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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Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice
Zhao, Fan ; Zhou, Guanghong ; Liu, Xinyue ; Song, Shangxin ; Xu, Xinglian ; Hooiveld, Guido ; Müller, Michael ; Liu, Li ; Kristiansen, Karsten ; Li, Chunbao - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
Akkermansia muciniphila - chicken protein - oxidative phosphorylation - soy protein

Scope: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated. Methods and results: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet. Conclusion: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.

Nonlinear responses of soil nematode community composition to increasing aridity
Xiong, Dan ; Wei, Cun Zheng ; Wubs, Jasper E.R. ; Veen, G.J. ; Liang, Wenju ; Wang, Xiaobo ; Li, Qi ; Putten, Wim H. Van der; Han, Xingguo - \ 2019
Global Ecology and Biogeography (2019). - ISSN 1466-822X
aridity - biodiversity - global climate change - grassland transect - nonlinear response - soil nematode community

Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have a poor understanding of how belowground communities respond. In order to understand the longer term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3,200 km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from.43 to.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used generalized additive (mixed) models to analyse the abundance, richness and community similarity patterns of soil nematodes. We used structural equation modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined nonlinearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred in arid conditions (aridity >.80). However, the shape of the response to aridity differed among nematode feeding groups. In arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than for fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but instead were affected directly by aridity. Main conclusions: Our results showed that in mesic grasslands, increasing aridity primarily caused a decline in nematode abundance, whereas increasing aridity in xeric grasslands led to a loss of nematode diversity. The nonlinear responses of nematodes to aridity could also result in nonlinear shifts in ecosystem functioning, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.

The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

The acclimation of leaf photosynthesis of wheat and rice to seasonal temperature changes in T-FACE environments
Cai, Chuang ; Li, Gang ; Di, Lijun ; Ding, Yunjie ; Fu, Lin ; Guo, Xuanhe ; Struik, Paul C. ; Pan, Genxing ; Li, Haozheng ; Chen, Weiping ; Luo, Weihong ; Yin, Xinyou - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
climate change - free-air CO enrichment - growth temperature - leaf nitrogen content - Oryza sativa L. - photosynthesis model - stomatal conductance - Triticum aestivum L.

Crops show considerable capacity to adjust their photosynthetic characteristics to seasonal changes in temperature. However, how photosynthesis acclimates to changes in seasonal temperature under future climate conditions has not been revealed. We measured leaf photosynthesis (An) of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) grown under four combinations of two levels of CO2 (ambient and enriched up to 500 µmol/mol) and two levels of canopy temperature (ambient and increased by 1.5–2.0°C) in temperature by free-air CO2 enrichment (T-FACE) systems. Parameters of a biochemical C3-photosynthesis model and of a stomatal conductance (gs) model were estimated for the four conditions and for several crop stages. Some biochemical parameters related to electron transport and most gs parameters showed acclimation to seasonal growth temperature in both crops. The acclimation response did not differ much between wheat and rice, nor among the four treatments of the T-FACE systems, when the difference in the seasonal growth temperature was accounted for. The relationships between biochemical parameters and leaf nitrogen content were consistent across leaf ranks, developmental stages, and treatment conditions. The acclimation had a strong impact on gs model parameters: when parameter values of a particular stage were used, the model failed to correctly estimate gs values of other stages. Further analysis using the coupled gs–biochemical photosynthesis model showed that ignoring the acclimation effect did not result in critical errors in estimating leaf photosynthesis under future climate, as long as parameter values were measured or derived from data obtained before flowering.

Self-assembled egg yolk peptide micellar nanoparticles as a versatile emulsifier for food-grade oil-in-water pickering nanoemulsions
Du, Zhenya ; Li, Qing ; Li, Junguang ; Su, Enyi ; Liu, Xiao ; Wan, Zhili ; Yang, Xiaoquan - \ 2019
Journal of Agricultural and Food Chemistry 67 (2019)42. - ISSN 0021-8561 - p. 11728 - 11740.
Egg yolk peptides - Food-grade pickering nanoemulsions - Nanomicelles - Particulate emulsifiers - Self-assembly

Pickering emulsions stabilized by food-grade particles have garnered increasing interest in recent years due to their promising applications in bio-related fields such as foods, cosmetics, and drug delivery. However, it remains a big challenge to formulate nanoscale Pickering emulsions from these edible particles. Herein, we show that a new Pickering nanoemulsion that is stable, monodisperse and controllable can be produced by employing the spherical micellar nanoparticles (EYPN), self- A ssembled from the food-derived, amphiphilic egg yolk peptides, as an edible particulate emulsifier. As natural peptide-based nanoparticles, the EYPN have small particle size, intermediate wettability, high surface activity, and deformability at the interface, which enable the formation of stable Pickering nanodroplets with a mean DLS diameter below 200 nm and a PDI below 0.2. This nanoparticle system is versatile for different oil phases with various polarities and demonstrates easy control of nanodroplet size through tuning the microfluidization conditions and/or the ratio of EYPN to oil phase. These food-grade Pickering nanoemulsions, obtained when the internal phase is an edible vegetable oil, have superior stability during long-term storage and spray-drying, based on the irreversible and compact adsorption of intact EYPN at the nanodroplet surface. This is the first finding of a natural edible nano-Pickering emulsifier that can be used solely to make stable food Pickering nanoemulsions with the qualities of simplicity, versatility, low cost, and the possibility of controllable and mass production, which make them viable for many sustainable applications.

Earthworms Coordinate Soil Biota to Improve Multiple Ecosystem Functions
Liu, Ting ; Chen, Xiaoyun ; Gong, Xin ; Lubbers, Ingrid M. ; Jiang, Yangyang ; Feng, Wen ; Li, Xianping ; Whalen, Joann K. ; Bonkowski, Michael ; Griffiths, Bryan S. ; Hu, Feng ; Liu, Manqiang - \ 2019
Current Biology 29 (2019)20. - ISSN 0960-9822 - p. 3420 - 3429.
bacterial-dominated channel - earthworm - ecosystem engineer - ecosystem service - soil fauna - soil microbe - sustainable agriculture

Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture.

Consumer confidence in the safety of milk and infant milk formula in China
Li, Saiwei ; Sijtsema, Siet J. ; Kornelis, Marcel ; Liu, Yumei ; Li, Shengli - \ 2019
Journal of Dairy Science 102 (2019)10. - ISSN 0022-0302 - p. 8807 - 8818.
ABA-mediated regulation of leaf and root hydraulic conductance in tomato grown at elevated CO2 is associated with altered gene expression of aquaporins
Fang, Liang ; Abdelhakim, Lamis Osama Anwar ; Hegelund, Josefine Nymark ; Li, Shenglan ; Liu, Jie ; Peng, Xiaoying ; Li, Xiangnan ; Wei, Zhenhua ; Liu, Fulai - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276

Elevated CO2 concentration in the air (e[CO2]) decreases stomatal density (SD) and stomatal conductance (gs) where abscisic acid (ABA) may play a role, yet the underlying mechanism remains largely elusive. We investigated the effects of e[CO2] (800 ppm) on leaf gas exchange and water relations of two tomato (Solanum lycopersicum) genotypes, Ailsa Craig (WT) and its ABA-deficient mutant (flacca). Compared to plants grown at ambient CO2 (400 ppm), e[CO2] stimulated photosynthetic rate in both genotypes, while depressed the gs only in WT. SD showed a similar response to e[CO2] as gs, although the change was not significant. e[CO2] increased leaf and xylem ABA concentrations and xylem sap pH, where the increases were larger in WT than in flacca. Although leaf water potential was unaffected by CO2 growth environment, e[CO2] lowered osmotic potential, hence tended to increase turgor pressure particularly for WT. e[CO2] reduced hydraulic conductance of leaf and root in WT but not in flacca, which was associated with downregulation of gene expression of aquaporins. It is concluded that ABA-mediated regulation of gs, SD, and gene expression of aquaporins coordinates the whole-plant hydraulics of tomato grown at different CO2 environments.

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling - \ 2019
GigaScience 8 (2019)9. - ISSN 2047-217X
Castanea mollissima - annotation - evolution - genome assembly

BACKGROUND: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

Transforming, Genome Editing and Phenotyping the Nitrogen-fixing Tropical Cannabaceae Tree Parasponia andersonii
Wardhani, Titis A.K. ; Roswanjaya, Yuda Purwana ; Dupin, Simon ; Li, Huchen ; Linders, Sidney ; Hartog, Marijke ; Geurts, Rene ; Zeijl, Arjan van - \ 2019
Journal of Visualized Experiments (2019)150. - ISSN 1940-087X - 17 p.

Parasponia andersonii is a fast-growing tropical tree that belongs to the Cannabis family (Cannabaceae). Together with 4 additional species, it forms the only known non-legume lineage able to establish a nitrogen-fixing nodule symbiosis with rhizobium. Comparative studies between legumes and P. andersonii could provide valuable insight into the genetic networks underlying root nodule formation. To facilitate comparative studies, we recently sequenced the P. andersonii genome and established Agrobacterium tumefaciens-mediated stable transformation and CRISPR/Cas9-based genome editing. Here, we provide a detailed description of the transformation and genome editing procedures developed for P. andersonii. In addition, we describe procedures for the seed germination and characterization of symbiotic phenotypes. Using this protocol, stable transgenic mutant lines can be generated in a period of 2-3 months. Vegetative in vitro propagation of T0 transgenic lines allows phenotyping experiments to be initiated at 4 months after A. tumefaciens co-cultivation. Therefore, this protocol takes only marginally longer than the transient Agrobacterium rhizogenes-based root transformation method available for P. andersonii, though offers several clear advantages. Together, the procedures described here permit P. andersonii to be used as a research model for studies aimed at understanding symbiotic associations as well as potentially other aspects of the biology of this tropical tree.

NSs Filament Formation Is Important but Not Sufficient for RVFV Virulence In Vivo
Li, Shufen ; Zhu, Xiangtao ; Guan, Zhenqiong ; Huang, Wenfeng ; Zhang, Yulan ; Kortekaas, Jeroen ; Lozach, Pierre Yves ; Peng, Ke - \ 2019
Viruses 11 (2019)9. - ISSN 1999-4915
filament - NSs - reverse genetics system - RVFV - virulence

Rift Valley fever virus (RVFV) is a mosquito-borne phlebovirus that represents as a serious health threat to both domestic animals and humans. The viral protein NSs is the key virulence factor of RVFV, and has been proposed that NSs nuclear filament formation is critical for its virulence. However, the detailed mechanisms are currently unclear. Here, we generated a T7 RNA polymerase-driven RVFV reverse genetics system based on a strain imported into China (BJ01). Several NSs mutations (T1, T3 and T4) were introduced into the system for investigating the correlation between NSs filament formation and virulence in vivo. The NSs T1 mutant showed distinct NSs filament in the nuclei of infected cells, the T3 mutant diffusively localized in the cytoplasm and the T4 mutant showed fragmented nuclear filament formation. Infection of BALB/c mice with these NSs mutant viruses revealed that the in vivo virulence was severely compromised for all three NSs mutants, including the T1 mutant. This suggests that NSs filament formation is not directly correlated with RVFV virulence in vivo. Results from this study not only shed new light on the virulence mechanism of RVFV NSs but also provided tools for future in-depth investigations of RVFV pathogenesis and anti-RVFV drug screening.

Prenatal infant feeding intentions and actual feeding practices during the first six months postpartum in rural Rwanda: a qualitative, longitudinal cohort study
Ahishakiye, J. ; Bouwman, L.I. ; Vaandrager, L. ; Koelen, M.A. ; Brouwer, I.D. - \ 2019
- 1 p.
Interactive effects of microplastics and glyphosate on the dynamics of soil dissolved organic matter in a Chinese loess soil
Liu, Hongfei ; Yang, Xiaomei ; Liang, Chutao ; Li, Yuanze ; Qiao, Leilei ; Ai, Z. ; Xue, Sha ; Liu, Guobin - \ 2019
Catena 182 (2019). - ISSN 0341-8162
Dissolved organic carbon (DOC) - Dissolved organic nitrogen (DON) - Dissolved organic phosphorus (DOP) - Excitation-emission matrix (EEM) - Glyphosate

The increased use of plastic films and pesticides on agricultural soil leads to the accumulation of plastic debris and pesticide residues in soil. This accumulation has become a serious environmental issue, as it threatens life of earthworms, inhibits the enzyme activities and microbial diversity, and contributes to the loss of soil microbial carbon and nitrogen. However, little information is available regarding the effects of pesticides on soil dissolved organic matter (DOM). It is also unknown how plastic debris, especially small-sized particles called microplastics, influences the effects of pesticides on soil DOM. In this study, we performed a 30-day soil incubation experiment. Three levels of the common herbicide glyphosate were applied to soil: 0 (control, CK), 3.6 kg ha 1 (G1) and 7.2 kg ha 1 (G2). We also tested four levels of glyphosate and microplastics (homopolymer polypropylene powder) co-addition: 3.6 kg ha 1 + 7% (w/w) (M1G1), 3.6 kg ha 1 + 28% (w/w) (M2G1), 7.2 kg ha 1 + 7% (w/w) (M1G2), and 7.2 kg ha 1 + 28% (w/w) (M2G2). Glyphosate addition slightly increased soil fluorescein diacetate hydrolase (FDAse) and phenol oxidase (PO) activities. Although the glyphosate addition significantly promoted the accumulation of dissolved organic phosphorus (DOP) within the first 14 days, the M2 treatment decreased DOP at day 30. M2G1 and M2G2 increased soil FDAse activity and promoted the accumulation of DOC and DOP relative to G1 and G2 respectively while M1G1 and M1G2 benefited DON accumulation. Our results highlighted that the interaction between glyphosate and low microplastics content negatively affected DOC and DOP dynamics, leading to the loss of bioavailable C and P loss. The interaction between glyphosate and high content microplastics negatively affected DON compared with glyphosate addition, possibly decreasing DON.

Deadly banana fungus reaches Latin America
Kema, G.H.J. - \ 2019
Super-resolution land cover mapping based on the convolutional neural network
Jia, Yuanxin ; Ge, Yong ; Chen, Yuehong ; Li, Sanping ; Heuvelink, Gerard B.M. ; Ling, Feng - \ 2019
Remote Sensing 11 (2019)15. - ISSN 2072-4292
Convolutional neural network - Land cover - Remote sensing imagery - Super-resolution mapping

Super-resolution mapping (SRM) is used to obtain fine-scale land cover maps from coarse remote sensing images. Spatial attraction, geostatistics, and using prior geographic information are conventional approaches used to derive fine-scale land cover maps. As the convolutional neural network (CNN) has been shown to be effective in capturing the spatial characteristics of geographic objects and extrapolating calibrated methods to other study areas, it may be a useful approach to overcome limitations of current SRM methods. In this paper, a new SRM method based on the CNN (SRMCNN) is proposed and tested. Specifically, an encoder-decoder CNN is used to model the nonlinear relationship between coarse remote sensing images and fine-scale land cover maps. Two real-image experiments were conducted to analyze the effectiveness of the proposed method. The results demonstrate that the overall accuracy of the proposed SRMCNN method was 3% to 5% higher than that of two existing SRM methods. Moreover, the proposed SRMCNN method was validated by visualizing output features and analyzing the performance of different geographic objects.

Consumer confidence in the safety of milk and infant milk formula in China
Li, Saiwei ; Sijtsema, Siet J. ; Kornelis, Marcel ; Liu, Yumei ; Li, Shengli - \ 2019
Journal of Dairy Science 102 (2019)10. - ISSN 0022-0302 - p. 8807 - 8818.
consumer confidence - food safety - infant milk formula - trust

A series of food safety incidents related to domestically produced dairy in China harmed consumer confidence and caused a dramatic decrease in dairy consumption from 2008 to 2010. Compared with previous studies that mainly assessed consumer confidence in food or dairy in general, this study focused on 2 specific dairy products, milk and infant milk formula (IMF). Based on data from 934 Chinese consumers, confidence in the safety of milk and IMF was measured by using a multi-item scale with 2 dimensions—optimism and pessimism. We found that Chinese consumers were optimistic about the safety of milk and IMF but, at the same time, were concerned about the risks related to milk and IMF. Chinese consumers have less confidence in IMF than in milk. Structural equation modeling indicated that consumer trust in manufacturers and third parties in the dairy supply chain and confidence in other foods, such as meat and fish, can foster consumer confidence in the safety of milk and IMF, while the extent of recall of the melamine infant formula incident in 2008 and trait worry exert negative effects. In addition, consumers with more children or less family income are likely to be more confident in domestically produced IMF. These insights into consumer confidence and its determinants can assist dairy supply chains and regulatory institutions in formulating effective risk communication strategies to strengthen consumer confidence.

Predicting hydrological impacts of the Yangtze-to-Huaihe Water Diversion Project on habitat availability for wintering waterbirds at Caizi Lake
Li, Chunlin ; Li, Haifeng ; Zhang, Yong ; Zha, D. ; Zhao, Binbin ; Yang, Sen ; Zhang, Baowei ; Boer, Willem F. de - \ 2019
Journal of Environmental Management 249 (2019). - ISSN 0301-4797
Hydrological regime - Water project - Waterbird conservation - Wetland management - Yangtze

Quantifying the relationship between hydrological regime and habitat availability is the first step to predict potential impacts of water engineering projects on waterbirds, particularly in periodically flooded wetlands. The proposed Yangtze-to-Huaihe Water Diversion Project (YHWD) cuts through Caizi Lake, which is of international importance for wintering waterbirds. In order to explore the potential impacts of the project on habitat availability for the wintering waterbirds, we first built linear models to fit relationships between land cover patterns and water level dynamics in the lake, and then used generalized linear mixed models to test effects of habitat variables (water area, grassland area and mudflat area) on bird abundances of different functional groups. The avian habitat use differed among guilds, and was correlated with the land cover pattern, which was strongly dependent on seasonal water level fluctuations. Following water recession in autumn, the exposure of riparian habitats was more prominent in the eastern part of the lake, where the channel of the proposed YHWD project is located. This part of the lake is also where we located most of the important bird areas. Compared to the current situation, 54.3% of the grassland and 60.5% of the mudflats are predicted to be lost during winter due to the projected water level rise, resulting in reduced habitat availability for grass foragers, invertebrate eaters and tuber feeders. In order to mitigate potential impacts of the YHWD project, we suggest habitat compensations by construction of artificial habitats, and maintenance of water level regime at the whole lake by restoring similarity in water level fluctuations between Xizi Lake and Caizi Lake.

The Major Hurdle for Effective Baculovirus Transduction into Mammalian Cells Is Passing Early Endosomes
Hu, Liangbo ; Li, Yimeng ; Ning, Yun Jia ; Deng, Fei ; Vlak, Just M. ; Hu, Zhihong ; Wang, Hualin ; Wang, Manli - \ 2019
Journal of Virology 93 (2019)15. - ISSN 0022-538X
baculovirus - early endosome - entry - fusion - gene delivery - mammalian cells - transduction

Baculoviruses, although they infect insects in nature, can transduce a wide variety of mammalian cells and are therefore promising gene therapy vectors. However, baculovirus transduction into many mammalian cells is very inefficient, and the limiting stages and factors remain unknown. An important finding is that a short-duration trigger with low pH can significantly enhance virus transduction efficiency, but the mechanism is poorly understood. Herein, we performed a detailed comparative study on entry mechanisms of the prototypical baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) into insect and mammalian cells. The results showed that AcMNPV could be internalized into mammalian cells efficiently, but fusion in early endosomes (EEs) appeared to be the major obstacle. Measurement of endosomal pH suggested that virus fusion might be restricted under relatively high-pH conditions in mammalian cells. Interestingly, mutations of the major viral fusion protein GP64 that conferred decreased fusogenicity did not affect virus infection of insect cells, whereas virus transduction into mammalian cells was severely impaired, suggesting a more stringent dependence on GP64 fusogenicity for AcMNPV entry into mammalian cells than into insect cells. An increase in the fusogenicity of GP64 mutants resulting from low pH triggered the rescue of fusion-deficient recombinant virus transduction efficiency. Based on the above-described findings, the pH of EEs was specifically reduced with a Na+/K+-ATPase inhibitor, and the AcMNPV transduction of many mammalian cells indeed became highly efficient. This study not only revealed the roadblocks to mammalian cell entry of baculovirus but also provides a new strategy for improving baculovirus-based gene delivery and therapy.IMPORTANCE Baculoviruses can transduce a wide variety of mammalian cells but do so with low efficiency, which greatly limits their practical application as potential gene delivery vectors. So far, the understanding of baculovirus entry into mammalian cells is obscure, and the limiting stages and factors are unclear. In this study, by comparatively analyzing the mechanisms of baculovirus entry into mammalian and insect cells, virus fusion during the early stage of endocytosis was revealed as the major obstacle for efficient baculovirus transduction into mammalian cells. A higher fusogenicity of the major viral fusion protein GP64 was found to be required for virus entry into mammalian cells than for entry into insect cells. Interestingly, by decreasing the pH of early endosomes with a specific agent, virus transduction of a wide range of mammalian cells was greatly enhanced. This study uncovers the roadblocks to mammalian cell entry of baculoviruses and presents mechanisms to overcome the roadblocks.

Pathogen suppression by microbial volatile organic compounds in soils
Boer, Wietse de; Li, Xiaogang ; Meisner, Annelein ; Garbeva, Paolina - \ 2019
FEMS microbiology ecology 95 (2019)8. - ISSN 0168-6496
disease suppression - fungistasis - microbial interactions - soil atmosphere - soil microbial community - sustainable management strategies - volatile organic compounds

There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.

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