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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    Water desalination with nickel hexacyanoferrate electrodes in capacitive deionization : Experiment, model and comparison with carbon
    Singh, K. ; Zhang, L. ; Zuilhof, H. ; Smet, L.C.P.M. de - \ 2020
    Desalination 496 (2020). - ISSN 0011-9164
    Capacitive deionization - Prussian blue analogues - Water desalination

    Capacitive deionization (CDI) is a water desalination technology in which ions are removed from water by creating a potential difference between two capacitive electrodes. Porous carbon has been extensively used as an electrode material in CDI. However, recent developments in the field of intercalation materials have led to their application in CDI due to their large ion storage capacity. One such intercalation material, nickel hexacyanoferrate (NiHCF), was used in this study as the electrode material. A symmetrical cell was assembled with two identical NiHCF electrodes separated by an anion-exchange membrane. The effect of operational parameters such as current density, feed concentration and flow rate on the desalination characteristics of the cell was investigated. The highest salt adsorption capacity of ≈ 35 mg/g was measured at a current density of 2.5 A/m2 in a 20 mM NaCl feed solution. Furthermore, a Nernst-Planck transport model was successfully used to predict the change in the outlet concentration and cell voltage of the symmetric CDI cell. Finally, performance of the symmetric NiHCF CDI cell was compared with an MCDI cell with porous carbon electrodes. The NiHCF cell, on average, consumed 2.5 times less energy than the carbon-based MCDI cell to achieve similar levels of salt removal from saline water in CDI.

    Aggregate-associated changes in nutrient properties, microbial community and functions in a greenhouse vegetable field based on an eight-year fertilization experiment of China
    Luan, Hao An ; Gao, Wei ; Tang, Ji Wei ; Li, Ruo Nan ; Li, Ming Yue ; Zhang, Huai Zhi ; Chen, Xinping ; Masiliunas, Dainius ; Huang, Shao Wen - \ 2020
    Journal of Integrative Agriculture 19 (2020)10. - ISSN 2095-3119 - p. 2530 - 2548.
    fertilization - microbial characteristics - soil aggregate distribution

    Soil aggregation, microbial community, and functions (i.e., extracellular enzyme activities; EEAs) are critical factors affecting soil C dynamics and nutrient cycling. We assessed soil aggregate distribution, stability, nutrients, and microbial characteristics within >2, 0.25–2, 0.053–0.25, and <0.053 mm aggregates, based on an eight-year field experiment in a greenhouse vegetable field in China. The field experiment includes four treatments: 100% N fertilizer (CF), 50% substitution of N fertilizer with manure (M), straw (S), and manure plus straw (MS). The amounts of nutrient (N, P2O5, and K2O) input were equal in each treatment. Results showed higher values of mean weight diameter in organic-amended soils (M, MS, and S, 2.43–2.97) vs. CF-amended soils (1.99). Relative to CF treatment, organic amendments had positive effects on nutrient (i.e., available N, P, and soil organic C (SOC)) conditions, microbial (e.g., bacterial and fungal) growth, and EEAs in the >0.053 mm aggregates, but not in the <0.053 mm aggregates. The 0.25–0.053 mm aggregates exhibited better nutrient conditions and hydrolytic activity, while the <0.053 mm aggregates had poor nutrient conditions and higher oxidative activity among aggregates, per SOC, available N, available P, and a series of enzyme activities. These results indicated that the 0.25–0.053 mm (<0.053 mm) aggregates provide suitable microhabitats for hydrolytic (oxidative) activity. Interestingly, we found that hydrolytic and oxidative activities were mainly impacted by fertilization (58.5%, P<0.01) and aggregate fractions (50.5%, P<0.01), respectively. The hydrolytic and oxidative activities were significantly (P<0.01) associated with nutrients (SOC and available N) and pH, electrical conductivity, respectively. Furthermore, SOC, available N, and available P closely (P<0.05) affected microbial communities within >0.25, 0.25–0.053, and <0.053 mm aggregates, respectively. These findings provide several insights into microbial characteristics within aggregates under different fertilization modes in the greenhouse vegetable production system in China.

    Circulating bilirubin levels and risk of colorectal cancer: serological and Mendelian randomization analyses
    Seyed Khoei, Nazlisadat ; Jenab, Mazda ; Murphy, Neil ; Banbury, Barbara L. ; Carreras-Torres, Robert ; Viallon, Vivian ; Kühn, Tilman ; Bueno-de-Mesquita, Bas ; Aleksandrova, Krasimira ; Cross, Amanda J. ; Weiderpass, Elisabete ; Stepien, Magdalena ; Bulmer, Andrew ; Tjønneland, Anne ; Boutron-Ruault, Marie Christine ; Severi, Gianluca ; Carbonnel, Franck ; Katzke, Verena ; Boeing, Heiner ; Bergmann, Manuela M. ; Trichopoulou, Antonia ; Karakatsani, Anna ; Martimianaki, Georgia ; Palli, Domenico ; Tagliabue, Giovanna ; Panico, Salvatore ; Tumino, Rosario ; Sacerdote, Carlotta ; Skeie, Guri ; Merino, Susana ; Bonet, Catalina ; Rodríguez-Barranco, Miguel ; Gil, Leire ; Chirlaque, Maria Dolores ; Ardanaz, Eva ; Myte, Robin ; Hultdin, Johan ; Perez-Cornago, Aurora ; Aune, Dagfinn ; Tsilidis, Konstantinos K. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Campbell, Peter T. ; Casey, Graham ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Cotterchio, Michelle ; Gallinger, Steven ; Gruber, Stephen B. ; Haile, Robert W. ; Hampe, Jochen ; Hoffmeister, Michael ; Hopper, John L. ; Hsu, Li ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Joshi, Amit D. ; Kampman, Ellen ; Larsson, Susanna C. ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Parfrey, Patrick S. ; Pharoah, Paul D.P. ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schmit, Stephanie L. ; Schoen, Robert E. ; Slattery, Martha L. ; Thibodeau, Stephen N. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Weigl, Korbinian ; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zhang, Xuehong ; Ferrari, Pietro ; Anton, Gabriele ; Peters, Annette ; Peters, Ulrike ; Gunter, Marc J. ; Wagner, Karl Heinz ; Freisling, Heinz - \ 2020
    BMC Medicine 18 (2020)1. - ISSN 1741-7015 - 1 p.
    Anti-oxidants - Bilirubin - Cancer - Colorectal cancer - Mendelian randomization analysis

    BACKGROUND: Bilirubin, a byproduct of hemoglobin breakdown and purported anti-oxidant, is thought to be cancer preventive. We conducted complementary serological and Mendelian randomization (MR) analyses to investigate whether alterations in circulating levels of bilirubin are associated with risk of colorectal cancer (CRC). We decided a priori to perform analyses separately in men and women based on suggestive evidence that associations may differ by sex. METHODS: In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition (EPIC), pre-diagnostic unconjugated bilirubin (UCB, the main component of total bilirubin) concentrations were measured by high-performance liquid chromatography in plasma samples of 1386 CRC cases and their individually matched controls. Additionally, 115 single-nucleotide polymorphisms (SNPs) robustly associated (P < 5 × 10-8) with circulating total bilirubin were instrumented in a 2-sample MR to test for a potential causal effect of bilirubin on CRC risk in 52,775 CRC cases and 45,940 matched controls in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colon Cancer Family Registry (CCFR), and the Colorectal Transdisciplinary (CORECT) study. RESULTS: The associations between circulating UCB levels and CRC risk differed by sex (Pheterogeneity = 0.008). Among men, higher levels of UCB were positively associated with CRC risk (odds ratio [OR] = 1.19, 95% confidence interval [CI] = 1.04-1.36; per 1-SD increment of log-UCB). In women, an inverse association was observed (OR = 0.86 (0.76-0.97)). In the MR analysis of the main UGT1A1 SNP (rs6431625), genetically predicted higher levels of total bilirubin were associated with a 7% increase in CRC risk in men (OR = 1.07 (1.02-1.12); P = 0.006; per 1-SD increment of total bilirubin), while there was no association in women (OR = 1.01 (0.96-1.06); P = 0.73). Raised bilirubin levels, predicted by instrumental variables excluding rs6431625, were suggestive of an inverse association with CRC in men, but not in women. These differences by sex did not reach formal statistical significance (Pheterogeneity ≥ 0.2). CONCLUSIONS: Additional insight into the relationship between circulating bilirubin and CRC is needed in order to conclude on a potential causal role of bilirubin in CRC development.

    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 (2020). - ISSN 0304-8608

    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.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Karolinska Institute
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics
    Background Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods We performed meta-analysis of Illumina’s HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4–18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. Results We identified 8899 CpGs in cord blood that were associated with gestational age (range 27–42 weeks), at Bonferroni significance, P
    Characterizing the changes of bovine milk serum proteins after simulated industrial processing
    Liu, Yaowei ; Zhang, Wenjin ; Zhang, Lina ; Hettinga, Kasper ; Zhou, Peng - \ 2020
    Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 133 (2020). - ISSN 0023-6438
    ELISA - Lactoferrin - LC-MS/MS - Proteomics - Thermal treatments

    This study investigated the changes and lactose glycosylation of milk serum proteins under simulated industrial processing conditions, including raw milk (R), holder pasteurization (L), high temperature short time pasteurization (H), extended shelf life (E), ultra-high temperature sterilization (U) and spray-drying (S). Through label-free proteomics, 433 proteins were identified in the samples. Several immune-related proteins, such as lactoferrin, complement C3, lactadherin, cystain, and lactoperoxidase, decreased in abundance after severe thermal treatments, while the abundance of caseins increased. No immunoglobulins and xanthine oxidase could be detected in milk after E, U or S treatments while 30%–60% of immunoglobulins was retained after pasteurizations. In detail, lactoferrin showed a better retention in H treatment while IgG showed a better retention in L treatment. UPLC-MS results showed that a slight lactose glycosylation occurred to α-LA and β-LG after severe thermal treatments (E, U and S). In addition, the results of LC-MS/MS based proteomics were verified by determining the lactoferrin and IgG content using ELISA. The observations here would update current information on the changes of milk proteins during traditional thermal processing and help to optimize current dairy processing.

    Phosphorus acquisition and yield gain in intercropping: empirical studies and meta-analyses
    Li, Chunjie - \ 2020
    Wageningen University. Promotor(en): E. Hoffland; Th.W. Kuyper, co-promotor(en): W. van der Werf; F.S. Zhang. - Wageningen : Wageningen University - ISBN 9789463954778 - 213
    Intercropping enables a sustainable intensification of agriculture
    Werf, Wopke van der; Li, Chunjie ; Cong, Wen Feng ; Zhang, Fusuo - \ 2020
    Frontiers of Agricultural Science and Engineering 7 (2020)3. - ISSN 2095-7505 - p. 254 - 256.
    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 (2020). - ISSN 1552-4450

    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.].

    Feature-based molecular networking in the GNPS analysis environment
    Nothias, Louis Félix ; Petras, Daniel ; Schmid, Robin ; Dührkop, Kai ; Rainer, Johannes ; Sarvepalli, Abinesh ; Protsyuk, Ivan ; Ernst, Madeleine ; Tsugawa, Hiroshi ; Fleischauer, Markus ; Aicheler, Fabian ; Aksenov, Alexander A. ; Alka, Oliver ; Allard, Pierre Marie ; Barsch, Aiko ; Cachet, Xavier ; Caraballo-Rodriguez, Andres Mauricio ; Silva, Ricardo R. Da; Dang, Tam ; Garg, Neha ; Gauglitz, Julia M. ; Gurevich, Alexey ; Isaac, Giorgis ; Jarmusch, Alan K. ; Kameník, Zdeněk ; Kang, Kyo Bin ; Kessler, Nikolas ; Koester, Irina ; Korf, Ansgar ; Gouellec, Audrey Le; Ludwig, Marcus ; Martin H, Christian ; McCall, Laura Isobel ; McSayles, Jonathan ; Meyer, Sven W. ; Mohimani, Hosein ; Morsy, Mustafa ; Moyne, Oriane ; Neumann, Steffen ; Neuweger, Heiko ; Nguyen, Ngoc Hung ; Nothias-Esposito, Melissa ; Paolini, Julien ; Phelan, Vanessa V. ; Pluskal, Tomáš ; Quinn, Robert A. ; Rogers, Simon ; Shrestha, Bindesh ; Tripathi, Anupriya ; Hooft, Justin J.J. van der; Vargas, Fernando ; Weldon, Kelly C. ; Witting, Michael ; Yang, Heejung ; Zhang, Zheng ; Zubeil, Florian ; Kohlbacher, Oliver ; Böcker, Sebastian ; Alexandrov, Theodore ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature Methods : techniques for life scientists and chemists 17 (2020)9. - ISSN 1548-7091 - p. 905 - 908.

    Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

    Height-diameter allometric relationships for seedlings and trees across China
    Zhang, Wei Ping ; Zhao, Lei ; Larjavaara, Markku ; Morris, E.C. ; Sterck, Frank J. ; Wang, Gen Xuan - \ 2020
    Acta Oecologica-International Journal of Ecology 108 (2020). - ISSN 1146-609X
    Allometric exponent - Canopy species - Gymnosperm - Scaling relationships - Seedling - Understory species

    Height–diameter allometric (H-D) relationships play an important role in the light capture and stability of a tree, and it is poorly understood whether the relationships changes with growth stages or functional groups along a large scale environmental gradients. We present a comparative study of H-D relationships of 6810 seedlings and 19,707 trees from about 1000 species in 9 different sites across China. We showed that allometric exponents for seedlings and trees differ between different sites and do not represent a single, constant theoretical value (e.g. 2/3, 1/2 or 1). Seedlings had greater exponents than trees in most sites. The exponents varied between canopy and understory trees in 5 sites, while were indistinguishable from each other in the remaining 4 sites. Canopy-tree seedlings had smaller exponents than understory-tree seedlings in 3 sites but had indistinguishable exponents in the other 6 sites. Gymnosperm trees had exponents greater than or indistinguishable from angiosperm trees. Elevation alone, or together with mean temperature of the warmest month explained variation of tree allometries for canopy-tree and understory-tree seedlings. The exponents of canopy trees decreased with mean annual precipitation. Our results do not support the predictions from metabolic scaling theory or biomechanical models that height–diameter allometries are invariant. Our study provides insight into how ontogeny, adult stature, phyletic affiliations and environmental limitations affect height–diameter allometric relationships at biogeographical scales.

    Pantothenic acid requirement of male White Pekin ducks from hatch to 21 days of age
    Tang, J. ; Zhang, B. ; Xue, M. ; Shi, W.B. ; Wu, Y.B. ; Feng, Y.L. ; Huang, W. ; Zhou, Z.K. ; Xie, M. ; Hou, S.S. - \ 2020
    Animal Feed Science and Technology 269 (2020). - ISSN 0377-8401
    Duck - Growth performance - Pantothenic acid - Requirement

    An experiment was conducted to determine the effects of dietary pantothenic acid levels on growth performance, carcass traits, and pantothenic acid status of male White Pekin ducks from hatch to 21 days of age, and to evaluate the requirement of this B-vitamin for starter ducks. Different levels pantothenic acid (0, 2, 4, 6, 8, 10, and 20 mg/kg) were supplemented to corn-soy isolate protein basal diet to produce 7 dietary treatments with different analyzed total pantothenic acid levels (4.65, 6.80, 8.39, 9.98, 12.04, 13.70, and 22.50 mg/kg). A total of 448 one-day-old male White Pekin ducks were allotted to 7 dietary treatments with 8 replicate pens of 8 birds per pen. At 21 days of age, body weight, average daily weight gain (ADG), average daily feed intake (ADFI), gain to feed ratio (G/F), liver pantothenic acid content, as well as percentage yield of breast meat, leg meat, and abdominal fat were examined. The growth depression, exudate on eyelids, dermatosis, poor feathering, and 100 % of mortality were observed in the ducks fed the basal diet without pantothenic acid supplementation, and these adverse effects were ameliorated by pantothenic acid supplementation. The starter ducks on the diet containing 6.80 mg/kg of pantothenic acid had a lower parameter profile of body weight, ADG, ADFI, G/F, breast meat yield, abdominal fat yield, and liver pantothenic acid content compared to the birds fed the diets with higher levels of pantothenic acid (P < 0.05). And these criteria showed a linear or quadratic response to increasing dietary pantothenic acid levels (P < 0.05). The pantothenic acid requirements (based on dietary total pantothenic acid) of starter male White Pekin ducks for body weight, ADG, ADFI, G/F, and liver pantothenic acid content were 8.95, 8.95, 8.59, 9.56, and 10.22 mg/kg based on broken-line regression, while were 10.04, 10.05, 9.18, 11.01, and 11.24 mg/kg based on quadratic broken-line regression, respectively.

    Short communication: Short-time freezing does not alter the sensory properties or the physical stability of ultra-high-temperature hydrolyzed-lactose milk
    Bottiroli, R. ; Zhang, C. ; Aprea, E. ; Fogliano, V. ; Hettinga, K. ; Gasperi, F. - \ 2020
    Journal of Dairy Science (2020). - ISSN 0022-0302
    aroma compound - freezing - hydrolyzed-lactose milk - physical stability - sensory property

    In this study, the effect of milk freezing was studied, focusing on the changes in 1% and 3% fat UHT hydrolyzed-lactose milk after slow- (−20°C) and fast-rate freezing (−80°C) for 72 h. Changes on the sensory properties were first assessed by discriminant analysis (triangle test), and then by volatile organic compounds and color analysis. The milk emulsion stability was characterized by optical centrifugation, particle size analysis, and confocal microscopy. The sensory panel was not able to distinguish the milk subjected to freezing from the control (72 h at 20°C). The volatile organic compounds and color analysis demonstrated that both freezing rates did not cause any significant changes in the milk aroma or color characteristics. The results of physical properties confirmed that short-time freezing did not lead to a distinct destabilization, except for a slight increase in the mean particle diameter at −80°C. Taking all the results together, UHT hydrolyzed-lactose milk was not significantly altered during the operation of freezing and thawing and, therefore, short-time freezing at both −20°C and −80°C can be used for milk storage without altering the product.

    Modelling urban meteorology with increasing refinements for the complex morphology of a typical Chinese city (Xi'an)
    Zhang, Xi ; Steeneveld, Gert Jan ; Zhou, Dian ; Ronda, Reinder J. ; Duan, Chengjiang ; Koopmans, Sytse ; Holtslag, Albert A.M. - \ 2020
    Building and Environment 182 (2020). - ISSN 0360-1323
    National urban database and access portal tool (NUDAPT) approach - Single-layer urban canopy model (SLUCM) - Urban canopy parameters (UCPs) - Urban heat island (UHI) - Weather research and forecasting model (WRF)

    Urban areas are vulnerable to intensive heatwave periods. In order to understand heat stress in cities, the single-layer urban canopy model (SLUCM) coupled with the weather research and forecasting model (WRF) have been widely used to quantify and forecast the urban climate. However, the model performance in WRF/SLUCM is limited by the coarse classification of urban canopy parameters (UCPs), and further improvements may require great effort. Therefore, this study was a new attempt at organizing the gridded UCPs in the ‘National Urban Database and Access Portal Tool (NUDAPT) approach’ and exploring its application in the WRF/SLUCM model in four simulations with contrasting UCP configurations. The model performances were evaluated for a heatwave period in 2018 in the typical Chinese city of Xi'an, using a near-surface observational network consisting of 39 meteorological stations in various urban spatial categories. We found that the increased accuracy in UCPs brought about gradual and overall improvements in the urban heat island effect (UHI) and air temperature (Ta), and had relatively slight effects on absolute humidity (ρν) and wind speed (WP). Furthermore, the station-to-station bias analyses indicated that optimization efficiency varied among urban spatial categories. Areas with an open form or areas densely covered with vegetation showed constant sensitivity to the increasing refinements of UCPs. Input of the gridded and multi-dimensional descriptions of urban canyon geometry contributed to more accurate results in dense urban areas and areas with mixed and inhomogeneous morphology.

    Assessing the combined toxicity effects of three neonicotinoid pesticide mixtures on human neuroblastoma SK-N-SH and lepidopteran Sf-9 cells
    Cheng, Lin ; Lu, Yangyang ; Zhao, Zhihui ; Hoogenboom, Ron L.A.P. ; Zhang, Qicai ; Liu, Xing ; Song, Wei ; Guan, Shuhui ; Song, Weiguo ; Rao, Qinxiong - \ 2020
    Food and Chemical Toxicology 145 (2020). - ISSN 0278-6915
    Combined toxicity - Human neuroblastoma cell line SK-N-SH - Lepidopteran (Spodoptera frugiperda) cell line Sf-9 - Mixtures - Neonicotinoid pesticides

    Neonicotinoid insecticides have been widely used in plant protection against pests worldwide. Generally, more than one neonicotinoids are detected in plants and foods, and such mixtures may show combined toxicity and increase the risk for both insects and higher organisms. In this study, the combined toxicity of imidacloprid (IM), acetamiprid (AC) and thiamethoxam (TH) was investigated using human neuroblastoma cell line (SK-N-SH) and lepidopteran cell line (Sf-9). Results showed that binary and ternary mixtures could enhance the inhibition of growth of both SK-N-SH and Sf-9 cells at low doses. In SK-N-SH cells, based on CompuSyn software analysis, all the mixtures of IM+AC, IM+TH, AC+TH and IM+AC+TH showed synergistic effects at concentrations < 50 mg/L, but IM+AC, IM+TH showed antagonistic effects at higher concentrations. For Sf-9 cells, all mixtures revealed synergistic effects at low concentrations (< 0.1 mg/L) except IM+AC, showing antagonism at higher concentrations (> 0.5 mg/L). The toxicity thresholds of mixtures denoted by BMDL10 values were all lower than those for single pesticides and the combined BMDL10 value of AC+TH was the lowest one. It is concluded that the co-occurrence of several neonicotinoid insecticides may enhance their toxicity and aggravate the health risk for both insects and human.

    Novel advances in biotransformation and bioactivation research-2019 year in review
    Khojasteh, S.C. ; Driscoll, James P. ; Jackson, Klarissa D. ; Miller, Grover P. ; Mitra, Kaushik ; Rietjens, Ivonne M.C.M. ; Zhang, Donglu - \ 2020
    Drug Metabolism Reviews 52 (2020)3. - ISSN 0360-2532 - p. 333 - 365.
    Biotransformation; bioactivation; reaction mechanism

    Biotransformation is one of the main mechanisms used by the body to eliminate drugs. As drug molecules become more complicated, the involvement of drug metabolizing enzymes increases beyond those that are typically studied, such as the cytochrome P450 enzymes. In this review, we try to capture the many outstanding articles that were published in the past year in the field of biotransformation (see Table 1). We have divided the articles into two categories of (1) metabolites and drug metabolizing enzymes, and (2) bioactivation and safety.  This annual review is the fifth of its kind since 2016 (Baillie et al. 2016; Khojasteh et al. 2017, 2018, 2019). This effort in itself also continues to evolve. We have followed the same format we used in previous years in terms of the selection of articles and the authoring of each section. I am pleased of the continued support of Rietjens, Miller, Zhang, Driscoll and Mitra to this review. We would like to welcome Klarissa D. Jackson as a new author for this year's issue. We strive to maintain a balance of authors from academic and industry settings.  We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. Cyrus Khojasteh, on behalf of the authors.

    A soil colour map of China
    Liu, Feng ; Rossiter, David G. ; Zhang, Gan-Lin ; Li, De-Cheng - \ 2020
    Geoderma 379 (2020). - ISSN 0016-7061
    Colour space - Digital soil mapping - Predictive soil mapping

    Soil colour can indicate soil physical, chemical and biological properties and processes, and is an important indicator for soil classification, soil quality evaluation and soil management. It varies in both horizontal and vertical dimensions, and thus regional maps of soil colour can reveal spatial patterns of these properties, processes, and indicators. However, although soil regions are sometimes named for their dominant soil colour, it is directly measured only at “point” support, i.e., during soil profile description, whereas it is desirable to know soil colour over the entire soilscape. To achieve this for China we used predictive soil mapping methods to produce soil colour maps (dry and moist colours) at 1 km2 grid cell size and over multiple depths from a consistent dataset of approximately 4 600 full profile descriptions taken as part of a national survey to define soil series in Chinese Soil Taxonomy, and a set of environmental covariates covering the national territory. The covariates characterized soil forming factors including climate, parent materials, terrain, vegetation, land surface water and thermal conditions. Soil colour descriptions in the Munsell system were extracted from the genetic horizon descriptions at the selected depths and converted to the sRGB and L*a*b* colour spaces. Dry and moist colour separates were not well-correlated in either space (r<0.76). Random forest models were constructed in both spaces, for dry and moist colours separately. Models in sRGB space were moderately successful (R2≈0.43,RMSE≈26/255) at 5 cm, with success decreasing with depth. Models smoothed the colour space and thus did not predict the more extreme values or chromas, nor the rarer hues. Models in L*a*b* space were less successful. The fitted sRGB models were used to produce predictive maps over all of China. Regional patterns as well as local detail are clearly shown. Solar radiation, wind exposure, regolith thickness, and Landsat TM bands 7 and 5 contributed most to the predictions, followed by elevation, mean annual precipitation, terrain wetness index, air temperature seasonality, precipitation standard deviation and standard deviation of NDVI. These suggest pedological processes acting on the development of soil colours, including weathering of parent materials, oxidation-reduction chemistry and biochemistry of the decomposing of organic matter. This study shows that predictive methods from points using suitable covariates are an alternative to spatial predictions over map units from their representative profiles.

    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.

    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    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.

    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.

    A systems analysis of microplastic pollution in Laizhou Bay, China
    Teng, Jia ; Zhao, Jianmin ; Zhang, C. ; Cheng, Bo ; Koelmans, A.A. ; Wu, Di ; Gao, Meng ; Sun, Xiyan ; Wang, Qing - \ 2020
    Science of the Total Environment 745 (2020). - ISSN 0048-9697
    Microplastic contamination is attracting increasing attention worldwide. In this study, the patterns of microplastic contamination in surface water and sediment from 58 sites, and living fish from 31 sites were investigated in a semi-closed bay (Laizhou Bay, China). Microplastics in Laizhou Bay were pervasively distributed, particularly in the form of fibers. Microplastic abundance exhibited no significant differences among regions in either surface waters or sediments, indicating multiple sources of microplastics pollution in the bay. Spatial hotspot (Getis-Ord Gi*) analysis demonstrated that microplastic pollution was mainly concentrated in the Laizhou-Weifang area, which in turn was mainly affected by ocean current dynamics. Although the spatial distribution of microplastics in sediments was different from surface water, it was also affected by geology, hydrogeology, and anthropogenic activities. The most common polymer in the surface waters was polyethylene terephthalate (PET), while cellophane (CP) was the most frequently observed polymer in sediment, suggesting different sinking behaviors of these microplastics. The proportion of low-density microplastics (PE and PP) in surface water was approximately 19.9%, but these microplastics accounted for only approximately 1.7% in the sediment, suggesting that low-density microplastic particles preferentially migrate to open sea. There were significant differences in shape, size and polymer type of the microplastics among surface water, sediment and biota (p < 0.05). Cluster analysis suggested that the Gudong, Yellow River Estuary and Laizhou-Weifang regions are three sources of microplastics, which might originate from river input, plastic recycling and marine raft aquaculture. Furthermore, microplastic particle diversity was greater in sediment at offshore sites, suggesting that these sites receive microplastics from multiple sources. Our results characterize the microplastic pollution pattern, clarify the possible transfer mechanisms between different environmental media, and will provide important information for risk evaluation and pollution control in this area.
    Salt stress and fluctuating light have separate effects on photosynthetic acclimation, but interactively affect biomass
    Zhang, Yuqi ; Kaiser, Elias ; Marcelis, Leo F.M. ; Yang, Qichang ; Li, Tao - \ 2020
    Plant, Cell & Environment 43 (2020)9. - ISSN 0140-7791 - p. 2192 - 2206.
    fluctuating light - light acclimation - photosynthesis - salt stress - stomatal conductance - tomato

    In nature, soil salinity and fluctuating light (FL) often occur concomitantly. However, it is unknown whether salt stress interacts with FL on leaf photosynthesis, architecture, biochemistry, pigmentation, mineral concentrations, as well as whole-plant biomass. To elucidate this, tomato (Solanum lycopersicum) seedlings were grown under constant light (C, 200 μmol m−2 s−1) or FL (5–650 μmol m−2 s−1), in combination with no (0 mM NaCl) or moderate (80 mM NaCl) salinity, for 14 days, at identical photoperiods and daily light integrals. FL and salt stress had separate effects on leaf anatomy, biochemistry and photosynthetic capacity: FL reduced leaf thickness as well as nitrogen, chlorophyll and carotenoid contents per unit leaf area, but rarely affected steady-state and dynamic photosynthetic properties along with abundance of key proteins in the electron transport chain. Salt stress, meanwhile, mainly disorganized chloroplast grana stacking, reduced stomatal density, size and aperture as well as photosynthetic capacity. Plant biomass was affected interactively by light regime and salt stress: FL reduced biomass in salt stressed plants by 17%, but it did not affect biomass of non-stressed plants. Our results stress the importance of considering FL when inferring effects of salt-stress on photosynthesis and productivity under fluctuating light intensities.

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

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

    Increasing yield and nitrogen use efficiency of spring maize in Northeast China through ecological intensification management
    Xu, Rui ; Xu, Rui ; Xu, Xin Peng ; Hou, Yun Peng ; Zhang, Jia Jia ; Huang, Shao Hui ; Ding, Wen Cheng ; Liu, Ying Xia ; He, Ping - \ 2020
    Journal of Plant Nutrition and Fertilizers 26 (2020)3. - ISSN 1008-505X - p. 461 - 471.
    Ecological intensive nutrient management - Nitrogen balance - Nitrogen use efficiency - Spring maize

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

    Lymphoid tissue in teleost gills : Variations on a theme
    Rességuier, Julien ; Dalum, Alf S. ; Pasquier, Louis Du; Zhang, Yaqing ; Koppang, Erling Olaf ; Boudinot, Pierre ; Wiegertjes, Geert F. - \ 2020
    Biology - open access biological sciences journal 9 (2020)6. - ISSN 2079-7737 - p. 1 - 14.
    Evolution - Fish - Gills - Ilt - Zap70

    In bony fish, the gill filaments are essential for gas exchanges, but also are vulnerable to infection by water‐borne microorganisms. Omnipresent across fish, gill‐associated lymphoid tissues (GIALT) regulate interactions with local microbiota and halt infection by pathogens. A special GIALT structure has recently been found in Salmonids, the interbranchial lymphoid tissue (ILT). However, the structural variation of GIALT across bony fish remains largely unknown. Here, we show how this critical zone of interaction evolved across fishes. By labeling a conserved T‐cell epitope on tissue sections, we find that several basal groups of teleosts possess typical ILT, while modern teleosts have lymphoepithelium of different shape and size at the base of primary gill filaments. Within Cypriniformes, neither body size variation between two related species, zebrafish and common carp, nor morphotype variation, did have a drastic effect on the structure of ILT. Thereby this study is the first to describe the presence of ILT in zebrafish. The ILT variability across fish orders seems to represent different evolutionary solutions to balancing trade‐offs between multiple adaptations of jaws and pharyngeal region, and immune responses. Our data point to a wide structural variation in gill immunity between basal groups and modern teleosts.

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

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

    Light from below matters: Quantifying the consequences of responses to far‐red light reflected upwards for plant performance in heterogeneous canopies
    Zhang, Ningyi ; Westreenen, Arian Van; He, Lizhong ; Evers, Jochem B. ; Anten, Niels P.R. ; Marcelis, Leo F.M. - \ 2020
    Plant, Cell & Environment (2020). - ISSN 0140-7791
    In vegetation stands, plants receive red to far‐red ratio (R:FR) signals of varying strength from all directions. However, plant responses to variations in R:FR reflected from below have been largely ignored despite their potential consequences for plant performance. Using a heterogeneous rose canopy, which consists of bent shoots down in the canopy and vertically growing upright shoots, we quantified upward far‐red reflection by bent shoots and its consequences for upright shoot architecture. With a three‐dimensional plant model, we assessed consequences of responses to R:FR from below for plant photosynthesis. Bent shoots reflected substantially more far‐red than red light, causing reduced R:FR in light reflected upwards. Leaf inclination angles increased in upright shoots which received low R:FR reflected from below. The increased leaf angle led to an increase in simulated plant photosynthesis only when this low R:FR was reflected off their own bent shoots and not when it reflected off neighbour bent shoots. We conclude that plant response to R:FR from below is an under‐explored phenomenon which may have contrasting consequences for plant performance depending on the type of vegetation or crop system. The responses are beneficial for performance only when R:FR is reflected by lower foliage of the same plants.
    Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling
    Shrestha, Neha ; Liu, Tongyu ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Li, Xin ; Zhang, Maria ; Tang, Chih-Hang Anthony ; Hu, Chih-Chi Andrew ; Liu, Chengyang ; Naji, Ali ; Liu, Ming ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling - \ 2020
    The Journal of Clinical Investigation 130 (2020)7. - ISSN 0021-9738 - p. 3499 - 3510.
    β Cell apoptosis and dedifferentiation are 2 hotly debated mechanisms underlying β cell loss in type 2 diabetes; however, the molecular drivers underlying such events remain largely unclear. Here, we performed a side-by-side comparison of mice carrying β cell-specific deletion of ER-associated degradation (ERAD) and autophagy. We reported that, while autophagy was necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex was required for the maintenance of β cell maturation and identity. Using single-cell RNA-Seq, we demonstrated that Sel1L deficiency was not associated with β cell loss, but rather loss of β cell identity. Sel1L-Hrd1 ERAD controlled β cell identity via TGF-β signaling, in part by mediating the degradation of TGF-β receptor 1. Inhibition of TGF-β signaling in Sel1L-deficient β cells augmented the expression of β cell maturation markers and increased the total insulin content. Our data revealed distinct pathogenic effects of 2 major proteolytic pathways in β cells, providing a framework for therapies targeting distinct mechanisms of protein quality control
    ER-associated degradation is required for the maintenance of β cell identity via TGFβ signaling
    Shrestha, Neha ; Liu, T. ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Zhang, M. ; Tang, C.A. ; Hu, C.A. ; Liu, Chengyang ; Naji, Ali ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling ; Hooiveld, Guido - \ 2020
    Wageningen University & Research
    Mus musculus - GSE143757 - PRJNA601502
    β cell apoptosis and dedifferentiation are two hotly-debated mechanisms underlying β cell loss in type 2 diabetes (T2D); however, the molecular drivers underlying such events remain largely unclear. Here, by performing a side-by-side comparison of mice carrying β cell-specific deletion of endoplasmic reticulum (ER)-associated degradation (ERAD) and autophagy, we report that while autophagy appears necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex is required for the maintenance of β cell maturation and identity. Notably, SEL1L expression is significantly reduced in human T2D islets compared to healthy human islets. At the single cell level, we demonstrate that Sel1L deficiency is not associated with β cell loss, but rather loss of β cell identity. Mechanistically, we find that Sel1L-Hrd1 ERAD controls β cell identity via TGFβ signaling, in part by mediating the degradation of TGF-β receptor 1 (TGFβRI). Inhibition of TGFβ signaling in Sel1L-deficient β cells augments the expression of β cell maturation markers and increases the total insulin content. Our data reveal profound but distinct pathogenic effects of two major proteolytic pathways in β cells, providing a new framework for therapies targeting distinct mechanisms of protein quality control
    Replication Data for: The stove, dome, and umbrella effects of pollutant aerosol on the planetary boundary layer: a large-eddy simulation and observations in Beijing
    Ma, Yongjing ; Ye, Jianhuai ; Xin, Jinyuan ; Zhang, Wenyu ; Vila-Guerau de Arellano, Jordi ; Zhao, Dandan ; Dai, Lindong ; Ma, Yongxiang ; Wu, Xiaoyan ; Xia, Xiangao ; Tang, Guiqian ; Shen, Pengke ; Lei, Yali ; Martin, Scot T. - \ 2020
    Harvard University
    Dataset for campaign observations and LES input file for the reference case.
    The Stove, Dome, and Umbrella Effects of Atmospheric Aerosol on the Development of the Planetary Boundary Layer in Hazy Regions
    Ma, Yongjing ; Ye, Jianhuai ; Xin, Jinyuan ; Zhang, Wenyu ; Vilà‐Guerau de Arellano, Jordi ; Wang, Shigong ; Zhao, Dandan ; Dai, Lindong ; Ma, Yongxiang ; Wu, Xiaoyan ; Xia, Xiangao ; Tang, Guiqian ; Wang, Yuesi ; Shen, Pengke ; Lei, Yali ; Martin, Scot T. - \ 2020
    Geophysical Research Letters 47 (2020)13. - ISSN 0094-8276
    Atmospheric aerosol plays critical roles in suppressing planetary boundary layer (PBL) and deteriorating air quality. However, comprehensive understanding on how aerosol optical properties (absorption and scattering) affect PBL remains lacking. Utilizing a large‐eddy simulation model incorporated with in situ observations, we demonstrate distinct impacts of absorption aerosol on PBL development when it is present below (stove effect and promotion) or above morning residual layer (dome effect and strong inhibition) and similar inhibition umbrella effects of scattering aerosol on PBL regardless of its vertical locations. There exists a transition height, above which absorption aerosol is more effective in suppressing PBL and below which scattering aerosol dominates the suppression. This height is highly related to the height of morning residual layer. Aerosol stove, dome, and umbrella effects enrich our knowledge on aerosol‐PBL interactions and the latter two can be interpreted as “double inhibitions” in promoting haze episodes in the North China Plain.
    Effect of dietary fiber fermentation on short-chain fatty acid production and microbial composition in vitro
    Bai, Yu ; Zhao, Jin Biao ; Tao, Shi Yu ; Zhou, Xing Jian ; Pi, Yu ; Gerrits, Walter J.J. ; Johnston, Lee J. ; Zhang, Shi Yi ; Yang, Hong Jian ; Liu, Ling ; Zhang, Shuai ; Wang, Jun Jun - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)11. - ISSN 0022-5142 - p. 4282 - 4291.
    fiber-rich co-products - gas production - in vitro fermentation - microbial community - short chain fatty acid

    BACKGROUND: The efficient utilization of fiber-rich co-products is important for optimizing feed resource utilization and animal health. This study was conducted to evaluate the fermentation characteristics of fiber-rich co-products, which had equal quantities of total dietary fiber (TDF), at different time points using batch in vitro methods. It considered their gas production, short-chain fatty acid (SCFA) production, and microbial composition. RESULTS: The fermentation of wheat bran (WB) and oat bran (OB) showed higher and faster (P < 0.05) gas and SCFA production than corn bran (CB), sugar beet pulp (SBP), and soybean hulls (SH). The α-diversity was higher in the CB, SBP, and SH groups than in the WB and OB groups (P < 0.05). At the phylum level, OB and WB fermentation showed lower (P < 0.05) relative abundance of Actinobacteria than the CB, SBP, and SH groups. At the genus level, OB and WB fermentation increased the Enterococcus population in comparison with the CB, SBP, and SH groups, whereas CB and SBP fermentation improved the relative abundance of the Christensenellaceae R-7 group more than the WB, OB, and SH groups (P < 0.05). CONCLUSION: Overall, WB and OB were rapidly fermented by fecal microbiota, in contrast with SBP, SH, and CB. Fermentation of different fiber-rich co-products with an equal TDF content gives different responses in terms of microbial composition and SCFA production due to variations in their physicochemical properties and molecular structure.

    Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum
    Yang, Meixin ; Zhang, Hao ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Feng, Jie ; Brankovics, Balázs ; Chen, Wanquan - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species
    Fertilization changes soil microbiome functioning, especially phagotrophic protists
    Zhao, Zhi Bo ; He, Ji Zheng ; Quan, Zhi ; Wu, Chuan Fa ; Sheng, Rong ; Zhang, Li Mei ; Geisen, Stefan - \ 2020
    Soil Biology and Biochemistry 148 (2020). - ISSN 0038-0717
    Fertilization - High-throughput sequencing - Microbiome functioning - Nitrogen - Phagotrophic protists

    The soil microbiome determines crop production and drives nutrient cycling, functions that are altered by fertilization. Yet, we have only begun to understand the effects of fertilization on taxonomic changes on soil microorganisms, while impacts on functional groups across the microbiome and therefore potential soil functioning have never been assessed. Here, using a range of methods including high-throughput sequencing, we identified 77 functional parameters of the main microbiome groups including bacteria, fungi, and protists in three common agricultural soil types in China (black, fluvo-aquic, and red soil), which were fertilized in the same way over two years. We show that fertilization most strongly and generally throughout soil types reduced the relative abundance of the main microbial predators, phagotrophic protists, by 31%. Ten functional groups within the microbiome showed soil type-specific responses to fertilization. For example, ammonia-oxidizing bacteria, and predatory/exoparasitic bacteria were reduced by fertilization in the acidic black and the red soils, while, no other microbial functional group than phagotrophic protists was suppressed by fertilization in the alkaline fluvo-aquic soil. The significant reductions in microbial functional groups especially in acidic soils could be explained by nitrogen enrichment, increased soil acidification and potential biotic links between the functional groups within the microbiome. Together, we show that the fertilization-induced abiotic changes alter microbial functions that depend on the soil and environmental conditions. Particularly the most profound changes on the group of microbial predators might subsequently affect other soil functions performed by bacteria and fungi.

    Impacts of nitrogen fertilizer type and application rate on soil acidification rate under a wheat-maize double cropping system
    Hao, Tianxiang ; Zhu, Qichao ; Zeng, Mufan ; Shen, Jianbo ; Shi, Xiaojun ; Liu, Xuejun ; Zhang, Fusuo ; Vries, Wim de - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Ammonium chloride - Cropland - Soil acidification - Soil pH - Urea

    Nitrogen (N) fertilizer-induced soil acidification in Chinese croplands is well-known, but insight in the impacts of different N fertilizer management approaches (fertilizer type and rate) on soil acidification rates is very limited. Here, we conducted a field experiment on a moderate acid soil to quantify soil acidification rates in response to N fertilization by different fertilizer types and N rates through monitoring the fate of elements (mainly nutrients) related to H+ production and consumption. Two N fertilizer types (urea and NH4Cl) and three N rates (control, optimized and conventional, 0/120/240 kg N ha−1 for wheat, 0/160/320 kg N ha−1 for maize) were included. Nitrogen addition led to an average H+ production of 4.0, 8.7, 11.4, 29.7 and 52.6 keq ha−1 yr−1, respectively, for the control, optimized urea, conventional urea, optimized NH4Cl and conventional NH4Cl plots. This was accompanied with a decline in soil base saturation of 1–10% and in soil pH of 0.1–0.7 units in the topsoil (0–20 cm). Removal of base cations by crop harvesting and N transformations contributed ~70% and ~20% to the H+ production in the urea treated plots, being ~20% and ~75% in the NH4Cl treated plots, respectively. The large NH4+ input via fertilization in the NH4Cl treated plots strongly enhanced the H+ production induced by N transformations. The low contribution of N transformations to the H+ production in the urea treated plots was due to the limited NO3 leaching, induced by the high N losses to air caused by denitrification. Increased N addition by urea, however, strongly increased H+ production by enhanced plant uptake of base cations, mainly due to a large potassium uptake in straw. Our results highlight the important role of optimizing fertilizer form and N rate as well as straw return to the field in alleviating soil acidification.

    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.

    Chain conformation and physicochemical properties of polysaccharide (glucuronoxylomannan) from Fruit Bodies of Tremella fuciformis
    Xu, Xiaoqi ; Chen, Aijun ; Ge, Xinyan ; Li, Sha ; Zhang, Tao ; Xu, Hong - \ 2020
    Carbohydrate Polymers 245 (2020). - ISSN 0144-8617
    Chain conformation - Glucuronoxylomannan - Moisture absorption and retention capacity - Rheological properties - Tremella fuciformis - Wormlike cylinder model

    Based on its potential bioactivities and sustainable source, polysaccharide (glucuronoxylomannan) from fruit bodies of Tremella fuciformis (TFP) aroused attention in food, pharmaceutical and cosmetic industry. The present study aimed at revealing its chain conformational and physicochemical properties. By using HPSEC-MALLS-Visc-RI measurement, worm-like cylinder model calculation and AFM observation, we manifested that TFP existed as flexible chains in 0.15 M NaCl (pH 7.4) solution, with the persistence length of 9.20 nm and chain diameter of 0.97 nm. Meanwhile, TFP solution exhibited shear-thinning behavior with C* at 5.3 mg mL−1, owning the feature of entangled polysaccharide. TFP solution changed from liquid-like to solid-like behavior as frequency increases, and the crossover points shifted to lower frequencies with concentration increasing. Besides, the strong moisture retention ability of TFP was evaluated. These characteristics indicated that TFP could be utilized to design microstructure system and applied as stabilizer or moisture holding ingredient in food, pharmaceutical and cosmetic system.

    Gut dysbacteriosis and intestinal disease: mechanism and treatment
    Meng, X. ; Zhang, G. ; Cao, H. ; Yu, D. ; Fang, X. ; Vos, W.M. de; Wu, H. - \ 2020
    Journal of Applied Microbiology (2020). - ISSN 1364-5072
    gut microbiome - immune response - intestinal diseases - prebiotics - probiotics

    The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota–derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.

    Steering protein and salt ad- and desorption by an electrical switch applied to polymer-coated electrodes
    Fritz, P.A. ; Zhang, P. ; Bruschinski, Tom ; Sahin, S. ; Smet, L.C.P.M. de; Chan-Park, M.B. ; Boom, R.M. ; Schroën, C.G.P.H. - \ 2020
    Separation and Purification Technology 250 (2020). - ISSN 1383-5866
    Although solid-phase chromatography is a well-established method for protein separation, chemically intensive and often costly regeneration steps are needed to make reuse of the adsorbent possible. Here, we demonstrate the use of electrochemical principles as sustainable alternative. We make use of spontaneous adsorption of proteins to solid electrodes and reverse this process by applying an electric potential to regenerate the interface. This allows for adsorption of proteins to take place at 0 V difference between the electrodes, due to electrostatic interactions between the protein and the electrode surface. The desorption is then triggered by applying a potential difference (−1.2 V) between the electrodes.

    It is demonstrated that the incorporation of negatively charged polystyrene sulfonate (PSS) or positively charged polydiallyldimethylammonium chloride (PDMAC) in or on top of the respective activated carbon electrodes increases the amount of exchanged protein from 1 to 10 mg g−1, as compared to simple activated carbon electrodes. Interestingly, salt ad- and desorption occurs in opposite cycles compared to protein ad- and desorption, resulting in simultaneous concentration and desalting of the protein when 0 V is applied. On top of that, we also found that an enrichment in β-lactoglobulin could be achieved starting from whey protein isolate. These results clearly demonstrate that electrochemical technologies can be used not only for protein separation (including removal of salt), but also for protein fractionation, while not requiring solvent use.
    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

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

    Genome-wide identification of small G protein ROPs and their potential roles in Solanaceous family
    Yang, Shuqing ; Yan, Ningning ; Bouwmeester, Klaas ; Na, Ren ; Zhang, Zhiwei ; Zhao, Jun - \ 2020
    Gene 753 (2020). - ISSN 0378-1119
    Genome-wide screening - Phylogenetic analysis - Plant growth and development - Plant immunity - Small GTPase ROPs - Solanaceous family

    Small GTPases function as molecular switches to active or inactive signaling cascades via binding or hydrolyzing GTP. A type of plant specific small GTPases, the ROPs are known to be involved in plant growth, development and immunity. We determined whether ROPs are conserved in Solanaceous species and whether they are involved in plant growth, development and resistance against Phytophthora capsisi. In genome-wide screening, a total of 66 ROPs in six Solanaceous species (SolROPs) were identified, including 16 ROPs in Solanum tuberosum L. (potato), 9 in Solanum lycopersicum L. (tomato), 5 in Solanum melongena L. (eggplant), 9 in Capsicum annuum L. (pepper), 13 in Nicotiana benthamiana Domin and 14 in Nicotiana tabacum L. (tobacco). Phylogenetic analysis revealed that 11 AtROPs and 66 SolROPs fall into five distinct clades (I-V) and hence a novel and systematic gene nomenclature was proposed. In addition, a comprehensive expression analysis was performed by making use of an online database. This revealed that ROP genes are differentially expressed during plant growth and development. Moreover, gene expression of SlROP-II.1 in S. lycopersicum could be significantly induced by P. capsici. Subsequently, SlROP-II.1 and its homologues in N. benthamiana and C. annuum (NbROP-II.1 and CaROP-II.1) were selected for functional analysis using virus-induced gene silencing. Infection assays with P. capsici on silenced plants revealed that SlROP-II.1, NbROP-II.1 and CaROP-II.1 play a role in P. capsici resistance, suggesting conserved function of ROP-II clade across different Solanaceous species. In addition, NbROP-II.1 is also involved in regulating plant growth and development. This study signified the diversity of Solanaceous ROPs and their potential roles in plant growth, development and immunity.

    Substantial differences occur between canopy and ambient climate : Quantification of interactions in a greenhouse-canopy system
    Westreenen, A. van; Zhang, N. ; Douma, J.C. ; Evers, J.B. ; Anten, N.P.R. ; Marcelis, L.F.M. - \ 2020
    PLoS ONE 15 (2020)5. - ISSN 1932-6203 - p. e0233210 - e0233210.

    Organ temperature and variation therein plays a key role in plant functioning and its responses to e.g. climate change. There is a strong feedback between organ, especially leaf, temperature and the climate within the canopy (canopy climate), which in turn interacts with the climate outside the canopy (ambient climate). For greenhouses, the determinants of this interplay and how they drive differences between canopy and ambient climate are poorly understood. Yet, as many experiments on both regular greenhouse crops and field crops are done in greenhouses, this is crucial to know. Therefore, we designed an experiment to quantify the differences between ambient and canopy climate and leaf temperature. A path analysis was performed to quantify the interactions between components of the greenhouse canopy-climate system. We found that with high radiation the canopy climate can be up to 5°C cooler than the ambient climate, while for cloudy days this was only 2°C. Canopy relative humidity (RH) was up to 25% higher compared to ambient RH. We showed that radiation is very important for these climate differences, but that this effect could be partly counteracted by turning off supplementary light (i.e. due to its indirect effects e.g. changing light distribution). Leaf temperature was substantially different, both higher and lower, from the canopy air temperature. This difference was determined by leaf area index (LAI), temperature of the heating pipe and the use of supplementary light, which all strongly influence radiation, either shortwave or thermal radiation. The difference between leaf and ambient air temperature could be decreased by decreasing the LAI or increasing the temperature of the heating pipe.

    Improvement in municipal wastewater treatment alters lake nitrogen to phosphorus ratios in populated regions
    Tong, Yindong ; Wang, Mengzhu ; Peñuelas, Josep ; Liu, Xueyan ; Paerl, Hans W. ; Elser, James J. ; Sardans, Jordi ; Couture, Raoul Marie ; Larssen, Thorjørn ; Hu, Hongying ; Dong, Xin ; He, Wei ; Zhang, Wei ; Wang, Xuejun ; Zhang, Yang ; Liu, Yi ; Zeng, Siyu ; Kong, Xiangzhen ; Janssen, Annette B.G. ; Lin, Yan - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Anthropogenic source - Aquatic ecosystem - Nutrient balance - Wastewater treatment - Water quality change

    Large-scale and rapid improvement in wastewater treatment is common practice in developing countries, yet this influence on nutrient regimes in receiving waterbodies is rarely examined at broad spatial and temporal scales. Here, we present a study linking decadal nutrient monitoring data in lakes with the corresponding estimates of five major anthropogenic nutrient discharges in their surrounding watersheds over time. Within a continuous monitoring dataset covering the period 2008 to 2017, we find that due to different rates of change in TN and TP concentrations, 24 of 46 lakes, mostly located in China's populated regions, showed increasing TN/TP mass ratios; only 3 lakes showed a decrease. Quantitative relationships between in-lake nutrient concentrations (and their ratios) and anthropogenic nutrient discharges in the surrounding watersheds indicate that increase of lake TN/TP ratios is associated with the rapid improvement in municipal wastewater treatment. Due to the higher removal efficiency of TP compared with TN, TN/TP mass ratios in total municipal wastewater discharge have continued to increase from a median of 10.7 (95% confidence interval, 7.6 to 15.1) in 2008 to 17.7 (95% confidence interval, 13.2 to 27.2) in 2017. Improving municipal wastewater collection and treatment worldwide is an important target within the 17 sustainable development goals set by the United Nations. Given potential ecological impacts on biodiversity and ecosystem function of altered nutrient ratios in wastewater discharge, our results suggest that long-term strategies for domestic wastewater management should not merely focus on total reductions of nutrient discharges but also consider their stoichiometric balance.

    Agriculture green development : A model for China and the world
    Shen, Jianbo ; Zhu, Qichao ; Jiao, Xiaoqiang ; Ying, Hao ; Wang, Hongliang ; Wen, Xin ; Xu, Wen ; Li, Tingyu ; Cong, Wenfeng ; Liu, Xuejun ; Hou, Yong ; Cui, Zhenling ; Oenema, Oene ; Davies, William J. ; Zhang, Fusuo - \ 2020
    Frontiers of Agricultural Science and Engineering 7 (2020)1. - ISSN 2095-7505 - p. 5 - 13.
    Agriculture green development - Food security - Interdisciplinary innovations - Resource use efficiency - Sustainable development - Sustainable intensification - Whole industry chain

    Realizing sustainable development has become a global priority. This holds, in particular, for agriculture. Recently, the United Nations launched the Sustainable Development Goals (SDGs), and the Nineteenth National People's Congress has delivered a national strategy for sustainable development in China-realizing green development. The overall objective of Agriculture Green Development (AGD) is to coordinate "green" with "development" to realize the transformation of current agriculture with high resource consumption and high environmental costs into a green agriculture and countryside with high productivity, high resource use efficiency and low environmental impact. This is a formidable task, requiring joint efforts of government, farmers, industry, educators and researchers. The innovative concept for AGD will focus on reconstructing the whole crop-animal production and food production-consumption system, with the emphasis on high thresholds for environmental standards and food quality as well as enhanced human well-being. This paper addresses the significance, challenges, framework, pathways and potential solutions for realizing AGD in China, and highlights the potential changes that will lead to a more sustainable agriculture in the future. Proposals include interdisciplinary innovations, whole food chain improvement and regional solutions. The implementation of AGD in China will provide important implications for the countries in developmental transition, and contribute to global sustainable development.

    Prevalence of milk fraud in the Chinese market and its relationship with fraud vulnerabilities in the chain
    Yang, Yuzheng ; Zhang, Liebing ; Hettinga, Kasper A. ; Erasmus, Sara W. ; Ruth, Saskia M. Van - \ 2020
    Foods 9 (2020)6. - ISSN 2304-8158
    China - Fourier transform-infrared spectroscopy - Fraud vulnerability - Milk adulteration - Milk composition - One-class classifications

    This study aimed to assess the prevalence of ultra-high-temperature (UHT) processed milk samples suspected of being adulterated on the Chinese market and, subsequently, relate their geographical origin to the earlier determined fraud vulnerability. A total of 52 UHT milk samples purchased from the Chinese market were measured to detect possible anomalies. The milk compositional features were determined by standardized Fourier transform-infrared spectroscopy, and the detection limits for common milk adulterations were investigated. The results showed that twelve of the analysed milk samples (23%) were suspected of having quality or fraud-related issues, while one sample of these was highly suspected of being adulterated (diluted with water). Proportionally, more suspected samples were determined among milks produced in the Central- Northern and Eastern areas of China than in those from the North-Western and North-Eastern areas, while those from the South were in between. Combining the earlier collected results on fraud vulnerability in the Chinese milk chains, it appears that increased fraud prevalence relates to poorer business relationships and lack of adequate managerial controls. Since very few opportunities and motivations differ consistently across high and low-prevalence areas, primarily the improvement of control measures can help to mitigate food fraud in the Chinese milk supply chains.

    Salt Tolerance Mechanisms of Plants
    Zelm, Eva Van; Zhang, Yanxia ; Testerink, Christa - \ 2020
    Annual Review of Plant Biology 71 (2020). - ISSN 1543-5008 - p. 403 - 433.
    ABA - auxin - developmental plasticity - ionic stress - osmotic stress - salinity

    Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context in order to link them to observed phases in growth rate that occur in response to stress. Recent advances in phenotyping can now functionally or genetically link cellular signaling responses, ion transport, water management, and gene expression to growth, development, and survival. Halophytes, which are naturally salt-tolerant plants, are highlighted as success stories to learn from. We emphasize that (a) filling the major knowledge gaps in salt-induced signaling pathways, (b) increasing the spatial and temporal resolution of our knowledge of salt stress responses, (c) discovering and considering crop-specific responses, and (d) including halophytes in our comparative studies are all essential in order to take our approaches to increasing crop yields in saline soils to the next level.

    Climate change impacts on agricultural suitability and yield reduction in a Mediterranean region
    Abd-Elmabod, Sameh K. ; Muñoz-Rojas, Miriam ; Jordán, Antonio ; Anaya-Romero, Mariá ; Phillips, Jonathan D. ; Laurence, Jones ; Zhang, Zhenhua ; Pereira, Paulo ; Fleskens, Luuk ; Ploeg, Martine van der; Rosa, Diego de la - \ 2020
    Geoderma 374 (2020). - ISSN 0016-7061
    Crop yield - Decision support systems - GIS - Global warming - Land suitability

    Climate change impacts are a serious threat to food provisioning, security and the economy. Thus, assessing agricultural suitability and yield reduction under climate change is crucial for sustainable agricultural production. In this study, we used two sub-models of the agro-ecological decision support system MicroLEIS (Terraza and Cervatana) to evaluate the impacts of climate change on land capability and yield reduction or wheat and sunflower as major rainfed crops in different Mediterranean soil types (in Andalucia, Southern Spain). The Terraza sub-model provides an experimental prediction for the bioclimate deficiency and yield reduction, while the Cervatana sub-model predicts the general land use suitability for specific agricultural uses. Sixty-two districts in Southern Spain were modeled and mapped using soil data and the A1B climate scenario (balanced scenario) for three 30-year periods ending in 2040, 2070 and 2100, respectively. Our results showed that the majority of agricultural soils were suitable for wheat production, and less for sunflowers, especially under projected climate change scenarios. Extreme impacts of climate change were observed in the soil types Typic Xerofluvents and Calcic Haploxerepts, where the land capability was reduced from Good and Moderate classes to the Marginal class. This was especially observed in sunflower crops by 2100. Yield reduction of sunflower was much higher than the reduction for wheat, especially under the projected climate periods, where the results for 2100 showed the severest effect on crop yields with about 95% of the sunflower area showing yield reductions. This high variability of the evaluation results demonstrates the importance of using soil factors, climate and crop information in conjunction in decision-making regarding the formulation of site-specific soil use and management strategies.

    Metabolic effects of PCSK9 inhibition with Evolocumab in subjects with elevated Lp(a)
    Zhang, Xiang ; Stiekema, Lotte C.A. ; Stroes, Erik S.G. ; Groen, Albert K. - \ 2020
    Lipids in Health and Disease 19 (2020)1. - ISSN 1476-511X
    Evolocumab - Lipoprotein(a) - Metabolomics - PCSK9 antibodies - VLDL

    Background: Epidemiological studies substantiated that subjects with elevated lipoprotein(a) [Lp(a)] have a markedly increased cardiovascular risk. Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) lowers both LDL cholesterol (LDL-C) as well as Lp(a), albeit modestly. Effects of PCSK9 inhibition on circulating metabolites such as lipoprotein subclasses, amino acids and fatty acids remain to be characterized. Methods: We performed nuclear magnetic resonance (NMR) metabolomics on plasma samples derived from 30 individuals with elevated Lp(a) (> 150 mg/dL). The 30 participants were randomly assigned into two groups, placebo (N = 14) and evolocumab (N = 16). We assessed the effect of 16 weeks of evolocumab 420 mg Q4W treatment on circulating metabolites by running lognormal regression analyses, and compared this to placebo. Subsequently, we assessed the interrelationship between Lp(a) and 14 lipoprotein subclasses in response to treatment with evolocumab, by running multilevel multivariate regression analyses. Results: On average, evolocumab treatment for 16 weeks resulted in a 17% (95% credible interval: 8 to 26%, P < 0.001) reduction of circulating Lp(a), coupled with substantial reduction of VLDL, IDL and LDL particles as well as their lipid contents. Interestingly, increasing concentrations of baseline Lp(a) were associated with larger reduction in triglyceride-rich VLDL particles after evolocumab treatment. Conclusions: Inhibition of PCSK9 with evolocumab markedly reduced VLDL particle concentrations in addition to lowering LDL-C. The extent of reduction in VLDL particles depended on the baseline level of Lp(a). Our findings suggest a marked effect of evolocumab on VLDL metabolism in subjects with elevated Lp(a). Trial registration: Clinical trial registration information is registered at on April 14, 2016 with the registration number NCT02729025.

    Energy consumption in membrane capacitive deionization and comparison with reverse osmosis
    Porada, S. ; Zhang, Li ; Dykstra, J.E. - \ 2020
    Desalination 488 (2020). - ISSN 0011-9164

    Membrane capacitive deionization (MCDI) is a technique for water desalination by adsorbing ions in charged porous electrodes. In the present experimental and theoretical study, we analyze the performance, in terms of energy consumption, salt rejection and water recovery, of MCDI operated in intermittent flow mode. With this mode, the water recovery of MCDI is increased by reducing the water flow ratio during regeneration. Both experimental and theoretical results show that high values for water recovery and salt rejection can be achieved with a lab-scale MCDI system for feed water with a salinity of 40 mM. Importantly, we find that the energy requirement of MCDI is a factor of 2.0–2.5 higher than of RO. For RO, the energy requirements were calculated with a system-scale model developed by Qin et al. [1]. Furthermore, we show that, based on our theoretical predictions, improved MCDI can reach high salt rejection and water recovery, without an additional energy penalty. In these conditions, the energy consumption of MCDI is lower than of RO. In the present work, we present new insights for a fair performance comparison of MCDI and RO.

    Syndromes of production in intercropping impact yield gains
    Li, Chunjie ; Hoffland, Ellis ; Kuyper, Thomas W. ; Yu, Yang ; Zhang, Chaochun ; Li, Haigang ; Zhang, Fusuo ; Werf, Wopke van der - \ 2020
    Nature Plants 6 (2020)6. - ISSN 2055-026X
    Intercropping, the simultaneous production of multiple crops on the same field, provides opportunities for the sustainable intensification of agriculture if it can provide a greater yield per unit land and fertilizer than sole crops. The worldwide absolute yield gain of intercropping as compared with sole crops has not been analysed. We therefore performed a global meta-analysis to quantify the effect of intercropping on the yield gain, exploring the effects of crop species combinations, temporal and spatial arrangements, and fertilizer input. We found that the absolute yield gains, compared with monocultures, were the greatest for mixtures of maize with short-grain cereals or legumes that had substantial temporal niche differentiation from maize, when grown with high nutrient inputs, and using multirow strips of each species. This approach, commonly practised in China, provided yield gains that were (in an absolute sense) about four times as large as those in another, low-input intercropping strategy, commonly practised outside China. The alternative intercropping strategy consisted of growing mixtures of short-stature crop species, often as full mixtures, with the same growing period and with low to moderate nutrient inputs. Both the low- and high-yield intercropping strategies saved 16–29% of the land and 19–36% of the fertilizer compared with monocultures grown under the same management as the intercrop. The two syndromes of production in intercropping uncovered by this meta-analysis show that intercropping offers opportunities for the sustainable intensification of both high- and low-input agriculture.
    Genomics of Rapid Evolution in Field Crickets
    Pascoal, Sonia ; Risse, Judith ; Zhang, Xiao ; Blaxter, Mark ; Cezard, Timothee ; Challis, Richard J. ; Gharbi, Karim ; Hunt, John ; Kumar, Sujai ; Langan, Emma ; Liu, Xuan ; Rayner, Jack G. ; Ritchie, Michael G. ; Snoek, Basten ; Trivedi, Urmi ; Bailey, Nathan W. - \ 2020
    University of Edinburgh
    PRJEB24786 - ERP106639 - Teleogryllus oceanicus - cricket - genomics
    This study reveals the genomic architecture of a rapidly evolving mutation which segregates as a single-locus, X-linked trait -- flatwing -- in wild Hawaiian field crickets (Teleogryllus oceanicus). Flatwingsilences males by eliminating sound-producing structures on their forewings. Silence protects them from an acoustically-orienting parasitoid fly (Ormia ochracea), but interferes with their ability to attract and court females for mating. Silent crickets spread rapidly on several Hawaiian islands under pressure from the flies, representing one of the fastest rates of evoutionary change documented in the wild. Here we present an annotated genome sequence of T. oceanicus along with a linkage map and QTL analysis of the trait derived from RAD-sequencing of a backcrossed mapping population. RNA-seq was used to probe the functional pathways affected by the mutation during early development, and pleiotropic effects on another signaling trait, cuticular hydrocarbons, were assessed and genetically mapped.
    Reproducible molecular networking of untargeted mass spectrometry data using GNPS
    Aron, Allegra T. ; Gentry, Emily C. ; McPhail, Kerry L. ; Nothias, Louis Félix ; Nothias-Esposito, Mélissa ; Bouslimani, Amina ; Petras, Daniel ; Gauglitz, Julia M. ; Sikora, Nicole ; Vargas, Fernando ; Hooft, Justin J.J. van der; Ernst, Madeleine ; Kang, Kyo Bin ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Koester, Irina ; Weldon, Kelly C. ; Bertrand, Samuel ; Roullier, Catherine ; Sun, Kunyang ; Tehan, Richard M. ; Boya P, Cristopher A. ; Christian, Martin H. ; Gutiérrez, Marcelino ; Ulloa, Aldo Moreno ; Tejeda Mora, Javier Andres ; Mojica-Flores, Randy ; Lakey-Beitia, Johant ; Vásquez-Chaves, Victor ; Zhang, Yilue ; Calderón, Angela I. ; Tayler, Nicole ; Keyzers, Robert A. ; Tugizimana, Fidele ; Ndlovu, Nombuso ; Aksenov, Alexander A. ; Jarmusch, Alan K. ; Schmid, Robin ; Truman, Andrew W. ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.

    Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

    Conifer and broadleaved trees differ in branch allometry but maintain similar functional balances
    Zhang, Lan ; Chen, Yajun ; Hao, Guangyou ; Ma, Keping ; Bongers, Frans ; Sterck, Frank J. - \ 2020
    Tree Physiology 40 (2020)4. - ISSN 0829-318X - p. 511 - 519.
    allometry - canopy - functional balance - wood anatomy - xylem growth

    Conifers and broadleaved trees coexist in temperate forests and are expected to differ in partitioning strategies between leaf and stem. We compare functional balances between water loss and water supply, and between sugar production and sugar transport/storage, and associate these with xylem growth to better understand how they contribute to these life form strategies. We sampled canopy branches from 14 common species in a temperate forest in northeast China and measured xylem area, phloem area, ray area, ray percentage, dry wood density, xylem conductivity and mean xylem growth rate for branch stems, and the leaf area and specific leaf area for leaves, and calculated the leaf-specific conductivity. Conifers and broadleaved trees did not differ significantly in tissue areas, xylem growth rate and the relation between phloem area and leaf area. Conifers had higher xylem area but lower ray area relative to leaf area. For the same xylem conductivity, phloem area and ray parenchyma area did not differ between conifers and broadleaved trees. Xylem growth rate was similar relative to leaf area and phloem area. Our results indicate that conifers tend to develop more xylem area per leaf area and more tracheid area at the cost of ray parenchyma area, probably to compensate for the low water transport ability of tracheid-based xylem. The divergent strategies between conifers and broadleaved tree species in leaf area and xylem area partitioning probably lead to the convergence of partitioning between leaf area and phloem area. Consequently, conifers tend to consume rather than store carbon to achieve a similar xylem expansion per year as coexisting broadleaved trees.

    UVA radiation promotes tomato growth through morphological adaptation leading to increased light interception
    Zhang, Yating ; Kaiser, Elias ; Zhang, Yuqi ; Zou, Jie ; Bian, Zhonghua ; Yang, Qichang ; Li, Tao - \ 2020
    Environmental and Experimental Botany 176 (2020). - ISSN 0098-8472
    Blue light - Leaf photosynthesis - Phenolics - Photomorphogenesis - Red light syndrome - UVA radiation

    UVA radiation (315−400 nm) is the main component of solar UV radiation. Although it shares photoreceptors (i.e. cryptochromes and phototropins) with blue light (400−500 nm), its function in plant biology is unclear to a large extent. This study aimed at exploring how UVA radiation affects plant morphology and physiology, and at distinguishing to what extent these effects differ from those of blue light. Tomato plants were grown under monochromatic red (R), dichromatic red and blue (R/B = 7:1), as well as red and two different levels of UVA radiation (R/UVA = 7:1 and 15:1, respectively), with identical photon flux density (250 μmol⋅m−2⋅s−1). Peak intensities of UVA, B and R were 370, 450 and 660 nm, respectively. We showed that replacing blue by UVA (in a background of red light) induced plant morphological modifications, as reflected by larger leaf area, steeper leaf angles, flatter leaves and longer stems. UVA had reduced effects on leaf secondary metabolism compared to blue light, resulting in significantly lower total phenolics and flavonoid contents, as well as concentrations of UV-absorbing compounds. In addition, UVA had a similar function as blue light in shaping the development of the photosynthetic apparatus, as both wavebands alleviated the ‘red light syndrome’ (i.e. low photosynthetic capacity, reduced photosynthetic electron transport, and unresponsive stomata). We conclude that: 1) UVA promotes tomato growth through morphological adaptation leading to increased light interception; 2) UVA affects leaf secondary metabolite accumulation less strongly than blue light; 3) UVA functions similarly to blue light in maintaining leaf photosynthetic functioning. Thus, unlike previously suggested, UVA cannot be unequivocally considered as an abiotic stress factor. This research adds to the understanding of plant processes in response to UVA radiation and provides a basis for future recipes for growing plants with artificial light.

    Can pedotransfer functions based on environmental variables improve soil total nutrient mapping at a regional scale?
    Song, Xiao Dong ; Rossiter, David G. ; Liu, Feng ; Wu, Hua Yong ; Zhao, Xiao Rui ; Cao, Qi ; Zhang, Gan Lin - \ 2020
    Soil & Tillage Research 202 (2020). - ISSN 0167-1987
    Digital soil mapping - Random forest - Regression analysis - Total nitrogen - Total phosphorus - Total potassium

    Numerous pedotransfer functions (PTFs) have been developed to predict the soil properties of interest from other soil properties and, less commonly, from environmental variables. However, only a few PTFs have been developed to predict soil nutrients using environmental variables and to extrapolate them to characterize spatial soil variations at a regional scale. In this study, we attempted to develop PTFs for the total nitrogen (TN), total phosphorus (TP) and total potassium (TK) concentrations in three typical pedo-climatic areas of China (Fujian Province, Jiangsu Province and Qilian Mountains) with diverse climate, terrain and soil types. A series of linear PTFs were developed to quantify the effect of terrain and climate on the predictive relations between the soil nutrients and other measured soil properties and environmental variables. In addition, digital soil mapping (DSM) based on the random forest (RF) technique was performed to test the hypothesis that the best-fit PTFs could be extrapolated, based on soil maps and environmental variables, to describe regional soil variations in the soil nutrients. The root mean square errors (RMSEs) of the best-fit PTFs for TN, TP and TK ranged from 0.21 to 0.79 g kg−1, 0.20 to 0.58 g kg−1, and 3.68 to 5.00 g kg−1, respectively. Different RMSEs were produced by DSM, namely 0.37-1.89 g kg−1, 0.19−0.56 g kg−1 and 3.79-4.83 g kg−1 for TN, TP and TK, respectively. PTFs provided a sound basis for database compilation if the soil properties were highly correlated. However, the extrapolation of best-fit PTFs to regional scales yielded greater errors than those produced by DSM. The comparison results reveal the limitations of PTFs and suggest that their performance could be improved by using environmental covariates or by fitting data in areas with relatively homogeneous soil landscapes. The DSM techniques may provide satisfactory alternatives to predict soil data at both regional and plot scales.

    Litter cover promotes biocrust decomposition and surface soil functions in sandy ecosystem
    Wu, Gao Lin ; Zhang, Meng Qi ; Liu, Yu ; López‐Vicente, Manuel - \ 2020
    Geoderma 374 (2020). - ISSN 0016-7061
    Ecological restoration - Sandy ecosystem - Soil crust - Soil nutrient - Soil organic matter - Soil particle size

    Ecological restoration of sandy inland ecosystems is important for achieving global sustainability. In the world's semi-arid regions, soil crusts play crucial roles in maintaining ecosystem functioning. However, the true extent of soil quality improvement during the development of crusts is an issue not solved. In this study, four development stages of natural soil crusts, i.e., physical crusts (PC), biocrusts (BC), litter covered biocrusts (LBC) and litter crusts (LC) were selected in a semi-arid sandy ecosystem, along with a bare sandy land (BSL) as control area, to evaluate soil physicochemical properties at different soil depths. The coverage of litter (mainly leaves of Populus simonii) increased soil moisture and reduced soil bulk density. Compared with BC, the content of total soil organic matter (SOM) decreased in LBC by 13.83% and increased in LC by 36.57%. In contrast with BC, LC promoted a significant increase in soil nutrients, such as total nitrogen (30.30%), total phosphorus (46.89%) and available potassium (34.40%) in the topsoil layer (0–2 cm). Besides, LC contained higher clay and silt contents (10.47% and 29.81%) and lower sand content (−1.02%) than BC. In the 0–10 cm soil layer, the D (fractal dimension of the soil particle size distribution) of LC was the largest, with a value 5.71%, 6.1%, 2.44% and 0.93% higher than D in BSL, PC, BC and LBC, respectively. These findings reveal that litter covering facilitate the disintegration of BC, which further forms LC, and these processes clearly promote the enhancement of soil quality under sandy semi-arid conditions. Our findings are particularly important for predicting the transformation processes of sandy soil crusts and are of interest in ecological restoration programs.

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

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

    Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild
    Pascoal, Sonia ; Risse, Judith E. ; Zhang, Xiao ; Blaxter, Mark ; Cezard, Timothee ; Challis, Richard J. ; Gharbi, Karim ; Hunt, John ; Kumar, Sujai ; Langan, Emma ; Liu, Xuan ; Rayner, Jack G. ; Ritchie, Michael G. ; Snoek, Basten L. ; Trivedi, Urmi ; Bailey, Nathan W. - \ 2020
    Evolution Letters 4 (2020)1. - ISSN 2056-3744 - p. 19 - 33.
    Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound‐producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome‐wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
    Organic amendment increases soil respiration in a greenhouse vegetable production system through decreasing soil organic carbon recalcitrance and increasing carbon-degrading microbial activity
    Luan, Haoan ; Gao, Wei ; Huang, Shaowen ; Tang, Jiwei ; Li, Mingyue ; Zhang, Huaizhi ; Chen, Xinping ; Masiliūnas, Dainius - \ 2020
    Journal of Soils and Sediments 20 (2020). - ISSN 1439-0108 - p. 2877 - 2892.
    Purpose: Recent works have shown that fertilization has an important influence on soil respiration (Rs); however, the underlying mechanisms involved in regulating Rs in greenhouse vegetable production (GVP) systems remain unclear.
    Materials and methods: Samples from six kinds of soils that were amended with different fertilization patterns (8 years) were incubated for 36 days to determine soil microbial community (PLFA), enzyme activities, soil organic C (SOC) quality (13C NMR), and Rs in a GVP system in Tianjin, China. Treatments included 100% chemical N (CN) and different substitution rates of CN with manure-N and/or straw-N.
    Results and discussion: Compared with 100%CN treatment, organic amendment strongly promoted microbial (e.g., fungi, bacteria, and actinomycetes) growth, enhanced the majority of C-degrading enzyme activities, affected SOC chemical composition with increasing O-alkyl (labile) C and reducing aromatic (stable) C, decreased SOC recalcitrance, and enhanced Rs. Redundancy analysis indicated that variations in microbial community and SOC chemical composition were closely linked to light fraction organic C (LFC) and readily oxidizable C (ROC), respectively. Further, structural equation modeling and linear regression analysis revealed that SOC recalcitrance (negative effects) and C-degrading enzyme activities (positive effects) together mediate Rs rates; meanwhile, microbial community can indirect affect Rs rates through altering C-degrading enzyme activities. Conclusions: Agricultural soil abiotic properties (mainly labile C fractions, i.e., LFC and ROC) are altered by adding organic resources (i.e., manure and straw), the changes of which can promote soil microbial growth, enhance C-degrading microbial activity, and reduce SOC recalcitrance, and in turn accelerate Rs in GVP systems.
    Border-row proportion determines strength of interspecific interactions and crop yields in maize/peanut strip intercropping
    Wang, Ruonan ; Sun, Zhanxiang ; Zhang, Lizhen ; Yang, Ning ; Feng, Liangshan ; Bai, Wei ; Zhang, Dongsheng ; Wang, Qi ; Evers, Jochem B. ; Liu, Yang ; Ren, Jianhong ; Zhang, Yue ; Werf, Wopke van der - \ 2020
    Field Crops Research 253 (2020). - ISSN 0378-4290
    border-row effect - relative yield total - row configuration - strip cropping - yield components

    Strip intercropping enables increases in yields and ecological services in agriculture. Crop yields of species grown in strip intercropping are often related to the yield responses (increases or decreases) in the outer rows of the strips: the border rows. This suggests that the yield response can be modulated by changing the proportion of border rows in the field. Here we studied the relationship between component species yields and proportion of border rows in strip intercrops of maize (Zea mays L.) and peanut (Arachis hypogaea Linn.). We tested four different intercrops with equal proportions of maize and peanut but a different number of rows per strip: M2P2 (2 rows maize intercropped with 2 rows peanut), M4P4, M6P6, M8P8, and sole maize (SM) and sole peanut (SP). The border-row proportions were 1, 0.5, 0.33 and 0.25 for the intercropping M2P2 to M8P8, respectively, and 0 for the pure stands. Yield responded positively to the proportion of border rows for maize, but negatively for peanut, confirming the dominance of maize in this system. Kernel number per ear of maize and pod number per plant of peanut were the main yield components that responded to the border-row proportion. Across three years, relative maize yield (yield in intercropping divided by yield in monoculture), varied from 0.76 in M2P2 to 0.56 in M8P8, while relative peanut yield varied from 0.19 in M2P2 to 0.39 in M8P8. Relative yield total was not significantly different from one in any of the mixtures. Yield of intercropped maize in border rows was 48% higher than in inner rows and the sole crop, in part due to a significantly higher kernel number per ear (13%). Yield of intercropped peanut in border rows was on average 29% lower than in inner rows and 48% lower than in sole peanut. Yield responses in border rows were independent from the border-row proportion. The results show that relative crop yields responded strongly to variation in border-row proportion resulting from variation in strip width from 1 to 4 m. Strip width thus provides a mechanism to control the strength of interspecific plant interactions and relative yields in strip intercropping.

    Impact of river discharge seasonality change on tidal duration asymmetry in the Yangtze River Estuary
    Yu, Xiayan ; Zhang, Wei ; Hoitink, A.J.F. - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322

    The Yangtze River Estuary (YRE) is one of the world’s largest river-tidal systems with rapidly changing hydrology and morphology following the construction of multiple dams. The effects of dam construction may extend to the region close to the coast, where channel stability depends on the asymmetry of the tide. Here, we focus on the possible effects of changing discharge regimes on tidal asymmetry in the YRE. Specifically, we focus on the difference in duration between ebb and flood, quantified as tidal duration asymmetry, because it has strong implications for residual sediment transport and can be derived from available water level data. To cope with nonstationary tides under the influence of a time-varying river discharge, a nonstationary harmonic analysis tool (NS_TIDE) is applied to explore the spatiotemporal variations in tidal duration asymmetry, under the influence of different combinations of tidal constituents. Tidal duration asymmetry initially increases, then slightly decreases, in an upstream direction. It experiences significant seasonal variations in response to rapidly varying discharge: tides are more asymmetric upstream of Zhenjiang in the dry season and more asymmetric downstream in the wet season. The combined effects of discharge regulation and morphological changes cause seasonal alterations in tidal duration asymmetry. In the wet season, reduced river discharge caused by water storage and climate change enhance the asymmetry upstream (+11.74% at Wuhu, +7.19 at Nanjing) while the asymmetry is weakened downstream (-2.90% at Zhenjiang, -7.19 at Jiangyin) following the TGD’s operation. Downstream channel erosion caused by post-TGD lower sediment loads has become the dominant factor weakening tidal asymmetry in most parts of the YRE in the dry season. Understanding these evolutions of tidal duration asymmetry under the hydrological and morphological effects has important implications for the management of estuarine ecosystem and navigation.

    Valuation of Wetland Ecosystem Services in National Nature Reserves in China’s Coastal Zones
    Li, Xiaowei ; Yu, Xiubo ; Hou, Xiyong ; Liu, Yubin ; Li, Hui ; Zhou, Yangming ; Xia, Shaoxia ; Liu, Yu ; Duan, Houlang ; Wang, Yuyu ; Dou, Yuehan ; Yang, Meng ; Zhang, Li - \ 2020
    Sustainability 12 (2020)8. - ISSN 2071-1050
    Wetlands provide ecosystem services for regional development, and, thus, have considerable economic value. In this study, a combination of evaluation methods was carried out to evaluate the wetland ecosystem services provided by national nature reserves in 11 coastal provinces/municipalities in China. We constructed a literature database containing 808observations (over 170 papers) on field-scale research for wetlands in China’s coastal zones. Using this literature database, as well as land use (LU) data, net primary productivity (NPP), and statistical data, and digital elevation model (DEM) data, we established a valuation framework and database for nine important ecosystem services of the 13 wetland types in the study area. After the large-scale academic literature review, the ordinary kriging offered by Geostatistical Analyst tools was used to interpolate the physical dimensions of the unmeasured locations. The results showed that: 1) the wetland ecosystem services in 35 national nature reserves have a total value of 33.168billion USD/year; 2) the values of wetland ecosystem services revealed considerable spatial variability along China’s coastal zones; and 3) assessments provide additional insights into the trade-offs between different ecosystem services and wetland types. The valuation framework and database established in this study can contribute to the mapping of wetland ecosystem services in coastal zones.
    Comparison of conditioned Latin hypercube and feature space coverage sampling for predicting soil classes using simulation from soil maps
    Ma, Tianwu ; Brus, Dick J. ; Zhu, Xing A. ; Zhang, Lei ; Scholten, Thomas - \ 2020
    Geoderma 370 (2020). - ISSN 0016-7061
    Calibration sampling - K-means - Random forest - Similarity-based predictive soil mapping - Simulated annealing - Soil sampling

    This study investigates sampling design for mapping soil classes based on multiple environmental features associated with the soil classes. Two types of sampling design for calibrating the prediction models are compared: conditioned Latin hypercube sampling (CLHS) and feature space coverage sampling (FSCS). Simple random sampling (SRS), which does not utilize the environmental features, is added as a reference design. The sample sizes used are 20, 30, 40, 50, 75, and 100 points, and at each sample size 100 sample sets were drawn using each of the three types of design. Each of these sample sets was then used to calibrate three prediction models: random forest (RF), individual predictive soil mapping (iPSM), and multinomial logistic regression (MLR). These sampling designs were compared based on the overall accuracy of predicted soil class maps obtained by these three prediction methods. The comparison was conducted in two study areas: Ammertal (Germany) and Raffelson (USA). For each of these two areas a detailed legacy soil class map is available. These soil class maps were used as references in a simulation study for the comparison. Results of both study areas show that on average FSCS outperforms CLHS and SRS for all three prediction methods. The difference in estimated medians of overall accuracy with CLHS and SRS was marginal. Moreover, the variation in overall accuracy among sample sets of the same size was considerably smaller for FSCS than that for CLHS. These results in the two study areas suggest that FSCS is a more effective sampling design.

    Examining the effects of forest fire on terrestrial carbon emission and ecosystem production in India using remote sensing approaches
    Sannigrahi, Srikanta ; Pilla, Francesco ; Basu, Bidroha ; Basu, Arunima Sarkar ; Sarkar, Konika ; Chakraborti, Suman ; Joshi, Pawan Kumar ; Zhang, Qi ; Wang, Ying ; Bhatt, Sandeep ; Bhatt, Anand ; Jha, Shouvik ; Keesstra, Saskia ; Roy, P.S. - \ 2020
    Science of the Total Environment 725 (2020). - ISSN 0048-9697
    Burn indices - Carbon emission - Forest fire - Greenhouse gas emission - Net primary productivity - Remote sensing

    Remote sensing techniques are effectively used for measuring the overall loss of terrestrial ecosystem productivity and biodiversity due to forest fires. The current research focuses on assessing the impacts of forest fires on terrestrial ecosystem productivity in India during 2003–2017. Spatiotemporal changes of satellite remote sensing derived burn indices were estimated for both fire and normal years to analyze the association between forest fires and ecosystem productivity. Two Light Use Efficiency (LUE) models were used to quantify the terrestrial Net Primary Productivity (NPP) of the forest ecosystem using the open-source and freely available remotely sensed data. A novel approach (delta NPP/delta burn indices) is developed to quantify the effects of forest fires on terrestrial carbon emission and ecosystem production. During 2003–2017, the forest fire intensity was found to be very high (>2000) across the eastern Himalayan hilly region, which is mostly covered by dense forest and thereby highly susceptible to wildfires. Scattered patches of intense forest fires were also detected in the lower Himalayan and central Indian states. The spatial correlation between the burn indices and NPP were mainly negative (−0.01 to −0.89) for the fire-prone states as compared to the other neighbouring regions. Additionally, the linear approximation between the burn indices and NPP showed a positive relation (0.01 to 0.63), suggesting a moderate to high impact of the forest fires on the ecosystem production and terrestrial carbon emission. The present approach has the potential to quantify the loss of ecosystem productivity due to forest fires.

    How Does a Simplified Recipe Collection Procedure in Dietary Assessment Tools Affect the Food Group and Nutrient Intake Distributions of the Population
    Zhang, Liangzi ; Boshuizen, Hendriek ; Ocké, Marga - \ 2020
    The British journal of nutrition 124 (2020)2. - ISSN 0007-1145 - p. 189 - 198.
    dietary assessment - Globodiet - population nutrient intake - recipe collection steps - self-administered

    Technology advancements have driven the use of self-administered dietary assessment methods in large-scale dietary surveys. Interviewer-assisted methods generally have a complicated recipe recording procedure enabling the adjustment from a standard recipe. In order to decide if this functionality can be omitted for self-administered dietary assessment, this study aimed to assess the extent of standard recipe modifications in the Dutch National Food Consumption Survey, and measure the impact on the food group and nutrient intake distributions of the population when the modifications were disregarded. A two-scenario simulation analysis was conducted. Firstly, the individual recipe scenario omitted the full modifications to the standard recipes made by people who knew their recipes. Secondly, the modified recipe scenario omitted the modifications made by those who partially modified the standard recipe due to their limited knowledge. The weighted percentage differences for the nutrient and food group intake distributions between the scenarios and the original dataset were calculated. The highest percentage of energy consumed through mixed dishes was 10% for females aged 19 to 79. Comparing the combined scenario and the original dataset, the average of the absolute percentage difference for the population mean intakes was 1.6% across all food groups and 0.6% for nutrients. The soup group (-6.6%) and docosahexaenoic acid (DHA) (-2.3%) showed the largest percentage difference. The recipe simplification caused a slight underestimation of the consumed amount of both foods (-0.2%) and nutrients (-0.4%). These results are promising for developing self-administered 24hR or food diary applications without complex recipe function.

    Impacts of agricultural industrial agglomeration on China's agricultural energy efficiency : A spatial econometrics analysis
    Wu, Jianzhai ; Ge, Zhangming ; Han, Shuqing ; Xing, Liwei ; Zhu, Mengshuai ; Zhang, Jing ; Liu, Jifang - \ 2020
    Journal of Cleaner Production 260 (2020). - ISSN 0959-6526
    Agriculture in China - Energy efficiency - Industrial agglomeration - Spatial econometrics

    The rapid development of traditional agriculture in China was achieved at the expense of high energy consumption and investments. However, the global green development trend made it necessary for the country to transform its agricultural energy utilization. Energy efficiency changes are affected by many factors, particularly industrial agglomeration. In recent years, the Chinese government has introduced a series of policies, including setting major producing regions for grains and advantageous regions for characteristic agricultural product. These have caused significant changes to the spatial layout of the agriculture industry. However, there is still a lack of research on the impact of these changes on agricultural energy efficiency (AEE). In this study, panel data of 30 Chinese provinces from 2000 to 2016 were entered into stochastic frontier models to measure the country's AEE at the provincial level. A series of spatial econometric models were also used to analyze the impact of agricultural industrial agglomeration on China's AEE. The results indicated that the country's AEE exhibited obvious spatial gradients and correlations. After controlling the impacts of spatial correlation and other factors in the models, agricultural industrial agglomeration was found to have an overall positive impact on China's AEE. In the future, policies should be formulated to increase AEE by establishing agricultural functional areas, strengthening the innovation and sharing of green development technologies at the farm level, and promoting the optimization of energy structures in agricultural and rural areas.

    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)3. - ISSN 1087-0156 - p. 272 - 276.
    Genome-wide detection of key genes and epigenetic markers for chicken fatty liver
    Tan, Xiaodong ; Liu, Ranran ; Xing, Siyuan ; Zhang, Yonghong ; Li, Qinghe ; Zheng, Maiqing ; Zhao, Guiping ; Wen, Jie - \ 2020
    International Journal of Molecular Sciences 21 (2020)5. - ISSN 1661-6596
    Chicken - DNA methylation - Epigenetics - Fatty liver - Lipid metabolism - Long noncoding RNA

    Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and long noncoding RNA (lncRNA) sequencing was conducted. A total of 1177 differentially expressed genes (DEGs) and 1442 differentially methylated genes (DMGs) were found. There were 72% of 83 lipid-and glucose-related genes upregulated; 81% of 150 immune-related genes were downregulated in fatty livers. Part of those genes was within differentially methylated regions (DMRs). Besides, sixty-seven lncRNAs were identified differentially expressed and divided into 13 clusters based on their expression pattern. Some lipid-and glucose-related lncRNAs (e.g., LNC_006756, LNC_012355, and LNC_005024) and immune-related lncRNAs (e.g., LNC_010111, LNC_010862, and LNC_001272) were found through a co-expression network and functional annotation. From the expression and epigenetic profiles, 23 target genes (e.g., HAO1, ABCD3, and BLMH) were found to be hub genes that were regulated by both methylation and lncRNAs. We have provided comprehensive epigenetic and transcriptomic profiles on FLS in chicken, and the identification of key genes and epigenetic markers will expand our understanding of the molecular mechanism of chicken FLS.

    Impact of conjugation with maltodextrin on rheological properties of sodium caseinate
    Zhang, Lu ; Versteege, Sabine ; Alting, Arno C. ; Schutyser, Maarten A.I. - \ 2020
    International Dairy Journal 105 (2020). - ISSN 0958-6946

    Aqueous dispersions of sodium caseinate-maltodextrin (NaCas-MD) conjugates were prepared by heating to study the impact of Maillard reaction on protein functionality. Conjugation with MD affected rheological properties, colour and microstructure of NaCas-MD dispersions. Gelation temperature of NaCas-MD dispersions increased by 7 °C after conjugation, whereas the gelation time was not significantly affected. Shear thickening of the dispersions occurred at high shear rates, and temperature-viscosity relationship was described by the Arrhenius equation. Gels formed at 25 °C had a lower gel strength after conjugation, associated with changes in microstructure. Strain hardening appeared at large amplitude oscillatory shear, which was more profound after conjugation. Moreover, a higher dextrose-equivalent-value of maltodextrin resulted in conjugates with higher degree of conjugation, darker colour, and larger particulates on a microscale. The study indicates that rheological properties of NaCas can be modified by conjugation with maltodextrin, which is in principle applicable for other protein-polysaccharide combinations.

    Stimulated biosynthesis of delphinidin-related anthocyanins in tea shoots reducing the quality of green tea in summer
    Zhang, Qunfeng ; Hu, Jianhui ; Liu, Meiya ; Shi, Yuanzhi ; Vos, C.H. de; Ruan, Jianyun - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)4. - ISSN 0022-5142 - p. 1505 - 1514.
    BACKGROUND: Greater proportions of purple tea buds and leaves usually appear in the summer, which seriously affects the
    color and taste quality of green tea products, yet the metabolism of purple tea shoots in summer remains unclear. Here, the metabolomic profiles and gene expression of related flavonoid metabolic pathways in the purple and normal green shoots of ‘Longjing 43’, and the quality of green teamade with these two phenotypes, were analyzed and compared.
    RESULTS: Differential metabolites identified using high-performance liquid chromatography–Orbitrap/mass spectrometry indicated that anthocyanin biosynthesis in purple leaves was enriched, with higher levels of anthocyanidins
    (delphinidin-hexose-coumaroyl showed the greatest increase), proanthocyanidins (oligomers of catechins) and kaempferol
    glycoside. Expression patterns of the genes ANR, ANS, FLS, LAR, C4H, PAL, CHI, CHS and DFR revealed that the metabolism of
    anthocyanin is positively regulated by high temperature and/or light levels in summer. Gas chromatography–mass spectrometry
    results showed that, in purple tea shoots, themetabolism of carbohydrates was enriched whereas that of amino acids was
    diminished, while their mannose, fructose, D-galactose, sorbose and D-glucose contents were more than double those found in green leaves. A sensory evaluation confirmed that a greater quantity of purple shoots had a greater negative impact on green tea quality because of a bitter taste and dark color (leaves and infusions were tested).
    CONCLUSIONS: These results highlight the need for and possibility of improving commercial tea quality via cultivation that
    controls the temperature or light of tea gardens during the summer.
    © 2019 Society of Chemical Industry
    Supporting information may be found in the
    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

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

    Meta-analysis of greenhouse gas and ammonia emissions from dairy manure composting
    Ba, Shidi ; Qu, Qingbo ; Zhang, Keqiang ; Groot, Jeroen C.J. - \ 2020
    Biosystems Engineering 193 (2020). - ISSN 1537-5110 - p. 126 - 137.
    Methane - Mitigation measure - Nitrous oxide - Silo - Turning - Windrow

    In order to minimise nutrient losses, comprehensive overviews of the magnitude of gaseous emissions from manure composting processes and the factors that influence these losses are urgently needed. This study presents a meta-analysis of greenhouse gases (GHGs) and ammonia (NH3) emissions from four main dairy manure composting methods (static, turning, windrow and silo) based on 41 scientific articles (153 treatments). Gaseous emissions and secondary variables such as average composting temperature, initial moisture content, initial total carbon (TC) and initial total nitrogen (TN) content from each compost treatment were extracted and normalised to enable inter-study comparison. Six mitigation measures for composting were selected and mitigation efficiency (Em) of each measure on different gas emissions were calculated. Gaseous emissions from different composting methods showed large differences. Turning composting resulted in larger carbon and nitrogen losses compared to other composting methods. Although silo composting significantly promoted NH3 emission, it reduced GHG losses by 82.84% compared with turning composting. Principal component analysis showed that the initial TC and TN content of the composted material were crucial in mediating gaseous emissions. Low TC and TN content can simultaneously reduce CH4, CO2 and N2O emissions. Applying compost biofilters was the most effective way to reduce NH3 emission with ME value of −97%. Adding sawdust or straw could reduce CH4 and N2O emissions by 66.3% and 44.0% respectively. Gaseous emissions from dairy manure composting varied a lot and were affected by physical characteristics of composted material and management practices of composting.

    The Chinese milk supply chain: A fraud perspective
    Yang, Yuzheng ; Huisman, Wim ; Hettinga, Kasper A. ; Zhang, Liebing ; Ruth, Saskia M. van - \ 2020
    Food Control 113 (2020). - ISSN 0956-7135
    China - Dairy farmer - Economically motivated adulteration - Fraud vulnerability assessment - Milk processor - Milk supply chain

    Food fraud has become a serious concern all over the world and especially in China. The melamine contaminated infant formula in 2008 has brought food fraud in the spotlights. This incident had grave consequences for the Chinese citizens as well as the Chinese milk industry. Fraud vulnerability assessments are the first step towards food fraud prevention and mitigation. To combat food fraud, one has to think like a criminal. In the current study, we determined the most vulnerable points in the Chinese milk supply chain, and examined the underlying causes. The fraud vulnerability perceived by 90 Chinese dairy farmers and 14 milk processors was evaluated with the SSAFE food fraud vulnerability assessment tool. Overall, actors perceived the milk supply chain as low to medium vulnerable to food fraud. Farmers appeared significantly more vulnerable than processors due to enhanced opportunities and motivations, and less adequate controls. Both geographical location of the farms and their size affected their perceived fraud vulnerability significantly.

    Substitution of manure for chemical fertilizer affects soil microbial community diversity, structure and function in greenhouse vegetable production systems
    Luan, Haoan ; Gao, Wei ; Huang, Shaowen ; Tang, Jiwei ; Li, Mingyue ; Zhang, Huaizhi ; Chen, Xinping ; Masiliūnas, Dainius - \ 2020
    PLoS ONE 15 (2020)2. - ISSN 1932-6203

    Soil microbial communities and enzyme activities together affect various ecosystem functions of soils. Fertilization, an important agricultural management practice, is known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research was to make a comparative study of the effects of different nitrogen (N) fertilizer rates and types (organic and inorganic) on soil physicochemical properties, enzyme activities and microbial attributes in a greenhouse vegetable production (GVP) system of Tianjin, China. Results showed that manure substitution of chemical fertilizer, especially at a higher substitution rate, improved soil physicochemical properties (higher soil organic C (SOC) and nutrient (available N and P) contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure application induced a higher fungi/bacteria ratio due to a lower response in bacterial than fungal growth. Also, manure application greatly increased bacterial stress indices, as well as microbial communities and functional diversity. The principal component analysis showed that the impact of manure on microbial communities and enzyme activities were more significant than those of chemical fertilizer. Furthermore, redundancy analysis indicated that SOC and total N strongly influenced the microbial composition, while SOC and ammonium-N strongly influenced the microbial activity. In conclusion, manure substitution of inorganic fertilizer, especially at a higher substitution rate, was more efficient for improving soil quality and biological functions.

    Optimizing rates and sources of nutrient input to mitigate nitrogen, phosphorus, and carbon losses from rice paddies
    Ding, Wencheng ; He, Ping ; Zhang, Jiajia ; Liu, Yingxia ; Xu, Xinpeng ; Ullah, Sami ; Cui, Zhenling ; Zhou, Wei - \ 2020
    Journal of Cleaner Production 256 (2020). - ISSN 0959-6526
    Enhanced-efficiency fertilizer - Greenhouse gas - Manure N - N threshold - Nutrient loss - Straw return

    Decreasing nutrient losses from excessive synthetic fertilizer inputs is the direct and valid way to address low nutrient use efficiency and the related environmental consequences. Here, we established a comprehensive database of nitrogen (N), phosphorus (P), and carbon (C) losses from rice paddy fields in China, which we used to evaluate fertilization-induced losses and the impact of environmental factors, and to mitigate losses by adopting alternative fertilization options and setting input thresholds. Our results showed that most N-loss pathways had exponential increases with additional N input. In average, 23.8% of the N applied was lost via NH3 (16.1%), N2O (0.3%), leaching (4.8%), and runoff (2.6%). Total P loss was approximately 2.7% of the input, composed of leaching (1.3%) and runoff (1.4%). C lost as CH4 accounted for 4.9% of the organic C input. A relative importance analysis indicated that climate or soil variation rather than fertilizer rate was the dominant factor driving N and P leaching, and CH4 emissions. Based on the sensitivity of multiple N-loss pathways to N fertilization, we propose upper thresholds for N inputs of 142–191 kg N ha−1 across four rice types, which would avoid dramatic increases in N losses. Compared to conventional chemical fertilization, alternative fertilization options had diverse performances: enhanced-efficiency N fertilizer reduced N loss rate by 7.8 percent points and the global warming potential (GWP, considering N2O and CH4 emissions) by 28.8%; combined manure and chemical N fertilizer reduced N loss rate by 9.0 percent points but increased the GWP by 56.9%; straw return had no effect on total N loss but almost doubled the GWP. Using nutrient sources most appropriate to site-specific conditions is demonstrated as a robust way to decrease nutrient losses. Setting nutrient input thresholds would also contribute to the mitigation of environmental pollution, especially in regions with poor fertilization recommendation systems.

    Examining effects of climate change and land use dynamic on biophysical and economic values of ecosystem services of a natural reserve region
    Sannigrahi, Srikanta ; Zhang, Qi ; Joshi, P.K. ; Sutton, Paul C. ; Keesstra, Saskia ; Roy, P.S. ; Pilla, Francesco ; Basu, Bidroha ; Wang, Ying ; Jha, Shouvik ; Paul, Saikat Kumar ; Sen, Somnath - \ 2020
    Journal of Cleaner Production 257 (2020). - ISSN 0959-6526
    CA-Markov - Climate change - Ecosystem services - InVEST - Land use - Sundarbans

    Ecosystem Service Valuation (ESV) is a process of evaluating and quantifying the monetary values of ESs and their functions. Using both biophysical and spatially explicit integrated models, biophysical and monetary values of key Ecosystem Services (ESs) were estimated in the Sundarbans Biosphere Region (SBR), India. Quantification was made both in time series (1982–2017) and individual years (1973, 1988, 2003, 2013, 2018, 2025, 2035, 2045) to understand the impact of climate change and land-use dynamics on the long-term ecological status of the region. The monetary and biophysical values of the ESs were then obtained from Net Primary Productivity (NPP) models, Integrated Valuation of Ecosystem Services and Trade-offs (InVEST), and Cellular Automata Markov Chain Model (CA-Markov). NPP increased significantly during the first half period (1982–1999), but significantly declined during the second period (2000–2017). The highest estimated ESVs (US$ ha−1) was found for habitat service (30780), nutrient cycling (12626), and gas regulation (7224.81), whereas, lower ESVs were approximated for water regulation (347.81), raw material production (777.82) and waste treatment (13.57) services. Among the nine ESs evaluated, climate regulation, gas regulation, and disturbance regulation were the most important regulating services of the SBR. The combined effects of climate change and land-use dynamics on ESs are much stringent in a vulnerable region like the SBR. Most of the regulating services were closely associated with the fluctuation of land use land cover input. Thus, land management policies and land reform strategies that will encourage the conversion of productive land, especially the highly productive mangrove forest, for the development or any other financial benefits, would disturb the ideal human-nature balance of this ecosystem. The outcomes of this study also provide an important reference to the land administrators, researchers, and decision-makers to comprehend the expected social-ecological juxtaposition in a protected natural reserve region like the Sundarbans.

    Controlled oleosome extraction to produce a plant-based mayonnaise-like emulsion using solely rapeseed seeds
    Romero-Guzmán, María Juliana ; Köllmann, Nienke ; Zhang, Lu ; Boom, Remko M. ; Nikiforidis, Constantinos V. - \ 2020
    Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 123 (2020). - ISSN 0023-6438
    Emulsion - Mayonnaise - Novel-ingredients - Oil-bodies - Oleosomes - Plant-based

    Oleosomes are oil storage structures in seeds, consisting of triglycerides surrounded by a protein-phospholipid mixed monolayer. They can be extracted aqueously together with other seed components such as proteins and soluble fibers. The co-extracted biomolecules can affect the properties of the extracts. Nevertheless, it is possible to control the electrostatic and hydrophobic interactions between these biomolecules and oleosomes by adjusting the extraction conditions. Hence, our aim was to adjust the extraction conditions in order to recover a natural emulsion with a specific functionality: a plant-based mayonnaise-like product, derived solely from rapeseed seeds. By varying the pH of extraction, the droplet size was customized and by increasing the number of purification steps, the right amount of co-extracted material was removed. A combination of these conditions shifted the rheological properties of the obtained natural emulsion to a range similar to the benchmark mayonnaises. This work shows that it is feasible to produce a plant-based mayonnaise with an oil content ranging from 61.7 g/100g to 72.0 g/100g through a simple and continuous oleosome extraction process by controlling the interactions between oleosomes and co-extracted material.

    Cereal dietary fibres influence retention time of digesta solid and liquid phases along the gastrointestinal tract
    Low, Dorrain Y. ; Pluschke, Anton M. ; Gerrits, Walter J.J. ; Zhang, Dagong ; Shelat, Kinnari J. ; Gidley, Michael J. ; Williams, Barbara A. - \ 2020
    Food Hydrocolloids 104 (2020). - ISSN 0268-005X
    Arabinoxylan - Digesta - Liquid phase - Retention time - Solid phase - β-glucan

    Nutrient digestion kinetics are determined by gastric emptying (GE) in the stomach and apparent mean retention time (aMRT) along the small and large intestine. This study aimed to evaluate the effects of cereal dietary fibres (DF), either as intrinsic components of plant foods or added ingredients, on the retention of solid and liquid phases of digesta along the gastrointestinal (GI) tract. Thirty pigs were fed one of five diets containing whole wheat (WW), wheat starch (WS) or wheat starch partially replaced by wheat arabinoxylan (AX) or oat β-glucan (βG), or in combination (WSAXβG). Indigestible solid and liquid phase markers were added to each diet and fed at i) constant and ii) pulse dose intervals. Constant markers (acid insoluble ash and chromium) provided aMRT along 11 sections of the GI tract, while pulse dose markers (cerium, ytterbium and cobalt), fed 2–6 h before anaesthesia, provided a GE time. aMRT was slowest in the caecum and large intestine (LI, 15.4h), followed by the small intestine (SI, 3.4h) and stomach (2.6h) with liquid phases moving faster compared to solid phases. Between DF, AX but not βG, delayed GE of solid and liquid contents and showed longer retention time in SI and LI. In the absence of isolated soluble fibres, WS and WW diets showed similar flow characteristics of solid and liquid phases. The aMRT was shown to be dependent on the structure and swellability of added DF.

    G protein α subunit suppresses sporangium formation through a serine/threonine protein kinase in Phytophthora sojae
    Qiu, Min ; Li, Yaning ; Zhang, Xin ; Xuan, Mingrun ; Zhang, Baiyu ; Ye, Wenwu ; Zheng, Xiaobo ; Govers, Francine ; Wang, Yuanchao - \ 2020
    PLoS Pathogens 16 (2020)1. - ISSN 1553-7366

    Eukaryotic heterotrimeric guanine nucleotide-binding proteins consist of α, β, and γ subunits, which act as molecular switches to regulate a number of fundamental cellular processes. In the oomycete pathogen Phytophthora sojae, the sole G protein α subunit (Gα; encoded by PsGPA1) has been found to be involved in zoospore mobility and virulence, but how it functions remains unclear. In this study, we show that the Gα subunit PsGPA1 directly interacts with PsYPK1, a serine/threonine protein kinase that consists of an N-terminal region with unknown function and a C-terminal region with a conserved catalytic kinase domain. We generated knockout and knockout-complemented strains of PsYPK1 and found that deletion of PsYPK1 resulted in a pronounced reduction in the production of sporangia and oospores, in mycelial growth on nutrient poor medium, and in virulence. PsYPK1 exhibits a cytoplasmic-nuclear localization pattern that is essential for sporangium formation and virulence of P. sojae. Interestingly, PsGPA1 overexpression was found to prevent nuclear localization of PsYPK1 by exclusively binding to the N-terminal region of PsYPK1, therefore accounting for its negative role in sporangium formation. Our data demonstrate that PsGPA1 negatively regulates sporangium formation by repressing the nuclear localization of its downstream kinase PsYPK1.

    A framework for nitrogen futures in the shared socioeconomic pathways
    Kanter, David R. ; Winiwarter, Wilfried ; Bodirsky, Benjamin L. ; Bouwman, Lex ; Boyer, Elizabeth ; Buckle, Simon ; Compton, Jana E. ; Dalgaard, Tommy ; Vries, Wim de; Leclère, David ; Leip, Adrian ; Müller, Christoph ; Popp, Alexander ; Raghuram, Nandula ; Rao, Shilpa ; Sutton, Mark A. ; Tian, Hanqin ; Westhoek, Henk ; Zhang, Xin ; Zurek, Monika - \ 2020
    Global environmental change : human and policy dimensions 61 (2020). - ISSN 0959-3780
    Environmental policy - Nitrogen pollution - Scenarios

    Humanity's transformation of the nitrogen cycle has major consequences for ecosystems, climate and human health, making it one of the key environmental issues of our time. Understanding how trends could evolve over the course of the 21st century is crucial for scientists and decision-makers from local to global scales. Scenario analysis is the primary tool for doing so, and has been applied across all major environmental issues, including nitrogen pollution. However, to date most scenario efforts addressing nitrogen flows have either taken a narrow approach, focusing on a singular impact or sector, or have not been integrated within a broader scenario framework – a missed opportunity given the multiple environmental and socio-economic impacts that nitrogen pollution exacerbates. Capitalizing on our expanding knowledge of nitrogen flows, this study introduces a framework for new nitrogen-focused narratives based on the widely used Shared Socioeconomic Pathways that include all the major nitrogen-polluting sectors (agriculture, industry, transport and wastewater). These new narratives are the first to integrate the influence of climate and other environmental pollution control policies, while also incorporating explicit nitrogen-control measures. The next step is for them to be used as model inputs to evaluate the impact of different nitrogen production, consumption and loss trajectories, and thus advance understanding of how to address environmental impacts while simultaneously meeting key development goals. This effort is an important step in assessing how humanity can return to the planetary boundary of this essential element over the coming century.

    Responses of ecosystem services to natural and anthropogenic forcings: A spatial regression based assessment in the world's largest mangrove ecosystem
    Sannigrahi, Srikanta ; Zhang, Qi ; Pilla, Francesco ; Joshi, Pawan Kumar ; Basu, Bidroha ; Keesstra, Saskia ; Roy, P.S. ; Wang, Ying ; Sutton, Paul C. ; Chakraborti, Suman ; Paul, Saikat Kumar ; Sen, Somnath - \ 2020
    Science of the Total Environment 715 (2020). - ISSN 0048-9697
    Biophysical and economic valuation - Climate change - Data dimensionality - Ecosystem services - Spatial regression - Sundarbans

    Most of the Earth's Ecosystem Services (ESs) have experienced a decreasing trend in the last few decades, primarily due to increasing human dominance in the natural environment. Identification and categorization of factors that affect the provision of ESs from global to local scales are challenging. This study makes an effort to identify the key driving factors and examine their effects on different ESs in the Sundarbans region, India. We carry out the analysis following five successive steps: (1) quantifying biophysical and economic values of ESs using three valuation approaches; (2) identifying six major driving forces on ESs; (3) categorizing principal data components with dimensionality reduction; (4) constructing multivariate regression models with variance partitioning; (5) implementing six spatial regression models to examine the causal effects of natural and anthropogenic forcings on ESs. Results show that climatic factors, biophysical factors, and environmental stressors significantly affect the ESs. Among the six driving factors, climate factors are highly associated with the ESs variation and explain the maximum model variances (R2 = 0.75–0.81). Socioeconomic (R2 = 0.44–0.66) and development (R2 = 27–0.44) factors have weak to moderate effects on the ESs. Furthermore, the joint effects of the driving factors are much higher than their individual effects. Among the six spatial regression models, Geographical Weighted Regression (GWR) performs the most accurately and explains the maximum model variances. The proposed hybrid valuation method aggregates biophysical and economic estimates of ESs and addresses methodological biases existing in the valuation process. The presented framework can be generalized and applied to other ecosystems at different scales. The outcome of this study could be a reference for decision-makers, planners, land administrators in formulating a suitable action plan and adopting relevant management practices to improve the overall socio-ecological status of the region.

    Benthic invertebrate and microbial biodiversity in sub-tropical urban rivers: Correlations with environmental variables and emerging chemicals
    Peng, Feng Jiao ; Pan, Chang Gui ; Zhang, Nai Sheng ; Braak, Cajo J.F. ter; Salvito, Daniel ; Selck, Henriette ; Ying, Guang Guo ; Brink, Paul J. Van den - \ 2020
    Science of the Total Environment 709 (2020). - ISSN 0048-9697
    Benthic bacterial community - Benthic macroinvertebrates - Double constrained ordination - Traits - Urban rivers - WWTP effluents

    Urban rivers often function as sinks for various contaminants potentially placing the benthic communities at risk of exposure. We performed a comprehensive biological survey of the benthic macroinvertebrate and bacterial community compositions in six rivers from the suburb to the central urban area of Guangzhou city (South China), and evaluated their correlations with emerging organic contaminants, heavy metals and nutrients. Overall, the benthic macroinvertebrate community shifted from molluscs to oligochaete from the suburban to the central urban rivers that receive treated and untreated sewage. An exception was the site in the Sha River where chironomids were most abundant. The differences in macroinvertebrate community assemblages were significantly associated with chromium, total phosphorus, galaxolide, triclosan and sand content in the sediment. There was no significant difference in benthic macroinvertebrate composition between the dry and wet season. As assessed by double constrained ordination, sexual reproduction was the only trait of benthic macroinvertebrates that showed a significant correlation with pollution variables, as it was significantly positively correlated with chromium and total phosphorus. This suggests that r-strategist occurs in polluted sampling sites. The benthic bacterial community composition showed a significant difference between seasons and among the Liuxi River, Zhujiang River and central urban rivers. The differences in community composition of the benthic bacteria were significantly correlated with galaxolide, total phosphorus, lead and triclosan. These results suggest that input of treated and untreated sewage significantly altered the benthic macroinvertebrate and bacterial community compositions in urban rivers.

    Development of a Generic Physiologically Based Kinetic Model to Predict In Vivo Uterotrophic Responses Induced by Estrogenic Chemicals in Rats Based on In Vitro Bioassays
    Zhang, Mengying ; Ravenzwaay, Bennard van; Rietjens, Ivonne M.C.M. - \ 2020
    Toxicological sciences 173 (2020)1. - ISSN 1096-6080 - p. 19 - 31.
    generic physiologically based kinetic modeling - quantitative in vitro–in vivo extrapolation - reverse dosimetry - uterotrophic assay

    The present study assessed the potential of a generic physiologically based kinetic (PBK) model to convert in vitro data for estrogenicity to predict the in vivo uterotrophic response in rats for diethylstibestrol (DES), ethinylestradiol (EE2), genistein (GEN), coumestrol (COU), and methoxychlor (MXC). PBK models were developed using a generic approach and in vitro concentration-response data from the MCF-7 proliferation assay and the yeast estrogen screening assay were translated into in vivo dose-response data. Benchmark dose analysis was performed on the predicted data and available in vivo uterotrophic data to evaluate the model predictions. The results reveal that the developed generic PBK model adequate defines the in vivo kinetics of the estrogens. The predicted dose-response data of DES, EE2, GEN, COU, and MXC matched the reported in vivo uterus weight response in a qualitative way, whereas the quantitative comparison was somewhat hampered by the variability in both in vitro and in vivo data. From a safety perspective, the predictions based on the MCF-7 proliferation assay would best guarantee a safe point of departure for further risk assessment although it may be conservative. The current study indicates the feasibility of using a combination of in vitro toxicity data and a generic PBK model to predict the relative in vivo uterotrophic response for estrogenic chemicals.

    Impact of trends in river discharge and ocean tides on water level dynamics in the Pearl River Delta
    Cao, Yu ; Zhang, Wei ; Zhu, Yuliang ; Ji, Xiaomei ; Xu, Yanwen ; Wu, Yao ; Hoitink, A.J.F. - \ 2020
    Coastal Engineering 157 (2020). - ISSN 0378-3839
    Nonstationary harmonic analysis - River discharge - Tidal amplitudes - Tidal forcing - Water levels

    The spectrum of tidal and subtidal water level variations in river deltas responds to river discharge variation, ocean tides, and human activities of many kinds. It remains a contemporary challenge to identify the main sources of changes in tidal dynamics in deltas, because of nonlinear interactions between tides and the river discharge in a changing setting. Understanding the main forcing factors controlling the evolution of mean water levels and the associated amplitudes and phases of tidal constituents can help to understand the causes of floods and the occurrence of low flows hindering navigation. Here, a nonstationary harmonic analysis tool (NS_TIDE) is applied to hydrological data from 14 stations in the Pearl River Delta (PRD) spanning the period 1961–2012. The water levels and main tidal constituent properties are decomposed into contributions of external forcing by river discharges and ocean tides, providing insight into the nonstationary tidal-fluvial processes. Significant temporal trends in mean water levels and tidal properties are observed in the PRD. Results indicate that there is spatial variability in the response of mean water levels and tidal properties to river discharge variation in the delta. The abrupt changes in bathymetry in the delta due to intensive sand excavation are likely responsible for the observed spatial variations in tidal response, which reduce the flood-dominant tidal asymmetry in this area.

    Modelling multi-regional urban growth with multilevel logistic cellular automata
    Shu, Bangrong ; Zhu, Shouhong ; Qu, Yi ; Zhang, Honghui ; Li, Xin ; Carsjens, Gerrit J. - \ 2020
    Computers, Environment and Urban Systems 80 (2020). - ISSN 0198-9715
    Logistic cellular automata - Multilevel modelling - Nonstationary - Tongshan County - Urban land expansion

    Simulation models based on cellular automata (CA) are useful for revealing the complex mechanisms and processes involved in urban growth and have become supplementary tools for urban land use planning and management. Although the urban growth mechanism is characterized by multilevel and spatiotemporal heterogeneity, most existing studies focus only on simulating the urban growth of singular regions without considering the heterogeneity of the urban growth process and the multilevel factors driving urban growth within regions that consist of multiple subregions. Thus, urban growth models have limited performance when simulating the urban growth of multi-regional areas. To address this issue, we propose a multilevel logistic CA model (MLCA) by incorporating a multilevel logistic regression model into the traditional logistic CA model (LCA). In the MLCA, multilevel driving factors are considered, and the multilevel logistic model allows the transition rules to not only vary in space, but also change when the subregional level factors change. To verify the MLCA's validity, it was applied to simulate the urban growth of Tongshan County, located in China's Xuzhou Prefecture. The results were compared with three comparative models, LCA1, which only considered grid cell-level factors; LCA2, which considered both grid cell- and subregional-level factors; and artificial neural network CA. Urban growth data for the periods 2000–2009 and 2009–2017 were used. The results show that the MLCA performs better on both visual comparison and indicators for accuracy verification. The Kappa of the results increased by <5%, but the improvement was significant, while increases for the accuracy of urban land and figure of merit were much higher than 5%. In addition, the results of MLCA had the smallest mean absolute percentage error when allocating new urban land areas to the various subregions. The results reveal that higher-level (e.g., town level) factors either strengthened or weakened the effects of grid cell-level factors on urban growth, which indirectly affected the spatial allocation of new urban land. The MLCA model is an effective step towards simulating nonstationary urban growth of multi-regional areas, using the comprehensive effects of multilevel driving factors.

    Modelling long-term impacts of fertilization and liming on soil acidification at Rothamsted experimental station
    Xu, Donghao ; Carswell, Alison ; Zhu, Qichao ; Zhang, Fusuo ; Vries, Wim de - \ 2020
    Science of the Total Environment 713 (2020). - ISSN 0048-9697
    Liming - Long-term experiments - Modelling - Soil acidification - VSD+

    Liming is widely used to reduce the impacts of soil acidification and optimize soil pH for agricultural production. Whether models can simulate the effect of liming on soil pH, and base saturation (BS), and thereby guide lime application, is still largely unknown. Long-term experimental data from a grassland (Park Grass, 1965–2012) and arable land (Sawyers Field, 1962–1972) at Rothamsted Research, UK, were thus used to assess the ability of the VSD+ model to simulate the effects of long-term fertilization and liming on soil acidification. The VSD+ model was capable of simulating observed soil pH and BS changes over time in the long-term liming experiments, except for a treatment in which sulphur (S) was added. Normalized Mean Absolute Errors (NMAE) and Normalized Root Mean Square Errors (NRMSE) of simulated and observed pH values, averaged over the observation periods varied between 0.02 and 0.08 (NMAE) and 0.01–0.05 (NRMSE). The acidity budget results for Park Grass suggest that nitrogen (N) transformations contributed most to acidity production, causing predominantly aluminium (Al) exchange in the topsoil (0–23 cm) followed by base cation (BC) release, but in the treatment with S addition, BC uptake had a nearly similar effect on acidity production. However, in Sawyers Field, the acidity budget suggested that BC uptake was the dominant cause of soil acidification, while the impacts of N transformations were limited. Liming was found to sufficiently replenish BC and decrease Al exchange in the topsoil layer. Overall, the VSD+ model can adequately reconstruct the impacts of fertilizer and liming applications on acid neutralizing processes and related soil pH and BC changes at the soil exchange complex.

    Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing
    Fuentes, Roven ; Hesselink, T. ; Nieuwenhuis, Ronald ; Bakker, L.V. ; Schijlen, E.G.W.M. ; Dooijeweert, W. van; Diaz Trivino, S. ; Haan, Jorn R. de; Sanchez Perez, G.F. ; Zhang, Xinyue ; Fransz, Paul ; Jong, J.H.S.G.M. de; Dijk, A.D.J. van; Ridder, D. de; Peters, S.A. - \ 2020
    The Plant Journal 102 (2020)3. - ISSN 0960-7412 - p. 480 - 492.
    Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non‐coding regions in the gene promoter and 5′UTR regions of genes. Poly‐A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non‐crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non‐homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
    Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
    Makarova, Kira S. ; Wolf, Yuri I. ; Iranzo, Jaime ; Shmakov, Sergey A. ; Alkhnbashi, Omer S. ; Brouns, Stan J.J. ; Charpentier, Emmanuelle ; Cheng, David ; Haft, Daniel H. ; Horvath, Philippe ; Moineau, Sylvain ; Mojica, Francisco J.M. ; Scott, David ; Shah, Shiraz A. ; Siksnys, Virginijus ; Terns, Michael P. ; Venclovas, Česlovas ; White, Malcolm F. ; Yakunin, Alexander F. ; Yan, Winston ; Zhang, Feng ; Garrett, Roger A. ; Backofen, Rolf ; Oost, John van der; Barrangou, Rodolphe ; Koonin, Eugene V. - \ 2020
    Nature Reviews Microbiology 18 (2020). - ISSN 1740-1526 - p. 67 - 83.

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

    Dynamic process-based modelling of crop growth and competitive water extraction in relay strip intercropping: Model development and application to wheat-maize intercropping
    Tan, Meixiu ; Gou, Fang ; Stomph, Tjeerd Jan ; Wang, Jing ; Yin, Wen ; Zhang, Lizhen ; Chai, Qiang ; Werf, Wopke van der - \ 2020
    Field Crops Research 246 (2020). - ISSN 0378-4290
    AquaCrop - LER - Water use efficiency - WER

    Strip intercropping increases land use efficiency but the effect on water use efficiency is less well-known. Here we develop a modelling method to simulate the growth of an intercrop taking into account the acquisition of light and water by the component species in order to calculate the efficacy of light and water acquisition in an intercropping system as compared to sole crops. The model is parameterized, calibrated and validated using data on wheat-maize intercropping in Gansu province, Northwest China. Observed above-ground biomass was 1630 g m−2 for sole wheat and 1334 g m−2 for intercropped wheat while it was 3023 g m−2 for sole maize and 2259 g m−2 for intercropped maize. The average water use was 405 mm in sole wheat, 595 mm in sole maize and 711 mm in wheat-maize intercropping. Based on observed yields, the land equivalent ratio (LER) was 1.59 and the water equivalent ratio (WER) was 1.14, where LER and WER express the relative amounts of land and water needed to achieve the yields obtained in a unit area of intercrop using sole crops. These results indicate that relay strip intercropping of wheat and maize achieves an increase of land use efficiency of 59% and of water use efficiency of 14%. Overall the intercrop model gave satisfactory predictions, with coefficients of efficiency (CE) in validation of 0.86–0.97, 0.90–0.95, 0.85–0.91 and 0.98 for biomass of sole wheat, sole maize, intercropped wheat, and intercropped maize, respectively. Overall CE of water use was 0.95. Simulated LER and WER were similar to observed LER and WER. The results show that intercropping could be used to obtain more yield on less land with less water. Policies that limit water use per unit land and prohibit the use of intercropping on the basis of its high water use per unit area may therefore be counter-productive. The model for intercrop growth and development under water limitation may be used for exploring production possibilities under land and water constraints.

    Intercropping maize and soybean increases efficiency of land and fertilizer nitrogen use; A meta-analysis
    Xu, Zhan ; Li, Chunjie ; Zhang, Chaochun ; Yu, Yang ; Werf, Wopke van der; Zhang, Fusuo - \ 2020
    Field Crops Research 246 (2020). - ISSN 0378-4290
    Fertilizer N equivalent ratio (FNER) - Intercropping - Land equivalent ratio (LER) - Maize - Soybean

    Intercropping exploits species complementarities to achieve sustainable intensification by increasing crop outputs per unit land with reduced anthropogenic inputs. Cereal/legume intercropping is a classical case. We carried out a global meta-analysis to assess land and fertilizer N use efficiency in intercropping of maize and soybean as compared to sole crops, based on 47 studies reported in English and 43 studies reported in Chinese. The data were extracted and analyzed with mixed effects models to assess land equivalent ratio (LER) of intercropping and factors affecting LER. The worldwide average LER of maize/soybean intercropping was 1.32 ± 0.02, indicating a substantial land sparing potential of intercropping over sole crops. This advantage increased as the temporal niche differentiation between the two species was increased by sowing or harvesting one crop earlier than the other as in relay intercropping, i.e. with only partial overlap of the growing periods of the two species The mean fertilizer N equivalent ratio (FNER) was 1.44 ± 0.03, indicating that intercrops received substantially less fertilizer N than sole crops for the same product output. These fertilizer savings are mainly due to the high relative maize yield and the lower N input in the intercrop compared to the input in sole maize. This meta-analysis thus shows that exploiting species complementarities by intercropping maize and soybean enables major increases in land productivity with less fertilizer N use. Both LER and FNER increased as the difference in growth duration increased for maize and soybean, but were not affected by fertilizer N rate. LER increased when soil organic matter increased but FNER did not change with soil organic matter.

    Can dietary manipulations improve the productivity of pigs with lower environmental and economic cost? A global meta-analysis
    Wang, Hongliang ; Long, Weitong ; Chadwick, Dave ; Velthof, Gerard L. ; Oenema, Oene ; Ma, Wenqi ; Wang, Junjun ; Qin, Wei ; Hou, Yong ; Zhang, Fusuo - \ 2020
    Agriculture, Ecosystems and Environment 289 (2020). - ISSN 0167-8809
    Ammonia emissions - Hydrogen sulfide - Livestock sustainability - Nitrogen - Phosphorus - Weight gain

    Inappropriate management of pig manure contributes considerably to pollution of waterbodies by nitrogen (N) and phosphorus (P), and to air pollution by ammonia (NH3) and hydrogen sulfide (H2S) emissions. Dietary manipulation is recognized as a possible pollution mitigation measure, but it may affect pig growth and thereby production costs. Here we present a global meta-analysis of the effects of dietary manipulation on nutrient (N and P) excretion, gaseous (NH3 and H2S) emissions from manure, and growth performance of pigs, using data from 245 published studies. Four groups of dietary manipulation were distinguished, namely i) lowering dietary crude protein (CP) content, (ii) supplementing exogenous enzymes, (iii) supplementing fermented feed ingredients, and (iv) supplementing other additives (e.g. fermentable carbohydrates, acidifying agent/salts and probiotics) in feed. In addition, the cost-effectiveness of dietary manipulations was evaluated, expressed as US $ per kg N excretion abated. Results show that lowering CP content significantly reduced both total N excretion (28.5%) and NH3 emissions (34.4%). Addition of protease reduced N excretion (18.2%) but did not affect NH3 emissions. Supplementing other additives simultaneously reduced NH3 emissions (21.5%) and H2S emissions (23.2%). Adding phytase to feed significantly decreased total P excretion by 31.4%. Diets with fermented feed ingredients tended to decrease N excretion and emissions, but this effect was not statistically significant. All dietary manipulations significantly improved the growth performance regarding the weight gain and feed efficiency, except for lowering CP content. But lowering dietary CP content within a moderate level in combination with adding additional amino acids did not impair pig growth. The cost-effectiveness analysis indicated that various diary manipulation measures were economically beneficial to farmers through improved feed-to-meat conversion efficiency. Our results can support to the design of proper dietary formulations so as to simultaneously reduce N and P excretion and associated emissions, meanwhile enhance the growth performance of pigs with lower economic cost.

    Revealing the nutrient limitation and cycling for microbes under forest management practices in the Loess Plateau – Ecological stoichiometry
    Zhang, Jiaoyang ; Yang, Xiaomei ; Song, Yahui ; Liu, Hongfei ; Wang, Guoliang ; Xue, Sha ; Liu, Guobin ; Ritsema, Coen J. ; Geissen, Violette - \ 2020
    Geoderma 361 (2020). - ISSN 0016-7061
    Ecological environment - Ecological stoichiometry - Forest management practices - Stoichiometric homeostasis - Threshold elemental ratio

    Forest management practices are commonly used in plantation forestry to obtain renewable energy and harvest biomass, in addition to maintaining the ecological environment, by changing the flow of carbon (C) and nutrients in the food webs of terrestrial ecosystems. To identify which forest management practices, alleviate soil nutrient limitation and impact stoichiometric homeostasis in relation to microbes, we used a Pinus tabuliformis plantation in the Loess Plateau where forest management practices were conducted since 1999. Five forest management practices were implemented: two at the forest level (P. tabuliformis with and without ground litter, CK, LRL) and three of different vegetation restorations after clear-cutting (P. tabuliformis seedlings (SPL), grass land (GL), and shrub land (SL)). Generally, the threshold elemental ratios for carbon:nitrogen (TERC:N; 7.77) and carbon:phosphorus (TERC:P; 44.37) were lower than the ratios influenced by forest management practices. The forest management practices significantly influenced ecoenzymatic activity and the ratios of ecoenzymes; however, the scale of the ecoenzyme activities for acquiring both organic N and organic P to that for acquiring C still follow the global pattern. The regression coefficients of C:N and C:P between the soil and microbial community at 0–20 cm and 20–40 cm depths were also influenced by these practices. Thus, the influence of forest management practices on the soil microbial community was limited by N and P in the Loess Plateau. The soil microbial community changed ecoenzymatic activities and ratios of ecoenzymes and even changed microbial community in order to balance elemental limitations in the soil. Finally, forest management practices have a minimal impact on the stoichiometric homeostasis of the microbial community at our study site.

    Biochar promotes the reduction of N2O to N2 and concurrently suppresses the production of N2O in calcareous soil
    Dong, Wenxu ; Walkiewicz, Anna ; Bieganowski, Andrzej ; Oenema, Oene ; Nosalewicz, Magdalena ; He, Chaohui ; Zhang, Yuming ; Hu, Chunsheng - \ 2020
    Geoderma 362 (2020). - ISSN 0016-7061
    Biochar - Calcareous soil - Denitrification - Nitrous oxide emissions

    Biochar additions may mitigate N2O emissions from soil. The mechanisms underpinning the mitigation of emissions remain to be elucidated. A series of incubation experiments were performed to investigate the effects of biochar on N2O production and reduction in columns with a low-fertility or high-fertility soil, with or without the injection of N2O in the subsoil and with and without glucose (to stimulate denitrification). Biochar was added to the calcareous soils in 0 and 1% (w/w) amounts and moisture was maintained at 70% water-filled pore space (WFPS) over the incubation period. The results revealed that biochar reduced the emissions of soil-produced N2O by 37–47% and those of injected N2O by 23–44%. The addition of glucose solution strongly increased N2O emissions, while biochar reduced total N2O emissions by as much as 64–81% and those of injected N2O alone by 29–51%. Differences between the low-fertility and high-fertility soils in the apparent N2O emission mitigation by biochar were relatively small, but tended to be larger for the low-fertility soil. The results suggest that biochar addition can suppress the production of N2O in soil and simultaneously stimulate the reduction of N2O to N2. Further studies are needed to elucidate the regulatory effects of biochar in soil.

    Rescue of tomato spotted wilt virus entirely fromcomplementary DNA clones
    Feng, Mingfeng ; Cheng, Ruixiang ; Chen, Minglong ; Guo, Rong ; Li, Luyao ; Feng, Zhike ; Wu, Jianyan ; Xie, Li ; Hong, Jian ; Zhang, Zhongkai ; Kormelink, R.J.M. ; Tao, Xiaorong - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)2. - ISSN 0027-8424BioRxiv - p. 1181 - 1190.
    Negative-stranded/ambisense RNA viruses (NSVs) include not only dangerous pathogens of medical importance but also serious plant pathogens of agronomic importance. Tomato spotted wilt virus (TSWV) is one of the most important plant NSVs, infecting more than 1,000 plant species, and poses major threats to global food security. The segmented negative-stranded/ambisense RNA genomes of TSWV, however, have been a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from complementary DNA (cDNA) clones. First, a replication- and transcription-competent minigenome replication system was established based on 35S-driven constructs of the S(−)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by the 5′ hammerhead and 3′ ribozyme sequence of hepatitis delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA-dependent RNA polymerase (RdRp) gene. Next, a movement-competent minigenome replication system was developed based on M(−)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. Finally, infectious TSWV and derivatives carrying eGFP reporters were rescued in planta via simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(−)-gRNA, and L(+)-agRNA in which the glycoprotein gene sequence of M(−)-gRNA was optimized. Viral rescue occurred with the addition of various RNAi suppressors including P19, HcPro, and γb, but TSWV NSs interfered with the rescue of genomic RNA. This reverse genetics system for TSWV now allows detailed molecular genetic analysis of all aspects of viral infection cycle and pathogenicity.
    Long-term fertilization alters microbial community but fails to reclaim soil organic carbon stocks in a land-use changed soil of the Tibetan Plateau
    Li, Meng ; Wang, Guoxi ; Kang, Xiaoming ; Hu, Hualing ; Wang, Yan ; Zhang, Xiangru ; Sun, Xiaolei ; Zhang, Hui ; Hu, Zhengyi ; Xi, Beidou - \ 2020
    Land Degradation and Development 31 (2020)4. - ISSN 1085-3278 - p. 531 - 524.
    16S rRNA sequencing - aggregates - manure compost - meadow - soil organic fractions

    The microbial community and soil organic carbon (SOC), which play vital roles in soil fertility and the global C cycle, have been heavily altered due to land-use changes and long-term fertilization. However, the effect of long-term fertilization on the microbial community and SOC in land-use changed soil is still unclear. In this study, a 26-year field experiment is conducted to detect the bacterial community and SOC stocks in the soils from meadow grasslands (M), croplands without fertilization (NF), and croplands with fertilization for 13 (F13a) and 26 years (F26a) in the Tibetan Plateau. The results show that land-use change from meadow grassland to cropland induced a decrease in the SOC stocks of total (TOC), free (FOC) and permanganate-oxidizable OC (POxC) by 61.8–85.0, 51.1–82.8, and 78.4–95.8%, respectively. Long-term fertilization increased the SOC stocks by 124.4–419.0%, which was still lower than those in the M soils. In addition, macroaggregates (MAA) and bacterial diversity displayed reductions when the land-use was changed from grassland to cropland, but they were enhanced after long-term fertilization. Land-use change and long-term fertilization both altered the microbial community. MAA served as a habitat for the microbial community and physical protection for SOC. This may be a key driver of changes in the bacterial community and SOC. This study demonstrates that long-term fertilization alters the microbial community but fails to restore SOC stocks to the level of uncropped meadow soils. Long-term fertilization integrated with macroaggregates are required to improve OC sequestration for developing sustainable agriculture and mitigating global climate change.

    Yield gain, complementary and competitive dominance in intercropping in China: a meta-analysis of drivers of yield gain using additive partitioning
    Li, C. ; Hoffland, E. ; Kuijper, T.W.M. ; Yu, Y. ; Li, Haigang ; Zhang, Chaochun ; Zhang, Fusuo ; Werf, W. van der - \ 2020
    European Journal of Agronomy 113 (2020). - ISSN 1161-0301
    Intercropping is known to increase the efficiency of land use, but no meta-analysis has so far been made on the yield gain of intercropping compared to sole cropping in terms of absolute yield per unit area. Yield gain could potentially be related to a relaxation of competition, due to complementarity or facilitation, and/or to the competitive dominance of the higher yielding species. The contributions of competitive relaxation and dominance were here estimated using the concepts of complementarity effect (CE) and selection effect (SE), respectively. We compiled a dataset on intercropping of grain-producing crops from China, a hotspot of strip intercropping in the world. We quantified the yield gain and its components and analysed the contribution to yield gain of species traits (C3, C4, legume, non-legume), complementarity in time and nutrient input. Total yield in intercrops exceeded the expected yield, estimated on the basis of sole crop yields, by 2.14 ± 0.16 Mg ha−1 (mean ± standard error). Ninety percent of this yield gain was due to a positive CE while the remaining 10 % was due to SE. The net yield gain increased with temporal niche differentiation (TND) which is the proportion of the total growing period of the crop mixture during which species grow alone. The mechanism underlying yield gain shifted from competitive dominance of the higher yielding species when there was more overlap in growth period between the two species, to competitive relaxation when there was less overlap, while competitive relaxation remained the major component of the yield gain. The yield gain was substantially greater in intercrops with maize than in intercrops without maize, but there was no difference in yield gain between systems with and without legumes. The yield gain increased with nitrogen (N) input in maize/C3-cereal intercrops but not in cereal/legume intercrops, illustrating the ability of legumes to compensate for low N input, and highlighting the need for N input for high productivity in intercropping systems without legumes. Yield gain did not respond to phosphorus (P) input. We conclude that competitive relaxation is the main contributing factor to yield gain in the investigated Chinese intercropping systems, which were mostly relay strip intercropping systems. The underlying drivers of yield gain were related to presence of maize and species complementarity in time, but we did not find strong evidence for the selection effect.

    Yield and nitrogen uptake of sole and intercropped maize and peanut in response to N fertilizer input
    Gao, Huaxin ; Meng, Weiwei ; Zhang, Chaochun ; Werf, Wopke van der; Zhang, Zheng ; Wan, Shubo ; Zhang, Fusuo - \ 2020
    Food and Energy Security 9 (2020)1. - ISSN 2048-3694
    intercropping - land equivalent ratio - N input - N uptake - yield

    Chinese agriculture needs to become less dependent on fertilizer inputs to enhance sustainability. Cereal/legume intercropping is a potential pathway to lower fertilizer inputs, but there is insufficient knowledge on the nitrogen (N) response in species mixtures. Here, we investigated N response in maize/peanut intercropping. Maize showed a stronger yield response to N input than peanut both in sole cropping and in intercropping, and so did sole crops relative to intercrops. Maize yield was the highest at the maximum level tested: 360 kg N/ha. Agronomic efficiency (AE) of sole maize was 7.8 kg/kg N input, averaged across five N levels (0, 90, 180, 270, and 360 kg/ha). Partial land equivalent ratios (pLERs) for maize decreased with N input, from 0.70 at zero to 0.64 at 360 kg/ha. Sole peanut showed an optimum yield response to N input, with the highest yield at 270 kg/ha and lower yield at 360 kg/ha. The average AE of sole peanut was 1.3 kg/kg. The pLER of peanut declined from 0.43 at zero to 0.32 at 360 kg/ha while the overall LER decreased from 1.13 to 0.96, indicating relative better performance of intercropping at low than at high N input. Apparent recovery (RE) for N was 27.2% for sole maize, 12.4% for sole peanut, and 7.2% for intercrops. Mean N uptake was 179 kg/ha in sole maize, 199 kg/ha in intercropping, and 264 kg/ha in sole peanut. Partial economic budgeting indicated that with the current low Chinese N fertilizer prices, gross margin is maximized with high N input in sole crops; however, for intercropping, the highest gross margin was attained at intermediate N inputs of 180 or 270 kg/ha. Fertilizer price incentives may facilitate a transition to intercropping at moderate N input in China.

    Stability of fat globules in UHT milk during proteolysis by the AprX protease from Pseudomonas fluorescens and by plasmin
    Zhang, Chunyue ; Bijl, Etske ; Muis, Karinska Eunike ; Hettinga, Kasper - \ 2020
    Journal of Dairy Science 103 (2020)1. - ISSN 0022-0302 - p. 179 - 190.
    AprX - fat stability - plasmin - proteolysis - UHT milk

    Fat separation is a limiting factor for the shelf life of UHT milk. It may be promoted by the proteolysis of fat surface-adsorbed proteins (FSAP) by proteases that remain active after UHT treatment. The aim of this research was to explore the relationship between the proteolysis of FSAP and fat destabilization. In this study, we developed a full-fat UHT milk-based model system and added either the major bacterial protease AprX from Pseudomonas fluorescens or the major native milk protease plasmin at high levels to induce fast destabilization of the milk fat globules. We monitored changes in physical properties and FSAP composition, and structural changes in fat globules, over 24 h. Our results showed that AprX-induced sedimentation as a result of the flocculation of fat globules, and plasmin induced cream to float as a result of the coalescence of fat globules. This study confirmed that AprX and plasmin can both lead to fat destabilization in full-fat UHT milk, and it provides insights in the underlying mechanisms.

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