Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    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.
    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.
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