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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    More Than Smell-COVID-19 Is Associated With Severe Impairment of Smell, Taste, and Chemesthesis
    Parma, Valentina ; Ohla, Kathrin ; Veldhuizen, Maria G. ; Niv, Masha Y. ; Kelly, Christine E. ; Bakke, Alyssa J. ; Cooper, Keiland W. ; Bouysset, Cédric ; Pirastu, Nicola ; Dibattista, Michele ; Kaur, Rishemjit ; Liuzza, Marco Tullio ; Pepino, Marta Y. ; Schöpf, Veronika ; Pereda-Loth, Veronica ; Olsson, Shannon B. ; Gerkin, Richard C. ; Rohlfs Domínguez, Paloma ; Albayay, Javier ; Farruggia, Michael C. ; Bhutani, Surabhi ; Fjaeldstad, Alexander W. ; Kumar, Ritesh ; Menini, Anna ; Bensafi, Moustafa ; Sandell, Mari ; Konstantinidis, Iordanis ; Pizio, Antonella Di; Genovese, Federica ; Öztürk, Lina ; Thomas-Danguin, Thierry ; Frasnelli, Johannes ; Boesveldt, Sanne ; Saatci, Özlem ; Saraiva, Luis R. ; Lin, Cailu ; Golebiowski, Jérôme ; Hwang, Liang Dar ; Ozdener, Mehmet Hakan ; Guàrdia, Maria Dolors ; Laudamiel, Christophe ; Ritchie, Marina ; Havlícek, Jan ; Pierron, Denis ; Roura, Eugeni ; Navarro, Marta ; Nolden, Alissa A. ; Lim, Juyun ; Whitcroft, Katherine L. ; Colquitt, Lauren R. - \ 2020
    Chemical Senses 45 (2020)7. - ISSN 0379-864X - p. 609 - 622.
    head and neck surgery - olfaction - somatosensation

    Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change ±100) revealed a mean reduction of smell (-79.7 ± 28.7, mean ± standard deviation), taste (-69.0 ± 32.6), and chemesthetic (-37.3 ± 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis. The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.

    Does forestland possession enhance households’ access to credit?—Examining China's forestland mortgage policy
    Dong, Jiayun ; Liang, Wenyuan ; Liu, Weiping ; Liu, Jinlong ; Managi, Shunsuke - \ 2020
    Economic Analysis and Policy 68 (2020). - ISSN 0313-5926 - p. 78 - 87.
    China's forest tenure reform - Forestland possession - Loan - Mortgage

    Many countries have seen a rising demand for forest policy reform. This paper explores the effects of China's forestland mortgage policy, a supporting measure for collective forest tenure reform, on household credit access. In theory, the forestland mortgage policy could have three impacts on households: (1) forestland possession could change households’ willingness to access credit (2) forestland possession could enhance household access to credit, and (3) the contract structure follows the theoretical predictions of the credit contract design mechanism. Our results show that households’ willingness to enroll in the mortgage policy as well as their potential to obtain credit increased when households possessed larger areas of forestland. However, the proportion of households that successfully obtained credit were fairly modest. Meanwhile, we found a positive relationship between collateralized forestland and the amount of the forestland mortgage loan, and a negative relationship between collateralized forestland and the interest rate. These findings are consistent with the theoretical predictions of the contract mechanism design. The existing forestland mortgage policy has increased households’ credit access to some extent; however, there is much room for improvement from a policy perspective. This requires divising policy arrangements that would facilitate a fully developed credit market available to households. Forest tenure mortgage loans alone may not be able to fully meet households’ financial needs.

    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.

    Assessing long-term spatial movement of wheat area across China
    Fan, Lingling ; Chen, Shi ; Liang, Shefang ; Sun, Xiao ; Chen, Hao ; You, Liangzhi ; Wu, Wenbin ; Sun, Jing ; Yang, Peng - \ 2020
    Agricultural Systems 185 (2020). - ISSN 0308-521X
    China - Climate change - Driving factors - Geographical centroid - Wheat area

    In the context of climate change, assessing spatiotemporal dynamics of crop production is becoming an important component of food security, which is one of the United Nations Sustainable Development Goals. Wheat is a major staple food that is grown worldwide. Although many studies have analyzed wheat production, spatial analyses, particularly geographical centroid (GC) studies, are rare. The GC studies are of important scientific value and policy implications. This study aims to estimate the GC movement of wheat area (including winter and spring wheat) from 1949 to 2014 in China (the largest wheat-producing country). A centroid model was adopted to measure GC movements, and then a regression analysis was conducted to understand the driving factors of wheat area changes (as area changes lead to GC movement). Then multiple scenario analyses were built to study GC movement driven by climatic factors alone. The net GC movements of winter and spring wheat area were estimated at 31 km northwestward and 692 km southwestward from 1949 to 2014, with both displaying a turning point in their movement routes around 1970s (the GC of winter wheat area moved 89 km before 1970s and 66 km after 1970s; while the GC of spring wheat area moved 89 km before 1970s and 799 km after 1970s); furthermore, the major driving factor of winter wheat GC movement is a socioeconomic factor (i.e., expanded irrigation area) while that of spring wheat GC movement is a climatic factor (i.e., temperature) among the factors considered in this study. Our “climate only” scenarios highlighted that the impact of temperature on GC movement of winter wheat is more significant than that of precipitation. We assessed the spatiotemporal movement of wheat area to better understand its production dynamics in response to climate change and human activities. This study provides scientific evidence for policymakers and related stakeholders in China and other countries regarding food production patterns and planting decisions.

    Spatiotemporal dynamics of the northern limit of winter wheat in China using MODIS time series images
    Chen, Shi ; Fan, Lingling ; Liang, Shefang ; Chen, Hao ; Sun, Xiao ; Hu, Yanan ; Liu, Zhenhuan ; Sun, Jing ; Yang, Peng - \ 2020
    Remote Sensing 12 (2020)15. - ISSN 2072-4292
    Crop mapping - MODIS EVI2 - Northern China - Northern limit of winter wheat - Time series classification

    Studying the spatiotemporal changes of the northern limit of winter wheat (NLWW) in China is important to ensure regional food security and deal with the effects of climate change. Previous studies mainly used climate indicators to analyze the variation of the potential NLWW in different historical periods, while little attention has been paid to the actual migrations and changes of the NLWW. The objectives of the present study were three-fold: (i) to map the spatial distribution of winter wheat in northern China in 2001, 2007, 2014 and 2019; (ii) to extract the actual NLWW; and (iii) to quantitatively explore the dynamics of the NLWW. First, we adopted the "combining variations before and after estimated heading dates" method to map the winter wheat in northern China based on time series MODIS EVI2 data. Second, we used the kernel density estimation algorithm to extract the actual NLWW in four historical periods. Finally, the fishnet method was utilized to quantitatively analyze the direction and distance of the spatiotemporal changes of the NLWW. The results demonstrated that the NLWW has exhibited a marked fluctuating trend of migration southward, with a 37-km shift in latitude over the past 20 years. The elevation limit of winter wheat planting was around 1600 m; however, the centroid of winter wheat planting has shifted slowly to lower elevations. There was a gap between the actual NLWW and the potential NLWW. The reason for this gap was that the actual NLWW moved southward under the interacting effects of human activities and climate change, while the potential NLWW moved northward due to climate change. The results of this study are of great scientific value in the formulation of winter wheat planting strategies in climate-sensitive areas to respond to climate change and ensure food security.

    Characteristics of circular rna expression profiles of porcine granulosa cells in healthy and atretic antral follicles
    Meng, Li ; Teerds, Katja ; Tao, Jian ; Wei, Hengxi ; Jaklofsky, Marcel ; Zhao, Zhihong ; Liang, Yaodi ; Li, Li ; Wang, Chi Chiu ; Zhang, Shouquan - \ 2020
    International Journal of Molecular Sciences 21 (2020)15. - ISSN 1661-6596 - p. 1 - 25.
    Antral follicular atresia - CircRNA expression profiles - Granulosa cell apoptosis

    Circular RNAs (circRNAs) are thought to play essential roles in multiple biological processes, including apoptosis, an important process in antral follicle atresia. We aimed to investigate the potential involvement of circRNAs in granulosa cell apoptosis and thus antral follicle atresia. CircRNA expression profiles were generated from porcine granulosa cells isolated from healthy antral (HA) and atretic antral (AA) follicles. Over 9632 circRNAs were identified, of which 62 circRNAs were differentially expressed (DE-circRNAs). Back-splicing, RNase R resistance, and stability of DE-circRNAs were validated, and miRNA binding sites and related target genes were predicted. Two exonic circRNAs with low false discovery rate (FDR) high fold change, miRNA binding sites, and relevant biological functions—circ_CBFA2T2 and circ_KIF16B—were selected for further characterization. qRT-PCR and linear regression analysis confirmed expression and correlation of the targeted genes—the antioxidant gene GCLC (potential target of circ_CBFA2T2) and the apoptotic gene TP53 (potential target of circ_KIF16B). Increased mRNA content of TP53 in granulosa cells of AA follicles was further confirmed by strong immunostaining of both p53 and its downstream target pleckstrin homology like domain family a member 3 (PHLDA3) in AA follicles compared to negligible staining in granulosa cells of HA follicles. Therefore, we concluded that aberrantly expressed circRNAs presumably play a potential role in antral follicular atresia.

    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.

    Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia
    Zohner, Constantin M. ; Mo, Lidong ; Renner, Susanne S. ; Svenning, Jens Christian ; Vitasse, Yann ; Benito, Blas M. ; Ordonez, Alejandro ; Baumgarten, Frederik ; Bastin, Jean François ; Sebald, Veronica ; Reich, Peter B. ; Liang, Jingjing ; Nabuurs, Gert Jan ; De-Migueln, Sergio ; Alberti, Giorgio ; Antón-Fernández, Clara ; Balazy, Radomir ; Brändli, Urs Beat ; Chen, Han Y.H. ; Chisholm, Chelsea ; Cienciala, Emil ; Dayanandan, Selvadurai ; Fayle, Tom M. ; Frizzera, Lorenzo ; Gianelle, Damiano ; Jagodzinski, Andrzej M. ; Jaroszewicz, Bogdan ; Jucker, Tommaso ; Kepfer-Rojas, Sebastian ; Khan, Mohammed Latif ; Kim, Hyun Seok ; Korjus, Henn ; Johannsen, Vivian Kvist ; Laarmann, Diana ; Langn, Mait ; Zawila-Niedzwiecki, Tomasz ; Niklaus, Pascal A. ; Paquette, Alain ; Pretzsch, Hans ; Saikia, Purabi ; Schall, Peter ; Seben, Vladimír ; Svoboda, Miroslav ; Tikhonova, Elena ; Viana, Helder ; Zhang, Chunyu ; Zhao, Xiuhai ; Crowther, Thomas W. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)22. - ISSN 0027-8424
    Climate change - Freezing damage - Late frost - Phenology - Spring leaf-out

    Late-spring frosts (LSFs) affect the performance of plants and animals across the world's temperate and boreal zones, but despite their ecological and economic impact on agriculture and forestry, the geographic distribution and evolutionary impact of these frost events are poorly understood. Here, we analyze LSFs between 1959 and 2017 and the resistance strategies of Northern Hemisphere woody species to infer trees' adaptations for minimizing frost damage to their leaves and to forecast forest vulnerability under the ongoing changes in frost frequencies. Trait values on leaf-out and leaf-freezing resistance come from up to 1,500 temperate and boreal woody species cultivated in common gardens. We find that areas in which LSFs are common, such as eastern North America, harbor tree species with cautious (late-leafing) leaf-out strategies. Areas in which LSFs used to be unlikely, such as broad-leaved forests and shrublands in Europe and Asia, instead harbor opportunistic tree species (quickly reacting to warming air temperatures). LSFs in the latter regions are currently increasing, and given species' innate resistance strategies, we estimate that ∼35% of the European and ∼26% of the Asian temperate forest area, but only ∼10% of the North American, will experience increasing late-frost damage in the future. Our findings reveal region-specific changes in the spring-frost risk that can inform decision-making in land management, forestry, agriculture, and insurance policy.

    Granule-based immobilization and activity enhancement of anammox biomass via PVA/CS and PVA/CS/Fe gel beads
    Wang, Jinxing ; Liang, Jidong ; Sun, Li ; Li, Gaigai ; Temmink, Hardy ; Rijnaarts, Huub H.M. - \ 2020
    Bioresource Technology 309 (2020). - ISSN 0960-8524
    Aggregation - Anammox - Gel beads - Immobilization

    Granule-based immobilization of anammox biomass assisted by polyvinyl alcohol/chitosan (PVA/CS) and PVA/CS/Fe gel beads was studied, via the operation of three identical up-flow reactors (R1 without gel beads, R2 with PVA/CS, R3 with PVA/CS/Fe) for 203 days. In the end, the nitrogen removal rates (NRR) were 5.3 ± 0.4, 10.0 ± 0.3 and 13.9 ± 0.5 kg-N m−3 d−1 for R1, R2 and R3, respectively. The porous PVA/CS and PVA/CS/Fe created a suitable eco-niche for anammox bacteria to grow and attach, thus being retained in the reactor. The EPS entangles newly grown cells within the gel beads, resulting in compact aggregation. The interaction between Fe ions added to PVA/CS/Fe gel beads and negatively charged EPS groups strongly promoted granule strength and compactness. The immobilization method proposed by this study was found to effectively improve biomass retention in the reactors, which is promising for advanced anammox process applications.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    Silicon-Free SuFEx Reactions of Sulfonimidoyl Fluorides : Scope, Enantioselectivity, and Mechanism
    Liang, Dong Dong ; Streefkerk, Dieuwertje E. ; Jordaan, Daan ; Wagemakers, Jorden ; Baggerman, Jacob ; Zuilhof, Han - \ 2020
    Angewandte Chemie-International Edition 59 (2020)19. - ISSN 1433-7851 - p. 7494 - 7500.
    enantioselectivity - kinetics - reaction mechanisms - SuFEx

    SuFEx reactions, in which an S−F moiety reacts with a silyl-protected phenol, have been developed as powerful click reactions. In the current paper we open up the potential of SuFEx reactions as enantioselective reactions, analyze the role of Si and outline the mechanism of this reaction. As a result, fast, high-yielding, “Si-free” and enantiospecific SuFEx reactions of sulfonimidoyl fluorides have been developed, and their mechanism shown, by both experimental and theoretical methods, to yield chiral products.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    Boric Acid Cross-linked 3D Polyvinyl Alcohol Gel Beads by NaOH-Titration Method as a Suitable Biomass Immobilization Matrix
    Sun, Li ; Wang, Jinxing ; Liang, Jidong ; Li, Gaigai - \ 2020
    Journal of Polymers and the Environment 28 (2020). - ISSN 1566-2543 - p. 532 - 541.
    Boric acid - Cross-linking - Gel beads - Immobilization - Polyvinyl alcohol

    Granule-base immobilization of biomass is a potential method for a decent quality granular sludge cultivation. In this study, 3D polyvinyl alcohol (PVA) gel beads were chemically cross-linked via a simple NaOH-titration method. The PVA gel beads’ porous morphology was characterized using scanning electron microscope (SEM) and Brunauer–Emmette–Teller (BET), and their mechanical properties were evaluated by swelling rate and compressive stress tests. When cross-linking time was 10 min, high quality gel beads (P10) were synthesized, which demonstrated a homogeneous porous structure, good swelling rate, and high compressive strength. A mechanism for synthesis of the gel beads was proposed based on the results of Fourier transform infrared (FTIR) and X-ray diffractometer (XRD) analysis. Briefly, the intermolecular hydrogen bonds of PVA were firstly broken by NaOH to generate active bond of O–Na, which easily reacted with B(OH)4 to produce the PVA-boric acid gel beads. P10 showed excellent biocompatibility for anaerobic ammonia oxidation (anammox) biomass’ immobilization. After incubation for three months, well granule-base immobilized sludge on P10 was developed in up-flow reactor. The sludge had high abundance of anammox biomass and was in balance with other functional bacteria. This work provides a simple method for the rapid preparation of 3D PVA gel beads and verifies their potential in granule-base immobilization of biomass.

    Interpreting forest diversity-productivity relationships : volume values, disturbance histories and alternative inferences
    Sheil, Douglas ; Bongers, Frans - \ 2020
    Forest Ecosystems 7 (2020)1. - ISSN 2095-6355
    Causation - Correlation - Diversity - Inference - Productivity - Richness - Tree-growth - Wood-density

    Understanding the relationship between stand-level tree diversity and productivity has the potential to inform the science and management of forests. History shows that plant diversity-productivity relationships are challenging to interpret—and this remains true for the study of forests using non-experimental field data. Here we highlight pitfalls regarding the analyses and interpretation of such studies. We examine three themes: 1) the nature and measurement of ecological productivity and related values; 2) the role of stand history and disturbance in explaining forest characteristics; and 3) the interpretation of any relationship. We show that volume production and true productivity are distinct, and neither is a demonstrated proxy for economic values. Many stand characteristics, including diversity, volume growth and productivity, vary intrinsically with succession and stand history. We should be characterising these relationships rather than ignoring or eliminating them. Failure to do so may lead to misleading conclusions. To illustrate, we examine the study which prompted our concerns —Liang et al. (Science 354:aaf8957, 2016)— which developed a sophisticated global analysis to infer a worldwide positive effect of biodiversity (tree species richness) on “forest productivity” (stand level wood volume production). Existing data should be able to address many of our concerns. Critical evaluations will improve understanding.

    Modelling root water uptake under deficit irrigation and rewetting in Northwest China
    Wang, Xiaowen ; Cai, Huanjie ; Zheng, Zhen ; Yu, Lianyu ; Wang, Zishen ; Li, Liang - \ 2020
    Agronomy Journal 112 (2020)1. - ISSN 0002-1962 - p. 158 - 174.

    The spatial and temporal distribution of root water uptake (RWU) under deficit irrigation are critical factors for crop growth. The SWAP (soil–water–atmosphere–plant) model was applied to analyze the pattern of RWU for winter wheat (Triticum aestivum L.) under three irrigation levels: no water deficit (100% evapotranspiration [ET]), moderate water deficit (80% ET) and severe water deficit (60% ET). The 2–yr experiments indicated that SWAP was highly accurate (mean relative error [MRE] <21.7%, root mean square error [RMSE] <0.07 cm3 cm−3) in simulating the soil water content (SWC). Root water uptake was significantly (P < 0.01) different in the 0- to 60-cm soil layer. The 0- to 60-cm soil layer was the main source of RWU, and the average value accounted for 89.4% of the total root zone. Water stress had the greatest adverse effect on heading to grain filling, reducing RWU by 0.0026 cm3 cm−3 d−1. The critical SWC was 67.9% of the field capacity, when the RWU dropped to 95% of the control treatment. After rewetting, compensation and hysteresis effects on RWU were observed. The ranking of RWU recovery ability after rewetting was: emergence to jointing > jointing to heading > grain filling to maturity > heading to grain filling. Recovery time of RWU was 2 to 11 d and gradually increased with growth stage. The simplified RWU model established using path analysis and regression performed well (R2 = 0.836; P < 0.01) for RWU. This provided a more convenient way to accurately estimate RWU with fewer variables.

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

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

    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 - \ 2020
    Global Ecology and Biogeography 29 (2020)1. - ISSN 1466-822X - p. 117 - 126.
    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.

    Data from: Nonlinear responses of soil nematode community composition to increasing aridity
    Xiong, Dan ; Wei, Cun Zheng ; Wubs, E.R.J. ; Veen, G.J. ; Liang, Wenju ; Wang, Xiaobo ; Li, Qi ; Putten, Wim van der; Han, Xingguo - \ 2019
    Dryad
    biodiversity - aridity - soil nematode community - non-linear response - global climate change - grassland transect
    Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have 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 3200-km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from 0.43 to 0.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used Generalized Additive (Mixed) Models to analyze 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 non-linearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred under arid conditions (aridity > 0.80). However, the shape of response to aridity differed among nematode feeding groups. Under arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but rather were directly affected by aridity. Main conclusions: Our results show that in mesic grasslands increasing aridity primarily caused decline in nematode abundance, whereas increasing aridity in xeric grasslands led to loss of nematode diversity. The non-linear responses of nematodes to aridity could result in non-linear shifts in ecosystem functioning as well, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.
    Ground cover rice production system reduces water consumption and nitrogen loss and increases water and nitrogen use efficiencies
    Liang, Hao ; Hu, Kelin ; Qin, Wei ; Zuo, Qiang ; Guo, Lin ; Tao, Yueyue ; Lin, Shan - \ 2019
    Field Crops Research 233 (2019). - ISSN 0378-4290 - p. 70 - 79.
    Conventional flooding paddy systems consume large amounts of water and results in water body pollution due to low water (WUE) and nitrogen use efficiencies (NUE). Therefore, rice production systems with water-saving and high resource use efficiencies need to be developed. A two-year field experiment was conducted in Fangxian County of Hubei Province in Central China. The experiment consisted of a conventional flooding paddy system (Paddy) and ground cover rice production system (GCRPS) with two different water management practices (i.e., GCRPSsat and GCRPS80%), factorially combined with three different N management practices (N1, no N fertilizer; N2, 150 kg urea N ha−1; and N3, 75 kg urea N ha−1 plus 75 kg N ha−1 as manure). In this study, we applied soil-crop system model (WHCNS, soil water heat carbon nitrogen simulator) coupled with simplified net mineralization model (LIXIM) to quantitatively evaluate water consumption, N fates, and rice growth under different N management practices for both Paddy and GCRPS. Results showed that the simulated soil water storage, soil mineral N content, leaf area index, dry matter, crop N uptake, and yield agreed well with the measured values. The Nash-Sutcliffe efficiency and index of agreement were greater than 0.51 and 0.86, respectively. Compared with Paddy, GCRPS significantly reduced the quantities of irrigation water (78.1%), nonproductive water consumption (evaporation, drainage, and runoff) (69.3%), and nitrate leaching (74.5%), and significantly enhanced yield (12.6%), WUE (42.8%), and NUE (20.0%). The WUE was ranked as follows: GCRPS80% > GCRPSsat > Paddy. In GCRPSs, GCRPS80% further decreased the nonproductive water consumption by 20.6% and did not reduce the yield compared with GCRPSsat. For different N management practices, no significant differences were found between the N2 and N3 treatments in terms of yields and NUEs. Meanwhile, the WUE of N3 (1.50 kg m-3) was significantly higher than that of N2 (1.41 kg m-3) in GCRPS. Hence, GCRPS80%_N3 was recommended as the best management practice for achieving high yield and high resource use efficiencies with the least environmental impact in the study region.
    Modelling groundwater level dynamics under different cropping systems and developing groundwater neutral systems in the North China Plain
    Liang, Hao ; Qin, Wei ; Hu, Kelin ; Tao, Hongbing ; Li, Baoguo - \ 2019
    Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 732 - 741.
    Over-exploitation of groundwater for irrigation has led to a series of ecological and environmental problems in the North China Plain (NCP). Identifying the water consumption and groundwater level dynamics under different cropping systems can help to develop groundwater neutral system in the NCP. The WHCNS (soil Water, Heat, Carbon and Nitrogen Simulator) model was applied to quantify the effects of different cropping systems (2H1Y, two harvests in one year; 3H2Y, three harvests in two years; and 1H1Y, one harvest in one year) on groundwater use and crop growth, and to explore the trade-offs of possible scenarios on the decline of groundwater level and cereal yield. Results showed that WHCNS performed well in simulating soil water content, leaf area index, dry matter and crop yield, as well as groundwater level dynamics, with the Nash and Sutcliffe Efficiency > 0.4 and index of agreement > 0.8. The simulated results indicated that the groundwater levels of 2H1Y decreased faster than those of other cropping systems, at a decline rate of 0.33 m yr−1. Irrigation of 300 mm yr−1 for the remaining high yield of winter wheat mainly resulted in the decline of groundwater level in the NCP. Scenario analyses showed that the groundwater levels would stop decreasing when the current planting area of winter wheat decreased by 76%. However, the reduction of wheat planting area (scenario 1) will also decrease the annual yield by 27% (from 13,547 to 9909 kg ha−1). Fallowing (scenario 2) may reduce annual yield by 50% (from 13,547 to 6834 kg ha−1) in order to maintain groundwater level. The SNWT (South to North Water Transfer) project (scenario 3) may have to provide 50% of irrigation water (130 mm yr−1), to prevent groundwater decline while maintaining the current yield. Scenario 3 could be better than scenario 1 only if the water price was less than 8 ¥m-3. In the future, reducing winter wheat planting area (especially for low-yield cropland) may be a good option to mitigate groundwater decline while maintaining relatively high yield and income for local farmers in the NCP.
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