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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    Digestible energy versus net energy approaches in feed evaluation for rainbow trout
    Groot, R. ; Lyons, Philip ; Schrama, J.W. - \ 2020
    In: Wias Annual Conference 2020. - WIAS - p. 40 - 40.
    Currently, a digestible energy (DE) approach is used in fish feed evaluation which assumes a constant utilisation of digestible energy for growth (kgDE). However, carbohydrates in rainbow trout (Oncorhynchus mykiss) feeds are, compared to protein and fat, not only considered to be lower in digestibility, but also to be utilised to a lesser extent for retained energy and thus growth. A lower utilisation of carbohydrates would thus suggest an over prediction of kgDE at higher dietary carbohydrate levels and an inaccuracy in the DE approach.Recently it has been proposed to use a net energy (NE) approach in feed evaluation for fish, which considers differences in the utilisation of the different digestible macronutrients (digestible protein, fat, carbohydrates). This study aimed to examine if a NE approach can increase the prediction precision of growth performance compared to a DE approach in feed evaluation for rainbow trout. Therefore, a feeding trial with feeds having different DElevels and with a wide contrast in macronutrient composition which reflect those found in practical rainbow trout diets was done. Eight different diets were formulated to include two protein levels (40 and 50%) and four different fat levels (14, 19, 25, 30%) coinciding in a wide range in carbohydrate levels (8-35%). NE was calculated both using linear efficiencies of digestible macronutrients (NElin=15.1×dCP+35.0×dFat+12.1×dCarb) and with a curvilinear effect of carbohydrates included (NEcurv=13.5×dCP+33.0×dFat+34.0×dCarb–3.64×(d-Carb)2) (NE as kJ/kg0.8 BW per d and dCP, dFat and dCarb as g/kg0.8 BW per d) (Schramaet al 2018). The results of the current study showed that growth was significantly (P < 0.5) linearly related to DE and NElin intake within each protein level, which suggested a constant efficiency of digestible carbohydrates even at the relatively high dietary carbohydrate levels used in this study. NElin showed the best prediction of growth (R2=0.94 compared toR2=0.93 for DE intake and R2=0.91 for NEcurv intake), which also showed that a NE approach with linear efficiencies of digestible macro nutrients can increase the prediction of growth performance in feed evaluation for rainbow trout. A NE approach, which assumed the utilisation of carbohydrates to be curvilinearly related to carbohydrate intake did not lead to an increased prediction of growth performance as compared to DE in the current study.
    Mycotoxins in Aquafeeds: Post-harvest measures for aquafeed producers to prevent contamination in the finished diets
    Koletsi, P. ; Lamberigts, Ben ; Lyons, Philip - \ 2018
    - 2 p.
    Mycotoxins in Aquafeeds: Post-harvest measures for aquafeed producers to prevent contamination in the finished diets
    Koletsi, P. ; Lamberigts, Ben ; Lyons, Philip - \ 2018
    Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
    O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
    Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
    Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
    Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
    Exploring urban metabolism—Towards an interdisciplinary perspective
    Dijst, M. ; Worrell, E. ; L., Böcker ; P., Brunner ; Davoudi, S. ; Geertman, S. ; Harmsen, R. ; Helbich, M. ; Holtslag, A.A.M. ; Kwan, Mei-Po ; Lenz, B. ; Lyons, G. ; Mokhtarian, P.L. ; Newman, P. ; Perrels, A. ; Ribeiro, A.P. ; Rosales Carreón, J. ; Thomson, G. ; Urge-Vorsatz, D. ; Zeyringer, M. - \ 2018
    Resources, Conservation and Recycling 132 (2018). - ISSN 0921-3449 - p. 190 - 203.
    The discussion on urban metabolism has been long dominated by natural scientists focussing on natural forces shaping the energy and material flows in urban systems. However, in the anthropocene human forces such as industrialization and urbanization are mobilizing people, goods and information at an increasing pace and as such have a large impact on urban energy and material flows. In this white paper, we develop a combined natural and social science perspective on urban metabolism. More specifically, innovative conceptual and methodological interdisciplinary approaches are identified and discussed to enhance the understanding of the forces that shape urban metabolism, and how these forces affect urban living and the environment. A challenging research agenda on urban metabolism is also presented.
    Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
    Bombarely, Aureliano ; Moser, Michel ; Amrad, Avichai ; Bao, Manzhu ; Bapaume, Laure ; Barry, Cornelius S. ; Bliek, Mattijs ; Boersma, Maaike R. ; Borghi, Lorenzo ; Bruggmann, Rémy ; Bucher, Marcel ; Agostino, Nunzio D'; Davies, Kevin ; Druege, Uwe ; Dudareva, Natalia ; Egea-Cortines, Marcos ; Delledonne, Massimo ; Fernandez-Pozo, Noe ; Franken, Philipp ; Grandont, Laurie ; Heslop-Harrison, J.S. ; Hintzsche, Jennifer ; Johns, Mitrick ; Koes, Ronald ; Lv, Xiaodan ; Lyons, Eric ; Malla, Diwa ; Martinoia, Enrico ; Mattson, Neil S. ; Morel, Patrice ; Mueller, Lukas A. ; Muhlemann, Joëlle ; Nouri, Eva ; Passeri, Valentina ; Pezzotti, Mario ; Qi, Qinzhou ; Reinhardt, Didier ; Rich, Melanie ; Richert-Pöggeler, Katja R. ; Robbins, Tim P. ; Schatz, Michael C. ; Schranz, Eric ; Schuurink, Robert C. ; Schwarzacher, Trude ; Spelt, Kees ; Tang, Haibao ; Urbanus, Susan L. ; Vandenbussche, Michiel ; Vijverberg, Kitty ; Villarino, Gonzalo H. ; Warner, Ryan M. ; Weiss, Julia ; Yue, Zhen ; Zethof, Jan ; Quattrocchio, Francesca ; Sims, Thomas L. ; Kuhlemeier, Cris - \ 2016
    Nature Plants 2 (2016). - ISSN 2055-026X

    Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

    Assessing silver nanoparticles behaviour in artificial seawater by mean of AF4 and spICP-MS
    António, D.C. ; Cascio, C. ; Jakšić, Z. ; Jurašin, D. ; Lyons, D.M. ; Nogueira, A.J.A. ; Rossi, F. ; Calzolai, L. - \ 2015
    Marine Environmental Research 111 (2015). - ISSN 0141-1136 - p. 162 - 169.
    Alginate - Asymmetric flow field-flow fractionation - Humic acid - Metal-organic interactions - Salinity - Silver nanoparticles - Single particle ICP-MS

    The use of nanotechnology-based products is constantly increasing and there are concerns about the fate and effect on the aquatic environment of antimicrobial products such as silver nanoparticles. By combining different characterization techniques (asymmetric flow field-flow fractionation, single particle ICP-MS, UV-Vis) we show that it is possible to assess in detail the agglomeration process of silver nanoparticles in artificial seawater. In particular we show that the presence of alginate or humic acid differentially affects the kinetic of the agglomeration process. This study provides an experimental methodology for the in-depth analysis of the fate and behaviour of silver nanoparticles in the aquatic environment.

    The COST model for calculation of forest operations costs
    Ackerman, P. ; Belbo, H. ; Eliasson, L. ; Jong, J.J. de; Lazdins, A. ; Lyons, J. - \ 2014
    International Journal of Forest Engineering 25 (2014)1. - ISSN 1494-2119 - p. 75 - 81.
    Since the late nineteenth century when high-cost equipment was introduced into forestry there has been a need to calculate the cost of this equipment in more detail with respect to, for example, cost of ownership, cost per hour of production, and cost per production unit. Machine cost calculations have been made using various standard economic methods, where costs have been subdivided into capital costs and operational costs. Because of differences between methods and between national regulations, mainly regarding tax rules and subsidies, international comparisons of machine costs are difficult. To address this, one of the goals of the European Cooperation in Science and Technology (COST) Action FP0902 was to establish a simple format for transparent cost calculations for machines in the forest biomass procurement chain. A working group constructed a Microsoft Excel–based spreadsheet model which is easy to understand and use. Input parameters are easy to obtain or possible to estimate by provided rules of thumb. The model gives users a simultaneous view of the input parameters and the resulting cost outputs. This technical note presents the model, explains how the calculations are made, and provides future users with a guide on how to use the model. Prospective users can view the model in the Supplementary Material linked to this article online.
    Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family.
    Hofberger, J.A. ; Lyons, E. ; Edger, P.P. ; Pires, J.C. ; Schranz, M.E. - \ 2013
    Genome Biology and Evolution 5 (2013). - ISSN 1759-6653 - p. 2155 - 2173.
    quantitative trait locus - arabidopsis-thaliana - gene duplication - secondary metabolism - insect resistance - natural variation - provides insight - biosynthesis - evolution - plants
    Plants share a common history of successive whole genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and Tandem Duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the Mustard Family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all Mustard Family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95 and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared to the 22% average for all protein-coding genes in Arabidopsis, 52 and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. While 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of tandem- and whole genome duplication events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.
    Composition of Human Skin Microbiota Affects Attractiveness to Malaria Mosquitoes
    Verhulst, N.O. ; Qiu, Y.T. ; Beijleveld, H. ; Maliepaard, C.A. ; Knights, D. ; Schulz, S. ; Berg-Lyons, D. ; Lauber, C.L. ; Verduijn, W. ; Haasnoot, G.W. ; Mumm, R. ; Bouwmeester, H.J. ; Claas, F.H.J. ; Dicke, M. ; Loon, J.J.A. van; Takken, W. ; Knight, R. ; Smallegange, R.C. - \ 2011
    PLoS ONE 6 (2011)12. - ISSN 1932-6203 - 7 p.
    major histocompatibility complex - human axillary odor - anopheles-gambiae - mating preferences - aedes-aegypti - microflora - spectrometry - diversity - responses - selection
    The African malaria mosquito Anopheles gambiae sensu stricto continues to play an important role in malaria transmission, which is aggravated by its high degree of anthropophily, making it among the foremost vectors of this disease. In the current study we set out to unravel the strong association between this mosquito species and human beings, as it is determined by odorant cues derived from the human skin. Microbial communities on the skin play key roles in the production of human body odour. We demonstrate that the composition of the skin microbiota affects the degree of attractiveness of human beings to this mosquito species. Bacterial plate counts and 16S rRNA sequencing revealed that individuals that are highly attractive to An. gambiae s.s. have a significantly higher abundance, but lower diversity of bacteria on their skin than individuals that are poorly attractive. Bacterial genera that are correlated with the relative degree of attractiveness to mosquitoes were identified. The discovery of the connection between skin microbial populations and attractiveness to mosquitoes may lead to the development of new mosquito attractants and personalized methods for protection against vectors of malaria and other infectious diseases
    Quality evaluation of gamma irradiated cereal grains for spawn production
    Sharma, H.S.S. ; Cunha, B. ; Kilpatrick, M. ; Lyons, G. ; Wichers, H.J. ; Hoozee, J. - \ 2008
    Properties of food that may modulate canine and feline behaviour
    Bosch, G. ; Beerda, B. ; Poel, A.F.B. van der; Hendriks, W.H. - \ 2007
    In: Nutritional Biotechnology in the Feed and Food Industries / Lyons, T.P., Jacques, K.A., Hower, J.M., Bath, England : Nottingham University Press - ISBN 9781897676400 - p. 395 - 406.
    Sil-All® 4x4: improving fermentation in the silo and in the rumen
    Vuuren, A.M. van - \ 2006
    In: Nutritional Biotechnology in the Feed and Food Industries: Proceedings of Alltech's 22nd Annual Symposium, Lexington, Kentucky, USA, 23-26 April 2006 / Lyons, T.P., Jacques, K.A., Hower, J.M., Stamford, UK : Alltech UK - ISBN 9781904761372 - p. 381 - 386.
    The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.) : polymorphism, linkage analysis and protein modelling
    Grimholt, U. ; Drablos, F. ; Jorgensen, S.M. ; Hoyheim, B. ; Stet, R.J.M. - \ 2002
    Immunogenetics 54 (2002). - ISSN 0093-7711 - p. 570 - 581.
    Abstract We show that a.s. all of the connected components of the Wired Spanning Forest are recurrent, proving a conjecture of Benjamini, Lyons, Peres and Schramm. Our analysis relies on a simple martingale involving the effective conductance between the endpoints of an edge in a uniform spanning tree. We believe that this martingale is of independent interest and will find further applications in the study of uniform spanning trees and forests.
    Effects of herd density on the course and control of FMD epidemics
    Mourits, M.C.M. ; Nielen, M. ; Tomassen, F.H.M. - \ 2002
    In: Foot and mouth disease. Control Strategies, Lyons, France, 2-5 June 2002 France : Thera McCann Healthcare/RCS Lyon - ISBN 9782840390909 - p. 145 - 145.
    A decision tree to optimise control measures during the early stage of a foot and mouth disease epidemic
    Tomassen, F.H.M. ; Koeijer, A. de; Mourits, M.C.M. ; Dekker, A. ; Bouma, A. ; Huirne, R.B.M. - \ 2002
    In: Foot and mouth disease. Control strategies., Lyons, France, 2-5 June 2002. - France : Thera McCann Healthcare/RCS Lyon B 398 160 242, 2002. - ISBN 2-84039-090-5 - p. 149 - 149.
    Microbial reference materials in seed health test standardization
    Bulk, R.W. van den; Langerak, C.J. ; Roberts, S.J. ; Lyons, N.F. - \ 1999
    In: Proceedings 3rd ISTA-PDC Seed Health Symposium, International Seed Testing Association, Zurich, Switzerland - p. 133 - 135.
    Dietary factors affecting ammonia and odour release from pig manure
    Aarnink, A.J.A. ; Sutton, A.L. ; Canh, T.T. ; Verstegen, M.W.A. ; Langhout, D.J. - \ 1999
    In: Biotechnology in the Feed Industry. Proceedings of Alltech's 14th Annual Symposium, Kentucky (USA), Nottingham Univ. Press (UK) / Lyons, T.P., Jacques, K.A., - p. 45 - 59.
    Modelling dynamic aspects of nitrogen in soils and plants
    Keulen, H. van - \ 1981
    In: Genetic engineering of symbiotic nitrogen fixation and conservation of fixed nitrogen / Lyons, J.M., New York : Plenum - p. 605 - 622.
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