiter, David G. ; Xiong, Liyang ; Tang, Guoan - \ 2020
    Geomorphology 364 (2020). - ISSN 0169-555X
    DEM - Loess landform - Terrain sketch map - Visual hierarchy division - Visual outline generalisation

    In geography, a terrain sketch map is necessary to understand the features and internal structures of a landscape due to its ability to depict key information in a geographical scene using as few lines as possible. Previous computer-drawn sketch maps have focused on the artistic effect rather than on depicting terrain features and landform structures, and thus, they differ considerably from hand-drawn sketch maps by geographers or geologists. This study develops a DEM-based method for terrain sketch mapping that considers the typical feature descriptions of a loess landform and the visual hierarchy expression in line with the law of visual perspective. The method was tested with experiments on two landforms of Chinese Loess Plateau, based on digital elevation models (DEM) with a horizontal resolution of 5 m. In the developed method, first, typical terrain features, including the visual outline, shoulder line, gully and flow lines, are extracted from the DEM. Second, the map is divided into three visual levels in accordance with the data extension and viewing point. Then, terrain feature lines are assigned to different visual levels. Finally, the visual outlines in the distant view are generalized following the law of visual perspective. Results are assessed through a questionnaire with specialists (experts) and students (non-experts). The sketch map was able to characterise loess landforms, and is somewhat similar to traditional hand-drawn maps. The generalisation method realises the near and distant view characteristics of a sketch map, which are detailed and simplified, respectively. The results of the questionnaire also showed that our method presents terrain morphology and geographical scene more accurately and reliably than a hand-drawn sketch map.

    Web-based system for mycotoxin prevention and control along the chain
    Fels-Klerx, Ine van der; Liu, Cheng ; Focker, Marlous ; Rossi, V. ; Manstretta, Valentina ; Montero Castro, I. ; Magan, N. ; Krska, R. - \ 2020
    A DMP-triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis
    Zhong, Yu ; Chen, Baojian ; Li, Mengran ; Wang, Dong ; Jiao, Yanyan ; Qi, Xiaolong ; Wang, Min ; Liu, Zongkai ; Chen, Chen ; Wang, Yuwen ; Chen, Ming ; Li, Jinlong ; Xiao, Zijian ; Cheng, Dehe ; Liu, Wenxin ; Boutilier, K.A. ; Liu, Chenxu ; Chen, Shaojiang - \ 2020
    Nature Plants 6 (2020). - ISSN 2055-026X - p. 466 - 472.
    Doubled haploid technology using inducer lines carrying mutations in ZmPLA1/MTL/NLD and ZmDMP1–4 has revolutionized traditional maize breeding. ZmPLA1/MTL/NLD is conserved in monocots and has been used to extend the system from maize to other monocots5–7, but no functional orthologue has been identified in dicots, while ZmDMP-like genes exist in both monocots and dicots4,8,9. Here, we report that loss-of-function mutations in the Arabidopsis thaliana ZmDMP-like genes AtDMP8 and AtDMP9 induce maternal haploids, with an average haploid induction rate of 2.1 ± 1.1%. In addition, to facilitate haploid seed identification in dicots, we established an efficient FAST-Red fluorescent marker-based haploid identification system that enables the identification of haploid seeds with >90% accuracy. These results show that mutations in DMP genes also trigger haploid induction in dicots. The conserved expression patterns and amino acid sequences of ZmDMP-like genes in dicots suggest that DMP mutations could be used to develop in vivo haploid induction systems in dicots.
    Corncob cellulose nanosphere as an eco-friendly detergent
    Liu, Bin ; Li, Tao ; Wang, Wenya ; Sagis, Leonard M.C. ; Yuan, Qipeng ; Lei, Xingen ; Cohen Stuart, Martien A. ; Li, Dan ; Bao, Cheng ; Bai, Jie ; Yu, Zhengquan ; Ren, Fazheng ; Li, Yuan - \ 2020
    Nature Sustainability (2020). - ISSN 2398-9629

    The daily use of synthetic detergents at a global scale is responsible for substantial environmental impacts but managerial and policy strategies to address them are largely inadequate. More sustainable and eco-friendly detergents are an appealing solution to reduce environmental impacts. Here, we developed a detergent based on cellulose nanospheres (CNSs) from agricultural waste corncob, an overlooked abundant and cheap natural source that is often discarded. Compared with conventional surfactants, CNSs stabilize at oil–water interfaces and form Pickering emulsions with enhanced stability and antiredeposition properties. CNSs show higher cleaning efficiency in removing stains from various surfaces compared with powder and liquid commercial detergents. In contrast to high toxicity of commercial detergents, CNSs are non-toxic to several mammalian cell lines, zebrafish and hydroponic lettuce. Overall, our results demonstrated the feasibility of using agriculturally derived waste CNSs as a safer, more cost-effective and sustainable alternative to commercial synthetic detergents.

    Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
    Li, Fay Wei ; Nishiyama, Tomoaki ; Waller, Manuel ; Frangedakis, Eftychios ; Keller, Jean ; Li, Zheng ; Fernandez-Pozo, Noe ; Barker, Michael S. ; Bennett, Tom ; Blázquez, Miguel A. ; Cheng, Shifeng ; Cuming, Andrew C. ; Vries, Jan de; Vries, Sophie de; Delaux, Pierre Marc ; Diop, Issa S. ; Harrison, Jill C. ; Hauser, Duncan ; Hernández-García, Jorge ; Kirbis, Alexander ; Meeks, John C. ; Monte, Isabel ; Mutte, Sumanth K. ; Neubauer, Anna ; Quandt, Dietmar ; Robison, Tanner ; Shimamura, Masaki ; Rensing, Stefan A. ; Villarreal, Juan Carlos ; Weijers, Dolf ; Wicke, Susann ; Wong, Gane K.S. ; Sakakibara, Keiko ; Szövényi, Péter - \ 2020
    Nature Plants 6 (2020)3. - ISSN 2055-026X - p. 259 - 272.

    Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

    Critical transitions in Chinese dunes during the past 12,000 years
    Xu, Zhiwei ; Mason, Joseph A. ; Xu, Chi ; Yi, Shuangwen ; Bathiany, Sebastian ; Yizhaq, Hezi ; Zhou, Yali ; Cheng, Jun ; Holmgren, Milena ; Lu, Huayu - \ 2020
    Science Advances 6 (2020)9. - ISSN 2375-2548 - p. eaay8020 - eaay8020.

    Dune systems can have alternative stable states that coexist under certain environmental conditions: a vegetated, stabilized state and a bare active state. This behavior implies the possibility of abrupt transitions from one state to another in response to gradual environmental change. Here, we synthesize stratigraphic records covering 12,000 years of dynamics of this system at 144 localities across three dune fields in northern China. We find side-by-side coexistence of active and stabilized states, and occasional sharp shifts in time between those contrasting states. Those shifts occur asynchronously despite the fact that the entire landscape has been subject to the same gradual changes in monsoon rainfall and other conditions. At larger scale, the spatial heterogeneity in dune dynamics averages out to produce relatively smooth change. However, our results do show different paths of recovery and collapse of vegetation at system-wide scales, implying that hysteretic behavior occurs in spatially extended systems.

    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.
    The chronic toxicity of emamectin benzoate to three marine benthic species using microcosms
    Cheng, Bo ; Smeden, Jasper Van; Deneer, John ; Belgers, Dick ; Foekema, Edwin ; Roessink, Ivo ; Matser, Arrienne ; Brink, Paul J. Van den - \ 2020
    Ecotoxicology and Environmental Safety 194 (2020). - ISSN 0147-6513
    Arenicola marina - Benthic invertebrates - Cerastoderma edule - Corophium volutator - Emamectin benzoate - Sediment bioassay

    The commercial farming of Atlantic salmon, Salmo salar, may require the periodic application of emamectin benzoate (EB) treatments to reduce the effects of biological pests, such as sea lice. As a result, EB is detected in sediments beneath these fish farms at considerable levels. Literature sediment toxicity data for EB for marine benthic species is only available for 10-day sediment toxicity tests, which might be too short to assess field effects. Here, we present a sediment toxicity test to determine 28-day mortality and growth effect concentrations for the non-target polychaete worm Arenicola marina, the crustacean Corophium volutator and the mollusk Cerastoderma edule using a marine microcosm setup. Results indicate that no concentration-dependent increase of mortality and growth rate was apparent to A. marina and C. edule. But for C. volutator, a concentration-dependent increase in mortality was observed, resulting in a calculated 28-d LC50 of 316 μg/kg dry sediment (95% confidence interval: 267–373 μg/kg dry sediment). There were significant effects on C. volutator growth rate at concentrations of 100 μg/kg dry sediment and above (NOEC = 30 μg/kg dry sediment). These observations show that C. volutator is more sensitive to EB than A. marina, which differs from results reported in previous studies. Comparison to the most sensitive NOEC (30 μg/kg dry sediment) found for C. volutator (organisms of 8–11 mm length), shows that the Environmental Quality Standard, derived by the Scottish Environment Protection Agency in 2017 which based on freshwater species data (NOEC = 1.175 μg/kg dry sediment), are relatively strict and is sufficiently protective for the marine species tested in this paper.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    Nationwide assessment of persistent halogenated compounds (PHCs) in farmed golden pompano of China
    Cheng, Bo ; Peng, Feng Jiao ; Liu, Qiao Rong ; Ke, Chang Liang ; Liu, Qi ; Pan, Chang Gui - \ 2020
    Food Chemistry 313 (2020). - ISSN 0308-8146
    Golden pompano - Health risk - Organochlorine pesticides (OCPs) - Persistent halogenated compounds (PHCs) - Polychlorinated biphenyls (PCBs)

    Persistent halogenated compounds (PHCs) contamination has become a major concern over the world. Here we investigated occurrence, spatial distributions, congener profiles, as well as health risks of PHCs in farmed golden pompano in China using gas chromatography/mass spectrometry (GC/MS). The concentrations of PCBs, PBDEs and OCPs were in the range of 0.78–4.79 ng/g wet weight (ww), not detected (nd)-1.14 ng/g ww and 1.1–38.8 ng/g ww, respectively. Furthermore, ρ,ρ′-DDT, ο,ρ′-DDT and PCB 101 were the dominant PHC contaminants. The estimated daily intakes of PHCs through consumption of golden pompano were up to 12.86 and 131.34 ng/kg body weight/day based on the mean and 95th concentrations determined in golden pompano, respectively. Risk-based analysis indicates that target PHCs in golden pompano would not pose risks to human. Our study presents the first report of a nationwide survey of PHCs contamination in farmed golden pompano in China.

    Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
    Makarova, Kira S. ; Wolf, Yuri I. ; Iranzo, Jaime ; Shmakov, Sergey A. ; Alkhnbashi, Omer S. ; Brouns, Stan J.J. ; Charpentier, Emmanuelle ; Cheng, David ; Haft, Daniel H. ; Horvath, Philippe ; Moineau, Sylvain ; Mojica, Francisco J.M. ; Scott, David ; Shah, Shiraz A. ; Siksnys, Virginijus ; Terns, Michael P. ; Venclovas, Česlovas ; White, Malcolm F. ; Yakunin, Alexander F. ; Yan, Winston ; Zhang, Feng ; Garrett, Roger A. ; Backofen, Rolf ; Oost, John van der; Barrangou, Rodolphe ; Koonin, Eugene V. - \ 2020
    Nature Reviews Microbiology 18 (2020). - ISSN 1740-1526 - p. 67 - 83.

    The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR–Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR–Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR–Cas.

    Rescue of tomato spotted wilt virus entirely fromcomplementary DNA clones
    Feng, Mingfeng ; Cheng, Ruixiang ; Chen, Minglong ; Guo, Rong ; Li, Luyao ; Feng, Zhike ; Wu, Jianyan ; Xie, Li ; Hong, Jian ; Zhang, Zhongkai ; Kormelink, R.J.M. ; Tao, Xiaorong - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)2. - ISSN 0027-8424BioRxiv - p. 1181 - 1190.
    Negative-stranded/ambisense RNA viruses (NSVs) include not only dangerous pathogens of medical importance but also serious plant pathogens of agronomic importance. Tomato spotted wilt virus (TSWV) is one of the most important plant NSVs, infecting more than 1,000 plant species, and poses major threats to global food security. The segmented negative-stranded/ambisense RNA genomes of TSWV, however, have been a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from complementary DNA (cDNA) clones. First, a replication- and transcription-competent minigenome replication system was established based on 35S-driven constructs of the S(−)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by the 5′ hammerhead and 3′ ribozyme sequence of hepatitis delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA-dependent RNA polymerase (RdRp) gene. Next, a movement-competent minigenome replication system was developed based on M(−)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. Finally, infectious TSWV and derivatives carrying eGFP reporters were rescued in planta via simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(−)-gRNA, and L(+)-agRNA in which the glycoprotein gene sequence of M(−)-gRNA was optimized. Viral rescue occurred with the addition of various RNAi suppressors including P19, HcPro, and γb, but TSWV NSs interfered with the rescue of genomic RNA. This reverse genetics system for TSWV now allows detailed molecular genetic analysis of all aspects of viral infection cycle and pathogenicity.
    Inhibition of oil digestion in Pickering emulsions stabilized by oxidized cellulose nanofibrils for low-calorie food design
    Liu, Bin ; Zhu, Yanli ; Tian, Jingnan ; Guan, Tong ; Li, Dan ; Bao, Cheng ; Norde, Willem ; Wen, Pengcheng ; Li, Yuan - \ 2019
    RSC Advances : An international journal to further the chemical sciences 9 (2019)26. - ISSN 2046-2069 - p. 14966 - 14973.

    Celluloses are renewable and biodegradable natural resources. The application of celluloses as oil-in-water Pickering emulsifiers is still quite limited. In this paper, cellulose nanofibrils (CNFs) with oxidation degrees (DOs) of 52.8% and 92.7% (DO50 and DO90) were obtained from TEMPO-mediate oxidation for microcrystalline cellulose (MC). The production of carboxyl groups of CNFs were confirmed by FT-IR and 13C solid-NMR. CNF-stabilized O/W Pickering emulsion showed excellent colloidal stability compared with un-oxidized cellulose by Turbiscan stability analysis. Additionally, CNF-stabilized Pickering emulsions showed stable colloidal properties in simulated intestinal fluid (SIF). Most importantly, in vitro fatty acid release kinetics under SIF showed that CNFs have strong inhibitory lipid digestion behavior. Our results suggest that the oxidation modification not only improves their emulsification activity but also promotes their application in oil digestion inhibition, providing inspiration for designing and developing low-calorie food products.

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