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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The antiSMASH database version 2 : a comprehensive resource on secondary metabolite biosynthetic gene clusters
Blin, Kai ; Pascal Andreu, Victòria ; Los Santos, Emmanuel L.C. de; Carratore, Francesco Del; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann - \ 2019
Nucleic Acids Research 47 (2019)D1. - ISSN 0305-1048 - p. D625 - D630.

Natural products originating from microorganisms are frequently used in antimicrobial and anticancer drugs, pesticides, herbicides or fungicides. In the last years, the increasing availability of microbial genome data has made it possible to access the wealth of biosynthetic clusters responsible for the production of these compounds by genome mining. antiSMASH is one of the most popular tools in this field. The antiSMASH database provides pre-computed antiSMASH results for many publicly available microbial genomes and allows for advanced cross-genome searches. The current version 2 of the antiSMASH database contains annotations for 6200 full bacterial genomes and 18,576 bacterial draft genomes and is available at

Unexpected role of canonical aerobic methanotrophs in upland agricultural soils
Ho, Adrian ; Lee, Hyo Jung ; Reumer, Max ; Meima-Franke, Marion ; Raaijmakers, Ciska ; Zweers, Hans ; Boer, Wietse de; Putten, Wim H. Van der; Bodelier, Paul L.E. - \ 2019
Soil Biology and Biochemistry 131 (2019). - ISSN 0038-0717 - p. 1 - 8.
C labelling - High-affinity methane oxidation - Methylocystaceae - PLFA analysis/ land-use change - pmoA

Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13C–CH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13C–CO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.

The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen.
Vossenberg, Bart T.L.H. van de; Brankovics, Balázs ; Nguyen, H.D.T. ; Gent-Pelzer, M.P.E. van; Smith, D. ; Dadej, K. ; Przetakiewicz, J. ; Kreuze, J.F. ; Boerma, M. ; Leeuwen, G.C.M. van; André Lévesque, C. ; Lee, T.A.J. van der - \ 2018
BMC Evolutionary Biology 18 (2018). - ISSN 1471-2148
Background: Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen. Results: We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence. Conclusions: Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.
Professional, easy to use and robust bioinformatic tools
Warris, S. ; Lee, T.A.J. van der - \ 2018
- 1 p.
Mitochondrial genomes and species boundaries in the genus Fusarium
Brankovics, Balázs ; Waalwijk, C. ; Lee, T.A.J. van der; Hoog, G.S. de; Diepeningen, A.D. van - \ 2018
Towards improved methods for detection of Xylella fastidiosa in plant material using triplex TaqMan PCR and NGS analysis
Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2018
Innovative detection methods to support plant health diagnostics
Bonants, P.J.M. ; Houwers, I.M. ; Dullemans, A.M. ; Griekspoor, Y. ; Mendes, O. ; Gent-Pelzer, M.P.E. van; Vlugt, R.A.A. van der; Bergervoet, J.H.W. ; Schoen, C.D. ; Wolf, J.M. van der; Lee, T.A.J. van der - \ 2018
Conjectural ‘Landscape Cities’ and the Gap of Imagination
Abbott, Mick ; Roncken, P.A. ; Lee, Woody ; Pickett, Tenille - \ 2018
Landscape Review 18 (2018)1. - ISSN 1173-3853 - 11 p.
This report discusses the results and layout of a design research studio focused on applying methods related to speculation and imagination. Three main findings are presented: a review of six methods that can direct designerly speculations; development of 11 'landscape city' scenarios; and a discussion of the role design 'challenges' can play in studio research settings. These outcomes reveal that creative discoveries are not bound to elaborative final outcomes only. Some of the intermediate results, particularly those with explicit habit-breaking effects on the imagination of the designers involved, and the process-driven materials produced, are equally valuable. This report seeks a reconsideration of the presentation and sharing of research results through designing, moving from the familiar focus on high-end, 'glossy' finalisations towards those more revealing of intermediate and abstract products of inquiry. In conclusion, an argument is made as to what can be framed as an 'imagination gap' that suggests possibility operates as a counterpoint to empiricism. L andscape architecture has a speculative role in imagining diverse, innovative and environmentally responsive futures (Waldheim, 2012; Weller, 2009). In its research, the discipline is prone to critique by a scientific community that either disqualifies speculative approaches or does not know how to assess the associative imaginations on which most design processes depend. Such critique is constructive as it urges clarification of what is both unique and systematic about design-directed research.
Comparative transcriptome analysis of Ethiopian indigenous chickens from low and high altitudes under heat stress condition reveals differential immune response
Park, W. ; Srikanth, K. ; Lim, D. ; Park, M. ; Hur, T. ; Kemp, S. ; Dessie, T. ; Kim, M.S. ; Lee, S.R. ; Pas, M.F.W. te; Kim, J.M. ; Park, J.E. - \ 2018
Animal Genetics (2018). - ISSN 0268-9146
highlands - lowlands - RNA-seq - thermal tolerance

Ethiopia is an ecologically diverse country; the low altitude regions are hot and humid whereas the high altitude regions are cooler. In this study we analyzed the transcriptome response of high altitude (Addis Ababa) and low altitude (Awash) chickens to heat stress conditions that are prevalent in the low altitude regions. The chickens were free ranged for 20 h in an enclosure in Awash, and then the heart, breast muscle and spleen tissues were collected at 6:00 am, 12:00 noon and 6:00 pm to follow a daily circadian cycle. Through RNA-sequencing analysis, we identified differentially expressed genes (DEGs) that were significant (q < 0.05). These DEGs were subjected to protein–protein interaction (PPI) network and gene co-expression network (GCN) analyses to understand their role. KEGG pathway analysis and Gene Ontology analysis of all the identified DEGs and the genes identified from the PPI network and GCN analyses revealed that several immune-related pathways, such as proteasome, focal adhesion, influenza A, the ErbB signaling pathway and glycerophospholipid metabolism, were enriched in response to heat stress. These results suggest that the high altitude chickens were under heat stress and might be immunologically susceptible. Our findings will help in developing a genetic approach to mitigate production loss due to heat stress.

Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.

This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

Targeting medium size commercial family farms : A pathway for development
Koomen, I. ; Lee, J. van der; Obwanga, B. ; Coninx, I. - \ 2018
Intensification and upgrading dynamics in emerging dairy clusters in the East African highlands
Lee, Jan van der; Klerkx, Laurens ; Bebe, Bockline Omedo ; Mengistu, Ashenafi ; Oosting, Simon - \ 2018
Sustainability 10 (2018)11. - ISSN 2071-1050
Agribusiness cluster - Commercialization - Dairy value chain - Ethiopia - Farming system - Kenya - Service arrangements - Sustainable intensification

Based on farmer and value chain actor interviews, this comparative study of five emerging dairy clusters elaborates on the upgrading of farming systems, value chains, and context shapes transformations from semi-subsistent to market-oriented dairy farming. The main results show unequal cluster upgrading along two intensification dimensions: dairy feeding system and cash cropping. Intensive dairy is competing with other high-value cash crop options that resource-endowed farmers specialize in, given conducive support service arrangements and context conditions. A large number of drivers and co-dependencies between technical, value chain, and institutional upgrading build up to system jumps. Transformation may take decades when market and context conditions remain sub-optimal. Clusters can be expected to move further along initial intensification pathways, unless actors consciously redirect course. The main theoretical implications for debate about cluster upgrading are that co-dependencies between farming system, market, and context factors determine upgrading outcomes; the implications for the debate about intensification pathways are that they need to consider differences in farmer resource endowments, path dependency, concurrency, and upgrading investments. Sustainability issues for consideration include enabling a larger proportion of resource-poor farmers to participate in markets; enabling private input and service provision models; attention for food safety; and climate smartness.

Higher Mediterranean Diet scores are not cross-sectionally associated with better cognitive scores in 20- to 70-year-old Dutch adults: The NQplus study
Brouwer, E.M. ; Benati, Anita ; Wiel, A.M. van de; Lee, L. van; Vries, J.H.M. de; Feskens, E.J.M. ; Rest, O. van de - \ 2018
Nutrition Research 59 (2018). - ISSN 0271-5317 - p. 80 - 89.
Adherence to the Mediterranean Diet (MedDiet) has been suggested to reduce
the risk of age-related cognitive decline. Therefore, we hypothesized that
adults consuming a more Mediterranean-like diet were more likely to have
better cognitive scores. We investigated cross-sectional associations between
MedDiet adherence and cognitive performance using data of 1607 Dutch men
and women aged 20–70 years. Dietary intake was assessed using a 183-item
Food Frequency Questionnaire. MedDiet adherence was defined by a 0–9 point
scale; which was based on intakes of vegetables, legumes, fruits/nuts, cereals,
fish/seafood, meat/poultry, dairy, ethanol and the MUFA:SFA ratio. Cognitive
function was assessed with a neuropsychological test battery. Linear regression
analyses adjusted for relevant covariates showed a significant inverse association
between MedDiet adherence and everyday memory: specifically β = −0.107
± 0.046 points (P = .02) for the total population and β = −0.139 ± 0.055 points
(P = .01) for those aged ≥50 years. Further exploration of the individual MedDiet
food groups suggested that the association between MedDiet and everyday
memory was predominantly driven by the MUFA:SFA ratio. Moreover, associations were observed between higher ethanol intake better semantic memory and language production (β = 0.016 ± 0.008 P = .05), higher
vegetable intake with better processing speed (β = 0.005 ± 0.002, P = .02), and
higher legumes intake with poorer processing speed (β = −0.014 ±0.006, P = 03). Thus, in this Dutch cohort, higher MedDiet adherence was associated with poorer everyday memory.
The role of pasture in the diet of ruminant livestock
Lee, Michael R.F. ; Jordana Rivero, M. ; Cone, J.W. - \ 2018
In: Improving grassland and pasture management in temperature agriculture / Marshall, Athole, Collins, Rosemary, Burleigh Dodds Science Publishing Limited - ISBN 9781786762009
Grazed pasture is the single most important forage feed for ruminants due to its low unit cost and widespread global availability. However, there is a growing use of arable crops in ruminant rations, which may exceed that used by humans by 2050. This chapter describes the ways in which grazed pasture provides the energy, proteins, minerals and vitamins and other nutritional factors required by ruminants. The chapter shows that the use of pasture and its by-products underpins the possibility of sustainably delivering future ruminant livestock production systems and ensuring their future role in food security.
The Bruce Lee statue in Mostar : 'Heritage from below' experiments in a divided city
Aceska, Ana ; Minca, C. - \ 2018
In: After Heritage / Muzaini, Hamzah, Minca, Claudio, London : Edward Elgar - ISBN 9781788110730 - p. 64 - 85.
Focusing on the practices and politics of heritage-making at the individual and the local level, this book uses a wide array of international case studies to argue for their potential not only to disrupt but also to complement formal heritage-making in public spaces. Providing a much-needed clarion call to reinsert the individual as well as the transient into more collective heritage processes and practices, this strong contribution to the field of Critical Heritage Studies offers insight into benefits of the ‘heritage from below approach’ for researchers, policy makers and practitioners.
The SPLENDID eating detection sensor : Development and feasibility study
Boer, Janet van den; Lee, Annemiek van der; Zhou, Lingchuan ; Papapanagiotou, Vasileios ; Diou, Christos ; Delopoulos, Anastasios ; Mars, Monica - \ 2018
Journal of Medical Internet Research 6 (2018)9. - ISSN 1438-8871
Chewing sensor - In-ear microphone - Mobile phone - Obesity prevention - Overweight - PPG sensor - Weight management

Background: The available methods for monitoring food intake-which for a great part rely on self-report-often provide biased and incomplete data. Currently, no good technological solutions are available. Hence, the SPLENDID eating detection sensor (an ear-worn device with an air microphone and a photoplethysmogram [PPG] sensor) was developed to enable complete and objective measurements of eating events. The technical performance of this device has been described before. To date, literature is lacking a description of how such a device is perceived and experienced by potential users. Objective: The objective of our study was to explore how potential users perceive and experience the SPLENDID eating detection sensor. Methods: Potential users evaluated the eating detection sensor at different stages of its development: (1) At the start, 12 health professionals (eg, dieticians, personal trainers) were interviewed and a focus group was held with 5 potential end users to find out their thoughts on the concept of the eating detection sensor. (2) Then, preliminary prototypes of the eating detection sensor were tested in a laboratory setting where 23 young adults reported their experiences. (3) Next, the first wearable version of the eating detection sensor was tested in a semicontrolled study where 22 young, overweight adults used the sensor on 2 separate days (from lunch till dinner) and reported their experiences. (4) The final version of the sensor was tested in a 4-week feasibility study by 20 young, overweight adults who reported their experiences. Results: Throughout all the development stages, most individuals were enthusiastic about the eating detection sensor. However, it was stressed multiple times that it was critical that the device be discreet and comfortable to wear for a longer period. In the final study, the eating detection sensor received an average grade of 3.7 for wearer comfort on a scale of 1 to 10. Moreover, experienced discomfort was the main reason for wearing the eating detection sensor <2 hours a day. The participants reported having used the eating detection sensor on 19/28 instructed days on average. Conclusions: The SPLENDID eating detection sensor, which uses an air microphone and a PPG sensor, is a promising new device that can facilitate the collection of reliable food intake data, as shown by its technical potential. Potential users are enthusiastic, but to be successful wearer comfort and discreetness of the device need to be improved.

Dissolved oxygen dynamics in drainage ditches along a eutrophication gradient
Lee, Gea H. van der; Verdonschot, Ralf C.M. ; Kraak, Michiel H.S. ; Verdonschot, Piet F.M. - \ 2018
Limnologica 72 (2018). - ISSN 0075-9511 - p. 28 - 31.
Dissolved oxygen saturation - Ecosystem functioning - Monitoring - Primary production - Respiration - Water quality

The impact of eutrophication on the functioning of drainage ditch ecosystems is understudied. Therefore, we performed a field study to quantify the dissolved oxygen dynamics of ditches at different depths and seasons along a eutrophication gradient. During summer, a clear distinction in daily variation in dissolved oxygen saturation of the top water layer was observed between the trophic states. We recommend including dissolved oxygen dynamics as a functional parameter in drainage ditch monitoring programmes.

Experimental investigation of low-angle dune morphodynamics
Naqshband, Suleyman ; Wullems, Bas ; Ruijsscher, Timo de; Hoitink, Ton - \ 2018
In: River Flow 2018 - Ninth International Conference on Fluvial Hydraulics. - EDP Sciences (E3S Web of Conferences ) - 5 p.

Dunes commonly dominate the bed of sandy rivers and they are of central importance in predicting flow resistance and water levels. In the present study, we show that by using light-weight polystyrene particles as substrate in a laboratory setting, promising morphodynamic similarity is obtained between dunes in shallow flow (flume) and deep flow (field) conditions. In particular, results from our flume experiments show that dune lee-side angles, which are crucial in turbulence production and energy dissipation, better approximate dune lee-side angles observed in natural channels. Furthermore, dune height evolution towards upper stage plane bed observed in the present experimental study, closely follows dune height evolution as observed in world's large rivers.

Biocatalytic C=C Bond Reduction through Carbon Nanodot-Sensitized Regeneration of NADH Analogues
Kim, Jinhyun ; Lee, Sahng Ha ; Tieves, Florian ; Choi, Da Som ; Hollmann, Frank ; Paul, Caroline E. ; Park, Chan Beum - \ 2018
Angewandte Chemie-International Edition 57 (2018)42. - ISSN 1433-7851 - p. 13825 - 13828.
alkene hydrogenation - asymmetric catalysis - carbon nanodot - NADH analogues - photobiocatalysis

Light-driven activation of redox enzymes is an emerging route for sustainable chemical synthesis. Among redox enzymes, the family of Old Yellow Enzyme (OYE) dependent on the nicotinamide adenine dinucleotide cofactor (NADH) catalyzes the stereoselective reduction of α,β-unsaturated hydrocarbons. Here, we report OYE-catalyzed asymmetric hydrogenation through light-driven regeneration of NADH and its analogues (mNADHs) by N-doped carbon nanodots (N-CDs), a zero-dimensional photocatalyst. Our spectroscopic and photoelectrochemical analyses verified the transfer of photo-induced electrons from N-CDs to an organometallic electron mediator (M) for highly regioselective regeneration of cofactors. Light triggered the reduction of NAD+ and mNAD+s with the cooperation of N-CDs and M, and the reduction behaviors of cofactors were dependent on their own reduction peak potentials. The regenerated cofactors subsequently delivered hydrides to OYE for stereoselective conversions of a broad range of substrates with excellent biocatalytic efficiencies.

Does the knowledge economy advance the green economy? An evaluation of green jobs in the 100 largest metropolitan regions in the United States
Lee, Taedong ; Heijden, Jeroen van der - \ 2018
Energy & Environment (2018). - ISSN 0958-305X
climate action - green economy - Green jobs - institutions of higher education - knowledge economy

Institutions of higher education are significant economic engines and innovative places in local economies: they directly employ large numbers of people, often with well-paying jobs; they are magnets for businesses that service the student population; they educate and often assist students in securing first jobs; and they partner with local organizations and businesses to provide students with hands-on experiences while “giving-back” to the community. In this article, we examine the impact that institutions of higher education have as an engine of growth for the green economy and, specifically, assess their impact on the development of green jobs. Green jobs have been touted as an important strategy to simultaneously address both the economic downturn and environmental degradation. This article empirically assesses the impact that the knowledge economy has on the presence of green jobs in the 100 largest metropolitan regions in the United States. Our findings suggest that enhanced higher education and sustainability-oriented departments and centers have a positive impact on green job development in urban regions.

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