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.

    We have a manual that explains all the features 

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    Towards recombinantly produced milk proteins : Physicochemical and emulsifying properties of engineered whey protein beta-lactoglobulin variants
    Keppler, Julia K. ; Heyse, Anja ; Scheidler, Eva ; Uttinger, Maximilian J. ; Fitzner, Laura ; Jandt, Uwe ; Heyn, Timon R. ; Lautenbach, Vanessa ; Loch, Joanna I. ; Lohr, Jonas ; Kieserling, Helena ; Günther, Gabriele ; Kempf, Elena ; Grosch, Jan Hendrik ; Lewiński, Krzysztof ; Jahn, Dieter ; Lübbert, Christian ; Peukert, Wolfgang ; Kulozik, Ulrich ; Drusch, Stephan ; Krull, Rainer ; Schwarz, Karin ; Biedendieck, Rebekka - \ 2021
    Food Hydrocolloids 110 (2021). - ISSN 0268-005X
    Two recombinant beta-lactoglobulin (BLG) B variants were produced in E. coli. Production/isolation resulted in native BLG without post-translational modifications. Properties of recombinant variants were compared to commercial BLG B and BLG AB. Minor differences in solubility and interface adsorption behavior were evident. Genetically engineered and natural BLGs show similar emulsifying properties.
    Global root traits (GRooT) database
    Guerrero-Ramírez, Nathaly R. ; Mommer, Liesje ; Freschet, Grégoire T. ; Iversen, Colleen M. ; McCormack, M.L. ; Kattge, Jens ; Poorter, Hendrik ; Plas, Fons van der; Bergmann, Joana ; Kuyper, Thom W. ; York, Larry M. ; Bruelheide, Helge ; Laughlin, Daniel C. ; Meier, Ina C. ; Roumet, Catherine ; Semchenko, Marina ; Sweeney, Christopher J. ; Ruijven, Jasper van; Valverde-Barrantes, Oscar J. ; Aubin, Isabelle ; Catford, Jane A. ; Manning, Peter ; Martin, Adam ; Milla, Rubén ; Minden, Vanessa ; Pausas, Juli G. ; Smith, Stuart W. ; Soudzilovskaia, Nadejda A. ; Ammer, Christian ; Butterfield, Bradley ; Craine, Joseph ; Cornelissen, Johannes H.C. ; Vries, Franciska T. de; Isaac, Marney E. ; Kramer, Koen ; König, Christian ; Lamb, Eric G. ; Onipchenko, Vladimir G. ; Peñuelas, Josep ; Reich, Peter B. ; Rillig, Matthias C. ; Sack, Lawren ; Shipley, Bill ; Tedersoo, Leho ; Valladares, Fernando ; Bodegom, Peter van; Weigelt, Patrick ; Wright, Justin P. ; Weigelt, Alexandra - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    Belowground ecology - functional biogeography - macroecological studies - plant form and function - publicly-available database - root traits

    Motivation: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready-to-use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks. Main types of variables contained: GRooT contains 114,222 trait records on 38 continuous root traits. Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies. Time period and grain: Data were recorded between 1911 and 2019. Major taxa and level of measurement: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values. Software format: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database.

    A Decision Support Model for Assessing the Water Regulation and Purification Potential of Agricultural Soils Across Europe
    Wall, David P. ; Delgado, Antonio ; O'Sullivan, Lilian ; Creamer, Rachel E. ; Trajanov, Aneta ; Kuzmanovski, Vladimir ; Bugge Henriksen, Christian ; Debeljak, Marko - \ 2020
    Frontiers in Sustainable Food Systems 4 (2020). - ISSN 2571-581X
    climate change - decision support tool - food security - soil functions - water purification - water quality - water regulation

    Water regulation and purification (WR) function is defined as “the capacity of the soil to remove harmful compounds and the capacity of the soil to receive, store and conduct water for subsequent use and to prevent droughts, flooding and erosion.” It is a crucial function that society expects agricultural soils to deliver, contributing to quality water supply for human needs and in particular for ensuring food security. The complexity of processes involved and the intricate tradeoff with other necessary soil functions requires decision support tools for best management of WR function. However, the effects of farm and soil management practices on the delivery of the WR function has not been fully addressed by decision support tools for farmers. This work aimed to develop a decision support model for the management of the WR function performed by agricultural soils. The specific objectives of this paper were (i) to construct a qualitative decision support model to assess the water regulation and purification capacity of agricultural soils at field level, to (ii) conduct sensitivity analysis of the model; and (iii) to validate the model with independent empirical data. The developed decision support model for WR is a hierarchical qualitative model with 5 levels and has 27 basic attributes describing the soil (S), environment (E), and management (M) attributes of the field site to be assessed. The WR model is composed of 3 sub-models concerning (1) soil water storage, (2) P and sediment loss in runoff, and (3) N leaching in percolating water. The WR decision support model was validated using a representative dataset of 94 field sites from across Europe and had an overall accuracy of 75% when compared to the empirically derived values across these sites. This highly accurate, reliable, and useful decision support model for assessing the capacity of agricultural soils to perform the WR function can be used by farmers and advisors help manage and protect their soil resources for the future. This model has also been incorporated into the Soil Navigator decision support tool which provides simultaneous assessment of the WR function and other important soil functions for agriculture.

    Altered energy partitioning across terrestrial ecosystems in the European drought year 2018
    Graf, Alexander ; Klosterhalfen, Anne ; Arriga, Nicola ; Bernhofer, Christian ; Bogena, Heye ; Bornet, Frédéric ; Brüggemann, Nicolas ; Brümmer, Christian ; Buchmann, Nina ; Chi, Jinshu ; Chipeaux, Christophe ; Cremonese, Edoardo ; Cuntz, Matthias ; Dušek, Jiří ; El-Madany, Tarek S. ; Fares, Silvano ; Fischer, Milan ; Foltýnová, Lenka ; Gharun, Mana ; Ghiasi, Shiva ; Gielen, Bert ; Gottschalk, Pia ; Grünwald, Thomas ; Heinemann, Günther ; Heinesch, Bernard ; Heliasz, Michal ; Holst, Jutta ; Hörtnagl, Lukas ; Ibrom, Andreas ; Ingwersen, Joachim ; Jurasinski, Gerald ; Klatt, Janina ; Knohl, Alexander ; Koebsch, Franziska ; Konopka, Jan ; Korkiakoski, Mika ; Kowalska, Natalia ; Kremer, Pascal ; Kruijt, Bart ; Lafont, Sebastien ; Léonard, Joël ; Ligne, Anne De; Longdoz, Bernard ; Loustau, Denis ; Magliulo, Vincenzo ; Mammarella, Ivan ; Manca, Giovanni ; Mauder, Matthias ; Migliavacca, Mirco ; Mölder, Meelis ; Neirynck, Johan ; Ney, Patrizia ; Nilsson, Mats ; Paul-Limoges, Eugénie ; Peichl, Matthias ; Pitacco, Andrea ; Poyda, Arne ; Rebmann, Corinna ; Roland, Marilyn ; Sachs, Torsten ; Schmidt, Marius ; Schrader, Frederik ; Siebicke, Lukas ; Šigut, Ladislav ; Tuittila, Eeva Stiina ; Varlagin, Andrej ; Vendrame, Nadia ; Vincke, Caroline ; Völksch, Ingo ; Weber, Stephan ; Wille, Christian ; Wizemann, Hans Dieter ; Zeeman, Matthias ; Vereecken, Harry - \ 2020
    Philosophical Transactions of the Royal Society B. Biological sciences 375 (2020)1810. - ISSN 0962-8436 - 1 p.
    eddy covariance - energy balance - evapotranspiration - heat flux - net carbon uptake - water-use efficiency

    Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO2 exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands). Each component of the surface radiation and energy balance observed in 2018 was compared to available data per site during a reference period 2004-2017. Based on anomalies in precipitation and reference evapotranspiration, we classified 46 sites as drought affected. These received on average 9% more solar radiation and released 32% more sensible heat to the atmosphere compared to the mean of the reference period. In general, drought decreased net CO2 uptake by 17.8%, but did not significantly change net evapotranspiration. The response of these fluxes differed characteristically between ecosystems; in particular, the general increase in the evaporative index was strongest in peatlands and weakest in croplands. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

    Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe
    Smith, Naomi E. ; Kooijmans, Linda M.J. ; Koren, Gerbrand ; Schaik, Erik van; Woude, Auke M. van der; Wanders, Niko ; Ramonet, Michel ; Xueref-Remy, Irène ; Siebicke, Lukas ; Manca, Giovanni ; Brümmer, Christian ; Baker, Ian T. ; Haynes, Katherine D. ; Luijkx, Ingrid T. ; Peters, Wouter - \ 2020
    Philosophical Transactions of the Royal Society B. Biological sciences 375 (2020)1810. - ISSN 0962-8436 - 1 p.
    CO2 - data assimilation - drought - European carbon balance - remote sensing

    We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated Carbon Observation System (ICOS) network, through biosphere and inverse modelling, and through remote sensing. Highly correlated yet independently-derived reductions in productivity from sun-induced fluorescence, vegetative near-infrared reflectance, and GPP simulated by the Simple Biosphere model version 4 (SiB4) suggest a 130-340 TgC GPP reduction in July-August-September (JAS) of 2018. This occurs over an area of 1.6 × 106 km2 with anomalously low precipitation in northwestern and central Europe. In this drought-affected area, reduced GPP, TER, NEE and soil moisture at ICOS ecosystem sites are reproduced satisfactorily by the SiB4 model. We found that, in contrast to the preceding 5 years, low soil moisture is the main stress factor across the affected area. SiB4's NEE reduction by 57 TgC for JAS coincides with anomalously high atmospheric CO2 observations in 2018, and this is closely matched by the NEE anomaly derived by CarbonTracker Europe (52 to 83 TgC). Increased NEE during the spring (May-June) of 2018 (SiB4 -52 TgC; CTE -46 to -55 TgC) largely offset this loss, as ecosystems took advantage of favourable growth conditions. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

    Mixing has limited impacts on the foliar nutrition of European beech and Scots pine trees across Europe
    Streel, Géraud de; Ammer, Christian ; Annighöfer, Peter ; Barbeito, Ignacio ; Bielak, Kamil ; Bravo-Oviedo, Andrés ; Brazaitis, Gediminas ; Buraczyk, Włodzimierz ; Collet, Catherine ; Hurt, Vaclav ; Kurylyak, Viktor ; Ouden, Jan den; Pach, Maciej ; Pretzsch, Hans ; Skrzyszewski, Jerzy ; Sramek, Vit ; Stankevičiūtė, Jolanta ; Strelcova, Katarina ; Svoboda, Miroslav ; Verheyen, Kris ; Zlatanov, Tzvetan ; Ponette, Quentin - \ 2020
    Forest Ecology and Management 479 (2020). - ISSN 0378-1127
    Complementarity - Fagus sylvatica L. - Foliar nutrition - Pinus sylvestris L. - Species mixture

    Tree species-mixing has been suggested as one option to counteract the adverse effects of global change on tree mineral nutrition, yet the effect of mixing on nutrient availability remains poorly documented. We therefore analyzed the current foliar nutrient (N, P, K, Ca, Mg) quantities and ilr balances (isometric log transformed ratios between elements or groups of elements) for 261 European beech and 248 Scots pine trees from 15 sites, each consisting of one beech-pine mixed stand and the respective monocultures, across a gradient of environmental conditions in Europe. We hypothesized an overall positive effect of mixing on tree foliar nutrient content, and that this mixing effect would be stronger on nutrient-poor sites. Using linear mixed models and multivariate linear regression models, we first tested for the effects of species (beech/pine) and composition (pure/mixed) across all sites; we then investigated whether the species-mixing effect was related to site fertility. The nutrient composition of beech leaves and pine needles differed significantly for all ilr balances. For both species, significant mixing effects were detected for some nutrients and ilr balances; those effects, however, could not be consistently related to contrasted nutrient composition between species. For most nutrients and ilr balances, the mixing effect was influenced by the site nutritional status, but the pattern differed from expectation: absence or minor differences between monocultures and mixtures at the lower end of the chemical fertility gradient, and maximum differences in rich soils. The contrasting foliar nutrient composition of pine and beech trees and the site nutrient status only partly explained the mixing effects on tree mineral nutrition. Our results claim for a better understanding of nutrient-related mechanisms associated with complementarity and points towards the need to further expand the existing frameworks to account for the multivariate nature of tree nutrition.

    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
    Erratum: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642 - 1 p.


    Progettazione urbana bioclimatica. Obiettivi e metodi
    Cortesão, J. - \ 2020
    In: Nuove sfide per l’architettura del paesaggio contemporanea Un ritorno verso la natura? / Burlando, Patrizia, Cortesão, João, Mazzino, Francesca, Piel, Christian, Florence : Altralinea Edizioni - ISBN 9788894869910 - p. 40 - 49.
    Bioclimatic urban design is a perspective on urban design fuelled by the belief that it is possible to mitigate urban climate problems through design and, thereby, actively contribute to a better mediation between man and climate. Bioclimatic urban design expands the scope of common urban design with the inclusion of design measures targeted at climate-resilience. This leads to including specific methods and tools, and looking at common urban design elements through a different lens. This book chapter presents an overview on what bioclimatic urban design is, on its fundamental goals and methods.
    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.

    COLOSS survey: global impact of COVID-19 on bee research
    Dall’Olio, Raffaele ; Blacquiere, Tjeerd ; Bouga, Maria ; Brodschneider, Robert ; Carreck, Norman L. ; Chantawannakul, Panuwan ; Dietemann, Vincent ; Kristiansen, Lotta Fabricius ; Gajda, Anna ; Gregorc, Ales ; Ozkirim, Aslı ; Pirk, Christian ; Soroker, Victoria ; Williams, Geoffrey R. ; Neumann, Peter - \ 2020
    Journal of Apicultural Research (2020). - ISSN 0021-8839
    Apis mellifera - COLOSS - coronavirus - COVID-19 - extension - honey bee - pandemic - research

    The socio-economic impacts of COVID-19 on society have yet to be truly revealed; there is no doubt that the pandemic has severely affected the daily lives of most of humanity. It is to be expected that the research activities of scientists could be impacted to varying degrees, but no data exist on how COVID-19 has affected research specifically. Here, we show that the still ongoing COVID-19 pandemic has already diversely and negatively affected bee research at a global level. An online survey disseminated through the global COLOSS honey bee research association showed that every participant (n = 230 from 56 countries) reported an impact on one or more of their activities. Activities that require travelling or the physical presence of people (meetings and conferences, teaching and extension) were affected the most, but also laboratory and field activities, daily operations, supervision and other activities were affected to varying degrees. Since the basic activities are very similar for many research fields, it appears as if our findings for bee research can be extrapolated to other fields. In the light of our data, we recommend that stakeholders such as governments and funding bodies who support research should facilitate the wide implementation of web-based information technology required for efficient online communication for research and education, as well as adequately loosened restriction measures with respect to field and laboratory work. Finally, increased flexibility in administration and extension of research grants and fellowships seem to be needed. It is apparent that adequate responses by all stakeholders are required to limit the impact of COVID-19 and future pandemics on bee science and other research fields.

    Analyzing the economics of food loss and waste reductions in a food supply chain
    Gorter, Harry de; Drabik, Dušan ; Just, David R. ; Reynolds, Christian ; Sethi, Geeta - \ 2020
    Food Policy (2020). - ISSN 0306-9192
    Cascading effects - Effective prices - Food waste - Purchases vs. sales - Supply chain

    The paper provides an economic model of food waste for consumers, intermediaries and farmers based on first principles. We distinguish between purchases and sales for each intermediary, purchases and consumption for consumers, and gross production versus sales for farmers. Because of waste at each stage of the supply chain, agents need higher sales prices to compensate. Our model is able to make more accurate predictions of how interventions (public policies or private initiatives) designed to reduce food waste influence the markets overall, including indirect (cascading) effects. We show the uniqueness of these interaction effects with a formal model and simulate an empirical model calibrated to market parameters and rates of waste for two commodities (chicken and fruit) in the UK. We show that the impacts of reducing waste vary by commodity, depending on supply and demand elasticities, degree of openness to international trade and the initial rates of food loss and waste at each stage of the value chain. The cascading effects up and down the supply chain mean that in some cases interventions to reduce food waste will be reinforced while in other cases partially offset.

    Lake trout growth is sensitive to spring temperature in southwest Alaska lakes
    Biela, Vanessa R. von; Black, Bryan A. ; Young, Daniel B. ; Sleen, Peter van der; Bartz, Krista K. ; Zimmerman, Christian E. - \ 2020
    Ecology of Freshwater Fish (2020). - ISSN 0906-6691
    biochronology - growth - lake trout - marine-derived nutrients - Pacific salmon - temperature

    In high-latitude lakes, air temperature is an important driver of ice cover thickness and duration, which in turn influence water temperature and primary production supporting lake consumers and predators. In lieu of multidecadal observational records necessary to assess the response of lakes to long-term warming, we used otolith-based growth records from a long-lived resident lake fish, lake trout (Salvelinus namaycush), as a proxy for production. Lake trout were collected from seven deep, oligotrophic lakes in Lake Clark National Park and Preserve on in southwest Alaska that varied in the presence of marine-derived nutrients (MDN) from anadromous sockeye salmon (Oncorhynchus nerka). Linear mixed-effects models were used to partition variation in lake trout growth by age and calendar-year and model comparisons tested for a mean increase in lake trout growth with sockeye salmon presence. Year effects from the best mixed-effects model were subsequently compared to indices of temperature, lake ice, and regional indices of sockeye salmon escapement. A strong positive correlation between annual lake trout growth and temperature suggested that warmer springs, earlier lake ice break-up, and a longer ice-free growing season increase lake trout growth via previously identified bottom-up increases in production with warming. Accounting for differences in the presence or annual escapement of sockeye salmon with available data did not improve model fit. Collectively with other studies, the results suggest that productivity of subarctic lakes has benefitted from warming spring temperatures and that temperature can synchronise otolith growth across lakes with and without sockeye salmon MDN.

    Next-generation biological control: the need for integrating genetics and genomics
    Leung, Kelley ; Ras, Erica ; Ferguson, Kim B. ; Ariëns, Simone ; Babendreier, Dirk ; Bijma, Piter ; Bourtzis, Kostas ; Brodeur, Jacques ; Bruins, Margreet A. ; Centurión, Alejandra ; Chattington, Sophie R. ; Chinchilla-Ramírez, Milena ; Dicke, Marcel ; Fatouros, Nina E. ; González-Cabrera, Joel ; Groot, Thomas V.M. ; Haye, Tim ; Knapp, Markus ; Koskinioti, Panagiota ; Hesran, Sophie Le; Lyrakis, Manolis ; Paspati, Angeliki ; Pérez-Hedo, Meritxell ; Plouvier, Wouter N. ; Schlötterer, Christian ; Stahl, Judith M. ; Thiel, Andra ; Urbaneja, Alberto ; Zande, Louis van de; Verhulst, Eveline C. ; Vet, Louise E.M. ; Visser, Sander ; Werren, John H. ; Xia, Shuwen ; Zwaan, Bas J. ; Magalhães, Sara ; Beukeboom, Leo W. ; Pannebakker, Bart A. - \ 2020
    Biological Reviews (2020). - ISSN 1464-7931
    artificial selection - biological control - genetics - genome assembly - genomics - insect breeding - microbiome - modelling

    Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

    Swimming alone? Why linking flood risk perception and behavior requires more than “it's the individual, stupid”
    Rufat, Samuel ; Fekete, Alexander ; Armaş, Iuliana ; Hartmann, Thomas ; Kuhlicke, Christian ; Prior, Tim ; Thaler, Thomas ; Wisner, Ben - \ 2020
    Wiley Interdisciplinary Reviews: Water 7 (2020)5. - ISSN 2049-1948
    behavior - disaster risk reduction - flood - flood risk management - risk perception

    A common assertion in discussions of flooding is that risk perception is critical and is linked to risk-mitigating behavior. Furthermore, many assert that the adverse effects of floods could be reduced by changes in risk communication, thereby influencing risk perception to foster mitigating behavior. We argue that these assertions are based on quite questionable underlying assumptions: That stakeholders are generally aware of flood risk, that they have the capacity to engage in disaster risk reduction, and that their actions can be effective. The belief in and policies influenced by these three questionable assertions support, in turn, policies that shift responsibility for flood risk reduction onto individuals and homeowners, without regard for social and spatial justice issues. In contrast, we argue that context matters to understanding the complexity of the relation between flood risk perception and behavior, local power relations, and other constraints and opportunities that affect stakeholders. While the academic community has long played a pivotal role in supporting practical flood risk management, future research should take a more critical perspective on the underlying assumptions and focus on improving coordination across theories, methods, and variables, fostering comparative studies across disciplines, contexts, and scales. This article is categorized under: Engineering Water > Planning Water Human Water > Water as Imagined and Represented Science of Water > Water Extremes.

    A Biostimulant Seed Treatment Improved Heat Stress Tolerance During Cucumber Seed Germination by Acting on the Antioxidant System and Glyoxylate Cycle
    Campobenedetto, Cristina ; Grange, Eric ; Mannino, Giuseppe ; Arkel, Jeroen van; Beekwilder, Jules ; Karlova, Rumyana ; Garabello, Christian ; Contartese, Valeria ; Bertea, Cinzia M. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    antioxidant molecules and enzymes - biostimulant - Cucumis sativus - gene expression - isocitrate lyase - seed treatment

    Seed enhancement technologies have the potential to improve germination and seedling growth under environmental stress. The effects of KIEM®, an innovative biostimulant based on lignin derivatives and containing plant-derived amino acids and molybdenum, were investigated on cucumber (Cucumis sativus L.) seed germination. To determine the metabolic targets of this product, biometric, transcriptional and biochemical analyses were carried out on both non-treated and KIEM®-treated seeds incubated for 24 and 48 h under standard (28°C) and heat stress (35°C) conditions. The application of the biostimulant as a seed treatment increased the percent germination (+6.54%) and fresh biomass (+13%) at 48 h, and decreased the content of H2O2 in treated seeds at 28°C (−70%) and at 35°C (−80%). These changes in biometric and biochemical properties were accompanied by changes in expression levels of the genes coding for ROS-producing (RBOH) and scavenging (SOD, CAT, GST) enzymes and their specific activity. In general, the treatment with KIEM® in heat-stress condition appeared to stimulate a higher accumulation of three scavenger gene transcripts: CuZnSOD (+1.78), MnSOD (+1.75), and CAT (+3.39), while the FeSOD isoform was dramatically downregulated (0.24). Moreover, the amount of non-protein thiols, important antioxidant molecules, was increased by the biostimulant after 48 h (+20%). Taken together these results suggest that KIEM® acts through mitigation of the effects of the oxidative stress. Moreover, after 48 h, the pre-sowing treatment with KIEM® increased the transcription levels (+1.5) and the activity of isocitrate lyase (+37%), a key enzyme of the glyoxylate cycle, suggesting a potential effect of this product in speeding up the germination process. Finally, the chemical characterization of KIEM® identified five essential and three non-essential amino acids, and others bioactive compounds, including five organic and inorganic acids that might be potentially involved in its activity. Based on these data, insights on the potential mechanism of action of the biostimulant, suggested that there are broader applications as a product able to increase seed tolerance to different abiotic stress typical of adverse environmental conditions.

    Calculation of ventilation rates and ammonia emissions : Comparison of sampling strategies for a naturally ventilated dairy barn
    Janke, David ; Willink, Dylia ; Ammon, Christian ; Hempel, Sabrina ; Schrade, Sabine ; Demeyer, Peter ; Hartung, Eberhard ; Amon, Barbara ; Ogink, Nico ; Amon, Thomas - \ 2020
    Biosystems Engineering 198 (2020). - ISSN 1537-5110 - p. 15 - 30.
    Air exchange rate - CO balance method - FTIR - Long-term measurements - Sampling positions

    Emissions and ventilation rates (VRs) in naturally ventilated dairy barns (NVDBs) are usually measured using indirect methods, where the choice of inside and outside sampling locations (i.e. sampling strategy) is crucial. The goal of this study was to quantify the influence of the sampling strategy on the estimation of emissions and VRs. We equipped a NVDB in northern Germany with an extensive measuring setup capable of measuring emissions under all wind conditions. Ammonia (NH3) and carbon dioxide (CO2) concentrations were measured with two Fourier-transform infrared spectrometers. Hourly values for ventilation rates and emissions for ammonia over a period of nearly a year were derived using the CO2 balance method and five different sampling strategies for the acquisition of indoor and outdoor concentrations were applied. When comparing the strategy estimating the highest emission level to the strategy estimating the lowest, the differences in NH3 emissions in winter, transition, and summer season were +26%, +19% and +11%, respectively. For the ventilation rates, the differences were +80%, +94%, and 63% for the winter, transition and summer season, respectively. By accommodating inside/outside concentration measurements around the entire perimeter of the barn instead of a reduced part of the perimeter (aligned to a presumed main wind direction), the amount of available data substantially increased for around 210% for the same monitoring period.

    Beneficial health effects of chitin and chitosan
    Dong, Liyou ; Wichers, H.J. ; Govers, C.C.F.M. - \ 2020
    In: Chitin and Chitosan / van den Broek, Lambertus A.M., Boeriu, Carmen G., Stevens, Christian V., John Wiley and Sons (Wiley Series in Renewable Research ) - ISBN 9781119450436 - p. 145 - 164.
    Chitin and chitosan have been recognised for their beneficial health effects since the 1980s. Over the past few decades, numerous studies and several clinical trials have been performed which demonstrated that these compounds can reduce body weight and cardiovascular disease (CVD), improve wound healing, but can also modulate the immune system and demonstrate antifungal and antibacterial activity. In particular, weight reduction and improvement of cardiovascular status are interesting targets as the prevalence of obesity and CVD are increasing. Both diseases are associated with various pathological disorders, including diabetes and hypertension and put a strain on healthcare costs and capacity. In general, lifestyle‐based interventions such as the oral intake of chitin and/or chitosan are becoming increasingly popular as these are easily integrated into current treatments and improve the self‐assertiveness of patients. Of interest, but beyond the scope of this chapter, is the use of chitin‐glucans as supplements in cosmetics. Several studies have demonstrated that chitin‐glucan reduced wrinkling and skin‐ageing, suggesting an interaction between the chitin‐glucan and cells of the epidermis. Although these effects may not be attributed to chitin alone, this does demonstrate the strong biological potential of chitin on cells of the human body. In this chapter, scientific literature has been reviewed that demonstrated the beneficial health effects of chitin and chitosan from an immunomodulatory point‐of‐view. First, we provide an overview of in vitro studies that offer in‐depth mechanistic insights, followed by describing preclinical animal studies. Finally, we list various human intervention trials that most clearly demonstrate the beneficial health effects of chitin and chitosan. Furthermore, we purposely discriminate between data on chitin and chitosan as they are chemically distinct and therefore possibly demonstrate unique effects on health
    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.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Functional relationship of particulate matter (PM) emissions, animal species, and moisture content during manure application
    Kabelitz, Tina ; Ammon, Christian ; Funk, Roger ; Münch, Steffen ; Biniasch, Oliver ; Nübel, Ulrich ; Thiel, Nadine ; Rösler, Uwe ; Siller, Paul ; Amon, Barbara ; Aarnink, André J.A. ; Amon, Thomas - \ 2020
    Environment International 143 (2020). - ISSN 0160-4120 - 12 p.
    Dry matter content - Fine dust - Manure management - Microorganism - Pig - Poultry

    Livestock manure is recycled to agricultural land as organic fertilizer. Due to the extensive usage of antibiotics in conventional animal farming, antibiotic-resistant bacteria are highly prevalent in feces and manure. The spread of wind-driven particulate matter (PM) with potentially associated harmful bacteria through manure application may pose a threat to environmental and human health. We studied whether PM was aerosolized during the application of solid and dried livestock manure and the functional relationship between PM release, manure dry matter content (DM), treatment and animal species. In parallel, manure and resulting PM were investigated for the survival of pathogenic and antibiotic-resistant bacterial species. The results showed that from manure with a higher DM smaller particles were generated and more PM was emitted. A positive correlation between manure DM and PM aerosolization rate was observed. There was a species-dependent critical dryness level (poultry: 60% DM, pig: 80% DM) where manure began to release PM into the environment. The maximum PM emission potentials were 1 and 3 kg t−1 of applied poultry and pig manure, respectively. Dried manure and resulting PM contained strongly reduced amounts of investigated pathogenic and antibiotic-resistant microorganisms compared to fresh samples. An optimal manure DM regarding low PM emissions and reduced pathogen viability was defined from our results, which was 55–70% DM for poultry manure and 75–85% DM for pig manure. The novel findings of this study increase our detailed understanding and basic knowledge on manure PM emissions and enable optimization of manure management, aiming a manure DM that reduces PM emissions and pathogenic release into the environment.

    Natuur als algoritme. Een dag met dieren in een datalandschap
    Driessen, C.P.G. ; Ernsten, Christian - \ 2020
    In: Voorland Groningen: Wandelingen door het Anthropoceen. / Visser, D.J., Ernsten, C., Minkema, M., Rotterdam : Nai 010 Uitgevers/Publishers - ISBN 9789462085909 - p. 150 - 159.
    The ovipositor actuation mechanism of a parasitic wasp and its functional implications
    Meer, Noraly M.M.E. van; Cerkvenik, Uroš ; Schlepütz, Christian M. ; Leeuwen, Johan L. van; Gussekloo, Sander W.S. - \ 2020
    Journal of Anatomy (2020). - ISSN 0021-8782
    hymenoptera - kinematics - musculature - ovipositor - synchrotron X-ray micro-computed tomography

    Parasitic wasps use specialized needle-like structures, ovipositors, to drill into substrates to reach hidden hosts. The external ovipositor (terebra) consists of three interconnected, sliding elements (valvulae), which are moved reciprocally during insertion. This presumably reduces the required pushing force on the terebra and limits the risk of damage whilst probing. Although this is an important mechanism, it is still not completely understood how the actuation of the valvulae is achieved, and it has only been studied with the ovipositor in rest position. Additionally, very little is known about the magnitude of the forces generated during probing. We used synchrotron X-ray microtomography to reconstruct the actuation mechanism of the parasitic wasp Diachasmimorpha longicaudata (Braconidae) in four distinct phases of the probing cycle. We show that only the paired first valvulae of the terebra move independently, while the second valvula moves with the metasoma (‘abdomen’). The first valvula movements are initiated by rotation of one chitin plate (first valvifer) with respect to another such plate (second valvifer). This is achieved indirectly by muscles connecting the non-rotating second valvifer and the abdominal ninth tergite. Contrary to previous reports, we found muscle fibres running inside the terebra, although their function remains unclear. The estimated maximal forces that can be exerted by the first valvulae are small (protraction 1.19 mN and retraction 0.874 mN), which reduces the risk of buckling, but are sufficient for successful probing. The small net forces of the valvulae on the substrate may still lead to buckling of the terebra; we show that the sheaths surrounding the valvulae prevent this by effectively increasing the diameter and second moment of area of the terebra. Our findings improve the comprehension of hymenopteran probing mechanisms, the function of the associated muscles, and the forces and damage-limiting mechanism that are involved in drilling a slender terebra into a substrate.

    The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642

    Bacterial strains of the phylum Planctomycetes occur ubiquitously, but are often found on surfaces of aquatic phototrophs, e.g. alga. Despite slower growth, planctomycetes are not outcompeted by faster-growing bacteria in biofilms on such surfaces; however, strategies allowing them to compensate for slower growth have not yet been investigated. Here, we identified stieleriacines, a class of N-acylated tyrosines produced by the novel planctomycete Stieleria maiorica Mal15T, and analysed their effects on growth of the producing strain and bacterial species likely co-occurring with strain Mal15T. Stieleriacines reduced the lag phase of Mal15T and either stimulated or inhibited biofilm formation of two bacterial competitors, indicating that Mal15T employs stieleriacines to specifically alter microbial biofilm composition. The genetic organisation of the putative stieleriacine biosynthetic cluster in strain Mal15T points towards a functional link of stieleriacine biosynthesis to exopolysaccharide-associated protein sorting and biofilm formation.

    Strategy in complexity: the shaping of communities and environments
    Assche, Kristof van; Beunen, R. ; Duineveld, M. - \ 2020
    In: Handbook on Planning and Complexity / de Roo, Gert, Yamu, Claudia, Zuidema, Christian, Edward Elgar (Research Handbooks in Planning series ) - ISBN 9781786439178 - p. 151 - 170.
    In this chapter, we reflect on the possibilities of purposeful community development in a non-linear understanding of society. Although the complexity and uncertainty that characterize the world put forward challenges for planning and steering, it doesn’t imply that purposive interventions are unlikely to be successful or that planning has become obsolete. It does, however, require a different understanding of how societies organize themselves and about how collective strategies sort reality-effects. Planning, as spatial planning, is a subset of strategy and provides a set of tools for others. In this chapter we highlight the importance of strategy in a world where many of the traditional planning rules and certainties have been challenged. We deepen the discussion about community development by placing it in the context of governance understood as a set of co-evolving actors, institutions, and power/knowledge configurations. Within these ever changing governance systems, forms of organization are necessarily linked to and co-evolve with narratives on identity, community, and governance itself, as the taking of collectively binding decisions. Taking into account the complexity and non-linearity that characterizes these co-evolutionary processes we discuss the links between community formation and the organization and transformation of space through planning. We explore how strategy should be understood in this context and we identify which forms of strategy can work under the structural conditions revealed through the lens of complexity theory and governance theory.
    Hepatocytic c-Jun N-terminal kinases (JNK)-1/2 function determines cell fate during carcinogenesis
    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 ; Davis, Roger J. ; Trautwein, Christian - \ 2020
    Wageningen University
    GSE140498 - PRJNA589901 - Mus musculus
    Aberrant biliary hyperproliferation resulting from lack of differentiating signals favoring the maintenance of an immature and proliferative phenotype by biliary epithelial cells are ultimately responsible for ducto/cystogenesis and intrahepatic cholangiocarcinoma (CCA) formation. Mitogen-activated protein kinase (MAPK) signaling is pivotal for CCA-related tumorigenesis. In particular, targeted inhibition of JNK signaling has shown therapeutic potential. However, the cell-type specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remains largely unknown. Here, we aimed to investigate the relevance of JNK function in hepatocytes in experimental carcinogenesis. JNK signaling in hepatocytes was inhibited by crossing AlbCre-JNK1LoxP/LoxP mice with JNK2-deficient mice to generate Jnk1LoxP/LoxP/Jnk2−/− (JNKΔhepa) mice. JNKΔhepa mice were further interbred with hepatocyte-specific Nemo-knockout mice (NEMOΔhepa), a model of chronic liver inflammation and spontaneous hepatocarcinogenesis, to generate NEMO/JNKΔhepa mice. The impact of JNK deletion on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development in NEMOΔhepa mice was determined. Moreover, regulation of essential genes was assessed by RT-PCR, immunoblottings and immunostains. Additionally, JNK2 inhibition, specifically in hepatocytes of NEMOΔhepa/JNK1Δhepa mice, was performed using siRNA (siJnk2) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of JNK1 and JNK2 in hepatocytes diminished hepatocarcinogenesis in both the DEN model of hepatocarcinogenesis and in NEMOΔhepa mice, but, in contrast, caused massive proliferation of the biliary ducts. Indeed, JNK deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression, but reduced hepatocarcinogenesis. 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 IL-6/Stat3 pathway in addition to EGFR-Raf-MEK-ERK cascade. The functional relevance was tested by administering lapatinib - a dual tyrosine kinase inhibitor (TKI) of ErbB2 and EGFR signaling - to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases and effectively blocked EGFR-Raf-MEK-ERK signaling. Our study defines a novel function of JNK in cell fate as well as hepatocarcinogenesis and opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.
    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.

    PCADD: SNV prioritisation in Sus scrofa
    Groß, Christian ; Derks, Martijn ; Megens, Hendrik Jan ; Bosse, Mirte ; Groenen, Martien A.M. ; Reinders, Marcel ; Ridder, Dick De - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X

    Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. Results: To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. Conclusions: We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.

    Model averaging for mapping topsoil organic carbon in France
    Chen, Songchao ; Mulder, Vera Leatitia ; Heuvelink, Gerard B.M. ; Poggio, Laura ; Caubet, Manon ; Román Dobarco, Mercedes ; Walter, Christian ; Arrouays, Dominique - \ 2020
    Geoderma 366 (2020). - ISSN 0016-7061
    Bias-corrected Variance Weighted - Data-poor countries - Digital soil mapping - Sample size requirement - Soil organic carbon

    The soil organic carbon (SOC) pool is the largest terrestrial carbon (C) pool and is two to three times larger than the C stored in vegetation and the atmosphere. SOC is a crucial component within the C cycle, and an accurate baseline of SOC is required, especially for biogeochemical and earth system modelling. This baseline will allow better monitoring of SOC dynamics due to land use change and climate change. However, current estimates of SOC stock and its spatial distribution have large uncertainties. In this study, we test whether we can improve the accuracy of the three existing SOC maps of France obtained at national (IGCS), continental (LUCAS), and global (SoilGrids) scales using statistical model averaging approaches. Soil data from the French Soil Monitoring Network (RMQS) were used to calibrate and evaluate five model averaging approaches, i.e., Granger-Ramanathan, Bias-corrected Variance Weighted (BC-VW), Bayesian Modelling Averaging, Cubist and Residual-based Cubist. Cross-validation showed that with a calibration size larger than 100 observations, the five model averaging approaches performed better than individual SOC maps. The BC-VW approach performed best and is recommended for model averaging. Our results show that 200 calibration observations were an acceptable calibration strategy for model averaging in France, showing that a fairly small number of spatially stratified observations (sampling density of 1 sample per 2500 km2) provides sufficient calibration data. We also tested the use of model averaging in data-poor situations by reproducing national SOC maps using various sized subsets of the IGCS dataset for model calibration. The results show that model averaging always performs better than the national SOC map. However, the Modelling Efficiency dropped substantially when the national SOC map was excluded in model averaging. This indicates the necessity of including a national SOC map for model averaging, even if produced with a small dataset (i.e., 200 samples). This study provides a reference for data-poor countries to improve national SOC maps using existing continental and global SOC maps.

    Politics versus Economics Philosophical Reflections on the Nature of Corporate Governance
    Blok, Vincent - \ 2020
    Philosophy of Management 19 (2020). - ISSN 1740-3812 - p. 69 - 87.
    In this article, we philosophically reflect on the nature of corporate governance. We raise thequestion whether control is still a feasible ideal of corporate governance and reflect on theimplications of the epistemic insufficiency of economic institutions with regard to grandchallenges like of global warming for our conceptualization of corporate governance. We firstintroduce the concept of corporate governance from the perspective of economics and politics.We then trace the genealogy of the concept of governance based on a selective reading ofGiorgio Agamben’s work, who has pointed at two interdependent paradigms of governance inthe Christian tradition, and apply his categories in the context of corporate governance. Wefinally engage in a critical reflection on the concept of corporate governance and develop fourcharacteristics of corporate governance that can guide future conceptual as well as empiricalresearch in the field of corporate social responsibility of economic institutions.
    Efectos de poda y fertilización en los rendimientos de jatropha bajo condiciones de pequeños agricultores en un bosque seco tropical de Ecuador
    Cañadas-López, Álvaro ; Rade-Loor, Diana ; Siegmund-Schultze, Marianna ; Vargas-Hernández, Jesús ; Wehenkel, Christian - \ 2020
    Revista Facultad Nacional de Agronomia Medellin 73 (2020)1. - ISSN 0304-2847 - p. 9089 - 9097.
    Biodiesel - Jatropha curcas - Marginal land - Seed productions

    Jatropha seed is a biomass suitable for bioenergy production that can be produced by smallholders, even on marginal lands. However, the current oilseed production is too low to meet the needs of the planned renewable electricity system in the Galapagos Islands. Pruning and fertilization are management options that can be used to increase the dry seed yields. The effects of both treatments were tested in a split-plot design with jatropha trees, which were monitored during a three-year production period. The average seed production was 643±58 kg ha-1 year-1 in the unpruned trees and 696±50 kg ha-1 year-1 in the pruned trees. Although this difference is small, it is expected to increase over time. The pruned trees developed more slowly than the unpruned trees but showed higher (and still increasing) yields at the end of the three-year test period, while the unpruned trees appeared to have reached their maximum production by the second year of the trial. The low fertilizer doses approved by the smallholders did not have a significant impact on the dry seed yield, and the management options that show benefits in the long term are generally not accepted or adopted by them. Cost-effective nutrient enhancement should be investigated, such as inoculation with arbuscular mycorrhizal fungi.

    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    Innovatiesubsidie voor medicijnmakers
    Wijffels, Rene ; Adamo, Sarah D'; Barbosa, Maria ; Martens, Dirk ; Südfeld, Christian - \ 2020
    TRY plant trait database – enhanced coverage and open access
    Kattge, Jens ; Bönisch, Gerhard ; Díaz, Sandra ; Lavorel, Sandra ; Prentice, Iain Colin ; Leadley, Paul ; Tautenhahn, Susanne ; Werner, Gijsbert D.A. ; Aakala, Tuomas ; Abedi, Mehdi ; Acosta, Alicia T.R. ; Adamidis, George C. ; Adamson, Kairi ; Aiba, Masahiro ; Albert, Cécile H. ; Alcántara, Julio M. ; Alcázar C, Carolina ; Aleixo, Izabela ; Ali, Hamada ; Amiaud, Bernard ; Ammer, Christian ; Amoroso, Mariano M. ; Anand, Madhur ; Anderson, Carolyn ; Anten, Niels ; Antos, Joseph ; Apgaua, Deborah Mattos Guimarães ; Ashman, Tia Lynn ; Asmara, Degi Harja ; Asner, Gregory P. ; Aspinwall, Michael ; Atkin, Owen ; Aubin, Isabelle ; Baastrup-Spohr, Lars ; Bahalkeh, Khadijeh ; Bahn, Michael ; Bekker, Renee ; Cromsigt, Joris P.G.M. ; Finegan, Bryan ; Kramer, Koen ; Lohbeck, Madelon ; Onoda, Yusuke ; Ozinga, Wim A. ; Prinzing, Andreas ; Robroek, Bjorn ; Slot, Martijn ; Sterck, Frank ; Beest, Mariska te; Bodegom, Peter M. van; Sande, Masha T. van der - \ 2020
    Global Change Biology 26 (2020)1. - ISSN 1354-1013 - p. 119 - 188.
    data coverage - data integration - data representativeness - functional diversity - plant traits - TRY plant trait database

    Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

    Partitioning main carbon pools in a semi-deciduous rainforest in eastern Cameroon
    Zekeng, Jules Christian ; Sande, Masha T. van der; Fobane, Jean Louis ; Mphinyane, Wanda N. ; Sebego, Reuben ; Mbolo, Marguerite Marie Abada - \ 2020
    Forest Ecology and Management 457 (2020). - ISSN 0378-1127
    Biomass - Cameroon - Carbon storage - Climate change - Terra-firme semi-deciduous forest - Tropical rainforest - Variation partitioning

    Tropical forests contribute to climate change mitigation by absorbing carbon from the atmosphere and storing this in biomass and soil organic matter. However, there is still considerable uncertainty about the above- and belowground quantity and distribution of carbon stocks in African forests. Here, we evaluate how different carbon pools (aboveground live biomass, aboveground dead biomass, belowground biomass) contribute to total carbon stocks, and how different carbon components (e.g. large trees, understorey trees, coarse woody debris, roots, soil organic carbon etc.) contribute to carbon pools and total carbon stocks. We evaluated data of extensive inventories within 30 1-ha plots spanning the terra-firme semi-deciduous forest in eastern Cameroon. Hence, the plots were placed at a mean distance of 1 km from the nearest plot and we analyzed the data using variation partitioning, linear regressions and correlation tests. We found that the terra-firme semi-deciduous forests store 283.97 ± 51.42 Mg C ha−1. The aboveground biomass pool, with a carbon stock of 180.99 ± 25.8 Mg C ha−1, mostly explained variation in total carbon stocks (R2 = 0.79). From all aboveground biomass components, carbon in large trees was most strongly correlated with total carbon stocks. The second most important carbon pool was belowground carbon (on average 85.06 ± 16.86 Mg C ha−1; R2 = 0.78), mainly explained by coarse root carbon. Carbon in dead biomass had only a small contribution to total carbon stocks (R2 = 0.04). Hence, our results indicate that aboveground live biomass is a good predictor for variation in total carbon storage within this semi-deciduous terra-firme forest. However, aboveground live carbon and belowground carbon and their interactions explained most of the variation in total carbon stock, indicating that a whole-ecosystem approach is necessary for a full understanding of the carbon cycle.

    Cost and effectiveness of in-season strategies for coping with weather variability in Pakistan's agriculture
    Shah, Hassnain ; Siderius, Christian ; Hellegers, Petra - \ 2020
    Agricultural Systems 178 (2020). - ISSN 0308-521X
    Compounded impacts - Coping - Critical moments - Crop stages - Weather variability

    Crops are vulnerable to weather hazards throughout the growth season, with periods of heightened risk described as critical moments. Farmers have a number of ex-ante and in-season options for coping with these events, and ex-post adjustments to farm-household portfolios to further limit the impact on livelihoods if these options fail. Adaptation-related research has focussed mainly on ex-ante or ex-post coping strategies, because in-season approaches tend to be seen as a given, meaning their cost effectiveness is ignored. Based on detailed survey data collected from 287 households in four of the main cropping systems in Pakistan, this study evaluates the impact pathways of hazards and the cost effectiveness of in-season coping strategies. Yield losses varied by 10–30% for 43% of the cases and by 31–50% for another 39%, with the most severe losses caused by the compounding effect of two hazards in one crop season or if both crops in a multi-crop rotation were affected simultaneously. In-season coping options were mostly restricted to the early crop stages and constrained by a short window of time for the response. The application of in-season coping strategies resulted in a yield recovery of 40–95%, with an additional cost of 4–34% of the value of recovered yield. The major critical moments identified were the harvest season, with farming often affected by un-seasonal precipitation, and the germination stage, with an additional high risk for low temperatures at high altitude. A better understanding of the differentiated risks and effectiveness of in-season coping strategies could support the promotion of sustainable crop production in similar agro-ecologies. Moreover, the effectiveness of present-day coping strategies, rather than the use of coping approaches itself, could signal a potential ability to adjust to future climate change.

    Towards an integrative understanding of soil biodiversity
    Thakur, Madhav P. ; Phillips, Helen R.P. ; Brose, Ulrich ; Vries, Franciska T. De; Lavelle, Patrick ; Loreau, Michel ; Mathieu, Jerome ; Mulder, Christian ; Putten, Wim H. Van der; Rillig, Matthias C. ; Wardle, David A. ; Bach, Elizabeth M. ; Bartz, Marie L.C. ; Bennett, Joanne M. ; Briones, Maria J.I. ; Brown, George ; Decaëns, Thibaud ; Eisenhauer, Nico ; Ferlian, Olga ; Guerra, Carlos António ; König-Ries, Birgitta ; Orgiazzi, Alberto ; Ramirez, Kelly S. ; Russell, David J. ; Rutgers, Michiel ; Wall, Diana H. ; Cameron, Erin K. - \ 2020
    Biological Reviews 95 (2020)2. - ISSN 1464-7931 - p. 350 - 364.
    alpha diversity - beta diversity - biodiversity theory - metacommunity theory - neutral theory - niche theory - spatial scale - species–energy relationship - theory of island biogeography

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

    Challenges at the marketing–operations interface in omni-channel retail environments
    Bijmolt, Tammo H.A. ; Broekhuis, Manda ; Leeuw, Sander de; Hirche, Christian ; Rooderkerk, Robert P. ; Sousa, Rui ; Zhu, Stuart X. - \ 2019
    Journal of Business Research (2019). - ISSN 0148-2963
    Assortment planning - Customer journey - Delivery - Digital business models - Distribution - Inventory control - Marketing–operations interface - Omni-channel - Product flow - Product returns

    To compete in today's omni-channel business context, it is essential for firms to co-ordinate their activities across channels and across different stages of the customer journey and the product flow. This requires firms to adopt an integrative approach, addressing each omni-channel design decision from a dual demand-side (marketing) and supply-side (operations) perspective. However, both in practice and in academic research, such an integrative approach is still in an immature stage. In this article, a framework is developed with the following key decision areas: (i) assortment & inventory, (ii) distribution & delivery and (iii) returns. These affect both the customer journey and the product flow. As a consequence of the resulting interdependencies between the firm's functions, addressing the issues that arise in the three decision areas requires an integrated marketing and operations perspective. For each of the areas, the key decisions that affect or involve both the customer journey and product flow are identified first. Next, for each decision, the marketing and operational goals and the tensions that arise when these goals are not perfectly aligned are described. The opportunities for relieving these tensions are also discussed and possible directions for future research aimed at addressing these tensions and opportunities are presented.

    ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest
    Ramos, Flavio Nunes ; Mortara, Sara Ribeiro ; Monalisa-Francisco, Nathalia ; Elias, João Pedro Costa ; Neto, Luiz Menini ; Freitas, Leandro ; Kersten, Rodrigo ; Amorim, André Márcio ; Matos, Fernando Bittencourt ; Nunes-Freitas, André Felippe ; Alcantara, Suzana ; Alexandre, Marcia Helena Nagahama ; Almeida-Scabbia, Renata Jimenez de; Almeida, Odair José Garcia de; Alves, Fernanda Eliane ; Oliveira Alves, Rogério Marcos de; Alvim, Francine Seehaber ; Andrade, Antônio Carlos Silva de; Andrade, Simone de; Aona, Lidyanne Yuriko Saleme ; Araujo, Andréa Cardoso ; Araújo, Kelianne Carolina Targino de; Ariati, Vanessa ; Assis, Julia Camara ; Azevedo, Cecília Oliveira de; Barbosa, Bruno Ferreira ; Barbosa, Daniel Elias Ferreira ; Reis Barbosa, Fernando dos; Barros, Fabio de; Basilio, Geicilaine Alves ; Bataghin, Fernando Antonio ; Bered, Fernanda ; Bianchi, Juliana Santos ; Blum, Christopher Thomas ; Boelter, Carlos Renato ; Bonnet, Annete ; Brancalion, Pedro Henrique Santin ; Breier, Tiago Bӧer ; Toledo Brion, Caio de; Buzatto, Cristiano Roberto ; Cabral, Andressa ; Cadorin, Tiago João ; Caglioni, Eder ; Canêz, Luciana ; Cardoso, Pedro Henrique ; Carvalho, Fábia Silva de; Carvalho, Renan Gonçalves ; Catharino, Eduardo Luis Martins ; Ceballos, Sergio Javier ; Cerezini, Monise Terra ; César, Ricardo Gomes ; Cestari, Cesar ; Chaves, Cleber Juliano Neves ; Citadini-Zanette, Vanilde ; Coelho, Luiz Francisco Mello ; Coffani-Nunes, João Vicente ; Colares, Renato ; Colletta, Gabriel Dalla ; Medeiros Corrêa, Nadjara de; Ferreira da Costa, Andrea ; Costa, Grênivel Mota da; Costa, Laís Mara Santana ; Costa, Natália Gabriela Souza ; Couto, Dayvid Rodrigues ; Cristofolini, Caroline ; Rodrigues da Cruz, Ana Carolina ; Neri, Leopoldo Angelo Del; Pasquo, Mercedes di; Santos Dias, Aline dos; Carmo Dutra Dias, Letícia do; Dislich, Ricardo ; Duarte, Marília Cristina ; Fabricante, Juliano Ricardo ; Farache, Fernando H.A. ; Gelli de Faria, Ana Paula ; Faxina, Claudenice ; Terrola Martins Ferreira, Mariana ; Fischer, Erich ; Fonseca, Carlos Roberto ; Fontoura, Talita ; Francisco, Talitha Mayumi ; Furtado, Samyra Gomes ; Galetti, Mauro ; Garbin, Mário Luís ; Gasper, André Luís de; Goetze, Márcia ; Gomes-da-Silva, Janaína ; Gonçalves, Mateus Felipe Araujo ; Gonzaga, Diego Rafael ; Granero e Silva, Ana Carolina ; Camargo Guaraldo, André de; Souza Gomes Guarino, Ernestino de; Votri Guislon, Aline ; Bitencourt Hudson, Luigy ; Jardim, Jomar Gomes ; Jungbluth, Patricia ; Santos Kaeser, Selma dos; Musauer Kessous, Igor ; Mossmann Koch, Natália ; Kuniyoshi, Yoshiko Saito ; Labiak, Paulo Henrique ; Lapate, Maria Esther ; Laurenti Santos, Ana Carolina ; Barbosa Leal, Roberta Luísa ; Leite, Felipe Silveira ; Leitman, Paula ; Liboni, Ana Paula ; Liebsch, Dieter ; Lingner, Débora Vanessa ; Lombardi, Julio Antonio ; Lucas, Eve ; Reis Luzzi, Jhonny dos; Mai, Patricia ; Mania, Luiz Felipe ; Mantovani, Waldir ; Maragni, Angelica Guidoni ; Marques, Marcia Cristina Mendes ; Marquez, Gonzalo ; Martins, Cristiane ; Nascimento Martins, Laura do; Luiz Sanglard Silva Martins, Pedro ; Fregolente Faracco Mazziero, Frederico ; Aguiar Melo, Camila de; Fiuza de Melo, Maria Margarida ; Mendes, Alex Fernando ; Mesacasa, Letícia ; Cerdeira Morellato, Leonor Patricia ; Souza Moreno, Vanessa de; Muller, Adelcio ; Silva Murakami, Mariana Moreira da; Cecconello, Edinete ; Nardy, Camila ; Nervo, Michelle Helena ; Neves, Beatriz ; Guimarães Cardoso Nogueira, Matheus ; Nonato, Fabiana Regina ; Oliveira-Filho, Ary Teixeira de; Oliveira, César Pedro Lopes de; Overbeck, Gerhard Ernst ; Marcusso, Gabriel Mendes ; Paciencia, Mateus Luís Barradas ; Padilha, Patricia ; Padilha, Peterson Teodoro ; Pereira, Ana Clara Alves ; Pereira, Luciana Carvalho ; Pereira, Rodrigo Augusto Santinelo ; Pincheira-Ulbrich, Jimmy ; Pires, José Salatiel Rodrigues ; Pizo, Marco Aurélio ; Pôrto, Kátia Cavalcanti ; Rattis, Ludmila ; Rodrigues de Mendonça Reis, Joice ; Gonçalves dos Reis, Simone ; Rocha-Pessôa, Thereza Christina da; Rocha, Carlos Frederico Duarte ; Rocha, Fernando Souza ; Rodrigues, Alba Regina Pereira ; Rodrigues, Ricardo Ribeiro ; Rogalski, Juliana Marcia ; Rosanelli, Roberta Luiza ; Rossado, Andrés ; Rossatto, Davi Rodrigo ; Rother, Débora Cristina ; Ruiz-Miranda, Carlos Ramon ; Saiter, Felipe Zamborlini ; Sampaio, Mauricio Bonesso ; Santana, Lucas Deziderio ; Silveira dos Santos, Juliana ; Sartorello, Ricardo ; Sazima, Marlies ; Schmitt, Juliane Luzía ; Schneider, Geniane ; Schroeder, Bruna Grosch ; Sevegnani, Lucia ; Júnior, Vasconcelos Oliveira Silva ; Silva, Fernando Rodrigues da; Silva, Maria Juliana da; Silva, Mércia Patrícia Pereira ; Silva, Rafaela Guimarães ; Silva, Sandro Menezes ; Singer, Rodrigo Bustos ; Siqueira, Geovane ; Soares, Luis Eduardo ; Sousa, Hildeberto Caldas de; Spielmann, Adriano ; Tonetti, Vinicius Rodrigues ; Toniato, Maria Teresa Zugliani ; Ulguim, Paulo Sérgio Bordoni ; Berg, Cássio van den; Berg, Eduardo van den; Varassin, Isabela Galarda ; Silva, Izabela Bitencourt Veloso da; Vibrans, Alexander Christian ; Waechter, Jorge Luiz ; Weissenberg, Erick Willy ; Windisch, Paulo Günter ; Wolowski, Marina ; Yañez, Agustina ; Yoshikawa, Vania Nobuko ; Zandoná, Luciano Ramos ; Zanella, Camila Martini ; Zanin, Elisabete Maria ; Zappi, Daniela Cristina ; Zipparro, Valesca Bononi ; Zorzanelli, João Paulo Fernandes ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)2. - ISSN 0012-9658
    abundance - Atlantic Forest - biodiversity data set - biodiversity hotspot - epiphyte - phorophyte - presence/absence - tropical forest

    Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

    Exploring the role of community self-organisation in the creation and creative dissolution of a community food initiative
    Hasanov, Mustafa ; Zuidema, Christian ; Horlings, Lummina G. - \ 2019
    Sustainability 11 (2019)11. - ISSN 2071-1050
    Citizen collectives - Collective action - Collective practices - Community food initiatives - Community self-organisation - Food activism - Food sharing - Food surplus - Food waste

    Community food initiatives are gaining momentum. Across various geographical contexts, community food initiatives are self-organising, providing communities with inspiration, knowledge and the opportunity to work towards responsible and socially acceptable transformations in food systems. In this article, we explore how self-organisation manifests itself in the daily activities and developments of community food initiatives. Through the conceptual lens of community self-organisation, we aim to provide a more detailed understanding of how community food initiatives contribute to broader and transformational shifts in food systems. Drawing on a multi-method approach, including community-based participatory research, interviews and observations, this article follows the creation and creative dissolution of the Free Café-a surplus food sharing initiative in Groningen, the Netherlands, which in the eye of the public remains unified, but from the volunteers' perspectives split up into three different initiatives. The results suggest that community self-organisation accommodates differing motivations and experiences embedded in the everyday collective performances of community rationalities and aspirations. This article also points to the changing individual and collective perspectives, vulnerabilities and everyday politics within community food initiatives. This paper contributes to emerging debates on community self-organising within food systems and the potential of community initiatives to promote broader social realignments.

    HIP-BB1.3 ‘Molecular markers for maturity and yield’
    Finkers, Richard ; Bachem, Christian - \ 2019
    Rule and rupture. State formation through the production of property and citizenship : by Christian Lund and Michael Eilenberg, Wiley Blackwell, Chichester, 2017, ix + 263 pp., $21,99 ISBN 9781119384809 (epub)
    Roth, Dik - \ 2019
    Journal of Legal Pluralism and Unofficial Law 51 (2019)3. - ISSN 0732-9113 - p. 406 - 409.
    Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage
    Petrasch, Stefan ; Silva, Christian J. ; Mesquida-Pesci, Saskia D. ; Gallegos, Karina ; Abeele, Casper Van Den; Papin, Victor ; Fernandez-Acero, Francisco J. ; Knapp, Steven J. ; Blanco-ulate, Barbara - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    Worldwide, 20–25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply chain due to rotting by fungal pathogens. Most postharvest pathogens exhibit necrotrophic or saprotrophic lifestyles, resulting in decomposition of the host tissues and loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit or remain quiescent until host conditions stimulate a successful infection. Previous research on infections of fruit has mainly been focused on the host’s genetic and physicochemical factors that inhibit or promote disease. Here, we investigated if fruit pathogens can modify their own infection strategies in response to the ripening stage of the host. To test this hypothesis, we profiled global gene expression of three fungal pathogens that display necrotrophic behavior—Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer—during interactions with unripe and ripe tomato fruit. We assembled and functionally annotated the transcriptomes of F. acuminatum and R. stolonifer as no genomic resources were available. Then, we conducted differential gene expression analysis to compare each pathogen during inoculations versus in vitro conditions. Through characterizing patterns of overrepresented pathogenicity and virulence functions (e.g., phytotoxin production, cell wall degradation, and proteolysis) among the differentially expressed genes, we were able to determine shared strategies among the three fungi during infections of compatible (ripe) and incompatible (unripe) fruit tissues. Though each pathogen’s strategy differed in the details, interactions with unripe fruit were commonly characterized by an emphasis on the degradation of cell wall components, particularly pectin, while colonization of ripe fruit featured more heavily redox processes, proteolysis, metabolism of simple sugars, and chitin biosynthesis. Furthermore, we determined that the three fungi were unable to infect fruit from the non-ripening (nor) tomato mutant, confirming that to cause disease, these pathogens require the host tissues to undergo specific ripening processes. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and the development of early detection tools and effective management strategies.
    Managing Forests for Both Downstream and Downwind Water
    Creed, Irena F. ; Jones, Julia A. ; Archer, Emma ; Claassen, Marius ; Ellison, David ; Mcnulty, Steven G. ; Noordwijk, Meine Van; Vira, Bhaskar ; Wei, Xiaohua ; Bishop, Kevin ; Blanco, Juan A. ; Gush, Mark ; Gyawali, Dipak ; Jobbágy, Esteban ; Lara, Antonio ; Little, Christian ; Martin-ortega, Julia ; Mukherji, Aditi ; Murdiyarso, Daniel ; Pol, Paola Ovando ; Sullivan, Caroline A. ; Xu, Jianchu - \ 2019
    Frontiers in Forests and Global Change 2 (2019). - ISSN 2624-893X
    Forests and trees are key to solving water availability problems in the face of climate change and to achieving the United Nations Sustainable Development Goals. A recent global assessment of forest and water science posed the question: How do forests matter for water? Here we synthesize science from that assessment, which shows that forests and water are an integrated system. We assert that forests, from the tops of their canopies to the base of the soils in which trees are rooted, must be considered a key component in the complex temporal and spatial dimensions of the hydrologic cycle. While it is clear that forests influence both downstream and downwind water availability, their actual impact depends on where they are located and their processes affected by natural and anthropogenic conditions. A holistic approach is needed to manage the connections between forests, water and people in the face of current governance systems that often ignore these connections. We need policy interventions that will lead to forestation strategies that decrease the dangerous rate of loss in forest cover and that—where appropriate—increase the gain in forest cover. We need collective interventions that will integrate transboundary forest and water management to ensure sustainability of water supplies at local, national and continental scales. The United Nations should continue to show leadership by providing forums in which interventions can be discussed, negotiated and monitored, and national governments must collaborate to sustainably manage forests to ensure secure water supplies and equitable and sustainable outcomes.
    European Weed Vegetation Database - a gap-focused vegetation-plot database
    Küzmic, Filip ; Šilc, Urban ; Lososová, Zdenka ; Mucina, Ladislav ; Chytrý, Milan ; Knollová, Ilona ; Hennekens, S.M. ; Berg, Christian ; Bergmeier, Erwin ; Biurrun, Idoia ; Fanfarillo, Emanuele ; Font, Xavier ; Iakushenko, Dmytro ; Kovacevic, Zlatan ; Meyer, Stefan ; Nagy, Katalin ; Pinke, Gyula ; Poranen, Eira ; Tereshenko, Svetlana - \ 2019
    Phytocoenologia 50 (2019)1. - ISSN 0340-269X - p. 93 - 100.
    This report presents the European Weed Vegetation Database, a new database of vegetation plots documenting short-lived vegetation of arable and ruderal habitats from Europe and Macaronesia. The database comprises the
    phytosociological classes Papaveretea rhoeadis, Sisymbrietea, Chenopodietea and Digitario sanguinalis-Eragrostietea minoris. It is a gap-focused database containing mainly plots of this vegetation from the areas not yet represented in the European Vegetation Archive (EVA), to facilitate its accessibility for researchers to answer various questions. As of the end of 2018, it contained 24,734 plots, predominantly from Southern Europe. The data can be used for phytosociological studies, various kinds of interdisciplinary research as well as for studies for agronomy, nature management and biodiversity conservation.
    Christian-Albrechts-Universität (External organisation)
    Hendriks, Wouter - \ 2019
    Evaluator for the vacant Chair in Animal Nutrition and Feed Science
    Rescuing Honiara, rescuing Gwou’ulu: negotiating frictional village–town relations and politico-religious (dis)unity in Solomon Islands
    Hobbis, Stephanie - \ 2019
    Journal of the Polynesian Society 128 (2019)4. - ISSN 0032-4000 - p. 435 - 456.
    Speaking to debates about the management of difference in and between towns and villages as well as secondary conversions and breakaway movements in Melanesia, this article examines the efforts of an Anglican village church to maintain social cohesion through politico-religious unity in Gwou’ulu, a multi-clan village in North Malaita, Solomon Islands, and its urban enclaves in Honiara. It focuses on an Anglican “rescue mission” that Gwou’ulu sends annually to Honiara to remind their urban relatives about the values, interests and priorities of their ancestral Anglican home. An analysis of this “rescue mission” and the controversies that surround it reveals an ongoing struggle between villagers for the politico-religious future of the village within and beyond its immediate geographic boundaries. Gwou’ulu villagers are increasingly questioning the capacity of the Anglican church and its leaders to provide stability in urban–rural insecurities, and, as a result, have begun breaking away from mainstream Anglicanism in a quest for alternative social and moral orders untainted by their religious leaders’ apparent spiritual impurity and even corrupt behaviours. By distancing themselves from Anglicanism as the force that has meant to unify the village since its inception as a Christian refuge in the early twentieth century, Gwou’ulu villagers then not only break away but also apart, exaggerating rural frictions with and alienations from (urban) modernity.
    Health and welfare of rabbits farmed in different production systems
    Saxmose Nielsen, Søren ; Alvarez, Julio ; Bicout, Dominique Joseph ; Calistri, Paolo ; Depner, Klaus ; Drewe, Julian Ashley ; Garin‐bastuji, Bruno ; Gonzales Rojas, Jose Luis ; Gortázar Schmidt, Christian ; Michel, Virginie ; Miranda Chueca, Miguel Ángel ; Roberts, Helen Clare ; Sihvonen, Liisa Helena ; Spoolder, Hans ; Stahl, Karl ; Velarde Calvo, Antonio ; Viltrop, Arvo ; Buijs, Stephanie ; Edwards, Sandra ; Candiani, Denise ; Mosbach‐schulz, Olaf ; Stede, Yves Van Der; Winckler, Christoph - \ 2019
    EFSA Journal 18 (2019)1. - ISSN 1831-4732 - 96 p.
    animal welfare - animal production - rabbits - animal housing - animal behaviour - animal health
    The AGRI committee of the European Parliament requested EFSA to assess the welfare of rabbits farmed in different production systems, including organic production, and to update its 2005 scientific opinion about the health and welfare of rabbits kept for meat production. Considering reproducing does, kits and growing rabbits, this scientific opinion focusses on six different housing systems, namely conventional cages, structurally enriched cages, elevated pens, floor pens, outdoor/partially outdoor systems and organic systems. To compare the level of welfare in the different housing systems and rabbit categories, welfare impact scores for 20 welfare consequences identified from the literature were calculated, taking their occurrence, duration and severity into account. Based on the overall welfare impact score (sum of scores for the single welfare consequences), obtained via a 2-step expert knowledge elicitation process, the welfare of reproducing does is likely (certainty 66–90%) to be lower in conventional cages compared to the five other housing systems. In addition, it is likely to extremely likely (certainty 66–99%) that the welfare of kits is lower in outdoor systems compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Finally, it is likely to extremely likely (certainty 66–99%) that the welfare of growing rabbits is lower in conventional cages compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Ranking of the welfare consequences allowed an analysis of the main welfare consequences within each system and rabbit category. It was concluded that for reproducing does, as well as growing rabbits, welfare consequences related to behavioural restrictions were more prominent in conventional cages, elevated pens and enriched cages, whereas those related to health problems were more important in floor pens, outdoor and organic systems. Housing in organic rabbit farming is diverse, which can result in different welfare consequences, but the overall welfare impact scores suggest that welfare in organic systems is generally good.
    Modelling approaches for mixed forests dynamics prognosis. Research gaps and opportunities
    Bravo, Felipe ; Fabrika, Marek ; Ammer, Christian ; Barreiro, Susana ; Bielak, Kamil ; Coll, Lluis ; Fonseca, Teresa ; Kangur, Ahto ; Löf, Magnus ; Merganičová, Katarina ; Pach, Maciej ; Pretzsch, Hans ; Stojanović, Dejan ; Schuler, Laura ; Peric, Sanja ; Rötzer, Thomas ; Río, Miren Del; Dodan, Martina ; Bravo-Oviedo, Andrés - \ 2019
    Forest Systems 28 (2019)1. - ISSN 2171-5068 - 18 p.
    Classification - Dynamics - Ecology - Empirical - Growth - Yield

    Aim of study: Modelling of forest growth and dynamics has focused mainly on pure stands. Mixed-forest management lacks systematic procedures to forecast the impact of silvicultural actions. The main objective of the present work is to review current knowledge and forest model developments that can be applied to mixed forests. Material and methods: Primary research literature was reviewed to determine the state of the art for modelling tree species mixtures, focusing mainly on temperate forests. Main results: The essential principles for predicting stand growth in mixed forests were identified. Forest model applicability in mixtures was analysed. Input data, main model components, output and viewers were presented. Finally, model evaluation procedures and some of the main model platforms were described. Research highlights: Responses to environmental changes and management activities in mixed forests can differ from pure stands. For greater insight into mixed-forest dynamics and ecology, forest scientists and practitioners need new theoretical frameworks, different approaches and innovative solutions for sustainable forest management in the context of environmental and social changes.

    Global carbon budget 2019
    Friedlingstein, Pierre ; Jones, Matthew W. ; O'Sullivan, Michael ; Andrew, Robbie M. ; Hauck, Judith ; Peters, Glen P. ; Peters, Wouter ; Pongratz, Julia ; Sitch, Stephen ; Quéré, Corinne Le; Bakker, Dorothee C.E. ; Canadell1, Josep G. ; Ciais1, Philippe ; Jackson, Robert B. ; Anthoni, Peter ; Barbero, Leticia ; Bastos, Ana ; Bastrikov, Vladislav ; Becker, Meike ; Bopp, Laurent ; Buitenhuis, Erik ; Chandra, Naveen ; Chevallier, Frédéric ; Chini, Louise P. ; Currie, Kim I. ; Feely, Richard A. ; Gehlen, Marion ; Gilfillan, Dennis ; Gkritzalis, Thanos ; Goll, Daniel S. ; Gruber, Nicolas ; Gutekunst, Sören ; Harris, Ian ; Haverd, Vanessa ; Houghton, Richard A. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Joetzjer, Emilie ; Kaplan, Jed O. ; Kato, Etsushi ; Goldewijk, Kees Klein ; Korsbakken, Jan Ivar ; Landschützer, Peter ; Lauvset, Siv K. ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lombardozzi, Danica ; Marland, Gregg ; McGuire, Patrick C. ; Melton, Joe R. ; Metzl, Nicolas ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Neill, Craig ; Omar, Abdirahman M. ; Ono, Tsuneo ; Peregon, Anna ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Resplandy, Laure ; Robertson, Eddy ; Rödenbeck, Christian ; Séférian, Roland ; Schwinger, Jörg ; Smith, Naomi ; Tans, Pieter P. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Werf, Guido R. Van Der; Wiltshire, Andrew J. ; Zaehle, Sönke - \ 2019
    Earth System Science Data 11 (2019)4. - ISSN 1866-3508 - p. 1783 - 1838.

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFF) are based on energy statistics and cement production data, while emissions from land use change (ELUC), mainly deforestation, are based on land use and land use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2009-2018), EFF was 9:5±0:5 GtC yr-1, ELUC 1:5±0:7 GtC yr-1, GATM 4:9±0:02 GtC yr-1 (2:3±0:01 ppm yr-1), SOCEAN 2:5±0:6 GtC yr-1, and SLAND 3:2±0:6 GtC yr-1, with a budget imbalance BIM of 0.4 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For the year 2018 alone, the growth in EFF was about 2.1% and fossil emissions increased to 10:0±0:5 GtC yr-1, reaching 10 GtC yr-1 for the first time in history, ELUC was 1:5±0:7 GtC yr-1, for total anthropogenic CO2 emissions of 11:5±0:9 GtC yr-1 (42:5±3:3 GtCO2). Also for 2018, GATM was 5:1±0:2 GtC yr-1 (2:4±0:1 ppm yr-1), SOCEAN was 2:6±0:6 GtC yr-1, and SLAND was 3:5±0:7 GtC yr-1, with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 407:38±0:1 ppm averaged over 2018. For 2019, preliminary data for the first 6-10 months indicate a reduced growth in EFF of C0:6% (range of.0:2% to 1.5 %) based on national emissions projections for China, the USA, the EU, and India and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. Overall, the mean and trend in the five components of the global carbon budget are consistently estimated over the period 1959-2018, but discrepancies of up to 1 GtC yr-1 persist for the representation of semi-decadal variability in CO2 fluxes. A detailed comparison among individual estimates and the introduction of a broad range of observations shows (1) no consensus in the mean and trend in land use change emissions over the last decade, (2) a persistent low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) an apparent underestimation of the CO2 variability by ocean models outside the tropics. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding of the global carbon cycle compared with previous publications of this data set (Le Quéré et al., 2018a, b, 2016, 2015a, b, 2014, 2013). The data generated by this work are available at https://doi.org/10.18160/gcp-2019 (Friedlingstein et al., 2019).

    Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology
    Wiegand, Sandra ; Jogler, Mareike ; Boedeker, Christian ; Pinto, Daniela ; Vollmers, John ; Rivas-Marín, Elena ; Kohn, Timo ; Peeters, Stijn H. ; Heuer, Anja ; Rast, Patrick ; Oberbeckmann, Sonja ; Bunk, Boyke ; Jeske, Olga ; Meyerdierks, Anke ; Storesund, Julia E. ; Kallscheuer, Nicolai ; Lücker, Sebastian ; Lage, Olga M. ; Pohl, Thomas ; Merkel, Broder J. ; Hornburger, Peter ; Müller, Ralph Walter ; Brümmer, Franz ; Labrenz, Matthias ; Spormann, Alfred M. ; Camp, Huub J.M. Op den; Overmann, Jörg ; Amann, Rudolf ; Jetten, Mike S.M. ; Mascher, Thorsten ; Medema, Marnix H. ; Devos, Damien P. ; Kaster, Anne Kristin ; Øvreås, Lise ; Rohde, Manfred ; Galperin, Michael Y. ; Jogler, Christian - \ 2019
    Nature Microbiology 5 (2019). - ISSN 2058-5276 - p. 126 - 140.

    When it comes to the discovery and analysis of yet uncharted bacterial traits, pure cultures are essential as only these allow detailed morphological and physiological characterization as well as genetic manipulation. However, microbiologists are struggling to isolate and maintain the majority of bacterial strains, as mimicking their native environmental niches adequately can be a challenging task. Here, we report the diversity-driven cultivation, characterization and genome sequencing of 79 bacterial strains from all major taxonomic clades of the conspicuous bacterial phylum Planctomycetes. The samples were derived from different aquatic environments but close relatives could be isolated from geographically distinct regions and structurally diverse habitats, implying that ‘everything is everywhere’. With the discovery of lateral budding in ‘Kolteria novifilia’ and the capability of the members of the Saltatorellus clade to divide by binary fission as well as budding, we identified previously unknown modes of bacterial cell division. Alongside unobserved aspects of cell signalling and small-molecule production, our findings demonstrate that exploration beyond the well-established model organisms has the potential to increase our knowledge of bacterial diversity. We illustrate how ‘microbial dark matter’ can be accessed by cultivation techniques, expanding the organismic background for small-molecule research and drug-target detection.

    Global distribution of earthworm diversity
    Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
    Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

    Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

    Design and quality criteria for archetype analysis
    Eisenack, Klaus ; Villamayor-Tomas, Sergio ; Epstein, Graham ; Kimmich, Christian ; Magliocca, Nicholas ; Manuel-Navarrete, David ; Oberlack, Christoph ; Roggero, Matteo ; Sietz, Diana - \ 2019
    Ecology and Society 24 (2019)3. - ISSN 1708-3087
    Abstraction - Archetype analysis - Generalization - Ideographic trap - Interdisciplinary collaboration - Panacea - Pattern - Qualitative - Quantitative - Research design - Social-ecological systems - Validity

    A key challenge in addressing the global degradation of natural resources and the environment is to effectively transfer successful strategies across heterogeneous contexts. Archetype analysis is a particularly salient approach in this regard that helps researchers to understand and compare patterns of (un)sustainability in heterogeneous cases. Archetype analysis avoids traps of overgeneralization and ideography by identifying reappearing but nonuniversal patterns that hold for well-defined subsets of cases. It can be applied by researchers working in inter-or transdisciplinary settings to study sustainability issues from a broad range of theoretical and methodological standpoints. However, there is still an urgent need for quality standards to guide the design of theoretically rigorous and practically useful archetype analyses. To this end, we propose four quality criteria and corresponding research strategies to address them: (1) specify the domain of validity for each archetype, (2) ensure that archetypes can be combined to characterize single cases, (3) explicitly navigate levels of abstraction, and (4) obtain a fit between attribute configurations, theories, and empirical domains of validity. These criteria are based on a stocktaking of current methodological challenges in archetypes research, including: to demonstrate the validity of the analysis, delineate boundaries of archetypes, and select appropriate attributes to define them. We thus contribute to a better common understanding of the approach and to the improvement of the research design of future archetype analyses.

    Genetic mapping of tuber size distribution and marketable tuber yield under drought stress in potatoes
    Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Eck, Herman J. van; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
    Euphytica 215 (2019)11. - ISSN 0014-2336
    Association panel - Drought - Marketable tubers - Modelling - Size - Yield

    Drought sensitivity of potato leads to a reduction in total tuber yield and marketable yield. An investigation of drought effects on tuber yield attributes will facilitate our understanding of how to reduce such huge yield losses. We have evaluated tuber yield, tuber size distribution and marketable yield of a set of 103 European commercial potato cultivars under irrigated and non-irrigated conditions in the field. The multi-year results from two locations, Connantre, France (2013–2015) and Nieuw-Namen in Zeeland, The Netherlands (2013–2014), were analysed. We used Normal and Gamma Distribution models to describe the tuber size distribution of tuber fresh weight and tuber number, respectively. The interactions among parameters of tuber size distribution and total/marketable tuber yield traits were analysed using correlation matrices and biplots. Finally, we used a 14K Infinium SNP marker array to find associations between the parameters or traits and genetic loci on the potato genome. Late foliage maturity facilitated a wider spread of tuber size distribution in favour of larger-sized tubers. Drought effects on total yield were representative of their impact on marketable yield, however, absolute values of total tuber number may not be indicative of marketable number of tubers. We found significant marker-trait associations between a region on chromosome 3 and the spread of tuber number distribution, size class with maximum tuber number and marketable fractions of tuber number and tuber weight. These findings will contribute to improvement and selection for drought tolerance in potato.

    Impacts of beekeeping and agroforestry initiatives, Upper Mara River Basin, Kenya
    Ingram, V.J. ; Kirui, Robert ; Rooij, S.A.M. van; Hitimana, Joseph ; Koopmans, Djuran - \ 2019
    In: 4th World Congress on Agroforestry, 20-22 May 2019, Montpellier, France. - - p. 533 - 533.
    Agroforestry as a mechanism for reforestation in Zambia : Scenarios within a REDD+ framework
    Ingram, V.J. ; Goes, A. van der; Phiri, G. ; Banda, T. - \ 2019
    In: 4th World Congress on Agroforestry, 20-22 May 2019, Montpellier, France. - - p. 285 - 285.
    Diagnostiek Ontwikkeling en Toepassing voor het optimaliseren van uiergezondheid
    Griffioen, Karien ; Velthuis, A.G.J. ; Wal, F.J. van der; Mevius, D.J. ; Achterberg, R.P. ; Cornelissen, J.B.W.J. ; Dijkman, Remco ; Heuvelink, Annet E. ; Hop, G.E. ; Holstege, Manon M.C. ; Scherpenzeel, Christian ; Lam, Theo - \ 2019
    Recommendation domains to scale out climate change adaptation in cocoa production in Ghana
    Bunn, Christian ; Läderach, Peter ; Quaye, Amos ; Muilerman, Sander ; Noponen, Martin R.A. ; Lundy, Mark - \ 2019
    Climate Services 16 (2019). - ISSN 2405-8807
    Climate impacts - Cocoa - Decision support - Ghana - Recommendation domains - West Africa

    Climate change is threatening cocoa production in West Africa and guidance towards site-specific adaptation is required. We developed recommendation domains with common degree of impact requiring incremental, systemic or incremental adaptation effort to provide decision support for interventions to scale out adaptive practices. We used Random Forests to divide the cocoa production belt into four zones with distinct climatic features under current and future climate conditions. To make model results actionable we used an expert validation approach. Cocoa experts evaluated and verified cocoa occurrence data for model input, prioritized climate and soil variables for modeling use and confirmed the validity of the distribution of climate zones. Climate change will reduce the available area for cocoa production in the north due to a shift of the northern transition to the Savanna zone. The current area for cocoa in central Ashanti will remain suitable but will face uncertain climatic conditions. Areas in the Western, Central and Eastern regions will likely become hotter and wetter. Each of these projected impacts will require site-specific adaptation strategies matching the degree of impacts. Failing to prepare may subject rural communities to high risks of losing their livelihoods. Our recommendation domains can support impact specific preparation so that the majority of Ghana's cocoa production area may be sustained despite adverse climatic changes. Institutional and private actors can use our work to scale out locally conceived interventions to alleviate impacts from drought, heat and erratic rainfall.

    Selection and gene flow shape niche-associated variation in pheromone response
    Lee, Daehan ; Zdraljevic, Stefan ; Cook, Daniel E. ; Frézal, Lise ; Hsu, Jung-Chen ; Sterken, Mark G. ; Riksen, Joost A.G. ; Wang, John ; Kammenga, Jan E. ; Braendle, Christian ; Félix, Marie-Anne ; Schroeder, Frank C. ; Andersen, Erik C. - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1455 - 1463.
    From quorum sensing in bacteria to pheromone signalling in social insects, chemical communication mediates interactions among individuals in local populations. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density; high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were previously shown to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world; this deletion underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbour individuals with a wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating the migration of species and providing a favourable niche for the recently arisen srg-37 deletion.

    Assessing the climate regulation potential of Agricultural soils using a decision support tool adapted to stakeholders' needs and possibilities
    Broek, Marijn Van de; Henriksen, Christian Bugge ; Ghaley, Bhim Bahadur ; Lugato, Emanuele ; Kuzmanovski, Vladimir ; Trajanov, Aneta ; Debeljak, Marko ; Sandén, Taru ; Spiegel, Heide ; Decock, Charlotte ; Creamer, Rachel ; Six, Johan - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X
    Soils perform many functions that are vital to societies, among which their capability to regulate global climate has received much attention over the past decades. An assessment of the extent to which soils perform a specific function is not only important to appropriately value their current capacity, but also to make well-informed decisions about how and where to change soil management to align the delivered soil functions with societal demands. To obtain an overview of the capacity of soils to perform different functions, accurate and easy-to-use models are necessary. A problem with most currently-available models is that data requirements often exceed data availability, while generally a high level of expert knowledge is necessary to apply these models. Therefore, we developed a qualitative model to assess how agricultural soils function with respect to climate regulation. The model is driven by inputs about agricultural management practices, soil properties and environmental conditions. To reduce data requirements on stakeholders, the 17 input variables are classified into either (1) three classes: low, medium and high or (2) the presence or absence of a management practice. These inputs are combined using a decision tree with internal integration rules to obtain an estimate of the magnitude of N2O emissions and carbon sequestration. These two variables are subsequently combined into an estimate of the capacity of a soil to perform the climate regulation function. The model was tested using data from long-term field experiments across Europe. This showed that the model is generally able to adequately assess this soil function across a range of environments under different management practices. In a next step, this model will be combined with models to assess other soil functions (soil biodiversity, primary productivity, nutrient cycling and water regulation and purification). This will allow the assessment of trade-offs between these soil functions for agricultural land across Europe.
    Parasite control in organic cattle farming: Management and farmers' perspectives from six European countries
    Takeuchi-Storm, Nao ; Moakes, Simon ; Thüer, Susann ; Grovermann, Christian ; Verwer, Cynthia ; Verkaik, Jan ; Knubben-Schweizer, Gabriela ; Höglund, Johan ; Petkevičius, Saulius ; Thamsborg, Stig ; Werne, Steffen - \ 2019
    Veterinary Parasitology: Regional Studies and Reports 18 (2019). - ISSN 2405-9390
    Anthelmintic use - Cattle - Europe - Fasciola hepatica - Gastrointestinal nematodes - Organic farming

    Organic ruminant production is expanding in the EU, but parasite management remains a constant challenge. Mandatory outdoor access for all age groups can increase exposure to pasture borne parasites, whilst restrictions in the prophylactic use of anthelmintics can limit parasite control. The scientific community has been working to deliver effective parasite control strategies and alternative approaches in order to slow down the development of anthelmintic resistance (AR). However, the current parasite control practices and overall awareness with regards to AR and alternative approaches on farms are largely unknown and may be causing a knowledge gap between the scientific and farming communities. Therefore, a structured survey was conducted in six European countries (Switzerland, Germany, Denmark, Netherlands, Lithuania, Sweden) to provide basic data on practices, management and farmers' perspectives for grazing and parasite control (gastrointestinal worms and liver flukes) on organic cattle farms. Overall, 375 surveys were collected (282 dairy and 93 beef farms) in 2015–2016, and analysed descriptively. Additionally, surveys from the 228 dairy farms were assessed using a double-hurdle adoption model to identify the factors involved in the decision to drench against gastrointestinal parasites. Generally, there are prominent differences between countries, with monitoring methods differing especially, which has important implications in terms of knowledge transfer. For example, media warning was the most common method in DE, while antibody testing in bulk tank milk was the common method in NL. In other countries, clinical signs (diarrhoea, hair coat quality, and reduced weight or yield) and liver condemnation data were used frequently. In general, organic farmers from the six participating countries indicated that they would accept alternative approaches despite greater cost and labour. The likelihood of drenching were higher on farms with smaller farm areas, higher number of young stock and total livestock units and farms where faecal egg counts were used to monitor the parasites. In conclusion, it was evident that grazing and parasite management varied between the countries even though they operate under the same basic principles. Parasite management strategies must therefore be country specific and disseminated with appropriate methods.

    Archetype analysis in sustainability research: meanings, motivations, and evidence-based policy making
    Oberlack, Christoph ; Sietz, Diana ; Bonanomi, Elisabeth Bürgi ; Bremond, Ariane de; Dell' Angelo, Jampel ; Eisenack, Klaus ; Ellis, Erle C. ; David, M. ; Giger, Markus ; Heinimann, Andreas ; Kimmich, Christian ; Kok, Marcel T.J. ; Navarrete, David Manuel ; Messerli, Peter ; Meyfroidt, Patrick ; Václavík, Tomás ; Villamayor-Tomas, Sergio - \ 2019
    Ecology and Society 24 (2019)2. - ISSN 1708-3087
    Archetype - Land systems - Social-ecological system - Sustainability - Vulnerability

    Archetypes are increasingly used as a methodological approach to understand recurrent patterns in variables and processes that shape the sustainability of social-ecological systems. The rapid growth and diversification of archetype analyses has generated variations, inconsistencies, and confusion about the meanings, potential, and limitations of archetypes. Based on a systematic review, a survey, and a workshop series, we provide a consolidated perspective on the core features and diverse meanings of archetype analysis in sustainability research, the motivations behind it, and its policy relevance. We identify three core features of archetype analysis: Recurrent patterns, multiple models, and intermediate abstraction. Two gradients help to apprehend the variety of meanings of archetype analysis that sustainability researchers have developed: (1) understanding archetypes as building blocks or as case typologies and (2) using archetypes for pattern recognition, diagnosis, or scenario development. We demonstrate how archetype analysis has been used to synthesize results from case studies, bridge the gap between global narratives and local realities, foster methodological interplay, and transfer knowledge about sustainability strategies across cases. We also critically examine the potential and limitations of archetype analysis in supporting evidence-based policy making through context-sensitive generalizations with case-level empirical validity. Finally, we identify future priorities, with a view to leveraging the full potential of archetype analysis for supporting sustainable development.

    Introducing rewilding to restoration to expand the conservation effort: a response to Hayward et al.
    Anderson, Robert M. ; Buitenwerf, Robert ; Driessen, Clemens ; Genes, Luísa ; Lorimer, Jamie ; Svenning, Jens Christian - \ 2019
    Biodiversity and Conservation 28 (2019)13. - ISSN 0960-3115 - p. 3691 - 3693.
    Synthesizing plausible futures for biodiversity and ecosystem services in europe and central asia using scenario archetypes
    Harrison, Paula A. ; Harmáčková, Zuzana V. ; Karabulut, Armağan Aloe ; Brotons, Lluis ; Cantele, Matthew ; Claudet, Joachim ; Dunford, Robert W. ; Guisan, Antoine ; Holman, Ian P. ; Jacobs, Sander ; Kok, Kasper ; Lobanova, Anastasia ; Morán-Ordóñez, Alejandra ; Pedde, Simona ; Rixen, Christian ; Santos-Martín, Fernando ; Schlaepfer, Martin A. ; Solidoro, Cosimo ; Sonrel, Anthony ; Hauck, Jennifer - \ 2019
    Ecology and Society 24 (2019)2. - ISSN 1708-3087
    Biodiversity - Drivers - Ecosystem services - Exploratory scenarios - Impacts - IPBES - Models - Nature - Nature’s contributions to people (NCP)

    Scenarios are a useful tool to explore possible futures of social-ecological systems. The number of scenarios has increased dramatically over recent decades, with a large diversity in temporal and spatial scales, purposes, themes, development methods, and content. Scenario archetypes generically describe future developments and can be useful in meaningfully classifying scenarios, structuring and summarizing the overwhelming amount of information, and enabling scientific outputs to more effectively interface with decision-making frameworks. The Intergovernmental Platform for Biodiversity and Ecosystem Services (IPBES) faced this challenge and used scenario archetypes in its assessment of future interactions between nature and society. We describe the use of scenario archetypes in the IPBES Regional Assessment of Europe and Central Asia. Six scenario archetypes for the region are described in terms of their driver assumptions and impacts on nature (including biodiversity) and its contributions to people (including ecosystem services): Business-as-usual, economic optimism, regional competition, regional sustainability, global sustainable development, and inequality. The analysis shows that trade-offs between nature’s contributions to people are projected under different scenario archetypes. However, the means of resolving these trade-offs depend on differing political and societal value judgements within each scenario archetype. Scenarios that include proactive decision making on environmental issues, environmental management approaches that support multifunctionality, and mainstreaming environmental issues across sectors, are generally more successful in mitigating tradeoffs than isolated environmental policies. Furthermore, those scenario archetypes that focus on achieving a balanced supply of nature’s contributions to people and that incorporate a diversity of values are estimated to achieve more policy goals and targets, such as the UN Sustainable Development Goals and the Convention on Biological Diversity Aichi targets. The scenario archetypes approach is shown to be helpful in supporting science-policy dialogue for proactive decision making that anticipates change, mitigates undesirable trade-offs, and fosters societal transformation in pursuit of sustainable development.

    Upcycling food leftovers and grass recources through farm animals
    Hal, O. van; Boer, I.J.M. de; Muller, A. ; Vries, S. de; Erb, K. ; Schader, Christian ; Zanten, H.H.E. van - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP book of abstracts ) - ISBN 9789086863396 - p. 316 - 316.
    Modeling of Soil Functions for Assessing Soil Quality: Soil Biodiversity and Habitat Provisioning
    Leeuwen, J.P. van; Creamer, Rachel ; Cluzeau, Daniel ; Debeljak, Marko ; Gatti, Fabio ; Henriksen, Christian Bugge ; Kuzmanovski, Vladimir ; Menta, Cristina ; Pérès, Guénola ; Picaud, Calypso ; Saby, N.P.A. ; Trajanov, Aneta ; Trinsoutrot-Gattin, Isabelle ; Visioli, Giovanna ; Rutgers, M. - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X - 13 p.
    Soil biodiversity and habitat provisioning is one of the soil functions that agricultural land provides to society. This paper describes assessment of the soil biodiversity function (SB function) as a proof of concept to be used in a decision support tool for agricultural land management. The SB function is defined as “the multitude of soil organisms and processes, interacting in an ecosystem, providing society with a rich biodiversity source and contributing to a habitat for aboveground organisms.” So far, no single measure provides the full overview of the soil biodiversity and how a soil supports a habitat for a biodiverse ecosystem. We have assembled a set of attributes for a proxy-indicator system, based on four “integrated attributes”: (1) soil nutrient status, (2) soil biological status, (3) soil structure, and (4) soil hydrological status. These attributes provide information to be used in a model for assessing the capacity of a soil to supply the SB function. A multi-criteria decision model was developed which comprises of 34 attributes providing information to quantify the four integrated attributes and subsequently assess the SB function for grassland and for cropland separately. The model predictions (in terms of low—moderate—high soil biodiversity status) were compared with expert judgements for a collection of 137 grassland soils in the Netherlands and 52 French soils, 29 grasslands, and 23 croplands. For both datasets, the results show that the proposed model predictions were statistically significantly correlated with the expert judgements. A sensitivity analysis indicated that the soil nutrient status, defined by attributes such as pH and organic carbon content, was the most important integrated attribute in the assessment of the SB function. Further progress in the assessment of the SB function is needed. This can be achieved by better information regarding land use and farm management. In this way we may make a valuable step in our attempts to optimize the multiple soil functions in agricultural landscapes, and hence the multifaceted role of soils to deliver a bundle of ecosystem services for farmers and citizens, and support land management and policy toward a more sustainable society.
    A Field-Scale Decision Support System for Assessment and Management of Soil Functions
    Debeljak, Marko ; Trajanov, Aneta ; Kuzmanovski, Vladimir ; Schroder, J.J. ; Sandén, Taru ; Spiegel, Heide ; Wall, David ; Broek, Marijn van de; Rutgers, Michiel ; Bampa, Francesca ; Creamer, Rachel ; Henriksen, Christian Bugge - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X
    Agricultural decision support systems (DSS) are mostly focused on increasing the supply of individual soil functions such as e.g. primary productivity or nutrient cycling, while neglecting other important soil functions, such as e.g. water purification and regulation, climate regulation and carbon sequestration, soil biodiversity and habitat provision. Making right management decisions for long-term sustainability is therefore challenging, and farmers and farm advisors would greatly benefit from an evidence-based DSS targeted for assessing and improving the supply of several soil functions simultaneously. To address this, need we designed the Soil Navigator DSS by applying a qualitative approach to multi criteria decision modelling using Decision Expert (DEX) integrative methodology. Multi-criteria decision models for the five main soil functions were developed, calibrated and validated using knowledge of involved domain experts and knowledge extracted from existing datasets by data mining. Subsequently, the five DEX models were integrated into a DSS to assess the soil functions simultaneously, and to provide management advises for improving the performance of prioritized soil functions. To enable communication between the users and the DSS, we developed a user-friendly computer-based graphical user interface, which enables users to provide the required data regarding their field to the DSS and to get textual and graphical results about the performance of each of the five soil functions in a qualitative way. The final output from the DSS is a list of soil mitigation measures that the end-users could easily apply in the field in order to achieve the desired soil function performance. The Soil Navigator DSS has a great potential to complement the Farm Sustainability Tools for Nutrients included in the Common Agricultural Policy 2021-2027 proposal adopted by the European Commission. The Soil Navigator has also a potential to be spatially upgraded to assist decisions on which soil functions to prioritize in a specific region or member state. Furthermore, the Soil Navigator DSS could be used as an educational tool for farmers, farm advisors and students, and its potential should be further exploited for the benefit of farmers and the society as a whole.
    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Basic Phytochrome B Calculations
    Smith, Robert W. ; Fleck, Christian - \ 2019
    In: Phytochromes / Hiltbrunner, Andreas, Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493996117 - p. 121 - 133.
    Computer programming - Mathematical modeling - Ordinary differential equations - Phytochromes

    Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
    Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
    Nature 571 (2019)7765. - ISSN 0028-0836

    In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following, https://inventaire-forestier.ign.fr/spip.php?rubrique159, site accessed on 01 January 2015)’. All of these errors have been corrected online.

    The nutritive value of black soldier fly larvae reared on common organic waste streams in Kenya
    Shumo, Marwa ; Osuga, Isaac M. ; Khamis, Fathiya M. ; Tanga, Chrysantus M. ; Fiaboe, Komi K.M. ; Subramanian, Sevgan ; Ekesi, Sunday ; Huis, Arnold van; Borgemeister, Christian - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    In Africa, livestock production currently accounts for about 30% of the gross value of agricultural production. However, production is struggling to keep up with the demands of expanding human populations, the rise in urbanization and the associated shifts in diet habits. High costs of feed prevent the livestock sector from thriving and to meet the rising demand. Insects have been identified as potential alternatives to the conventionally used protein sources in livestock feed due to their rich nutrients content and the fact that they can be reared on organic side streams. Substrates derived from organic by-products are suitable for industrial large-scale production of insect meal. Thus, a holistic comparison of the nutritive value of Black Soldier Fly larvae (BSFL) reared on three different organic substrates, i.e. chicken manure (CM), brewers’ spent grain (SG) and kitchen waste (KW), was conducted. BSFL samples reared on every substrate were collected for chemical analysis after the feeding process. Five-hundred (500) neonatal BSFL were placed in 23 × 15 cm metallic trays on the respective substrates for a period of 3–4 weeks at 28 ± 2 °C and 65 ± 5% relative humidity. The larvae were harvested when the prepupal stage was reached using a 5 mm mesh size sieve. A sample of 200 grams prepupae was taken from each replicate and pooled for every substrate and then frozen at −20 °C for chemical analysis. Samples of BSFL and substrates were analyzed for dry matter (DM), crude protein (CP), ether extracts (EE), ash, acid detergent fibre (ADF), neutral detergent fibre (NDF), amino acids (AA), fatty acids (FA), vitamins, flavonoids, minerals and aflatoxins. The data were then subjected to analysis of variance (ANOVA) using general linear model procedure. BSFL differed in terms of nutrient composition depending on the organic substrates they were reared on. CP, EE, minerals, amino acids, ADF and NDF but not vitamins were affected by the different rearing substrates. BSFL fed on different substrates exhibited different accumulation patterns of minerals, with CM resulting in the largest turnover of minerals. Low concentrations of heavy metals (cadmium and lead) were detected in the BSFL, but no traces of aflatoxins were found. In conclusion, it is possible to take advantage of the readily available organic waste streams in Kenya to produce nutrient-rich BSFL-derived feed.

    Hybrid Software Development Approaches in Practice : A European Perspective
    Kuhrmann, Marco ; Diebold, Philipp ; Munch, Jurgen ; Tell, Paolo ; Trektere, Kitija ; McCaffery, Fergal ; Garousi, Vahid ; Felderer, Michael ; Linssen, Oliver ; Hanser, Eckhart ; Prause, Christian R. - \ 2019
    IEEE Software 36 (2019)4. - ISSN 0740-7459 - p. 20 - 31.
    agile practices - computing milieux - hybrid development approach - management of computing and information systems - software development method - software development practice - software management - software process - traditional development approach

    The surveyed companies applied hybrid development approaches to specific projects even when company-wide policies for process usage existed. These approaches emerged from the evolution of different work practices and were consistently used regardless of company size or industry sector.

    A conceptual and empirical framework to analyze the economics of consumer food waste
    Drabik, Dušan ; Gorter, Harry de; Reynolds, Christian - \ 2019
    Resources, Conservation and Recycling 149 (2019). - ISSN 0921-3449 - p. 500 - 509.
    Consumer purchases - Consumption - Downstream - Economic model - Effective consumption price - Food waste

    We develop a microeconomic model to understand food waste of consumers. We capture at-home and away-from home food consumption and distinguish between food purchases and food consumption. We allow the consumer to choose the rate of food waste at home optimally to maximize her utility. We show that consumer purchases can decline or increase with a cut in the rate of consumer waste, depending on the elasticity of food demand. Using the UK data for poultry in 2012, we also show a case where for a price elastic demand food consumption increases with a reduction in the food waste rate, but food purchases (retail sales) increase.

    Live cell imaging of meiosis in Arabidopsis thaliana
    Prusicki, Maria A. ; Keizer, Emma M. ; Rosmalen, Rik P. van; Komaki, Shinichiro ; Seifert, Felix ; Müller, Katja ; Wijnker, Erik ; Fleck, Christian ; Schnittger, Arp - \ 2019
    eLife 8 (2019). - ISSN 2050-084X
    A. thaliana - cell biology - cyclin - development - meiosis - phragmoplast - plant biology - reproduction - spindle

    To follow the dynamics of meiosis in the model plant Arabidopsis, we have established a live cell imaging setup to observe male meiocytes. Our method is based on the concomitant visualization of microtubules (MTs) and a meiotic cohesin subunit that allows following five cellular parameters: cell shape, MT array, nucleus position, nucleolus position, and chromatin condensation. We find that the states of these parameters are not randomly associated and identify 11 cellular states, referred to as landmarks, which occur much more frequently than closely related ones, indicating that they are convergence points during meiotic progression. As a first application of our system, we revisited a previously identified mutant in the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM). Our imaging system enabled us to reveal both qualitatively and quantitatively altered landmarks in tam, foremost the formation of previously not recognized ectopic spindle- or phragmoplast-like structures that arise without attachment to chromosomes.

    Understanding Genetic Load in Potato for Hybrid Diploid Breeding
    Bachem, Christian W.B. ; Eck, Herman J. van; Vries, Michiel E. de - \ 2019
    Molecular Plant 12 (2019)7. - ISSN 1674-2052 - p. 896 - 898.
    Data from: The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agro-ecosystem services across Europe
    Martin, Emily A. ; Dainese, Matteo ; Clough, Yann ; Báldi, András ; Bommarco, R. ; Gagic, Vesna ; Garratt, Michael P.D. ; Holzschuh, Andrea ; Kleijn, D. ; Kovács-Hostyánszki, Anikó ; Marini, Lorenzo ; Potts, Simon G. ; Smith, Henrik G. ; Hassan, Diab Al; Albrecht, Matthias ; Andersson, Georg K.S. ; Asís, Josep D. ; Aviron, Stéphanie ; Balzan, M.V. ; Baños-Picón, Laura ; Bartomeus, Ignasi ; Batáry, Péter ; Burel, Francoise ; Caballero-lópez, Berta ; Concepción, Elena D. ; Coudrain, Valérie ; Dänhardt, Juliana ; Diaz, Mario ; Diekötter, Tim ; Dormann, Carsten F. ; Duflot, Rémi ; Entling, Martin H. ; Farwig, Nina ; Fischer, Christina ; Frank, Thomas ; Garibaldi, Lucas A. ; Hermann, John ; Herzog, Felix ; Inclán, Diego J. ; Jacot, Katja ; Jauker, Frank ; Jeanneret, Philippe ; Kaiser, Marina ; Krauss, Jochen ; Féon, Violette Le; Marshall, Jon ; Moonen, Anna Camilla ; Moreno, Gerardo ; Riedinger, Verena ; Rundlöf, Maj ; Rusch, Adrien ; Scheper, J.A. ; Schneider, Gudrun ; Schüepp, Christof ; Stutz, Sonja ; Sutter, Louis ; Tamburini, Giovanni ; Thies, Carsten ; Tormos, José ; Tscharntke, Teja ; Tschumi, Matthias ; Uzman, Deniz ; Wagner, Christian ; Zubair Anjum, Muhammad ; Steffan-Dewenter, Ingolf - \ 2019
    University of Würzburg
    biodiversity - agroecosystem - landscape composition - landscape configuration - functional traits - arthropods - natural pest control - pollination - yields
    Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with the proportions of crop and non‐crop habitats, and species’ dietary, dispersal and overwintering traits led to contrasting responses to landscape variables. Overall, however, in landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7‐ and 1.4‐fold respectively. Arable‐dominated landscapes with high edge densities achieved high yields. This suggests that enhancing edge density in European agroecosystems can promote functional biodiversity and yield‐enhancing ecosystem services.
    Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
    Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
    forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

    Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

    Alpha diversity of vascular plants in European forests
    Večeřa, Martin ; Divíšek, Jan ; Lenoir, Jonathan ; Jiménez-Alfaro, Borja ; Biurrun, Idoia ; Knollová, Ilona ; Agrillo, Emiliano ; Campos, Juan Antonio ; Čarni, Andraž ; Crespo Jiménez, Guillermo ; Ćuk, Mirjana ; Dimopoulos, Panayotis ; Ewald, Jörg ; Fernández-González, Federico ; Gégout, Jean Claude ; Indreica, Adrian ; Jandt, Ute ; Jansen, Florian ; Kącki, Zygmunt ; Rašomavičius, Valerijus ; Řezníčková, Marcela ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Svenning, Jens Christian ; Swacha, Grzegorz ; Vassilev, Kiril ; Venanzoni, Roberto ; Willner, Wolfgang ; Wohlgemuth, Thomas ; Chytrý, Milan - \ 2019
    Journal of Biogeography 46 (2019)9. - ISSN 0305-0270 - p. 1919 - 1935.
    diversity - Europe - European Vegetation Archive (EVA) - forest vegetation - plant community - predictive modelling - Random Forests - species-richness patterns - vascular plants - vegetation-plot database

    Aim: The former continental-scale studies modelled coarse-grained plant species-richness patterns (gamma diversity). Here we aim to refine this information for European forests by (a) modelling the number of vascular plant species that co-occur in local communities (alpha diversity) within spatial units of 400 m2; and (b) assessing the factors likely determining the observed spatial patterns in alpha diversity. Location: Europe roughly within 12°W–30°E and 35–60°N. Taxon: Vascular plants. Methods: The numbers of co-occurring vascular plant species were counted in 73,134 georeferenced vegetation plots. Each plot was classified by an expert system into deciduous broadleaf, coniferous or sclerophyllous forest. Random Forest models were used to map and explain spatial patterns in alpha diversity for each forest type separately using 19 environmental, land-use and historical variables. Results: Our models explained from 51.0% to 70.9% of the variation in forest alpha diversity. The modelled alpha-diversity pattern was dominated by a marked gradient from species-poor north-western to species-rich south-eastern Europe. The most prominent richness hotspots were identified in the Calcareous Alps and adjacent north-western Dinarides, the Carpathian foothills in Romania and the Western Carpathians in Slovakia. Energy-related factors, bedrock types and terrain ruggedness were identified as the main variables underlying the observed richness patterns. Alpha diversity increases especially with temperature seasonality in deciduous broadleaf forests, on limestone bedrock in coniferous forests and in areas with low annual actual evapotranspiration in sclerophyllous forests. Main conclusions: We provide the first predictive maps and analyses of environmental factors driving the alpha diversity of vascular plants across European forests. Such information is important for the general understanding of European biodiversity. This study also demonstrates a high potential of vegetation-plot databases as sources for robust estimation of the number of vascular plant species that co-occur at fine spatial grains across large areas.

    Genetic and molecular analysis of trichome development in Arabis alpina
    Chopra, Divykriti ; Mapar, Mona ; Stephan, Lisa ; Albani, Maria C. ; Deneer, Anna ; Coupland, George ; Willing, Eva Maria ; Schellmann, Swen ; Schneeberger, Korbinian ; Fleck, Christian ; Schrader, Andrea ; Hülskamp, Martin - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)24. - ISSN 0027-8424 - p. 12078 - 12083.
    Arabis alpina - Genetic analysis - Trichomes

    The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabis alpina. In general, we found most trichome mutant classes known in A. thaliana. We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2. Moreover, we show that overexpression of the GL3 basic helix–loop–helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana. Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.

    Science-based wildlife disease response
    Vicente, Joaquín ; Apollonio, Marco ; Blanco-Aguiar, Jose A. ; Borowik, Tomasz ; Brivio, Francesca ; Casaer, Jim ; Croft, Simon ; Ericsson, Göran ; Ferroglio, Ezio ; Gavier-Widen, Dolores ; Gortázar, Christian ; Jansen, Patrick A. ; Keuling, Oliver ; Kowalczyk, Rafał ; Petrovic, Karolina ; Plhal, Radim ; Podgórski, Tomasz ; Sange, Marie ; Scandura, Massimo ; Schmidt, Krzysztof ; Smith, Graham C. ; Soriguer, Ramon ; Thulke, Hans Hermann ; Zanet, Stefania ; Acevedo, Pelayo - \ 2019
    Science 364 (2019)6444. - ISSN 0036-8075 - p. 943 - 944.
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