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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A research roadmap for quantifying non-state and subnational climate mitigation action
Hsu, Angel ; Höhne, Niklas ; Kuramochi, Takeshi ; Roelfsema, Mark ; Weinfurter, Amy ; Xie, Yihao ; Lütkehermöller, Katharina ; Chan, Sander ; Corfee-Morlot, Jan ; Drost, Philip ; Faria, Pedro ; Gardiner, Ann ; Gordon, David J. ; Hale, Thomas ; Hultman, Nathan E. ; Moorhead, John ; Reuvers, Shirin ; Setzer, Joana ; Singh, Neelam ; Weber, Christopher ; Widerberg, Oscar - \ 2019
Nature Climate Change 9 (2019)1. - ISSN 1758-678X - p. 11 - 17.

Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.

Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants
Cho, Jungnam ; Benoit, Matthias ; Catoni, Marco ; Drost, Hajk Georg ; Brestovitsky, Anna ; Oosterbeek, Matthijs ; Paszkowski, Jerzy - \ 2019
Nature Plants 5 (2019). - ISSN 2055-026X - p. 26 - 33.

Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. Such studies provide important ‘snapshots’ reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5′ LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.

Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development
Drost, Hajk Georg ; Bellstädt, Julia ; Ó'Maoiléidigh, Diarmuid S. ; Silva, Anderson T. ; Gabel, Alexander ; Weinholdt, Claus ; Ryan, Patrick T. ; Dekkers, Bas J.W. ; Bentsink, Leónie ; Hilhorst, Henk W.M. ; Ligterink, Wilco ; Wellmer, Frank ; Grosse, Ivo ; Quint, Marcel - \ 2016
Molecular Biology and Evolution 33 (2016)5. - ISSN 0737-4038 - p. 1158 - 1163.
developmental hourglass - floral transition - germination - plant development - transcriptomics

The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found postembryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.

Monitoring soil bacteria with community-level physiological profiles using Biolog™ ECO-plates in the Netherlands and Europe
Rutgers, Michiel ; Wouterse, Marja ; Drost, Sytske M. ; Breure, Anton M. ; Mulder, Christian ; Stone, Dorothy ; Creamer, Rachel E. ; Winding, Anne ; Bloem, Jaap - \ 2016
Applied Soil Ecology 97 (2016). - ISSN 0929-1393 - p. 23 - 35.
Biolog - Indicator - Method - Microbial community - MicroResp - Soil

Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ ECO-plates in the Netherlands Soil Monitoring Network (NSMN; 704 samples) and in a European-wide transect (73 samples). The selection of sites was based on a representative sample of major soil texture types, land uses and climate zones. This method for determination of CLPP was specifically designed to be applied in large and long-term monitoring activities. It encompassed a solution for the inoculum-density dependence of colour formation patterns in ECO-plates, through stepwise dilution to extinction of the bacterial inoculum. The CLPP in Dutch and European soil samples appeared to be reproducible and sensitive to land use and/or soil texture. Although the method is selective, CLPP based parameters correlated well with other microbial parameters and soil characteristics. Consistent patterns in CLPP and soil habitat characteristics are emerging, as brought about by environmental disturbances, land management and soil texture. The applicability of CLPP analysis in monitoring systems is discussed.

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination
Dekkers, S.J.W. ; Pearce, S. ; Bolderen-Veldkamp, R.P. ; Marshall, A. ; Widera, P. ; Gilbert, J. ; Drost, H.G. ; Bassel, G. ; Muller, K. ; King, J.R. ; Wood, A. ; Grosse, I. ; Bentsink, L. - \ 2013
Plant Physiology 163 (2013)1. - ISSN 0032-0889 - p. 205 - 215.
thaliana seeds - abscisic-acid - leaf senescence - gene activity - endosperm - reveals - dormancy - metabolism - embryo - touch
Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high-resolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.
Linking theories of change and observed reality: the Shea value chain partnership case in Burkina
Drost, S. ; Wijk, J. van; Vellema, S. - \ 2012
Maastricht : Maastricht School of Management (MSM Working Paper 2012/03) - 50 p.
This case study found out how a public-private partnership in Burkina Faso helped female shea nut producers to link up with the cosmetic industry. Empirical data collected from October-December 2011 revealed that the shea value chain partnership between a international shea processing company, a development organisation, and a local service provider, enabled the connection between the dynamics of the shea market in Burkina Faso, wherein the demand for shea kernels by international and local buyers affects price setting mechanisms, and the logic of locally embedded organisations, wherein local practices of managing information and financial flows and leadership affect the commitment to collaboration. But could a bilateral agreement between a buying company and producer organisation not have lead to the same result? In this case, the likely answer is no. The case study suggests that the added value of the shea value chain partnership lies beyond the technicalities and practicalities of a collaboration protocol between a private buyer and female producer organisations, and comes down to the way in which the protocol stimulates joint navigation by the company and producer organisations. The research found that the ‘hands-on approach’ of an ‘institutional entrepreneur’, the service provider in the partnership, played an important role in the processes of joint navigation under whimsical market conditions and stubborn local practices.
Value chain partnerships: A process-based view on how partnerships generate institutional change
Vellema, S. ; Wijk, J. van; Roo, N. de; Douma, M. ; Drost, S. - \ 2012
Looking beyond upgrading: How value chains partnerships create institutional change
Vellema, S. ; Wijk, J. van; Roo, N. de; Douma, M. ; Drost, S. - \ 2012
Biomass in peat soils? Feasibility of bioenergy production under a climate change scenario
Kuhlman, J.W. ; Verburg, R.W. ; Dijk, J. van; Phan-Drost, N. - \ 2011
In: Land-Use modelling in planning practice / Koomen, E., Borsboom-van Beurden, J., Dordrecht, Heidelberg, London, New York : Springer (The GeoJournal Library 101) - ISBN 9789400718210 - 214 p.
Biomass on Peat Soils? Feasibility of bioenergy production under a climate change scenario
Kuhlman, J.W. ; Verburg, R.W. ; Dijk, Janneke van; Phan-Drost, N. - \ 2011
In: Land-Use Modelling in Planning Practice / Koomen, Eric, Borsboom-van Beurden, Judith, Dordrecht : Springer (1st Edition XVI) - ISBN 9789400718210 - p. 97 - 116.
Energy security has become a priority as the world’s population increases and its standard of living improves, thus increasing energy consumption. As the demand for energy increases, there is growing concern about the possible exhaustion of finite supplies of fossil fuels in the not-too-distant future. In addition to the problem of availability, combustion of fossil fuels also has negative environmental effects: air pollution (e.g. particulates, nitrogen oxides, carbon monoxide and sulphur dioxide) produced through the combustion of fossil fuels, threatens human health as well as plant and animal life. Furthermore, the combustion of fossil fuels releases carbon dioxide and other greenhouse gases into the atmosphere, thus contributing to an increase in global temperature. These considerations lead to a search for alternative, renewable sources of energy, one of which is bioenergy.
Development value chains meet business supply chains: the concept of global value chains unraveled
Drost, S. ; Wijk, J. van; Vellema, S. - \ 2010
Rotterdam : the Partnerships Resource Centre (working paper 2) - 13 p.
Conceptual challenges in the concept of Global Value Chain
Drost, S. ; Wijk, J. van; Vellema, S. - \ 2010
Rotterdam : Partnerships Resource Centre
Coleoptera - Kevers In: Entomofauna van de noordelijke Achterhoek. Verslag van de 163e zomerbijeenkomst te Vorden (ed. Cuppen & Drost)
Cuppen, J.G.M. ; Vorst, O. ; Heijerman, Th. ; Nunen, F. ; Jansen, R.P. ; Drost, M.B.P. ; Tiemersma, S. ; Maanen, B. van; Langeveld, S.C. ; Burgers, J. ; Threels, A. - \ 2009
Entomologische Berichten 69 (2009)5. - ISSN 0013-8827 - p. 180 - 188.
Heteroptera - wantsen In: Entomofauna van de noorderlijke Achterhoek. Verslag van de 163e zomerbijeenkomst te Vorden (ed Cuppen & Drost)
Cuppen, J.G.M. ; Aukema, B. ; Heijerman, Th. ; Chen, P.P. ; Nieser, N. ; Jansen, R.P. - \ 2009
Entomologische Berichten 69 (2009)5. - ISSN 0013-8827 - p. 175 - 176.
De nomenclatuur en volgorde van de soorten zijn gebaseerd op de vijf delen van de ‘Catalogue of the Heteroptera of the Palaearctic Region’ (Aukema & Rieger 1995, 1996, 1999, 2001, 2006). Voor nieuwe waarnemingen van wantsen uit de provincie Gelderland werden het overzicht in Aukema (1989) en de eerste twee delen van de ‘Verspreidingsatlas van de Nederlandse wantsen’ (Aukema et al. 2002; Aukema & Hermes 2006) geraadpleegd. Hieruit is gebleken dat slechts Psallus montanus Josifov niet in deze werken werd genoemd. Deze soort werd echter onlangs als nieuw voor Nederland gemeld door Aukema (2008) met daarbij diverse, ook oude waarnemingen uit de provincie Gelderland. Derhalve kunnen hier geen nieuwe soorten wantsen aan de lijst aan deze provincie worden toegevoegd. Het merendeel van de terrestrische wantsen werd gedetermineerd door Berend Aukema die helaas de zomerbijeenkomst niet kon bijwonen.
Coleoptera - kevers. In: Verslag van de 162e zomerbijeenkomst te Mechelen (ed. Drost & Cuppen)
Cuppen, J.G.M. ; Vorst, O. ; Nunen, F. ; Drost, M.B.P. ; Jansen, R. - \ 2008
Entomologische Berichten 68 (2008)4. - ISSN 0013-8827 - p. 142 - 151.
Coleoptera - Kevers. In: Entomofauna van Zuid-Limburg. Verslag van de 162e zomerbijeenkomst te Mechelen
Cuppen, J.G.M. ; Vorst, O. ; Nunen, F. ; Heijerman, Th. ; Drost, M.B.P. ; Jansen, R. ; Muilwijk, M. ; Sande, J.C. - \ 2008
Entomologische Berichten 64 (2008)4. - ISSN 0013-8827 - p. 142 - 153.
Omschakelen naar geïntegreerde of biologische teelt - motieven en randvoorwaarden
Lauwere, C.C. de; Buck, A.J. de; Smit, A.L. ; Buurma, J.S. ; Drost, H. ; Prins, H. ; Theuws, L.W. - \ 2008
conversie - biologische landbouw - bedrijfsvoering - motivatie - geïntegreerde bedrijfssystemen - conversion - organic farming - management - motivation - integrated farming systems
Posterpresentatie. Onderzoek naar het omschakelen naar geïntegreerde of biologische teelt
Heteroptera - Wantsen In: Entomofauna van de De Kempen, Noord-Brabant. Verslag van de 161 zomerbijeenkomst te Baarschot (ed. Cuppen & Drost)
Cuppen, J.G.M. ; Aukema, B. ; Heijerman, Th. - \ 2007
Entomologische Berichten 67 (2007). - ISSN 0013-8827 - p. 125 - 127.
Coleoptera-Kevers. Verslag van de 161e zomerbijeenkomst te Baarschot.
Cuppen, J.G.M. ; Vorst, O. ; Heijerman, Th. ; Drost, M.P.B. ; Nunen, B.M.P.J. van; Jansen, R.P. ; Maanen, B. van; Muilwijk, M. ; Huijbregts, J. ; Langeveld, S.C. ; Threels, A. - \ 2007
Entomologische Berichten 67 (2007). - ISSN 0013-8827 - p. 132 - 140.
Arbeid door jongeren in de agrarische sector : 1. nadere beschrijving van de problematiek
Oude Vrielink, H.H.E. ; Kroeze, G.H. ; Drost, W.C. - \ 2007
arbeid (werk) - landbouwsector - minderjarige werknemers - arbeidswetgeving - Nederland - labour - agricultural sector - young workers - labour legislation - Netherlands
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