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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    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.

    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.

    Examining Health of Wetlands with Multiple Ecosystem Services as Targets in China’s Coastal Regions
    Zhou, Yangming ; Dou, Yuehan ; Yu, Xiubo ; Zhang, Li ; Huang, Chong ; Wang, Yuyu ; Li, Xiaowei ; Li, He ; Jia, Yifei ; Bakker, Martha ; Carsjens, Gerrit Jan ; Zhou, Yan ; Duan, Houlang - \ 2020
    Chinese Geographical Science 30 (2020)4. - ISSN 1002-0063 - p. 600 - 613.
    coastal zones - ecosystem services - Wetland Health Index (WHI) - wetland utilization

    Coastal zones are key interconnectors of terrestrial and marine ecosystems. Due to the degradation and fragmentation of coastal wetlands, there is an urgent need to develop assessment methodology to compare the health of wetland ecosystems at different spatial scales. This will help efficiently develop and implement protections using easy-to-access ecosystem health data. This study aims to understand the spatial distribution of coastal and inland wetland health for China’s coastal regions. A Wetland Health Index (WHI) was developed to provide a basis for policy and decision making. Four utilization models—Long Term Model, Open Model, Nature Reserve Model, and Protected and Economic Model—were defined in the context of China’s coastal regions to specifically examine wetland health. Results show that the average WHI score was 63.6 with the range of 44.8–84.3 for 35 National Nature Reserves (NNRs), and the southern NNRs generally performed better than the northern NNRs. The wetlands in the southern provinces/municipalities are relatively healthier than their northern counterparts. The competent authority has slight influence on WHI scores but duration of conservation establishment does not show a clear correlation. With increasing economic activity, the differences in health conditions (WHI scores) of China’s coastal regions also increase. Gross Domestic Product (GDP) or economic intensification does not relate to WHI scores. Appropriate trade-offs between wetland management and economic development could contribute to improve health conditions, conservation and utilization of coastal and inland wetlands.

    Estimation of nitrogen supply for winter wheat production through a long-term field trial in China
    Huang, Shaohui ; Ding, Wencheng ; Yang, Junfang ; Zhang, Jiajia ; Ullah, Sami ; Xu, Xinpeng ; Liu, Yingxia ; Yang, Yunma ; Liu, Mengchao ; He, Ping ; Jia, Liangliang - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Nitrogen use efficiency - Relative yield - Total nitrogen supply - Winter wheat

    Excessive synthetic nitrogen (N) applications, high mineral N accumulation and low N use efficiency (NUE) are current issues in intensively cultivated winter wheat production system impeding the sustainable development of agriculture in China. To solve these problems, soil accumulated N in the top 1 m of the soil profile before sowing (Nsoil), returned straw-N from the previous maize crop (Nstraw) and fertilizer N application (Nfertilizer) should be comprehensively considered N supply sources in N management. As such, the objective of this research was to determine the optimal total N supply (TNsupply) level needed to meet crop requirements while minimizing environmental impacts. A 9-year on-farm experiment was conducted in accordance with a split-plot design involving two different fertilizer management systems (main treatments) and three N application strategies (sub treatments). Extensive TNsupply levels (ranging from 61 kg ha−1 to 813 kg ha−1) were detected, and relative yield (RY), N input and N output in response to the TNsupply were measured. The relationships between TNsupply and RY, N input, and N output strongly fit linear-plateau, linear, and linear-plateau models, respectively. The minimum TNsupply levels needed to achieve the maximum RY and N output were 325 and 392 kg ha−1, respectively. On the basis of N supply capacity, the TNsupply was removed from the growing system by 61% (N input). As the N input increased past 209 kg ha−1, the NUE declined, at which point the TNsupply reached 433 kg ha−1. Therefore, the suitable TNsupply should range from 325 kg ha−1 (ensuring a total N supply for high yield and N uptake) to 433 kg ha−1 (obtaining a relatively higher NUE and less N loss to the environment). The TNsupply was highlighted to be an indicator for use in N management recommendations. Considering the average high N accumulation in winter wheat production systems, N management should essentially take into account the consumption of Nsoil, the levels of Nstraw and the minimum application of Nfertilizer to obtain high yields while minimizing environmental impacts under suitable TNsupply levels.

    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.

    Direct and quantitative in-situ analysis of third-hand smoke in and on various matrices by ambient desorption corona beam ionization mass spectrometry
    Min, Ke ; Guo, Ping ; Chen, Dongying ; Huang, Si ; Luo, Wei ; Ma, Ming ; Chen, Bo ; Yao, Shouzhou ; Zuilhof, H. - \ 2020
    Talanta 219 (2020). - ISSN 0039-9140
    Third-hand smoke (THS) is composed of surface-deposited remnants resulting from tabacco-smoking. Because THS components have properties of remaining on, re-emitting from and reacting on and with surfaces, in-situ analysis of the components on different surfaces is both in high demand and challenging. The aim of this study is to establish desorption corona beam ionization (DCBI)-MS/MS as an analytical tool for THS research. To this end, an in-situ DCBI-MS/MS approach was developed for the quantitative analysis of typical THS environmental markers, i.e. nicotine and cotinine on different surfaces such as fruits, cotton clothing, glass, and toys etc. The limits of detection of nicotine and cotinine were both 1.4 μg m-2. Low-temperature DCBI-MS/MS was applied to the direct detection of THS on fingers without any skin damage. Smoking-related biomarkers analyses in urine were accomplished, with a 10 s DCBI analysis time. The on-surface tobacco-specific nitrosamines (TSNAs), such as 1-(N-methyl-N-nitrosamino)-1-(3-pyridinyl)-4-butanal) (NNA), 4-(methylnitrosamino)-1-(3-pyridinyl)-1-butanone (NNK), and N-nitroso nornicotine (NNN) were in-situ successfully detected in dust samples.
    Effects of migration network configuration and migration synchrony on infection prevalence in geese
    Yin, Shenglai ; Knegt, Henrik J. de; Jong, Mart C.M. de; Si, Yali ; Prins, Herbert H.T. ; Huang, Zheng Y.X. ; Boer, Willem F. de - \ 2020
    Journal of Theoretical Biology 502 (2020). - ISSN 0022-5193
    Avian influenza - Cumulative infection - Environmental transmission - SIR model - Stopover site

    Migration can influence dynamics of pathogen-host interactions. However, it is not clearly known how migration pattern, in terms of the configuration of the migration network and the synchrony of migration, affects infection prevalence. We therefore applied a discrete-time SIR model, integrating environmental transmission and migration, to various migration networks, including networks with serial, parallel, or both serial and parallel stopover sites, and with various levels of migration synchrony. We applied the model to the infection of avian influenza virus in a migratory geese population. In a network with only serial stopover sites, increasing the number of stopover sites reduced infection prevalence, because with every new stopover site, the amount of virus in the environment was lower than that in the previous stopover site, thereby reducing the exposure of the migratory population. In a network with parallel stopover sites, both increasing the number and earlier appearance of the stopover sites led to an earlier peak of infection prevalence in the migratory population, because the migratory population is exposed to larger total amount of virus in the environment, speeding-up the infection accumulation. Furthermore, higher migration synchrony reduced the average number of cumulative infection, because the majority of the population can fly to a new stopover site where the amount of virus is still relatively low and has not been increased due to virus shedding of infected birds. Our simulations indicate that a migration pattern with multiple serial stopover sites and with highly synchronized migration reduces the infection prevalence.

    Trade-offs of dryland forage production and soil water consumption in a semi-arid area
    Huang, Ze ; Dunkerley, David ; López-Vicente, Manuel ; Wu, Gao Lin - \ 2020
    Agricultural Water Management 241 (2020). - ISSN 0378-3774
    Dryland farming - Forage - Nutritional quality - Precipitation utilization efficiency - Soil water consumption - Yield

    Drought-tolerant forage crops have huge development potential in drylands taking into account the current global challenges (climate change, natural resources overexploitation and increasing food demand). However, little is known about the trade-off among yield, nutritional quality, and soil water consumption for dryland forage farming production in semi-arid regions. This research compared the two-year yield and soil water consumption characteristics of sweet sorghum (Sorghum dochna), sudangrass (Sorghum sudanense) and forage maize (Zea mays) under natural rainfall condition. The soil water content up to 200 cm soil depth –at 10-cm intervals– and dry matter yield of the different forage crops were evaluated in a set of plots in 2017 and 2018, and the nutritional quality of these crops were measured in 2018. Three replicate plots were established for each forage crop. Results showed that the neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents of sudangrass were significantly lower than those of sweet sorghum and forage maize (P < 0.05). Sudangrass presented the higher in vitro dry matter digestibility coefficient (IVDMD). The yield of sweet sorghum was significantly higher than that of sudangrass and forage maize. Different soil water consumption patterns were observed among the forage crops, happening mostly in the 0–150 cm soil layer in the forage maize plots, and in the 0–100 cm soil layer in the sweet sorghum and sudangrass plots. The average daily evapotranspiration (ETd) of forage maize was about 10 % and 15 % higher than that of sweet sorghum and sudangrass, respectively. Forage sorghum presented the highest yield, less soil water consumption, and similar nutritional quality to forage maize, and thus, it is an advisable option for forage production in the soil water-limited semi-arid regions.

    Neighbourhood-dependent root distributions and the consequences on root separation in arid ecosystems
    Chen, Bin J.W. ; Xu, Chi ; Liu, Mao Song ; Huang, Zheng Y.X. ; Zhang, Ming Juan ; Tang, Jian ; Anten, Niels P.R. - \ 2020
    Journal of Ecology 108 (2020)4. - ISSN 0022-0477 - p. 1635 - 1648.
    dryland - growth form - niche partitioning - plant–plant interactions - root competition - root distribution - root separation - species coexistence

    Interspecific root separation is an important example of spatial niche differentiation that drives species coexistence in many ecosystems. Particularly under water-stressed conditions, it is believed to be an inevitable outcome of species interactions. However, evidence for and against this idea has been found. So far, studies aiming at reconciling the debate have mainly focused on abiotic determinants. It remains unclear if and to what extent root separation depends on the type and growth form of interacting plants. We conducted a detailed field study in three adjacently located (with pairwise distances <500 m) arid patchy communities where a common tussock grass species Achnatherum splendens grew in association with either a tree Elaeagnus angustifolia, a shrub Nitraria tangutorum or a perennial forb species Sophora alopecuroides. In each community, roots and soils were sampled along the soil layers from five depths (0–10, 10–30, 30–60, 60–100 and 100–150 cm) in the patches and in the adjacent bare ground outside the patches. Significant vertical interspecific root separation occurred in the species-association patches of tree-grass and forb-grass communities, but not in the shrub-grass community. As the neighbour changed going from trees to shrubs and to forbs, rooting profiles of the grass Achnatherum became progressively deeper, with progressively less roots allocated in the upmost 10 cm soil layer and more in the subsequent two layers. After controlling for the differences in soil water and nutrient conditions among the three communities, the effects of neighbour type on grass rooting profiles remained robust. Synthesis. We found that the root distributions of plants in the dryland strongly depend on the type of neighbour plants, which can, at least partially, determine the extent of interspecific root separation at the community scale. Our work poses new questions about plasticity in root distribution and helps to better understand species interactions and coexistence under stressful conditions.

    Blockchain Technology for Agriculture: Applications and Rationale
    Xiong, Hang ; Dalhaus, Tobias ; Wang, P. ; Huang, J. - \ 2020
    Frontiers in Blockchain 3 (2020). - ISSN 2624-7852
    The blockchain is a ledger of accounts and transactions that are written and stored by all participants. It promises a reliable source of truth about the state of farms, inventories and contracts in agriculture, where the collection of such information is often incredibly costly. The blockchain technology can track the provenance of food and thus helps create trustworthy food supply chains and build trust between producers and consumers. As a trusted way of storing data, it facilitates the use of data-driven technologies to make farming smarter. In addition, jointly used with smart contracts, it allows timely payments between stakeholders that can be triggered by data changes appearing in the blockchain This article examines the applications of blockchain technology in food supply chains, agricultural insurance, smart farming, transactions of agricultural products for both theoretical and practical perspectives. We also discuss the challenges of recording transactions made by smallholder farmers and creating the ecosystem for utilizing the blockchain technology in the food and agriculture sector.
    Combining stressors: heat stress and Orsay virus infection in Caenorhabditis elegans
    Huang, Yuqing ; Zwet, Koen van; Grashuis, Thijs ; Pijlman, G.P. ; Kammenga, J.E. - \ 2020
    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.

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

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

    Body mass variation is negatively associated with brain size: Evidence for the fat-brain trade-off in anurans
    Huang, Yan ; Mai, Chun Lan ; Liao, Wen Bo ; Kotrschal, Alexander - \ 2020
    Evolution 74 (2020)7. - ISSN 0014-3820 - p. 1551 - 1557.
    body mass - Brain size - fat storage - trade-off

    Species can evolve diverse strategies to survive periods of uncertainty. Animals may either invest in energy storage, allowing them to decrease foraging costs, such as locomotion or risk of predation, or they may invest in better cognitive abilities helping them to flexibly adapt their behavior to meet novel challenges. Here, we test this idea of a fat-brain trade-off in 38 species of Chinese anurans by relating the coefficient of variation of body mass (CVbodymass; as an indicator of how much animals invest into storage over the season) to brain anatomical features. After correcting for shared ancestry and body mass, we found a negative relationship between relative brain size and CVbodymass. This indicates that anurans seem to trade-off physiological and cognitive buffering during energy shortages. As similar patterns have been reported in arboreal mammals and primates our findings suggest that the fat-brain trade-off, where animals either invest into physiological or cognitive strategies to survive harsh conditions, may be a general pattern across vertebrates.

    Aryl hydrocarbon Receptor activation during In vitro and in vivo digestion of raw and cooked broccoli (brassica oleracea var. Italica)
    Koper, Jonna E.B. ; Kortekaas, Maaike ; Loonen, Linda M.P. ; Huang, Zhan ; Wells, Jerry M. ; Gill, Chris I.R. ; Pourshahidi, L.K. ; McDougall, Gordon ; Rowland, Ian ; Pereira-Caro, Gema ; Fogliano, Vincenzo ; Capuano, Edoardo - \ 2020
    Food & Function 11 (2020)5. - ISSN 2042-6496 - p. 4026 - 4037.

    Broccoli is rich in glucosinolates, which can be converted upon chewing and processing into Aryl hydrocarbon Receptor (AhR) ligands. Activation of AhR plays an important role in overall gut homeostasis but the role of broccoli processing on the generation of AhR ligands is still largely unknown. In this study, the effects of temperature, cooking method (steaming versus boiling), gastric pH and further digestion of broccoli on AhR activation were investigated in vitro and in ileostomy subjects. For the in vitro study, raw, steamed (t = 3 min and t = 6 min) and boiled (t = 3 min and t = 6 min) broccoli were digested in vitro with different gastric pH. In the in vivo ileostomy study, 8 subjects received a broccoli soup or a broccoli soup plus an exogenous myrosinase source. AhR activation was measured in both in vitro and in vivo samples by using HepG2-Lucia™ AhR reporter cells. Cooking broccoli reduced the AhR activation measured after gastric digestion in vitro, but no effect of gastric pH was found. Indole AhR ligands were not detected or detected at very low levels both after intestinal in vitro digestion and in the ileostomy patient samples, which resulted in no AhR activation. This suggests that the evaluation of the relevance of glucosinolates for AhR modulation in the gut cannot prescind from the way broccoli is processed, and that broccoli consumption does not necessarily produce substantial amounts of AhR ligands in the large intestine.

    Belowground soil water response in the afforestation-cropland interface under semi-arid conditions
    Huang, Ze ; Yang, Wen Jin ; Liu, Yu ; Shen, Weibo ; López-Vicente, Manuel ; Wu, Gao Lin - \ 2020
    Catena 193 (2020). - ISSN 0341-8162
    Agroforestry system interface - Semi-arid area - Soil water deficit degree - Soil water storage

    Agroforestry is an effective measure to control soil erosion and maintain or increase productivity in semi-arid areas. However, the belowground soil water responses in the afforestation-cropland interface (ACI) is not well known. This study analyzed the variability of soil water storage (SWS) and deficit in three ACIs taking into account the distance between the forest and cropland. The variations of soil water content up to 4 m depth and at five distances from the interface (−5 m (in forest), 0 m (interface), 1 m, 3 m and 5 m (in cropland)) were estimated in three artificial forests (Salix matsudana, Sophora japonica, and Populus cathayana) and their adjacent croplands (maize). The results showed that soil water at the interfaces was significantly affected by forest. This effect was effective up to 160–170 cm of soil depth, and the ACI of S. matsudana had the greatest impact on the farmland soil water. There was no significant relative soil water deficit between 1 and 3 m length, and the ACI of P. cathayana showed the lowest changes in the lateral direction. The SWS of S. japonica in the ACI was clearly higher than the other two artificial forests (P < 0.05). Our findings indicated that S. japonica was the most suitable forest species for agriculture sustainability in the study area. The tree species and the distance between cropland and forest should be considered during the establishment of agroforestry systems. This study provided insights for water conservation and effective management of ACIs in semi-arid areas.

    A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone
    Huang, Zhaobin ; Petersen, Jillian M. ; Martijn, Joran ; Ettema, Thijs J.G. ; Shao, Zongze - \ 2020
    Environmental Microbiology Reports 12 (2020)4. - ISSN 1758-2229 - p. 387 - 395.

    We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.

    Social-psychological factors in food consumption of rural residents : The role of perceived need and habit within the theory of planned behavior
    Huang, Jiaqi ; Antonides, Gerrit ; Nie, Fengying - \ 2020
    Nutrients 12 (2020)4. - ISSN 2072-6643
    Food consumption - Habit - Perceived need - Rural residents - Theory of planned behavior (TPB)

    To address the problem of malnutrition in poor rural areas of China, this study aims to examine the effects of social-psychological factors in food consumption of rural residents in poor counties of Southwest China. In addition, it investigates the role of perceived need and habit within the theory of planned behavior (TPB) in predicting food consumption. A survey with random sampling was conducted on rural residents (n = 424), and the theoretical frameworks of both the standard and extended TPB were applied for comparison purposes. Structural equation modeling was applied to test the relationships among constructs. Consumption of five food items was studied, respectively: meat, eggs, dairy, fish, and fruits. Results showed that incorporation of perceived need and habit substantially increased the explanatory power of the TPB, but these factors only had significant direct effects on intention rather than behavior. Perceived need and habit are stronger predictors of intention than any other TPB construct for consumption of all food items except for meat. We found indirect effects of the constructs in the extended TPB model on consumption to be different across food items. Practical implications to improve consumption of different food items were proposed accordingly.

    Pathogen manipulation of chloroplast function triggers a light-dependent immune recognition
    Gao, Chuyun ; Xu, Huawei ; Huang, Jie ; Sun, Biying ; Zhang, Fan ; Savage, Zachary ; Duggan, Cian ; Yan, Tingxiu ; Wu, Chih Hang ; Wang, Yuanchao ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien ; Bozkurt, Tolga O. ; Dong, Suomeng - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)17. - ISSN 0027-8424 - p. 9613 - 9620.
    Chloroplast - Disease resistance - Light - NLR - Potato blight

    In plants and animals, nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune sensors that recognize and eliminate a wide range of invading pathogens. NLR-mediated immunity is known to be modulated by environmental factors. However, how pathogen recognition by NLRs is influenced by environmental factors such as light remains unclear. Here, we show that the agronomically important NLR Rpi-vnt1.1 requires light to confer disease resistance against races of the Irish potato famine pathogen Phytophthora infestans that secrete the effector protein AVRvnt1. The activation of Rpi-vnt1.1 requires a nuclear-encoded chloroplast protein, glycerate 3-kinase (GLYK), implicated in energy production. The pathogen effector AVRvnt1 binds the full-length chloroplast-targeted GLYK isoform leading to activation of Rpi-vnt1.1. In the dark, Rpi-vnt1.1-mediated resistance is compromised because plants produce a shorter GLYK-lacking the intact chloroplast transit peptide-that is not bound by AVRvnt1. The transition between full-length and shorter plant GLYK transcripts is controlled by a light-dependent alternative promoter selection mechanism. In plants that lack Rpi-vnt1.1, the presence of AVRvnt1 reduces GLYK accumulation in chloroplasts counteracting GLYK contribution to basal immunity. Our findings revealed that pathogen manipulation of chloroplast functions has resulted in a light-dependent immune response.

    Organic amendment increases soil respiration in a greenhouse vegetable production system through decreasing soil organic carbon recalcitrance and increasing carbon-degrading microbial activity
    Luan, Haoan ; Gao, Wei ; Huang, Shaowen ; Tang, Jiwei ; Li, Mingyue ; Zhang, Huaizhi ; Chen, Xinping ; Masiliūnas, Dainius - \ 2020
    Journal of Soils and Sediments 20 (2020). - ISSN 1439-0108 - p. 2877 - 2892.
    Purpose: Recent works have shown that fertilization has an important influence on soil respiration (Rs); however, the underlying mechanisms involved in regulating Rs in greenhouse vegetable production (GVP) systems remain unclear.
    Materials and methods: Samples from six kinds of soils that were amended with different fertilization patterns (8 years) were incubated for 36 days to determine soil microbial community (PLFA), enzyme activities, soil organic C (SOC) quality (13C NMR), and Rs in a GVP system in Tianjin, China. Treatments included 100% chemical N (CN) and different substitution rates of CN with manure-N and/or straw-N.
    Results and discussion: Compared with 100%CN treatment, organic amendment strongly promoted microbial (e.g., fungi, bacteria, and actinomycetes) growth, enhanced the majority of C-degrading enzyme activities, affected SOC chemical composition with increasing O-alkyl (labile) C and reducing aromatic (stable) C, decreased SOC recalcitrance, and enhanced Rs. Redundancy analysis indicated that variations in microbial community and SOC chemical composition were closely linked to light fraction organic C (LFC) and readily oxidizable C (ROC), respectively. Further, structural equation modeling and linear regression analysis revealed that SOC recalcitrance (negative effects) and C-degrading enzyme activities (positive effects) together mediate Rs rates; meanwhile, microbial community can indirect affect Rs rates through altering C-degrading enzyme activities. Conclusions: Agricultural soil abiotic properties (mainly labile C fractions, i.e., LFC and ROC) are altered by adding organic resources (i.e., manure and straw), the changes of which can promote soil microbial growth, enhance C-degrading microbial activity, and reduce SOC recalcitrance, and in turn accelerate Rs in GVP systems.
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