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.

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