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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    Matching scope, purpose and uses of planetary boundaries science
    Downing, Andrea S. ; Bhowmik, Avit ; Collste, David ; Cornell, Sarah E. ; Donges, Jonathan ; Fetzer, Ingo ; Häyhä, Tiina ; Hinton, Jennifer ; Lade, Steven ; Mooij, Wolf M. - \ 2019
    Environmental Research Letters 14 (2019)7. - ISSN 1748-9318
    footprints approach - global sustainability science - human dimensions - life cycle analysis - Planetary boundaries - resilience - safe operating space

    Background: The Planetary Boundaries concept (PBc) has emerged as a key global sustainability concept in international sustainable development arenas. Initially presented as an agenda for global sustainability research, it now shows potential for sustainability governance. We use the fact that it is widely cited in scientific literature (>3500 citations) and an extensively studied concept to analyse how it has been used and developed since its first publication. Design: From the literature that cites the PBc, we select those articles that have the terms 'planetary boundaries' or 'safe operating space' in either title, abstract or keywords. We assume that this literature substantively engages with and develops the PBc. Results: We find that 6% of the citing literature engages with the concept. Within this fraction of the literature we distinguish commentaries - that discuss the context and challenges to implementing the PBc, articles that develop the core biogeophysical concept and articles that apply the concept by translating to sub-global scales and by adding a human component to it. Applied literature adds to the concept by explicitly including society through perspectives of impacts, needs, aspirations and behaviours. Discussion: Literature applying the concept does not yet include the more complex, diverse, cultural and behavioural facet of humanity that is implied in commentary literature. We suggest there is need for a positive framing of sustainability goals - as a Safe Operating Space rather than boundaries. Key scientific challenges include distinguishing generalised from context-specific knowledge, clarifying which processes are generalizable and which are scalable, and explicitly applying complex systems' knowledge in the application and development of the PBc. We envisage that opportunities to address these challenges will arise when more human social dimensions are integrated, as we learn to feed the global sustainability vision with a plurality of bottom-up realisations of sustainability.

    Modeling water quality in the Anthropocene: directions for the next-generation aquatic ecosystem models
    Mooij, W.M. ; Wijk, Dianneke van; Beusen, A.H.W. ; Brederveld, R.J. ; Chang, M. ; Cobben, Marleen M.P. ; DeAngelis, D.L. ; Downing, A.S. ; Janssen, A.B.G. ; Hengeveld, G.M. - \ 2019
    Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 85 - 95.
    Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
    Social vulnerability to climate change in European cities – state of play in policy and Practice
    Breil, M. ; Downing, C. ; Kazmierczak, A. ; Mäkinen, K. ; Romanovska, L. ; Terämä, E. ; Swart, R.J. - \ 2018
    Copenhagen : EEA - European Environment Agency (ETC/CCA Technical Paper 2018/1) - 85 p.
    Climate change impacts do not affect all citizens in the same way. They often cause worse impacts on certain vulnerable groups within cities. The aim of this technical paper is to provide the state-of-play in policy and practice for addressing social vulnerability to climate change in urban areas.
    Sharing adaptation knowledge across Europe: Evidence for the evaluation of Climate-ADAPT
    Mattern, Kati ; Giannini, Valentina ; Downing, Claire ; Gomes, Ana ; Ramieri, Emiliano ; Karali, Eleni ; Capela Lourenco, T. ; Jong, F. de; Coninx, I. ; Marras, Serena ; Medri, Silvia ; Kazmierczak, Aleksandra - \ 2018
    Bologna : ETC CCA (ETC/CCA Technical paper 2018/2) - 214 p.
    This report (termed 'ETC/CCA Technical Paper') collects the annexes (“Key evidence”) supporting the outcomes of the evaluation of the European Climate Adaptation Platform (Climate-ADAPT), that are presented in the European Environment Agency (EEA) Report (2018) “Sharing adaptation knowledge across Europe – Evaluation of the European Climate Adaptation Platform”.
    Final release of the network database and associated documentation : Deliverable D 2.2, Work Package 2 Stocktaking of the decision making context
    Karali, Eleni ; Giupponi, Carlo ; Bojovic, Dragana ; Coninx, I. ; Calliari, E. ; Allenbach, Karin ; Downing, C. ; Rohat, Guillaume ; Michalek, Gabriela ; Schwarze, Reimund ; Vetter, Patrick - \ 2017
    Placard - 164 p.
    Task 2.2 “Clustering and network analysis” of the PLACARD project aimed at supporting the mapping of interactions within and between CCA and DRR communities and assessing quantitatively the roles that different actors have in them, using a Social Network Analysis (SNA). SNA techniques are used to answer questions about how actors are connected to each other, how strong their relationships are and which actors are best positioned to connect other actors in a network through the calculation of indicators such as degree, closeness, betweenness centrality and clustering coefficient. In the context of the PLACARD project, two SNA exercises were carried out to investigate the intensity of actors’ interactions (i.e. on a scale from 1 to 5 representing lack of interaction, weak and strong communication, and weak and strong collaboration), as well as the type of interactions (i.e., whether an interaction is related to CCA, DRR, or both fields). Social network metrics were calculated to quantitatively assess the roles of different actors in the network and their interrelationships. In particular, we focused on centrality measures – degree, in‐ degree, betweenness and eigenvector – that are considered good indicators of an actor’s power position, meaning the strength of the role played by an actor in influencing interactions in a network. The first exercise took place in summer 2016 and focused on the interactions between CCA and DRR actors operating at the European and International level. Data was collected from the responses of 32 out of the 35 actors that were invited to participate in an online SNA survey. The European Climate Adaptation Platform (Climate‐ADAPT) emerged as the actor with the highest degree, eigenvector and betweenness centrality values. Besides Climate-ADAPT, the Directorate‐General for Research and Innovation (DG R&I), the European Environment Agency (EEA) and the Directorate‐ General for Climate Action (DG CLIMA) were identified as actors with high centrality values. The actor with the highest in‐degree centrality, an indicator that considers the number of ties that a certain actor has as specified by other actors in the network, was DG CLIMA, followed by EEA and IPCC. When it comes to the analysis of whether interactions are related to CCA and/or DRR issues, collaboration appeared to be most often related to both CCA and DRR, while communication mostly related to one of the two areas when these were considered separately. Cluster analysis was applied to explore if actors could be grouped on the basis of SNA metrics. The application of Clauset‐ Newman‐Moore algorithm revealed two large groups, which clearly depicted the two main communities: DRR and CCA, and one significantly smaller cluster. A detailed description of the first SNA can be found in the PLACARD Milestone 10 report (Bojovic et al., 2017). The second round of the SNA initiated in autumn 2017. This aimed at exploring the two-way interactions between national level actors in four European countries: Germany, Italy, Switzerland and the United Kingdom, as well as the one-way interactions between national level actors and a small group of international actors whose role was identified as important based on the output of the first SNA. Data collection took place in parallel in all four countries, while data was analysed separately for each one of them. The output of the analyses along with a description of the methodological approach employed in this study and a review of CCA and DRR studies that have used SNA during the last two decades are presented in detail in this report (PLACARD Deliverable 2.2 report) (Karali et al., 2018). Selected observations and general remarks from this second exercise are presented below: Governmental actors and research institutes were well represented in all four countries. Output of the SNA analyses confirmed our hypothesis that these actors have a central role in national CCA / DRR networks. • Knowledge platforms and businesses were less equally represented across the four countries, yet they had an important role in the networks in which they were present. Especially for the case of business / companies, relevant actors appeared to be very active in networking, reaching out to a large number of actors (see the out-degree centrality metric). The importance of these actors’ role in the CCA / DRR networks is expected to increase further in the near future. • In many cases the same actors occupied the top places in the ranking of more than one of the calculated SNA metrics. This observation reflects the key role of certain actors in interacting with other actors in their networks as well as in setting up interactions with actors that are less well-connected. • The one-way interactions of national level actors in the four countries with the six international actors (as indicated by the former) suggest that the former interact more with international actors with whom share a similar field of expertise. • Differences exist in the type and intensity of interactions among national level actors in the four countries and the ranking of the different types of actors considered in each network. While some general remarks can be made based on the output of the four SNAs, a full crosscountry comparison is not considered useful in this study due to the differences in the composition of the four networks. • Both CCA and DRR are dynamic and highly evolving fields. This implies that the roles and the importance of actors may change over time as a result of the changing needs in the different networks. Already in this study, the important role of actors such as networks, nongovernmental organisations or non-governmental advisory boards emerged. • Ensuring the diversity of voices and the involvement of actors that are often neglected in relevant exercises is expected to benefit the network in terms of its potential to expand and increase its strength and relevance in the long-term. • Several challenges emerged at the different stages of the SNA exercise. Setting the network and identifying suitable survey participants were key challenges during the design of the SNA. High workload, fatigue, scepticism about the way that data will be used and the repetitive pattern of the SNA questionnaire were identified as barriers during the data collection process that had to be overcome in order to minimize their impact on the response rates of the surveys and the completeness of the collected responses. Finally, during the phase of the data analysis and the interpretation of the results, we were confronted with two ‘weak’ points of the SNA method: (i) the fact that the method is a rather static, as it can reflect actors’ interactions only at a specific point in time, and (ii) that it cannot capture the reasons why certain patterns emerge. These challenges reinforce the idea that the applications of SNA need to be complemented by other methodological tools (i.e. interviews, focus groups) to support a more insightful interpretation of their results.
    Predicting bee community responses to land-use changes : Effects of geographic and taxonomic biases
    Palma, Adriana De; Abrahamczyk, Stefan ; Aizen, Marcelo A. ; Albrecht, Matthias ; Basset, Yves ; Bates, Adam ; Blake, Robin J. ; Boutin, Céline ; Bugter, Rob ; Connop, Stuart ; Cruz-López, Leopoldo ; Cunningham, Saul A. ; Darvill, Ben ; Diekötter, Tim ; Dorn, Silvia ; Downing, Nicola ; Entling, Martin H. ; Farwig, Nina ; Felicioli, Antonio ; Fonte, Steven J. ; Fowler, Robert ; Franzén, Markus ; Goulson, Dave ; Grass, Ingo ; Hanley, Mick E. ; Hendrix, Stephen D. ; Herrmann, Farina ; Herzog, Felix ; Holzschuh, Andrea ; Jauker, Birgit ; Kessler, Michael ; Knight, M.E. ; Kruess, Andreas ; Lavelle, Patrick ; Féon, Violette Le; Lentini, Pia ; Malone, Louise A. ; Marshall, Jon ; Pachón, Eliana Martínez ; McFrederick, Quinn S. ; Morales, Carolina L. ; Mudri-Stojnic, Sonja ; Nates-Parra, Guiomar ; Nilsson, Sven G. ; Öckinger, Erik ; Osgathorpe, Lynne ; Parra-H, Alejandro ; Peres, Carlos A. ; Persson, Anna S. ; Petanidou, Theodora ; Poveda, Katja ; Power, Eileen F. ; Quaranta, Marino ; Quintero, Carolina ; Rader, Romina ; Richards, Miriam H. ; Roulston, Tai ; Rousseau, Laurent ; Sadler, Jonathan P. ; Samnegård, Ulrika ; Schellhorn, Nancy A. ; Schüepp, Christof ; Schweiger, Oliver ; Smith-Pardo, Allan H. ; Steffan-Dewenter, Ingolf ; Stout, Jane C. ; Tonietto, Rebecca K. ; Tscharntke, Teja ; Tylianakis, Jason M. ; Verboven, Hans A.F. ; Vergara, Carlos H. ; Verhulst, Jort ; Westphal, Catrin ; Yoon, Hyung Joo ; Purvis, Andy - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 14 p.

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

    Exploring, exploiting and evolving diversity of aquatic ecosystem models : a community perspective
    Janssen, A.B.G. ; Arhonditsis, G.B. ; Beusen, Arthur ; Bolding, Karsten ; Bruce, Louise ; Bruggeman, Jorn ; Couture, Raoul Marie ; Downing, Andrea S. ; Alex Elliott, J. ; Frassl, M.A. ; Gal, Gideon ; Gerla, Daan J. ; Hipsey, M.R. ; Hu, Fenjuan ; Ives, S.C. ; Janse, J.H. ; Jeppesen, Erik ; Jöhnk, K.D. ; Kneis, David ; Kong, Xiangzhen ; Kuiper, J.J. ; Lehmann, M.K. ; Lemmen, Carsten ; Özkundakci, Deniz ; Petzoldt, Thomas ; Rinke, Karsten ; Robson, B.J. ; Sachse, René ; Schep, S.A. ; Schmid, Martin ; Scholten, Huub ; Teurlincx, Sven ; Trolle, Dennis ; Troost, T.A. ; Dam, A.A. Van; Gerven, L.P.A. Van; Weijerman, Mariska ; Wells, S.A. ; Mooij, W.M. - \ 2015
    Aquatic Ecology 49 (2015)4. - ISSN 1386-2588 - p. 513 - 548.
    Ecology - Geochemistry - Hydraulics - Hydrodynamics - Hydrology - Linking - Model availability - Physical environment - Socio-economics - Standardization - Water quality

    Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5–10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.

    Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
    Gerven, L.P.A. van; Brederveld, R.J. ; Klein, J.J.M. de; DeAngelis, D.L. ; Downing, A.S. ; Faber, M. ; Gerla, D.J. ; Hoen, J. 't; Janse, J.H. ; Janssen, A.B.G. ; Jeuken, Michel ; Kooi, B.W. ; Kuiper, J.J. ; Lischke, B. ; Liu, Sien ; Petzoldt, Thomas ; Schep, S.A. ; Teurlincx, Sven ; Thiange, C. ; Trolle, D. ; Nes, E.H. van; Mooij, W.M. - \ 2015
    Fundamental and Applied Limnology 186 (2015)1-2. - ISSN 1863-9135 - p. 5 - 20.
    Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches. PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework – including runtime performance – can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
    Coupled human and natural system dynamics as key to the sustainability of Lake Victoria’s ecosystem services
    Downing, A.S. ; Nes, E.H. van; Balirwa, J.S. ; Beuving, J. ; Bwathondi, P.O.J. ; Chapman, L.J. ; Cornelissen, I.J.M. ; Cowx, I.G. ; Goudswaard, P.C. ; Hecky, R.E. ; Janse, J.H. ; Janssen, A.B.G. ; Kaufman, L. ; Kishe-Machumu, M.A. ; Kolding, J. ; Ligtvoet, W. ; Mbabazi, D. ; Medard, M. ; Mkumbo, O.C. ; Mlaponi, E. ; Munyaho, A.T. ; Nagelkerke, L.A.J. ; Ogutu-Ohwayo, R. ; Ojwang, W.O. ; Peter, H.K. ; Schindler, D.E. ; Seehausen, O. ; Sharpe, D. ; Silsbe, G.M. ; Sitoki, L. ; Tumwebaze, R. ; Tweddle, D. ; Wolfshaar, K.E. van de; Dijk, J.W.M. van; Donk, E. van; Rijssel, J.C. van; Zwieten, P.A.M. van; Wanink, J. ; Witte, F. ; Mooij, W.M. - \ 2014
    Ecology and Society 19 (2014)4. - ISSN 1708-3087
    cyprinid rastrineobola-argentea - perch lates-niloticus - nile perch - east-africa - water hyacinth - mwanza gulf - oreochromis-niloticus - morphological-changes - introduced predator - biological-control
    East Africa’s Lake Victoria provides resources and services to millions of people on the lake’s shores and abroad. In particular, the lake’s fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria’s system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake’s social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks’ vulnerability to exploitation but reduce society’s vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.
    Methodological approach
    Isoard, S. ; Prutsch, A. ; MCCallum, S. ; Biesbroek, G.R. ; Mäkinen, K. ; Hildén, M. ; Downing, C. ; Street, R. - \ 2014
    In: National adaptation policy processes in European countries - 2014 Luxembourgh : European Environment Agency (EEA Report 4/2014) - ISBN 9789292134853 - p. 14 - 14.
    Serving many at once: How a database approach can create unity in dynamical ecosystem modelling
    Mooij, W.M. ; Brederveld, R.J. ; Klein, J.J.M. de; DeAngelis, D.L. ; Downing, A.S. ; Faber, M. ; Gerla, D.J. ; Hipsey, M.R. ; Hoen, J. 't; Janse, J.H. ; Janssen, A.B.G. ; Jeuken, M. ; Kooi, B.W. ; Lischke, B. ; Petzoldt, T. ; Postma, L. ; Schep, S.A. ; Scholten, H. ; Teurlincx, S. ; Thiange, C. ; Trolle, D. ; Dam, A.A. van; Gerven, L.P.A. van; Nes, E.H. van; Kuiper, J.J. - \ 2014
    Environmental Modelling & Software 61 (2014). - ISSN 1364-8152 - p. 266 - 273.
    shallow lakes - simulation - eutrophication - management - package - pclake
    Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. © 2014 The Authors.
    Socio-economic assessment methods for adaptation to climate change: Application in the case studies of MEDIATION
    Zhu, X. ; Ierland, E.C. van; Watkiss, P. ; Bisaro, S. ; Aydemir, G. ; Khovanskaia, M. ; Hinkel, J. ; Varela-ortega, C. ; Blanco, I. ; Esteve, P. ; Bharwani, S. ; Downing, T.E. ; Fronzek, S. ; Juarez, E. ; Tainio, A. ; Heikkinen, R.K. ; Heliola, T.R. ; Leikola, N. ; Lotjonen, S. ; Mashkina, O. ; Carter, T.R. ; Taylor, R. ; Moriondo, M. ; Trombi, G. ; Bindi, M. ; Pol, T.D. van der; Weikard, H.P. - \ 2013
    Mediation - 2 p.
    Early host response in the mammary gland after experimental Streptococcus uberis challenge in heifers
    Greeff, A. de; Zadoks, R.N. ; Ruuls, L. ; Toussaint, M. ; Nguyen, T.K. ; Downing, A. ; Rebel, J.M.J. ; Stockhofe-Zurwieden, N. ; Smith, H.E. - \ 2013
    Journal of Dairy Science 96 (2013)6. - ISSN 0022-0302 - p. 3723 - 3736.
    innate immune-response - lipopolysaccharide-binding protein - clinical mastitis - intramammary infections - staphylococcus-aureus - lipoteichoic acid - bovine mastitis - dairy-cattle - 2 strains - epidemiology
    Streptococcus uberis is a highly prevalent causative agent of bovine mastitis, which leads to large economic losses in the dairy industry. The aim of this study was to examine the host response during acute inflammation after experimental challenge with capsulated Strep. uberis. Gene expression in response to Strep. uberis was compared between infected and control quarters in 3 animals. All quarters (n=16) were sampled at 16 different locations. Microarray data showed that 239 genes were differentially expressed between infected and control quarters. No differences in gene expression were observed between the different locations. Microarray data were confirmed for several genes using quantitative PCR analysis. Genes differentially expressed due to early Strep. uberis mastitis represented several stages of the process of infection: (1) pathogen recognition; (2) chemoattraction of neutrophils; (3) tissue repair mechanisms; and (4) bactericidal activity. Three different pathogen recognition genes were induced: ficolins, lipopolysaccharide binding protein, and toll-like receptor 2. Calgranulins were found to be the most strongly upregulated genes during early inflammation. By histology and immunohistochemistry, we demonstrated that changes in gene expression in response to Strep. uberis were induced both in infiltrating somatic milk cells and in mammary epithelial cells, demonstrating that the latter cell type plays a role in milk production as well as immune responsiveness. Given the rapid development of inflammation or mastitis after infection, early diagnosis of (Strep. uberis) mastitis is required for prevention of disease and spread of the pathogen. Insight into host responses could help to design immunomodulatory therapies to dampen inflammation after (early) diagnosis of Strep. uberis mastitis. Future research should focus on development of these early diagnostics and immunomodulatory components for mastitis treatment.
    Was Lates Late? A Null Model for the Nile Perch Boom in Lake Victoria
    Downing, A.S. ; Galic, N.G. ; Goudswaard, P.C. ; Nes, E.H. van; Scheffer, M. ; Witte, F. ; Mooij, W.M. - \ 2013
    PLoS ONE 8 (2013)10. - ISSN 1932-6203
    east-africa - niloticus l - fisheries - impact - ecosystems - resurgence - lessons - tilapia - kyoga - l.
    Nile perch (Lates niloticus) suddenly invaded Lake Victoria between 1979 and 1987, 25 years after its introduction in the Ugandan side of the lake. Nile perch then replaced the native fish diversity and irreversibly altered the ecosystem and its role to lakeshore societies: it is now a prised export product that supports millions of livelihoods. The delay in the Nile perch boom led to a hunt for triggers of the sudden boom and generated several hypotheses regarding its growth at low abundances – all hypotheses having important implications for the management of Nile perch stocks. We use logistic growth as a parsimonious null model to predict when the Nile perch invasion should have been expected, given its growth rate, initial stock size and introduction year. We find the first exponential growth phase can explain the timing of the perch boom at the scale of Lake Victoria, suggesting that complex mechanisms are not necessary to explain the Nile perch invasion or its timing. However, the boom started in Kenya before Uganda, indicating perhaps that Allee effects act at smaller scales than that of the whole Lake. The Nile perch invasion of other lakes indicates that habitat differences may also have an effect on invasion success. Our results suggest there is probably no single management strategy applicable to the whole lake that would lead to both efficient and sustainable exploitation of its resources.
    Letters to the editor : Assembling the pieces of Lake Victoria's many food webs: Reply to Kolding
    Downing, A.S. ; Nes, E.H. van; Janse, J.H. ; Witte, F. ; Cornelissen, J.J.L.M. ; Scheffer, M. ; Mooij, W.M. - \ 2013
    Ecological Applications 23 (2013)3. - ISSN 1051-0761 - p. 671 - 675.
    tilapia oreochromis-niloticus - nile tilapia - lates-niloticus - mwanza gulf - perch - kenya - l.
    Stockholm University, Department of Systems Ecology, SE-10691, Stockholm, Sweden Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University, P.O. Box 47, NL-6700 AA Wageningen, Netherlands Netherlands Environmental Assessment Agency, P.O. Box 303, 3720 AH Bilthoven, Netherlands Institute of Biology, Leiden University, Sylviusweg 72, 2300 RA Leiden, Netherlands Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700 AH Wageningen, Netherlands Department of Aquatic Ecology, Netherlands Institute of Ecology, P.O. Box 50, NL-6700 AB, Wageningen, Netherlands
    Effects of resources and mortality on the growth and reproduction of Nile perch in Lake Victoria
    Downing, A.S. ; Nes, E.H. van; Wolfshaar, K.E. van de; Scheffer, M. ; Mooij, W.M. - \ 2013
    Freshwater Biology 58 (2013)4. - ISSN 0046-5070 - p. 828 - 840.
    lates-niloticus l - size-structured populations - life-history traits - haplochromine cichlids - east-africa - mwanza gulf - nyanza-gulf - competition - predation - dynamics
    1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30 million people. Furthermore, changes in Nile perch population size-structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over-estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long-term effects of human impact.
    A community-based framework for aquatic ecosystem models
    Trolle, D. ; Hamilton, D.P. ; Hipsey, M.R. ; Bolding, K. ; Bruggeman, J. ; Mooij, W.M. ; Janse, J.H. ; Nielsen, A. ; Jeppesen, E. ; Elliott, J.A. ; Makler-Pick, V. ; Petzoldt, T. ; Rinke, K. ; Flindt, M.R. ; Arhonditsis, G.B. ; Gal, G. ; Bjerring, R. ; Tominaga, K. ; Hoen, J. 't; Downing, A.S. ; Marques, D.M. ; Fragoso, C.R. ; Sondergaard, M. ; Hanson, P.C. - \ 2012
    Hydrobiologia 683 (2012)1. - ISSN 0018-8158 - p. 25 - 34.
    climate-change - lake kinneret - phytoplankton - management - fish
    Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid 're-inventing the wheel', thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework.
    The resilience and resistance of an ecosystem to a collapse of diversity
    Downing, A.S. ; Nes, E.H. van; Mooij, W.M. ; Scheffer, M. - \ 2012
    PLoS ONE 7 (2012)9. - ISSN 1932-6203
    lake victoria - stable states - east-africa - coral-reefs - nile perch - food-web - biodiversity - productivity - communities - populations
    Diversity is expected to increase the resilience of ecosystems. Nevertheless, highly diverse ecosystems have collapsed, as did Lake Victoria's ecosystem of cichlids or Caribbean coral reefs. We try to gain insight to this paradox, by analyzing a simple model of a diverse community where each competing species inflicts a small mortality pressure on an introduced predator. High diversity strengthens this feedback and prevents invasion of the introduced predator. After a gradual loss of native species, the introduced predator can escape control and the system collapses into a contrasting, invaded, low-diversity state. Importantly, we find that a diverse system that has high complementarity gains in resilience, whereas a diverse system with high functional redundancy gains in resistance. Loss of resilience can display early-warning signals of a collapse, but loss of resistance not. Our results emphasize the need for multiple approaches to studying the functioning of ecosystems, as managing an ecosystem requires understanding not only the threats it is vulnerable to but also pressures it appears resistant to
    Seeing the water for the fish: building on perspectives of Lake Victoria
    Downing, A.S. - \ 2012
    Wageningen University. Promotor(en): Wolf Mooij; Marten Scheffer, co-promotor(en): Egbert van Nes. - S.l. : s.n. - ISBN 9789461733672 - 187
    waterkwaliteit - victoriameer - vissen - voedselwebben - aquatische ecosystemen - rivierbaars - groei - voortplanting - water quality - lake victoria - fishes - food webs - aquatic ecosystems - perch - growth - reproduction

    Over the past century, Lake Victoria, in East Africa, has been stage to the most dramatic social, economical and ecological changes: it saw a hundreds-rich diversity of fish species collapse; an introduced predator (Nile perch) invade and become the product of a valuable international fish export trade – a trade that invited an insurge of migrants to work on the lake’s shores.

    Since the 1990s, there has been an increase in dependence on the lake’s resources – including Nile perch and the other commercial fishes of the lake – and a decrease in the predictability and reliability of these resources.

    We here use a variety of ecological models to explore how changes in fishing and water quality influence changes in the lake’s food webs and Nile perch stocks. We describe the lake in its social-ecological perspective, and define the makers and breakers of the system’s resilience and recommend holistic and adaptive management policies.

    Exploitation or eutrophication as threats for fisheries? Social and ecological drivers of ecosystem changes in Lake Victoria
    Zwieten, P.A.M. van; Peter, H.K. ; Medard Ntara, M. ; Cornelissen, I.J.M. ; Downing, A.S. ; Nagelkerke, L.A.J. ; Mooij, W.M. ; Dijk, H. van - \ 2012
    Lake Victoria is the second largest freshwater lake and supports the largest freshwater commercial fishery in the world. Eutrophication and fisheries drive Lake Victoria’s changing ecosystem with far-reaching consequences for exploitation patterns, livelihoods and trade. The SEDEC research program attempts to link the two processes to understand feedbacks in food webs, resource use patterns and trade. Our main objective is to unravel the social and ecological drivers of ecosystem change and to develop longterm strategies to deal with the risks of these ecosystem changes. The working hypothesis is that continued eutrophication presents a much graver risk to the resource base and livelihoods of coastal populations than fishing pressure. Initially eutrophication resulted in a higher carrying capacity for Nile perch, because food availability increased through enhanced primary production. This increased carrying capacity resulted in an apparent resilience of the exploited Nile perch stocks to increased fishing pressure. However, the compensation of increased fishing pressure by increased production could fail when eutrophication becomes too strong, because of increasing self-shading by algae and by an increasing anoxic hypolimnion, which can cause catastrophic fish kills. Optimal nutrient concentrations to support fisheries may have already been exceeded, which could negatively affect Nile perch biomass. The responses of the fishery to changes caused by increased eutrophication as well as the responses of Nile perch stocks to the combined impacts of size selective fishing and eutrophication are researched in four inter-related projects that (1) analyse social factors that drive decision-making processes of individuals in the fishery; (2) analyse ecological factors, including size-selection, that drive decisions about spatial effort allocation by fishermen; (3) analyse the impact of eutrophication and Nile perch predation on food web structure, and (4) model the interactions and feedbacks resulting from eutrophication and fishery, as most likely factors driving changes in Lake Victoria’s food web. Scenarios to assess management under non-steady state conditions are developed in collaboration with international scientific experts and with regional and national government and research institutions.
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