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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    Are the planning targets of liquid biofuel development achievable in China under climate change?
    Yan, Dan ; Liu, Litao ; Li, Jinkai ; Wu, Jiaqian ; Qin, Wei ; Werners, Saskia E. - \ 2021
    Agricultural Systems 186 (2021). - ISSN 0308-521X
    Climate change - Liquid biofuels - Marginal land - Non-grain energy crops
    Liquid biofuels from non-grain energy crops on marginal land could become an important substitute of gasoline in the transport sector, and offer the possibility to reduce competition with food crops for land resources. However, the cultivation of energy crops is facing profound challenges due to changing temperature and precipitation in the future. To assess the impact of climate change on the potential of liquid biofuels on marginal land in China, this study used a geographic information system-based approach combined with multiple factor analysis to identify the spatial distribution of marginal land suitable for nine major energy crops in China. Climate scenarios were generated based on bias-corrected results of five different climate models under two representative concentration pathways (RCP2.6 and 8.5). Results show that climate change is projected to have a substantial impact on the land availability for biofuel production in the 2050s under both RCPs. The total amount of marginal land suitable for energy crops was 170.2 million hectares for the period of 2010–2019, and would increase in the 2050s under both RCPs. The changing pattern of area are similar under both RCP 2.6 and 8.5, only the magnitude is different. All the species are projected to have a northward spread in China. The amount of marginal land suitable for all the energy crops is projected to increase in the 2050s, except for Miscanthus floridulus, and Miscanthus lutarioriparius under RCP 8.5. However, the potential productivity of the energy crops is projected to have a substantial decrease in the 2050s. The average yields of the energy crops are only about one fourth of their yields in the 2010s due to climate change. Combined with high costs of producing biofuels and numerous ecological tradeoffs, it is likely that liquid biofuels development using 1.5 and 2-generation energy crops does not have an optimistic perspective in China.
    Decoupling livestock and crop production at the household level in China
    Jin, Shuqin ; Zhang, Bin ; Wu, Bi ; Han, Dongmei ; Hu, Yu ; Ren, Chenchen ; Zhang, Chuanzhen ; Wei, Xun ; Wu, Yan ; Mol, Arthur P.J. ; Reis, Stefan ; Gu, Baojing ; Chen, Jie - \ 2020
    Nature Sustainability (2020). - ISSN 2398-9629

    Animal manure used to be the major source of additional nutrients and crucial for maintaining soil fertility and crop yield in traditional farming systems. However, it is increasingly not recycled, wasting vital resources and damaging the environment. By using long-term (1986–2017) data from a rural household survey (>20,000 households) across China, here we show that the share of rural households with both crop planting and livestock raising (CPLR) has sharply declined from 71% in 1986 to only 12% in 2017. Compared with households with only crop planting, the CPLR households apply less synthetic fertilizer and more manure per cropland area. However, manure production in one-third of CPLR households has exceeded the nutrient requirement of crop growth on their croplands. Rebuilding the links between livestock and croplands at a regional scale thus provides vital opportunities for the sustainable intensification of agriculture in China.

    OsPIN9, an auxin efflux carrier, is required for the regulation of rice tiller bud outgrowth by ammonium
    Hou, Mengmeng ; Luo, Feifei ; Wu, Daxia ; Zhang, Xuhong ; Lou, Manman ; Shen, Defeng ; Yan, Ming ; Mao, Chuanzao ; Fan, Xiaorong ; Xu, Guohua ; Zhang, Yali - \ 2020
    New Phytologist (2020). - ISSN 0028-646X
    ammonium - auxin transport - nitrate - OsPIN9 - rice - tiller bud elongation
    The degree of rice tillering is an important agronomic trait that can be markedly affected by nitrogen supply. However, less is known about how nitrogen-regulated rice tillering is related to polar auxin transport. Compared with nitrate, ammonium induced tiller development and was paralleled with increased 3H-indole-acetic acid (IAA) transport and greater auxin into the junctions. OsPIN9, an auxin efflux carrier, was selected as the candidate gene involved in ammonium-regulated tillering based on GeneChip data. Compared with wild-type plants, ospin9 mutants had fewer tillers, and OsPIN9 overexpression increased the tiller number. Additionally, OsPIN9 was mainly expressed in vascular tissue of the junction and tiller buds, and encoded a membrane-localised protein. Heterologous expression in Xenopus oocytes and yeast demonstrated that OsPIN9 is a functional auxin efflux transporter. More importantly, its RNA and protein levels were induced by ammonium but not by nitrate, and tiller numbers in mutants did not respond to nitrogen forms. Further advantages, including increased tiller number and grain yield, were observed in overexpression lines grown in the paddy field at a low-nitrogen rate compared with at a high-nitrogen rate. Our data revealed that ammonium supply and an auxin efflux transporter co-ordinately control tiller bud elongation in rice.
    Liming reduces soil phosphorus availability but promotes yield and P uptake in a double rice cropping system
    Liao, Ping ; Ros, Mart ; Gestel, Natasja van; Sun, Yan Ni ; Zhang, Jun ; Huang, Shan ; Zeng, Yong Jun ; Wu, Zi Ming ; Groeningen, Kees Jan van - \ 2020
    Journal of Integrative Agriculture 19 (2020)11. - ISSN 2095-3119 - p. 2807 - 2814.
    crop yield - phosphatase activity - phosphorus availability - soil acidification - subtropical

    Liming is often applied to alleviate soil acidification and increase crop yield on acidic soils, but its effect on soil phosphorus (P) availability is unclear, particularly in rice paddies. The objective of this study was to examine the effect of liming on rice production, yield and P uptake in a three-year field experiment in a double rice cropping system in subtropical China. We also conducted an incubation experiment to investigate the direct effect of liming on soil available P and phosphatase activities on paddy soils in the absence of plants. In the incubation experiment, liming reduced soil P availability (measured as Olsen-extractable P) by 14–17% and inhibited the activity of soil acid phosphatase. Nonetheless, lime application increased grain yield, biomass, and P uptake in the field. Liming increased grain yield and P uptake more strongly for late rice (26 and 21%, respectively) than for early rice (15 and 8%, respectively). Liming reduced the concentration of soil available P in the field as well, reflecting the increase in rice P uptake and the direct negative effect of liming on soil P availability. Taken together, these results suggest that by stimulating rice growth, liming can overcome direct negative effects on soil P availability and increase plant P uptake in this acidic paddy soil where P is not the limiting factor.

    A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema
    Ta, Le Duc Huy ; Chan, James Chun Yip ; Yap, Gaik Chin ; Purbojati, Rikky W. ; Drautz-Moses, Daniela I. ; Koh, Yanqing Michelle ; Tay, Carina Jing Xuan ; Huang, Chiung Hui ; Kioh, Dorinda Yan Qin ; Woon, Jia Yun ; Tham, Elizabeth Huiwen ; Loo, Evelyn Xiu Ling ; Shek, Lynette P.C. ; Karnani, Neerja ; Goh, Anne ; Bever, Hugo P.S. Van; Teoh, Oon Hoe ; Chan, Yiong Huak ; Lay, Christophe ; Knol, Jan ; Yap, Fabian ; Tan, Kok Hian ; Chong, Yap Seng ; Godfrey, Keith M. ; Kjelleberg, Staffan ; Schuster, Stephan C. ; Chan, Eric Chun Yong ; Lee, Bee Wah - \ 2020
    Gut Microbes 12 (2020)1. - ISSN 1949-0976 - p. 1 - 21.
    allergen sensitization - atopic dermatitis - atopic eczema - Early life - gut metabolome - gut microbiome - SCFA

    Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk. We measured the functionality of the gut microbiome and metabolome of 63 infants between ages 3 weeks and 12 months with well-defined eczema cases and controls in a sub-cohort from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) mother-offspring cohort. At 3 weeks, the microbiome and metabolome of allergen-sensitized atopic eczema infants were characterized by an enrichment of Escherichia coli and Klebsiella pneumoniae, associated with increased stool D-glucose concentration and increased gene expression of associated virulence factors. A delayed colonization by beneficial Bacteroides fragilis and subsequent delayed accumulation of butyrate and propionate producers after 3 months was also observed. Here, we describe an aberrant developmental trajectory of the gut microbiome and stool metabolome in allergen sensitized atopic eczema infants. The infographic describes an impaired developmental trajectory of the gut microbiome and metabolome in allergen-sensitized atopic eczema (AE) infants and infer its contribution in modulating allergy risk in the Singaporean mother-offspring GUSTO cohort. The key microbial signature of AE is characterized by (1) an enrichment of Escherichia coli and Klebsiella pneumoniae which are associated with accumulation of pre-glycolysis intermediates (D-glucose) via the trehalose metabolic pathway, increased gene expression of associated virulence factors (invasin, adhesin, flagellin and lipopolysaccharides) by utilizing ATP from oxidative phosphorylation and delayed production of butyrate and propionate, (2) depletion of Bacteroides fragilis which resulted in lower expression of immunostimulatory bacterial cell envelope structure and folate (vitamin B9) biosynthesis pathway, and (3) accompanied depletion of bacterial groups with the ability to derive butyrate and propionate through direct or indirect pathways which collectively resulted in reduced glycolysis, butyrate and propionate biosynthesis.

    Bayesian linear inverse problems in regularity scales
    Gugushvili, Shota ; Vaart, Aad Van Der; Yan, Dong - \ 2020
    Annales de l'Institut Henri Poincaré, Probabilités et Statistiques 56 (2020)3. - ISSN 0246-0203 - p. 2081 - 2107.
    Adaptive estimation - Gaussian prior - Hilbert scale - Linear inverse problem - Nonparametric Bayesian estimation - Posterior contraction rate - Random series prior - Regularity scale - White noise

    We obtain rates of contraction of posterior distributions in inverse problems defined by scales of smoothness classes. We derive abstract results for general priors, with contraction rates determined by Galerkin approximation. The rate depends on the amount of prior concentration near the true function and the prior mass of functions with inferior Galerkin approximation. We apply the general result to non-conjugate series priors, showing that these priors give near optimal and adaptive recovery in some generality, Gaussian priors, and mixtures of Gaussian priors, where the latter are also shown to be near optimal and adaptive. The proofs are based on general testing and approximation arguments, without explicit calculations on the posterior distribution. We are thus not restricted to priors based on the singular value decomposition of the operator. We illustrate the results with examples of inverse problems resulting from differential equations.

    COSTE: Complexity-based OverSampling TEchnique to alleviate the class imbalance problem in software defect prediction
    Feng, Shuo ; Keung, Jacky ; Yu, Xiao ; Xiao, Yan ; Bennin, Kwabena Ebo ; Kabir, Md Alamgir ; Zhang, Miao - \ 2020
    Information and Software Technology 129 (2020). - ISSN 0950-5849
    Class imbalance - Effort-aware defect prediction - MAHAKIL - Oversampling - SMOTE - Software defect prediction
    Context: Generally, there are more non-defective instances than defective instances in the datasets used for software defect prediction (SDP), which is referred to as the class imbalance problem. Oversampling techniques are frequently adopted to alleviate the problem by generating new synthetic defective instances. Existing techniques generate either near-duplicated instances which result in overgeneralization (high probability of false alarm, pf) or overly diverse instances which hurt the prediction model's ability to find defects (resulting in low probability of detection, pd). Furthermore, when existing oversampling techniques are applied in SDP, the effort needed to inspect the instances with different complexity is not taken into consideration. Objective: In this study, we introduce Complexity-based OverSampling TEchnique (COSTE), a novel oversampling technique that can achieve low pf and high pd simultaneously. Meanwhile, COSTE also performs better in terms of Norm(popt) and ACC, two effort-aware measures that consider the testing effort. Method: COSTE combines pairs of defective instances with similar complexity to generate synthetic instances, which improves the diversity within the data, maintains the ability of prediction models to find defects, and takes the different testing effort needed for different instances into consideration. We conduct experiments to compare COSTE with Synthetic Minority Oversampling TEchnique, Borderline-SMOTE, Majority Weighted Minority Oversampling TEchnique and MAHAKIL. Results: The experimental results on 23 releases of 10 projects show that COSTE greatly improves the diversity of the synthetic instances without compromising the ability of prediction models to find defects. In addition, COSTE outperforms the other oversampling techniques under the same testing effort. The statistical analysis indicates that COSTE's ability to outperform the other oversampling techniques is significant under the statistical Wilcoxon rank sum test and Cliff's effect size. Conclusion: COSTE is recommended as an efficient alternative to address the class imbalance problem in SDP.
    A Web Tool to Map Research Impacts Via Altmetrics
    Fernando Monsores Passos Maia, Luís ; Lenzi, Marcia ; Rabello, Elaine ; Oliveira, Jonice - \ 2020
    In: The Web Conference 2020 - Companion of the World Wide Web Conference, WWW 2020. - Association for Computing Machinery (The Web Conference 2020 - Companion of the World Wide Web Conference, WWW 2020 ) - ISBN 9781450370240 - p. 235 - 239.
    altmetrics - bibliometrics - chikungunya - social network analysis - zika
    Currently, there is a big concern on governments and research institutes on assessing the population awareness about the scientific innovations, such as new food production technologies and the development of drugs against emerging and neglected diseases. There is an unmet demand for new ways to show the impact of scientific research on social media (population's main communication vehicles) and assess the social outreach of the scientific output. This article presents a novel web tool to map research impacts via Altmetrics, wich are alternative metrics based on the exchange of scientific knowledge on social media and online environments.
    The NLR Protein Encoded by the Resistance Gene Ty-2 Is Triggered by the Replication-Associated Protein Rep/C1 of Tomato Yellow Leaf Curl Virus
    Shen, Xuexue ; Yan, Zhe ; Wang, Xiaoxuan ; Wang, Yinlei ; Arens, Marjon ; Du, Yongchen ; Visser, Richard G.F. ; Kormelink, Richard ; Bai, Yuling ; Wolters, Anne Marie A. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    avirulence factor - cloning - NLR gene - Rep/C1 - Ty-2 - TYLCV

    The whitefly-transmitted tomato yellow leaf curl virus (TYLCV) is one of the most destructive viral pathogens of cultivated tomato. To combat TYLCV, resistance gene Ty-2 has been introduced into cultivated tomato (Solanum lycopersicum) from wild tomato species Solanum habrochaites by interspecific crossing. Introgression lines with Ty-2 contain a large inversion compared with S. lycopersicum, which causes severe suppression of recombination and has hampered the cloning of Ty-2 so far. Here, we report the fine-mapping and cloning of Ty-2 using crosses between a Ty-2 introgression line and several susceptible S. habrochaites accessions. Ty-2 was shown to encode a nucleotide-binding leucine-rich repeat (NLR) protein. For breeding purposes, a highly specific DNA marker tightly linked to the Ty-2 gene was developed permitting marker-assisted selection. The resistance mediated by Ty-2 was effective against the Israel strain of TYLCV (TYLCV-IL) and tomato yellow leaf curl virus-[China : Shanghai2] (TYLCV-[CN : SH2]), but not against tomato yellow leaf curl Sardinia virus (TYLCSV) and leafhopper-transmitted beet curly top virus (BCTV). By co-infiltration experiments we showed that transient expression of the Rep/C1 protein of TYLCV, but not of TYLCSV triggered a hypersensitive response (HR) in Nicotiana benthamiana plants co-expressing the Ty-2 gene. Our results indicate that the Rep/C1 gene of TYLCV-IL presents the avirulence determinant of Ty-2-mediated resistance.

    2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
    Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
    Archives of Virology 165 (2020). - ISSN 0304-8608 - p. 3023 - 3072.

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

    High-intensity ultrasound treatment on soy protein after selectively proteolyzing glycinin component: Physical, structural, and aggregation properties
    Xia, Wenjie ; Pan, Siyi ; Cheng, Zhe ; Tian, Yan ; Huang, Xingjian - \ 2020
    Foods 9 (2020)6. - ISSN 2304-8158
    Gelation - High-intensity ultrasound - Pepsin - Selective proteolysis - Soluble aggregates

    In this study, a novel method called selective proteolysis was applied to the glycinin component of soy protein isolate (SPI), and a degraded glycinin hydrolysate (DGH) was obtained. The effects of high-intensity ultrasound (HIU) treatment (20 kHz at 400 W, 0, 5, 20, and 40 min) on the physical, structural, and aggregation properties of DGH were investigated with the aim to reveal the influence of the selectively hydrolyzing glycinin component on the HIU treatment of soy protein. The effects of HIU on DGH and a control SPI (CSPI) were both time-dependent. HIU induced the formation of soluble aggregates in both samples at an early stage, while it dissociated these newly formed aggregates after a longer duration. Selectively hydrolyzing glycinin contributed to the soluble aggregation by exposing the compact protein structure and producing small protein fractions. The larger extent of hydrophobic interactions and disulfide bonds imparted a higher stability to the soluble protein aggregates formed in DGH. As a result, DGH displayed more ordered secondary structures, a higher solubility, and better gelling properties after the HIU treatment, especially at 20 min. The results of this study will be beneficial to the scientific community as well as industrial application.

    Structural basis for diamide modulation of ryanodine receptor
    Ma, Ruifang ; Haji-Ghassemi, Omid ; Ma, Dan ; Jiang, Heng ; Lin, Lianyun ; Yao, Li ; Samurkas, Arthur ; Li, Yuxin ; Wang, Yiwen ; Cao, Peng ; Wu, Shian ; Zhang, Yan ; Murayama, Takashi ; Moussian, Bernard ; Petegem, Filip Van; Yuchi, Zhiguang - \ 2020
    Nature Chemical Biology 16 (2020). - ISSN 1552-4450 - p. 1246 - 1254.

    The diamide insecticide class is one of the top-selling insecticides globally. They are used to control a wide range of pests by targeting their ryanodine receptors (RyRs). Here, we report the highest-resolution cryo-electron microscopy (cryo-EM) structure of RyR1 in the open state, in complex with the anthranilic diamide chlorantraniliprole (CHL). The 3.2-Å local resolution map facilitates unambiguous assignment of the CHL binding site. The molecule induces a conformational change by affecting the S4–S5 linker, triggering channel opening. The binding site is further corroborated by mutagenesis data, which reveal how diamide insecticides are selective to the Lepidoptera group of insects over honeybee or mammalian RyRs. Our data reveal that several pests have developed resistance via two mechanisms, steric hindrance and loss of contact. Our results provide a foundation for the development of highly selective pesticides aimed at overcoming resistance and therapeutic molecules to treat human myopathies. [Figure not available: see fulltext.].

    A new TROPOMI product for tropospheric NO2 columns over East Asia with explicit aerosol corrections
    Liu, Mengyao ; Lin, Jintai ; Kong, Hao ; Boersma, K.F. ; Eskes, Henk ; Kanaya, Yugo ; He, Qin ; Tian, Xin ; Qin, Kai ; Xie, Pinhua ; Spurr, Robert ; Ni, Ruijing ; Yan, Yingying ; Weng, Hongjian ; Wang, Jingxu - \ 2020
    Atmospheric Measurement Techniques 13 (2020)8. - ISSN 1867-1381 - p. 4247 - 4259.

    We present a new product with explicit aerosol corrections, POMINO-TROPOMI, for tropospheric nitrogen dioxide (NO2) vertical column densities (VCDs) over East Asia, based on the newly launched TROPOspheric Monitoring Instrument with an unprecedented high horizontal resolution. Compared to the official TM5-MP-DOMINO (OFFLINE) product, POMINO-TROPOMI shows stronger concentration gradients near emission source locations and better agrees with MAX-DOAS measurements (R2 D 0:75; NMB D 0:8% versus R2 D 0:68, NMB D 41:9 %). Sensitivity tests suggest that implicit aerosol corrections, as in TM5-MP-DOMINO, lead to underestimations of NO2 columns by about 25%over the polluted northern East China region. Reducing the horizontal resolution of a priori NO2 profiles would underestimate the retrieved NO2 columns over isolated city clusters in western China by 35% but with overestimates of more than 50% over many offshore coastal areas. The effect of a priori NO2 profiles is more important under calm conditions.

    Yield components, reproductive allometry and the tradeoff between grain yield and yield stability in dryland spring wheat
    Du, Yan Lei ; Xi, Yue ; Cui, Ting ; Anten, Niels P.R. ; Weiner, Jacob ; Li, Xinmao ; Turner, Neil C. ; Zhao, Yi Min ; Li, Feng Min - \ 2020
    Field Crops Research 257 (2020). - ISSN 0378-4290
    Risk reduction - Smallholder farms - Variety screening - Wheat breeding - Yield stability

    Yield improvement for smallholder farmers in developing countries via crop breeding has been slow, in part because breeders have focused primarily on higher yields rather than stability of yield across environments. We investigated the relationships between (i) grain yield and yield-component traits, (ii) grain yield and yield stability, and (iii) reproductive (R) and vegetative (V) biomass in a field experiment with 18 spring wheat genotypes varying from landraces to recently-released breeding lines in a semiarid region under three different levels of precipitation. Genotypic differences in grain yield varied with the environment. The relationship between grain yield and yield components was also dependent on the environment, making it difficult to identify early-screening parameters for use in breeding programs. A genotype main effects and genotype by environment interaction effect analysis (GGE) showed a negative relationship between mean grain yield and yield stability across environments. There were significant differences among genotypes in the allometric exponent of the R-V relationship (slope of the log R – log V relationship). For the three highest yielding but less stable genotypes, this slope value was > 1, while the five lowest yielding, but more stable genotypes, it was < 1. We hypothesize that the tradeoff between grain yield and yield stability reported here is biologically constrained and cannot be eliminated through breeding. Therefore, a balance between yield stability and high yield should be considered in future wheat breeding programs for smallholder farmers, rather than attempting to improve both.

    Resistance to Fusarium head blight and mycotoxin accumulation among 129 wheat cultivars from different ecological regions in China
    Yan, Z. ; Zhang, H. ; Lee, T.A.J. Van Der; Waalwijk, C. ; Diepeningen, A.D. Van; Deng, Y. ; Feng, J. ; Liu, T. ; Chen, W. - \ 2020
    World Mycotoxin Journal 13 (2020)2. - ISSN 1875-0710 - p. 189 - 199.
    Disease index - Fusarium head blight - Resistance - Toxin - Wheat

    A total of 129 wheat cultivars collected from local breeders in four ecological regions in China was evaluated for Fusarium head blight resistance after natural infection under epidemic conditions. The disease index was scored and seven toxins concentrations were determined by UPLC-MS/MS. The disease index ranged from 6.3 to 80.9% and a strong correlation was found between the regions from which the cultivars originate and disease index. The middle and lower reaches of Yangtze River Region showed the highest disease resistance, followed by the upper reaches of the Yangtze River Region. FHB resistance of cultivars from northern and southern Huanghuai Region was lowest and all cultivars in these regions are highly or moderately susceptible. Disease index was significantly correlated with toxin accumulation on nation scale, but no clear correlation was found within most ecological regions. The toxin accumulation was also not well correlated with resistant levels. As the incidence of FHB has increased dramatically over the last decade, improved FHB resistance in cultivars is urgently needed. We recommend that besides scoring for disease index also mycotoxin accumulation in cultivars is incorporated in breeding procedures and the evaluation of cultivars.

    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.

    The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion
    Gu, Yian ; Dong, Ke ; Geisen, Stefan ; Yang, Wei ; Yan, Yaner ; Gu, Dalu ; Liu, Naisen ; Borisjuk, Nikolai ; Luo, Yuming ; Friman, Ville Petri - \ 2020
    Plant and Soil 452 (2020). - ISSN 0032-079X - p. 105 - 117.
    Diversity - Microbial inoculation - Microbial transplants - Plant growth-promotion - Rhizosphere microbiota - Soil functioning

    Aims: Microbial inoculation has been proposed as a potential approach for rhizosphere engineering. However, it is still unclear to what extent successful plant growth-promoting effects are driven by the origin of the microbial inocula and which taxa are responsible for the plant-beneficial effects. Methods: We conducted a microbial transplant experiment by using different microbial inocula (and nutrient controls) isolated from forest, soybean and tomato field soils and determined their effects on tomato plant biomass and nutrient assimilation in sterilized tomato soil. Rhizosphere bacterial communities were compared at the end of the experiment and correlative and machine learning analyses used to identify potential keystone taxa associated with the plant growth-promotion. Results: Microbial inoculants had a clear positive effect on plant growth compared to control nutrient inoculants. Specifically, positive effects on the plant biomass were significantly associated with microbial inoculants from the forest and soybean field soils, while microbial inoculants from the forest and tomato field soils had clear positive effects on the plant nutrient assimilation. Soil nutrients alone had relatively minor effects on rhizosphere bacterial communities. However, the origin of microbial inoculants had clear effects on the structure of bacterial community structure with tomato and soybean inoculants having positive effects on the diversity and abundance of bacterial communities, respectively. Specifically, Streptomyces, Luteimonas and Enterobacter were identified as the potential keystone genera affecting plant growth. Conclusions: The origin of soil microbiome inoculant can predictably influence plant growth and nutrient assimilation and that these effects are associated with certain key bacterial genera.

    Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System
    Wang, Shilei ; Xiong, Wu ; Wang, Yuqiao ; Nie, Yao ; Wu, Qun ; Xu, Yan ; Geisen, Stefan - \ 2020
    mSystems 5 (2020)4. - ISSN 2379-5077
    We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.
    Plant architectural responses in simultaneous maize/soybean strip intercropping do not lead to a yield advantage
    Li, Shuangwei ; Evers, Jochem B. ; Werf, Wopke van der; Wang, Ruili ; Xu, Zhaoli ; Guo, Yan ; Li, Baoguo ; Ma, Yuntao - \ 2020
    Annals of Applied Biology 177 (2020)2. - ISSN 0003-4746 - p. 195 - 210.
    architectural response - border row effect - growth - intercropping - land equivalent ratio

    Maize/soybean strip intercropping is a commonly used system throughout China with high crop yields at reduced nutrient input compared to sole maize. Maize is the taller crop, and due to its dominance in light capture over soybean in the intercrop, maize is expected to outperform maize in sole cropping. Conversely, soybean is the subordinate crop and intercropped soybean plants are expected to perform worse than sole soybean. Crop plants show plastic responses in plant architecture to their growing conditions to forage for light and avoid shading. There is little knowledge on plant architectural responses to growing conditions in simultaneous (non-relay) intercropping and their relationship to species yields. A two-year field experiment with two simultaneous maize/soybean intercropping systems with narrow and wide strips was conducted to characterise architectural traits of maize and soybean plants grown as intercrop and sole crops. Intercropped maize plants, especially those in border rows, had substantially greater leaf area, biomass and yield than maize plants in sole crops. Intercropped soybean plants, especially those in border rows, had lower leaf area, biomass and yield than sole soybean plants. Overall intercrop performance was similar to that of sole crops, with the land equivalent ratio (LER) being only slightly greater than one (1.03–1.08). Soybean displayed typical shade avoidance responses in the intercrop, such as greater internode elongation and changes in specific leaf area, but these responses could not overcome the consequences of the competition with the taller maize plants. Therefore, in contrast to relay intercrop systems, in the studied simultaneous maize/soybean system, plastic responses did not contribute to practically relevant increases in resource capture and yield at whole system (i.e., intercrop) level.

    The gender wage gap among China’s rural–urban migrants
    Wu, Yan ; Pieters, Janneke ; Heerink, Nico - \ 2020
    Review of Development Economics (2020). - ISSN 1363-6669
    China - gender wage gap - migration

    In this study, we present new empirical evidence on gender wage differences among rural–urban migrants in China. We use a data set that includes migrants residing in urban communities and those living at their workplaces—the latter were not included in the previous studies. We find that the gender wage gap among migrants is 16%–18% and does not differ between migrants living at workplaces and those living in urban communities. However, gender differences in industry sorting play a more important role for migrants living at their workplaces, whereas differences in education and experience are of importance for those living in urban communities. Overall, differences in the returns to characteristics are the main driver of the gender wage gap, especially for migrants living in urban communities.

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