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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    Loss of c‐Jun N‐terminal Kinase 1 and 2 Function in Liver Epithelial Cells Triggers Biliary Hyperproliferation Resembling Cholangiocarcinoma
    Cubero, Francisco Javier ; Mohamed, Mohamed Ramadan ; Woitok, Marius M. ; Zhao, Gang ; Hatting, Maximilian ; Nevzorova, Yulia A. ; Chen, Chaobo ; Haybaeck, Johannes ; Bruin, Alain de; Avila, Matias A. ; Boekschoten, Mark V. ; Davis, Roger J. ; Trautwein, Christian - \ 2020
    Hepatology Communications 4 (2020)6. - ISSN 2471-254X - p. 834 - 851.
    Targeted inhibition of the c‐Jun N‐terminal kinases (JNKs) has shown therapeutic potential in intrahepatic cholangiocarcinoma (CCA)‐related tumorigenesis. However, the cell‐type‐specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remain largely unknown. Here, we aimed to investigate the relevance of JNK1 and JNK2 function in hepatocytes in two different models of experimental carcinogenesis, the dethylnitrosamine (DEN) model and in nuclear factor kappa B essential modulator (NEMO)hepatocyte‐specific knockout (Δhepa) mice, focusing on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development. Moreover, regulation of essential genes was assessed by reverse transcription polymerase chain reaction, immunoblottings, and immunostainings. Additionally, specific Jnk2 inhibition in hepatocytes of NEMOΔhepa/JNK1Δhepa mice was performed using small interfering (si) RNA (siJnk2 ) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of Jnk1 and Jnk2 in hepatocytes diminished hepatocellular carcinoma (HCC) in both the DEN model and in NEMOΔhepa mice but in contrast caused massive proliferation of the biliary ducts. Indeed, Jnk1/2 deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression but reduced HCC. Furthermore, siJnk2 treatment in NEMOΔhepa/JNK1Δhepa mice recapitulated the phenotype of NEMOΔhepa/JNKΔhepa mice. Next, we sought to investigate the impact of molecular pathways in response to compound JNK deficiency in NEMOΔhepa mice. We found that NEMOΔhepa/JNKΔhepa livers exhibited overexpression of the interleukin‐6/signal transducer and activator of transcription 3 pathway in addition to epidermal growth factor receptor (EGFR)‐rapidly accelerated fibrosarcoma (Raf)‐mitogen‐activated protein kinase kinase (MEK)‐extracellular signal‐regulated kinase (ERK) cascade. The functional relevance was tested by administering lapatinib, which is a dual tyrosine kinase inhibitor of erythroblastic oncogene B‐2 (ErbB2) and EGFR signaling, to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases, and effectively blocked EGFR‐Raf‐MEK‐ERK signaling. Conclusion : We define a novel function of JNK1/2 in cholangiocyte hyperproliferation. This opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.
    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.

    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.

    The future of phenomics in dairy cattle breeding
    Cole, John B. ; Eaglen, Sophie A.E. ; Maltecca, Christian ; Mulder, Han A. ; Pryce, Jennie E. - \ 2020
    Animal Frontiers 10 (2020)2. - ISSN 2160-6056 - p. 37 - 44.
    Analytics - Big data - Dairy cattle - Machine learning - Phenomics - Sensors

    Increasingly complex dairy cattle production systems require that all aspects of animal performance are measured across individuals' lifetimes. Selection emphasis is shifting away from traits related to animal productivity toward those related to effcient resource utilization and improved health and welfare/ resilience. The goal of phenomics is to provide information for making decisions related to on-farm management, as well as genetic improvement.

    Future of the human climate niche
    Xu, Chi ; Kohler, Timothy A. ; Lenton, Timothy M. ; Svenning, Jens Christian ; Scheffer, Marten - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Climate - Migration - Societies

    All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ~11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same conditions, and the same optimum has been found for agricultural and nonagricultural economic output of countries through analyses of year-to-year variation. We show that in a business-as-usual climate change scenario, the geographical position of this temperature niche is projected to shift more over the coming 50 y than it has moved since 6000 BP. Populations will not simply track the shifting climate, as adaptation in situ may address some of the challenges, and many other factors affect decisions to migrate. Nevertheless, in the absence of migration, one third of the global population is projected to experience a MAT >29 °C currently found in only 0.8% of the Earth's land surface, mostly concentrated in the Sahara. As the potentially most affected regions are among the poorest in the world, where adaptive capacity is low, enhancing human development in those areas should be a priority alongside climate mitigation.

    Turning autophobic wetting on biomimetic surfaces into complete wetting by wetting additives
    Leermakers, Frans A.M. ; Luengo, Gustavo S. ; Baghdadli, Nawel ; Mazilier, Christian ; Potter, Anne ; Léonforte, Fabien - \ 2020
    Soft Matter 16 (2020)20. - ISSN 1744-683X - p. 4823 - 4839.

    Autophobicity or pseudo partial wetting, a phenomenon of a liquid not spreading on its own monolayer, is characterized by an energy barrier that prevents the growth of a wetting film beyond the monolayer thickness. Applying a molecularly detailed self-consistent field theory we illustrate how autophobic wetting can be overcome by wetting additives. More specifically we use an emulsifier which keeps the interfacial tension between the wetting component and the majority solvent low, and a co-solvent additive which partitions inside the film and then destroys the molecular order in it so that the barrier for film growth is cleared. An application wherein it is believed that autophobic wetting is counteracted by such a set of wetting additives is found in an antidandruff shampoo formulation. We have experimental results that show thick deposits onto hydrophobic hair surfaces by administration of the antidandruff shampoo. The complementary modeling of such a system suggests that the active ingredient plays the role of the co-solvent additive. As significant amounts of the co-solvent additives are needed to approach the completely wet state, the formulation naturally brings large amounts of active ingredient to the root of the hair where its presence is required.

    Antenatal multiple micronutrient supplementation: call to action for change in recommendation
    Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu‐Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle‐Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, L. ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2020
    Annals of the New York Academy Of Sciences 1465 (2020)1. - ISSN 0077-8923 - p. 5 - 7.
    A schematic sampling protocol for contaminant monitoring in raptors
    Espín, Silvia ; Andevski, Jovan ; Duke, Guy ; Eulaers, Igor ; Gómez-Ramírez, Pilar ; Hallgrimsson, Gunnar Thor ; Helander, Björn ; Herzke, Dorte ; Jaspers, Veerle L.B. ; Krone, Oliver ; Lourenço, Rui ; María-Mojica, Pedro ; Martínez-López, Emma ; Mateo, Rafael ; Movalli, Paola ; Sánchez-Virosta, Pablo ; Shore, Richard F. ; Sonne, Christian ; Brink, Nico W. van den; Hattum, Bert van; Vrezec, Al ; Wernham, Chris ; García-Fernández, Antonio J. - \ 2020
    Ambio (2020). - ISSN 0044-7447
    Best practices - Birds of prey - Falcons - Large-scale biomonitoring - Owls - Pan-European network

    Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

    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.

    Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs
    Cao, Lu ; Liu, Huiming ; Mulder, Han A. ; Henryon, Mark ; Thomasen, Jørn Rind ; Kargo, Morten ; Sørensen, Anders Christian - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    across-environment selection of sires - genetic gain - joint genetic evaluation - long-term cooperation - rate of inbreeding - stochastic simulation

    Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (rg) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point rg that is the lowest value of rg for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point rg than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

    Determinants of legacy effects in pine trees – implications from an irrigation-stop experiment
    Zweifel, Roman ; Etzold, Sophia ; Sterck, Frank ; Gessler, Arthur ; Anfodillo, Tommaso ; Mencuccini, Maurizio ; Arx, Georg von; Lazzarin, Martina ; Haeni, Matthias ; Feichtinger, Linda ; Meusburger, Katrin ; Knuesel, Simon ; Walthert, Lorenz ; Salmon, Yann ; Bose, Arun K. ; Schoenbeck, Leonie ; Hug, Christian ; Girardi, Nicolas De; Giuggiola, Arnaud ; Schaub, Marcus ; Rigling, Andreas - \ 2020
    New Phytologist 227 (2020)4. - ISSN 0028-646X - p. 1081 - 1096.
    cambial activity - drought stress - ecological memory - irrigation experiment - osmoregulation - point dendrometer - radial stem growth - TreeNet

    Tree responses to altered water availability range from immediate (e.g. stomatal regulation) to delayed (e.g. crown size adjustment). The interplay of the different response times and processes, and their effects on long-term whole-tree performance, however, is hardly understood. Here we investigated legacy effects on structures and functions of mature Scots pine in a dry inner-Alpine Swiss valley after stopping an 11-yr lasting irrigation treatment. Measured ecophysiological time series were analysed and interpreted with a system-analytic tree model. We found that the irrigation stop led to a cascade of downregulations of physiological and morphological processes with different response times. Biophysical processes responded within days, whereas needle and shoot lengths, crown transparency, and radial stem growth reached control levels after up to 4 yr only. Modelling suggested that organ and carbon reserve turnover rates play a key role for a tree’s responsiveness to environmental changes. Needle turnover rate was found to be most important to accurately model stem growth dynamics. We conclude that leaf area and its adjustment time to new conditions is the main determinant for radial stem growth of pine trees as the transpiring area needs to be supported by a proportional amount of sapwood, despite the growth-inhibiting environmental conditions.

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

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

    Combining recent nutritional data with prospective cohorts to quantify the impact of modern dietary patterns on disability–adjusted life years : A feasibility study
    Krieger, Jean Philippe ; Pestoni, Giulia ; Frehner, Anita ; Schader, Christian ; Faeh, David ; Rohrmann, Sabine - \ 2020
    Nutrients 12 (2020)3. - ISSN 2072-6643
    DALYs - Dietary patterns - MenuCH

    Unhealthy diets are commonly associated with increased disability-adjusted life years (DALYs) from noncommunicable diseases. The association between DALYs and dietary patterns can be quantified with individual longitudinal data. This assessment, however, is often based on dietary data collected once at cohort entry, therefore reflecting the impact of “old” dietary habits on morbidity and mortality. To overcome this limitation, we tested the association of contemporary diets with DALYs. First, we defined contemporary dietary patterns consumed in Switzerland with the national nutrition survey menuCH (2014–2015). Second, we identified individuals who consumed similar diets in the NRP–MONICA census-linked cohort (1977–2015). In this cohort, individual data on disease and mortality were used to calculate the DALYs-dietary patterns association using a mixed regression model. A total of 58,771 DALYs from NCDs were recorded in a mean follow-up time of 25.5 years. After multivariable adjustments, the “Swiss traditional” pattern was not associated with an increase in DALYs compared to the “Prudent” pattern. However, individuals following a “Western” pattern had, on average 0.29 DALYs (95% CI 0.02, 0.56) more than those following a “Prudent” pattern, equating to a loss of healthy life of more than three months. These data highlight the feasibility of quantifying the impact of contemporary diets on DALYs without the establishment of new cohorts or the use of nationally aggregated data.

    Scaling carbon fluxes from eddy covariance sites to globe : Synthesis and evaluation of the FLUXCOM approach
    Jung, Martin ; Schwalm, Christopher ; Migliavacca, Mirco ; Walther, Sophia ; Camps-Valls, Gustau ; Koirala, Sujan ; Anthoni, Peter ; Besnard, Simon ; Bodesheim, Paul ; Carvalhais, Nuno ; Chevallier, Frederic ; Gans, Fabian ; Goll, Daniel S. ; Haverd, Vanessa ; Köhler, Philipp ; Ichii, Kazuhito ; Jain, Atul K. ; Liu, Junzhi ; Lombardozzi, Danica ; Nabel, Julia E.M.S. ; Nelson, Jacob A. ; O'Sullivan, Michael ; Pallandt, Martijn ; Papale, Dario ; Peters, Wouter ; Pongratz, Julia ; Rödenbeck, Christian ; Sitch, Stephen ; Tramontana, Gianluca ; Walker, Anthony ; Weber, Ulrich ; Reichstein, Markus - \ 2020
    Biogeosciences 17 (2020)5. - ISSN 1726-4170 - p. 1343 - 1365.

    FLUXNET comprises globally distributed eddy-covariance-based estimates of carbon fluxes between the biosphere and the atmosphere. Since eddy covariance flux towers have a relatively small footprint and are distributed unevenly across the world, upscaling the observations is necessary to obtain global-scale estimates of biosphere-atmosphere exchange. Based on cross-consistency checks with atmospheric inversions, sun-induced fluorescence (SIF) and dynamic global vegetation models (DGVMs), here we provide a systematic assessment of the latest upscaling efforts for gross primary production (GPP) and net ecosystem exchange (NEE) of the FLUXCOM initiative, where different machine learning methods, forcing data sets and sets of predictor variables were employed. Spatial patterns of mean GPP are consistent across FLUXCOM and DGVM ensembles ( at 1 spatial resolution) while the majority of DGVMs show, for 70 of the land surface, values outside the FLUXCOM range. Global mean GPP magnitudes for 2008-2010 from FLUXCOM members vary within 106 and 130 PgC class with the largest uncertainty in the tropics. Seasonal variations in independent SIF estimates agree better with FLUXCOM GPP (mean global pixel-wise) than with GPP from DGVMs (mean global pixel-wise). Seasonal variations in FLUXCOM NEE show good consistency with atmospheric inversion-based net land carbon fluxes, particularly for temperate and boreal regions. Interannual variability of global NEE in FLUXCOM is underestimated compared to inversions and DGVMs. The FLUXCOM version which also uses meteorological inputs shows a strong co-variation in interannual patterns with inversions (for 2001-2010). Mean regional NEE from FLUXCOM shows larger uptake than inversion and DGVM-based estimates, particularly in the tropics with discrepancies of up to several hundred grammes of carbon per square metre per year. These discrepancies can only partly be reconciled by carbon loss pathways that are implicit in inversions but not captured by the flux tower measurements such as carbon emissions from fires and water bodies. We hypothesize that a combination of systematic biases in the underlying eddy covariance data, in particular in tall tropical forests, and a lack of site history effects on NEE in FLUXCOM are likely responsible for the too strong tropical carbon sink estimated by FLUXCOM. Furthermore, as FLUXCOM does not account for fertilization effects, carbon flux trends are not realistic. Overall, current FLUXCOM estimates of mean annual and seasonal cycles of GPP as well as seasonal NEE variations provide useful constraints of global carbon cycling, while interannual variability patterns from FLUXCOM are valuable but require cautious interpretation. Exploring the diversity of Earth observation data and of machine learning concepts along with improved quality and quantity of flux tower measurements will facilitate further improvements of the FLUXCOM approach overall.

    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.
    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.

    From GWAS Peak to Causal Mutation; Utilizing p(ig)CADD Scores to Prioritize Sequence Variation
    Derks, Martijn ; Gross, Christian ; Lopes, M.S. ; Reinders, M.J.T. ; Bosse, Mirte ; Gjuvsland, Arne B. ; Megens, Hendrik-Jan ; Ridder, Dick de; Groenen, Martien - \ 2020
    The genotype-phenotype link is a major research topic in life sciences, but remains highly complex to disentangle. Part of the complexity arises from the polygenicity of phenotypes, in which many (interacting) genes contribute to the observed phenotype. Genome wide association studies have been instrumental to associate genomic markers to important phenotypes. However, despite the vast increase of molecular data (e.g. whole genome sequences), pinpointing the causal variant underlying a phenotype of interest is still a major challenge, especially due to high levels of linkage disequilibrium.

    In this study we present a method to prioritize genomic variation underlying traits of interest from genome wide association studies in pigs. First, we select all sequence variants associated with the trait. Subsequently, we prioritize variation by utilizing and integrating predicted variant impact scores, gene expression data, epigenetic marks for promotor and enhancer identification, and associated phenotypes in other (well-studied) mammalian species. The power of the method heavily relies on variant impact scores, for which we used pCADD, a tool which can assign scores to any
    variant in the genome including those in non-coding regions. Using our methodology, we are able to either pinpoint the likely causal mutation or substantially narrow down the list of potential causal candidates from any association result. We demonstrate the efficacy of the tool by reporting known and novel causal variants, of which many affect (non-coding) regulatory sequences associated with important phenotypes in pigs.

    This study provides a framework to pinpoint likely causal variation and genes underlying important phenotypes in pigs. Hence, the tool accelerates the discovery of new causal variants that could be directly implemented to improve selection. Finally, we report several common pathways and molecular mechanisms involved in analogous phenotypes between human and pig, proving the suitability of pig as a model to study human (metabolic) disease.
    Synchronization of developmental, molecular and metabolic aspects of source–sink interactions
    Fernie, Alisdair R. ; Bachem, Christian W.B. ; Helariutta, Yrjö ; Neuhaus, H.E. ; Prat, Salomé ; Ruan, Yong Ling ; Stitt, Mark ; Sweetlove, Lee J. ; Tegeder, Mechthild ; Wahl, Vanessa ; Sonnewald, Sophia ; Sonnewald, Uwe - \ 2020
    Nature Plants 6 (2020). - ISSN 2055-026X - p. 55 - 66.

    Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source–sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.

    Soil carbon sequestration in grazing systems: managing expectations
    Godde, Cécile M. ; Boer, Imke J.M. de; Ermgassen, Erasmus zu; Herrero, Mario ; Middelaar, Corina E. van; Muller, Adrian ; Röös, Elin ; Schader, Christian ; Smith, Pete ; Zanten, Hannah H.E. van; Garnett, Tara - \ 2020
    Climatic Change (2020). - ISSN 0165-0009
    Cattle - Climate change - Grasslands - Greenhouse gases - Livestock - Soil carbon

    Grazing systems emit greenhouse gases, which can, under specific agro-ecological conditions, be partly or entirely offset by soil carbon sequestration. However, any sequestration is time-limited, reversible, and at a global level outweighed by emissions from grazing systems. Thus, grazing systems are globally a net contributor to climate change and the time scale of key processes needs to be factored into any mitigation efforts. Failing to do so leads to unrealistic expectations of soil carbon management in grazing systems as a mitigation strategy. Protecting the large carbon stocks in grazing lands is also essential in order to avoid further climate change from additional CO2 release. Despite the time-limited and reversible nature of soil carbon sequestration in grazing lands, sequestration should be promoted in cases where it delivers environmental and agronomic benefits as well as for its potential, particularly on degraded land, to increase the feasibility of limiting global warming to less than 2 or preferably 1.5 °C. Some peer-reviewed sequestration estimates are of a similar order of magnitude to other food systems mitigation options over a 10–20 years period, such as reducing food loss and waste by 15% or aligning diets with current health related dietary-recommendations. However, caution should be applied to such comparisons since mitigation estimates are associated with large uncertainties and will ultimately depend on the economic cost-benefit relation, feasibility of implementation and time frame considered.

    A thin layer of activated carbon deposited on polyurethane cube leads to new conductive bioanode for (plant) microbial fuel cell
    Sudirjo, Emilius ; Constantino Diaz, Paola Y. ; Cociancich, Matteo ; Lisman, Rens ; Snik, Christian ; Buisman, Cees J.N. ; Strik, David P.B.T.B. - \ 2020
    Energies 13 (2020)3. - ISSN 1996-1073
    Activated carbon - Bioanode - Conductive biofilms - Microbial fuel cell - Plant microbial fuel cell - Polyurethane

    Large-scale implementation of (plant) microbial fuel cells is greatly limited by high electrode costs. In this work, the potential of exploiting electrochemically active self-assembled biofilms in fabricating three-dimensional bioelectrodes for (plant) microbial fuel cells with minimum use of electrode materials was studied. Three-dimensional robust bioanodes were successfully developed with inexpensive polyurethane foams (PU) and activated carbon (AC). The PU/AC electrode bases were fabricated via a water-based sorption of AC particles on the surface of the PU cubes. The electrical current was enhanced by growth of bacteria on the PU/AC bioanode while sole current collectors produced minor current. Growth and electrochemical activity of the biofilm were shown with SEM imaging and DNA sequencing of the microbial community. The electric conductivity of the PU/AC electrode enhanced over time during bioanode development. The maximum current and power density of an acetate fed MFC reached 3 mA·m−2 projected surface area of anode compartment and 22 mW·m−3 anode compartment. The field test of the Plant-MFC reached a maximum performance of 0.9 mW·m−2 plant growth area (PGA) at a current density of 5.6 mA·m−2 PGA. A paddy field test showed that the PU/AC electrode was suitable as an anode material in combination with a graphite felt cathode. Finally, this study offers insights on the role of electrochemically active biofilms as natural enhancers of the conductivity of electrodes and as transformers of inert low-cost electrode materials into living electron acceptors.

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