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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Deciphering landscapes through the lenses of locals: The “Territorial Social-Ecological Networks” Framework applied to a Brazilian maroon case
Ayaviri Matuk, Fernanda ; Behagel, Jelle ; Gonçalves Reynaud Schaefer, Carlos Ernesto ; Duque-Brasil, Reinaldo ; Turnhout, Esther - \ 2019
Geoforum 100 (2019). - ISSN 0016-7185 - p. 101 - 115.
Adaptive co-management - Indigenous and local knowledge systems - Integration - Landscape approaches - Social-ecological systems - Territory

Landscape approaches are prominent in current policy debates about how to achieve ecological, economic and social sustainability. These approaches assess local social-ecological contexts to plan adaptive management and often include indigenous peoples and local communities (IPLC). An important aim of landscape approaches is to integrate different scientific disciplines, indigenous and local knowledge systems (ILK) and Western science, and global and local needs. In practice, such integration tends to favor globalized knowledge models and global needs over local ones. This article introduces a Territorial Social-Ecological Networks (TSEN) Framework for an integrated assessment of landscape settings and dynamics to overcome such tendencies. We argue that both scientific knowledge and ILK are entwined with practice and informed by worldviews. Moreover, these assemblages of knowledges-practice-worldviews are produced by social and ecological interrelations (or networks) that shape human appropriation of territory. We use an approach of methodological bricolage to apply the TSEN Framework to the case of the Brazilian Malhada Grande Maroon Territory. The results highlight how social-ecological networks of different space-time scales co-produce landscapes. Trade-offs and synergies between global and local needs are also discussed and used to identify priority needs that can be addressed by a landscape approach in the area. The analysis suggests that the TSEN Framework may be used by both scientists and practitioners to perform environmental assessments that are inclusive of social and ecological disciplines, of local and Western scientific knowledge, and of global and local needs in a landscape.

Identifying barriers and levers of biodiversity mainstreaming in four cases of transnational governance of land and water
Karlsson-Vinkhuyzen, S.I.S.E. ; Boelee, E. ; Cools, J. ; Hoof, L.J.W. van; Hospes, O. ; Kok, M. ; Peerlings, J.H.M. ; Tatenhove, J.P.M. van; Termeer, C.J.A.M. ; Visseren-Hamakers, I.J. - \ 2018
Environmental Science & Policy 85 (2018). - ISSN 1462-9011 - p. 132 - 140.
Biodiversity - Mainstreaming - Integration - Values-based leadership - Governance - Certification - Economic sectors - Fisheries - Palm Oil - FDI - Land - Mangroves
Mainstreaming biodiversity into the governance of economic sectors such as agriculture, forestry and fisheries is required to reverse biodiversity loss and achieve globally adopted conservation targets. Governments have recognized
this but little progress has been made. This paper addresses the following research question: What are the barriers and levers for mainstreaming biodiversity into economic sectors that exert high pressure on biodiversity?
This question is approached through applying an analytical framework developed from literature on mainstreaming and Environmental Policy Integration as well as governance theory and practice to four cases in
agriculture, agro-forestry and fisheries covering multi-level and transnational governance contexts. Decisionmaking and governance in these cases look quite different compared to the kind of public policy machinery of governmental bureaucracies that much EPI literature has focused on. Our analysis demonstrates mainstreaming efforts in some of our cases at the degree of harmonization and even coordination among key actors. It further identifies a number of ‘additional’ barriers and levers that from an Environmental Policy Integration perspective would be considered as external factors out of reach for mainstreaming efforts. The results are pertinent for the evaluation of EPI performance because the governance perspective expands the borders of who can initiate, enable and sustain mainstreaming, what scope of regulatory norms they can use and the potentially useful resources for the process.
Conceptual description of an integrated biomass logistics centre (IBLC)
Annevelink, Bert ; Gogh, Bart Van; Nogués, Fernando Sebastián ; Espatolero, Sergio ; La Cruz, Teresa De; Luzzini, Davide ; Karampinis, Manolis ; Kougioumtzis, Michalis ; Olsson, Johanna - \ 2017
European Biomass Conference and Exhibition Proceedings 2017 (2017)25thEUBCE. - ISSN 2282-5819 - p. 200 - 203.
Biobased economy - Integration - Logistics - Supply chain
The main goal of the AGROinLOG project is the demonstration of Integrated Biomass Logistic Centres (IBLCs) for food and non-food products, evaluating their technical, environmental and economic feasibility. Applying IBLCs in existing agro-industries can have a positive impact on the final product price, giving a clear competitive strength to these agro-industries in comparison with a new biomass supply business that is built from scratch. The main challenges are being able to integrate logistics, harvesting and equipment in food and non-food applications, and ensuring the marketability of the final bio-commodities. The first task of the AGROinLOG project was to provide a conceptual description of the features and characteristics of an IBLC. With this IBLC description the researchers intend to provide a theoretical framework that builds further on results from previous projects (such as SUCELLOGucellog), describing the current thoughts on Agro-Industry Logistics Centres (ALCs).
Crops in silico : Generating virtual crops using an integrative and multi-scale modeling platform
Marshall-Colon, Amy ; Long, Stephen P. ; Allen, Douglas K. ; Allen, Gabrielle ; Beard, Daniel A. ; Benes, Bedrich ; Caemmerer, Susanne Von; Christensen, A.J. ; Cox, Donna J. ; Yin, Xinyou - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Computational framework - Crop yield - Integration - Model - Multiscale

Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (, an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

Mainstreaming biodiversity in economic sectors : An analytical framework
Karlsson-Vinkhuyzen, Sylvia ; Kok, Marcel T.J. ; Visseren-Hamakers, Ingrid J. ; Termeer, Katrien - \ 2017
Biological Conservation 210 (2017). - ISSN 0006-3207 - p. 145 - 156.
Biodiversity - Certification - Forests - Governance - Integration - Mainstreaming

One of the major challenges in halting biodiversity loss is finding ways to address the issue in places where it would matter most; in the economic sectors of society that exert the strongest pressures on biodiversity such as agriculture, forestry and fisheries. Governments have acknowledged the need for this so termed mainstreaming under the Convention on Biological Diversity, but in practice have made little progress and struggle to find ways forward. In this paper we argue that the concept of mainstreaming was originally developed for situations where governments or intergovernmental organizations with explicit public mandates took the lead, but it is increasingly extended into various governance contexts where multiple types of actors at different levels (could) engage in conserving biodiversity. This paper aims to enable the identification of innovative repertoires of mainstreaming opportunities that optimally and realistically benefits from the broader governance context. Therefore it presents a framework, consisting of institutional, motivational and means dimensions for identifying key barriers and levers for mainstreaming biodiversity into economic sectors. By applying the framework on the forestry sector we show that it does not only help to identify new mainstreaming opportunities but it also shows directions for improving existing schemes as well.

The importance of endophenotypes to evaluate the relationship between genotype and external phenotype
Pas, Marinus F.W. te; Madsen, Ole ; Calus, Mario P.L. ; Smits, Mari A. - \ 2017
International Journal of Molecular Sciences 18 (2017)2. - ISSN 1661-6596
Bioinformatics - Genomic variation and environment - Integration - Livestock science - Metabolome - Methylome - Phenome - Proteome - Systems biology - Transcriptome

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal’s transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal’s genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals’ microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

Integrated assessment of emerging science and technologies as creating learning processes among assessment communities
Forsberg, Ellen Marie ; Ribeiro, Barbara ; Heyen, Nils B. ; Nielsen, Rasmus Øjvind ; Thorstensen, Erik ; Bakker, Erik de; Klüver, Lars ; Reiss, Thomas ; Beekman, Volkert ; Millar, Kate - \ 2016
Life Sciences, Society and Policy 12 (2016)1. - ISSN 2195-7819
Assessment - Dialogue - Emerging science and technologies - Integration - Transparency - TranSTEP

Emerging science and technologies are often characterised by complexity, uncertainty and controversy. Regulation and governance of such scientific and technological developments needs to build on knowledge and evidence that reflect this complicated situation. This insight is sometimes formulated as a call for integrated assessment of emerging science and technologies, and such a call is analysed in this article. The article addresses two overall questions. The first is: to what extent are emerging science and technologies currently assessed in an integrated way. The second is: if there appears to be a need for further integration, what should such integration consist in? In the article we briefly outline the pedigree of the term ‘integrated assessment’ and present a number of interpretations of the concept that are useful for informing current analyses and discussions of integration in assessment. Based on four case studies of assessment of emerging science and technologies, studies of assessment traditions, literature analysis and dialogues with assessment professionals, currently under-developed integration dimensions are identified. It is suggested how these dimensions can be addressed in a practical approach to assessment where representatives of different assessment communities and stakeholders are involved. We call this approach the Trans Domain Technology Evaluation Process (TranSTEP).

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