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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    Effects of climate and land-use changes on fish catches across lakes at a global scale
    Kao, Yu Chun ; Rogers, Mark W. ; Bunnell, David B. ; Cowx, Ian G. ; Qian, Song S. ; Anneville, Orlane ; Beard, T.D. ; Brinker, Alexander ; Britton, J.R. ; Chura-Cruz, René ; Gownaris, Natasha J. ; Jackson, James R. ; Kangur, Külli ; Kolding, Jeppe ; Lukin, Anatoly A. ; Lynch, Abigail J. ; Mercado-Silva, Norman ; Moncayo-Estrada, Rodrigo ; Njaya, Friday J. ; Ostrovsky, Ilia ; Rudstam, Lars G. ; Sandström, Alfred L.E. ; Sato, Yuichi ; Siguayro-Mamani, Humberto ; Thorpe, Andy ; Zwieten, Paul A.M. van; Volta, Pietro ; Wang, Yuyu ; Weiperth, András ; Weyl, Olaf L.F. ; Young, Joelle D. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Globally, our knowledge on lake fisheries is still limited despite their importance to food security and livelihoods. Here we show that fish catches can respond either positively or negatively to climate and land-use changes, by analyzing time-series data (1970–2014) for 31 lakes across five continents. We find that effects of a climate or land-use driver (e.g., air temperature) on lake environment could be relatively consistent in directions, but consequential changes in a lake-environmental factor (e.g., water temperature) could result in either increases or decreases in fish catch in a given lake. A subsequent correlation analysis indicates that reductions in fish catch was less likely to occur in response to potential climate and land-use changes if a lake is located in a region with greater access to clean water. This finding suggests that adequate investments for water-quality protection and water-use efficiency can provide additional benefits to lake fisheries and food security.

    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Following the water: Characterising de facto wastewater reuse in agriculture in the Netherlands
    Beard, Jack E. ; Bierkens, Marc F.P. ; Bartholomeus, Ruud P. - \ 2019
    Sustainability 11 (2019)21. - ISSN 2071-1050
    Circular economy - Drought - Irrigation - Wastewater reuse - Water quality

    De facto (or indirect) wastewater reuse is the practice of extracting from surface water bodies which are impacted by treated wastewater (TWW) for anthropogenic use. The extent to which surface water bodies in the Netherlands are impacted by TWW is poorly understood, and the distribution of de facto reuse even more so. This study addresses these knowledge gaps, with a focus on reuse for agricultural irrigation. This is achieved via a novel application of the Water Framework Directive (WFD) Explorer water quality model, allowing for the distribution of different flow components-namely TWW and flow from transboundary rivers-to be discerned for the national surface water network. When paired with data on surface water extractions for irrigation, this identifies notable areas of de facto reuse. Results show that during dry conditions, TWW is a significant flow component in many surface water bodies, particularly in smaller streams located close to WWTPs. De facto reuse is indicated as widespread, with several key areas identified in which extractions are from impacted surface water bodies. This study represents a first attempt to directly link TWW emissions to agricultural irrigation, highlighting a mechanism by which wastewater-associated contaminants can propagate through the hydrological system.

    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 (cropsinsilico.org), 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.

    A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens
    Guo, Ying ; Gu, Xiaorong ; Sheng, Zheya ; Wang, Yanqiang ; Luo, Chenglong ; Liu, Ranran ; Qu, Hao ; Shu, Dingming ; Wen, Jie ; Crooijmans, Richard P.M.A. ; Carlborg, Örjan ; Zhao, Yiqiang ; Hu, Xiaoxiang ; Li, Ning - \ 2016
    Plos Genetics 12 (2016)6. - ISSN 1553-7404

    Muffs and beard (Mb) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face (muffs) and below the beak (beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. Here we use genome-wide association (GWA) analysis, linkage analysis, Identity-by-Descent (IBD) mapping, array-CGH, genome re-sequencing and expression analysis to show that the Mb allele causing the Mb phenotype is a derived allele where a complex structural variation (SV) on GGA27 leads to an altered expression of the gene HOXB8. This Mb allele was shown to be completely associated with the Mb phenotype in nine other independent Mb chicken breeds. The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27. The duplications contain total seven annotated genes and their expression was tested during distinct stages of Mb morphogenesis. A continuous high ectopic expression of HOXB8 was found in the facial skin of Mb chickens, strongly suggesting that HOXB8 directs this regional feather-development. In conclusion, our results provide an interesting example of how genomic structural rearrangements alter the regulation of genes leading to novel phenotypes. Further, it again illustrates the value of utilizing derived phenotypes in domestic animals to dissect the genetic basis of developmental traits, herein providing novel insights into the likely role of HOXB8 in feather development and differentiation.

    Data mining methods for quality assurance in an environmental monitoring network
    Athanasiadis, Ioannis N. ; Rizzoli, Andrea Emilio ; Beard, Daniel W. - \ 2010
    In: Artificial Neural Networks – ICANN 2010. - Springer (Lecture Notes in Computer Science ) - ISBN 9783642158247 - p. 451 - 456.

    The paper presents a system architecture that employs data mining techniques for ensuring quality assurance in an environmental monitoring network. We investigate how data mining techniques can be incorporated in the quality assurance decision making process. As prior expert decisions are available, we demonstrate that expert knowledge can be effectively extracted and reused for reproducing human experts decisions on new data. The framework is demonstrated for the Saudi Aramco air quality monitoring network and yields trustworthy behavior on historical data. A variety of data-mining algorithms was evaluated, resulting to an average predictive accuracy of over 80%, while best models reached 90% of correct decisions.

    Case study on iron in mental development - in memory of John Beard (1947-2009)
    Osendarp, S.J.M. ; Murray-Kolb, L.E. ; Black, M.M. - \ 2010
    Nutrition Reviews 68 (2010)11. - ISSN 0029-6643 - p. S48 - S52.
    randomized controlled-trials - sprague-dawley rats - deficiency anemia - infant development - brain iron - child-development - supplementation - alters - transferrin - preschool
    Iron deficiency (ID) anemia is associated with poor neurocognitive development in infants and children. Depending on the stage of development at the time of deficiency, these adverse effects may be reversible. Recent investigations using sensitive measurements have confirmed that the deposition of iron in the brain varies according to brain region and age, and that dopamine-dependent behaviors are among the core deficits in ID. Dr John Beard (1947-2009) has been one of the leading scientists and pioneers in the area of iron and child development. His legacy to this area of science will grow through the continuation of his work by his co-workers and colleagues.
    Estimating static and dynamic perceived landscape openness with visibility measurements
    Weitkamp, S.G. - \ 2008
    In: Proceedings of the ifth International Conference on Geographic Information Science, GIScience 2008, Utah, USA, 23 - 26 September, 2008. - Park City, Utah : - p. 188 - 192.
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