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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    Highly efficient mono-functionalization of knob-in-hole antibodies with strain-promoted click chemistry
    Bruins, Jorick J. ; Wouw, Criss van de; Koen, Wagner ; Lina, Bartels ; Albada, Bauke ; Delft, F.L. van - \ 2019
    Journal of the American Chemical Society 4 (2019). - ISSN 0002-7863 - p. 11801 - 11807.
    Knob-in-hole antibodies can be utilized to introduce a single tag for chemo-enzymatic functionalization. By either introducing a single C-terminal sortase tag (sortase-tag expressed protein ligation) or tyrosine tag (G4Y), mono-functionalization of the monoclonal antibody trastuzumab was achieved rapidly and in high yields. This method was applied to selectively and efficiently introduce a single fluorescent tag, cytokine or single-chain variable fragment, as well as produce clean homo dimers of trastuzumab.

    Inducible, selective labeling of proteins via enzymatic oxidation of tyrosine
    Bruins, Jorick J. ; Wouw, Criss van de; Keijzer, Jordi F. ; Albada, Bauke ; Delft, Floris L. van - \ 2019
    In: Methods in Molecular Biology Hertfordshire : Springer (Methods in Molecular Biology ) - ISBN 9781493995455 - p. 357 - 368.
    Antibody–drug conjugates (ADC) - Bioconjugate chemistry - Bioorthogonal click - Protein functionalization - SPOCQ - Tyrosine modification

    Proteins can be labeled site-specifically and in inducible fashion by exposing a small peptide tag (G4Y) on any of its termini and activating the newly exposed tyrosine residue with the enzyme mushroom tyrosinase. The enzyme generates a quinone by oxidizing the tyrosine, which in turn can perform strain-promoted oxidation-controlled ortho-quinone cycloaddition (SPOCQ) with strained alkynes and alkenes, generating a stable conjugation product. Here, we describe a protocol to perform SPOCQ reaction on proteins, along with notes to optimize yield and reaction rates. Conjugation efficiencies of over 95% to antibodies have been reported using this protocol.

    Fly the coop! Vertical structures influence the distribution and behaviour of laying hens in an outdoor range
    Rault, J.L. ; Wouw, A. van de; Hemsworth, P. - \ 2013
    Australian Veterinary Journal 91 (2013)10. - ISSN 0005-0423 - p. 423 - 426.
    egg-production systems - domestic-fowl - cover - runs
    BackgroundThe number of free-range farms has greatly increased in the Australian egg industry, up by 64% over the past 5 years and representing 34% of the retail egg sales last year. Nonetheless, free-range systems offer particular challenges to farmers. The use of the outdoor range is variable among hens; their distribution is usually not uniform across the range and they tend to stay close to features such as walls or fences, resulting in high stocking density in particular areas, with associated welfare and environmental concerns. MethodsUsing video recordings, we investigated the effect of erecting a series of vertical structures in the range on the hens' numbers, distribution and behaviour. ResultsHens were very attracted to the structures, which altered their distribution and behaviour. Up to 160 hens were seen around each structure, giving a density of 6.4 hens/m(2). The hens spent 40% of their time pecking at the structures and standing in these areas and less time walking, preening or ground pecking. ConclusionElucidating which physical features fulfil hens' biological needs could improve their use of outdoor ranges.
    A historical analysis of diversity trends in French and Dutch lettuce cultivars
    Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van - \ 2013
    Euphytica 190 (2013)2. - ISSN 0014-2336 - p. 229 - 239.
    genetische erosie - genetische diversiteit - lactuca sativa - slasoorten - rassen (planten) - oude plantenrassen - diversiteit - frankrijk - nederland - bladgroenten - groenten - genetic erosion - genetic diversity - lactuca sativa - lettuces - varieties - old varieties - diversity - france - netherlands - leafy vegetables - vegetables - genebank collection - erosion
    Using historical seed catalogues in combination with molecular fingerprinting data, diversity trends of lettuce, representing an important vegetable with active breeding programmes, were studied. Seed catalogues originating from France and the Netherlands from five different decades, the earliest dating from the 1840s, were checked for the occurence of lettuce cultivars. A total of 225 catalogues, with 7,311 records of lettuce, representing 878 different cultivars were found. The number of unique cultivars on offer by French and Dutch companies showed a small continuous increase until the 1960s, after which the number of cultivars on offer more than doubled to a total of 534 in the 1990s. Only a relatively small overlap between France and the Netherlands in the range of cultivars offered was observed. The 1960s appeared to be a period with many changes: the lowest genetic diversity in lettuce cultivars was found for this decade, whereas after the 1960s the number of companies supplying lettuce seeds reduced dramatically. The percentage of companies in a decade offering an identical cultivar decreased over time, and in the 1990s almost all cultivars were unique to only a single company. The possible relations of the observed trends with the developments in plant variety protection and in the plant breeding industry are discussed.
    News - Seed banks susceptible to sham samples
    Wouw, Mark van de - \ 2013
    Genetic erosion by modern plant breeding: fact or fiction?
    Treuren, R. van; Wouw, M.J. van de; Hintum, T.J.L. van; Kik, C. ; Visser, L. - \ 2012
    Genebanks Could Be Storing the Wrong Seeds - Dutch study investigates the authenticity of heirloom cultivars stored at genebanks
    Wouw, M.J. van de - \ 2011
    Crop Science News release
    The error of genebanks’ ways, by Luigi
    Wouw, M.J. van de - \ 2011
    Agricultural Biodiversity Weblog
    Collecting vegetative material of forage grasses and legumes
    Hanson, J. ; Wouw, M.J. van de - \ 2011
    In: Collecting plant genetic diversity: Technical guidelines. 2011 update / Guarino, L, Ramanatha Rao, V, Goldberg, E., - p. 22 - 22.
    Genetic erosion of crop diversity
    Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van; Kik, C. ; Visser, L. - \ 2011
    Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations
    Rouxel, T. ; Grandaubert, J. ; Hane, J.K. ; Hoede, C. ; Wouw, A. ; Couloux, A. ; Dominguez, V. ; Anthouard, V. ; Bally, P. ; Bourras, S. ; Cozijnsen, A.J. ; Ciuffetti, L.M. ; Degrave, A. ; Dilmaghani, A. ; Duret, L. ; Fudal, L. ; Goodwin, S.B. ; Gout, L. ; Glaser, N. ; Linglin, J. ; Kema, G.H.J. ; Lapalu, N. ; Lawrence, C.B. ; May, K. ; Meyer, M. ; Ollivier, B. ; Poulain, J. ; Schoch, C.L. ; Simon, A. ; Spatafora, J.W. ; Stachowiak, A. ; Turgeon, B.G. ; Tyler, B.M. ; Vincent, D. ; Weissenbach, J. ; Amselem, J. ; Quesneville, H. ; Oliver, R.P. ; Wincker, P. ; Balesdent, M.H. ; Howlett, B.J. - \ 2011
    Nature Communications 2 (2011). - ISSN 2041-1723 - p. 202 - 202.
    transposable elements - molecular evolution - pathogen effectors - brassica-napus - gene-transfer - oilseed rape - stem canker - avirulence - plant - fungal
    Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints
    Persistent Acacia savannas replace Mediterranean sclerophyllous forests in South America
    Wouw, P. van de; Echeverria, C. ; Rey-Benayas, J.M. ; Holmgren, M. - \ 2011
    Forest Ecology and Management 262 (2011)6. - ISSN 0378-1127 - p. 1100 - 1108.
    central chile - seedling establishment - vegetation structure - plant invasions - slope aspect - management - fire - conservation - regeneration - germination
    Mediterranean ecosystems are global hotspots of biodiversity threaten by human disturbances. Growing evidence indicates that regeneration of Mediterranean forests can be halted under certain circumstances and that successional stages can become notoriously persistent. The Mediterranean sclerophyllous forest in central Chile is been largely transformed into savannas dominated by the invasive legume tree Acacia caven as result of interacting management and ecological factors. We used multi-temporal satellite imagery to study the transition dynamics of these major vegetation types over the last four decades (1975–2008). Vegetation changes were related to indicators of resource availability (topography, water availability, solar radiance), potential propagule availability (distance to forest remnant patches) and disturbance regimes (grazing, fire occurrence and distance to roads and cities). During this study period, forests were mostly converted into Acacia savannas (46.1%). Acacia savanna was the most persistent natural vegetation type. The probability of sclerophyllous forest degradation into Acacia savanna increased on drier northern-exposed slopes, close to roads and further away from forest remnants. In contrast, forest regeneration from Acacia savanna was higher on moister southern-exposed slopes and closer to forest remnants. Acacia savannas are increasingly being converted into cultivated land on the moister locations or switching into a bare soil state in locations close to cities and further away from forest remnants. These results highlight the vulnerability of diverse sclerophyllous forests and its increasing conversion into persistent Acacia savannas in the Mediterranean region of central Chile and identify the ecological conditions for successful conservation and restoration of the native sclerophyllous forest vegetation that can be used for sensible land use planning.
    Authenticity of old cultivars in genebank collections: a case study on lettuce
    Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van - \ 2011
    Crop Science 51 (2011)2. - ISSN 0011-183X - p. 736 - 746.
    genenbanken - slasoorten - aflp - oude plantenrassen - ex-situ conservering - cultivarauthenticiteit - lactuca sativa - rassen (planten) - cultivars - gene banks - lettuces - amplified fragment length polymorphism - old varieties - ex situ conservation - cultivar authenticity - lactuca sativa - varieties - cultivars - genetic diversity - maintenance - accessions - longevity - level - l.
    Ex situ collections in genebanks conserve many old cultivars that had disappeared from mainstream agriculture before modern genebanks were established. The collections incorporated cultivars from many sources, such as botanical gardens and working collections, sometimes with little further information on their origin. Many old cultivars with identical or synonymous names are maintained in multiple collections and often more than once within collections. This research investigates the authenticity of old cultivars in genebanks using a large lettuce (Lactuca sativa L.) collection as a case study. Accessions presumed to be identical, based on the cultivar names accompanying the accessions, were compared for their DNA marker profiles, based on amplified fragment length polymorphisms (AFLPs). Using the genetic similarity of these accessions, the probability of authenticity of the old cultivars maintained in the collection was estimated. Separate analyses were done for different classes of cultivars, on the basis of the year of release or the donor history of the cultivar. The two largest cultivar groups within the collection, Sans Rivale à Graine Blanche and Maikönig, were analyzed in detail. Nonauthenticity of the investigated cultivars appeared to be high. This was especially true for the oldest cultivars, but even for the cultivars released from the 1960s to 1990 it was estimated that approximately 10% was not authentic. Recommendations to improve authenticity of cultivars in ex situ collections were presented
    Juridica; De rode wouw als ecosysteemdienst
    Kistenkas, F.H. - \ 2011
    Vakblad Natuur Bos Landschap 8 (2011)5. - ISSN 1572-7610 - p. 36 - 37.
    vogels - kadaververwijdering - ecosysteemdiensten - inventarisaties - birds - carcass disposal - ecosystem services - inventories
    Aan de hand van de vroegere functie van de wouw (namelijk als vuilnis- en kadaveropruimer) beschrijft Kistenkas het huidige begrip ecosysteemdienst. Zijn pleidooi: bij duurzame gebiedsontwikkeling zouden ecosysteemdiensten meegewogen moeten worden
    Crop diversity increasing says dutch researchers
    Wouw, M.J. van de - \ 2010
    Crop Biotech Update
    Biodiversiteit in gewassen neemt toe, niet af
    Wouw, M.J. van de - \ 2010
    Wageningen UR
    Crop biodiversity going up, not down - News release
    Wouw, M.J. van de - \ 2010
    Genetic diversity trends in twentieth century crop cultivars: a meta analysis
    Wouw, M.J. van de; Hintum, T.J.L. van; Kik, C. ; Treuren, R. van; Visser, L. - \ 2010
    Theoretical and Applied Genetics 120 (2010)6. - ISSN 0040-5752 - p. 1241 - 1252.
    veredelde rassen - plantenveredeling - genetische diversiteit - meta-analyse - improved varieties - plant breeding - genetic diversity - meta-analysis - triticum-aestivum l. - assessing temporal-changes - spring wheat germplasm - hordeum-vulgare l. - winter-wheat - microsatellite markers - molecular diversity - ssr markers - breeding programs - gliadin alleles
    In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.
    Genetic erosion in crops: concept, research results and challenges
    Wouw, M.J. van de; Kik, C. ; Hintum, T.J.L. van; Treuren, R. van; Visser, L. - \ 2010
    Plant genetic resources: characterization and utilization 8 (2010)1. - ISSN 1479-2621 - p. 1 - 15.
    genetische diversiteit - plantenveredeling - veredelde rassen - landrassen - genetische erosie - modernisering - genetic diversity - plant breeding - improved varieties - landraces - genetic erosion - modernization - spring bread wheat - oryza-sativa l. - allelic diversity changes - farmers seed selection - triticum-aestivum l. - microsatellite markers - molecular diversity - green-revolution - temporal trends - durum desf.
    The loss of variation in crops clue to the modernization of agriculture has been described as genetic erosion The current paper discusses the different views that exist on the concept of genetic erosion in crops Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop Two stages in this bottleneck are recognized the initial replacement of landraces by modern cultivars, and further trends in diversity as a consequence of modern breeding practices Genetic erosion may occur at three levels of integration crop, variety and allele The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following a reduction in diversity clue to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed
    Water vasthouden aan de bron: inzicht door modelberekeningen
    Bakel, J. van; Wouw, M. van de; Poelman, A. ; Stuyt, L.C.P.M. - \ 2007
    H2O : tijdschrift voor watervoorziening en afvalwaterbehandeling 40 (2007)14/15. - ISSN 0166-8439 - p. 35 - 38.
    wateropslag - waterbeheer - watersystemen - kwel - stroomgebieden - modellen - grondwaterstand - gegevensanalyse - noord-brabant - water storage - water management - water systems - seepage - watersheds - models - groundwater level - data analysis - noord-brabant
    De meest effectieve strategie voor de reductie van piekafvoeren, water vasthouden, is bergen van water bij de bron, waarbij de afstroming van water op perceelsniveau wordt bemoeilijkt. Om een onderbouwd inzicht in effect en relevantie van water vasthouden te krijgen zijn, in samenspraak met betrokken instanties, vijf maatregelen met behulp van de computercode SIMGRO geëvalueerd in de stroomgebieden Peelsche Loop, Groote Wetering en Raamsloop. Piekafvoeren kunnen met 3 tot 45% worden gereduceerd. De meest effectieve manier om water vast te houden is het voorkómen van maaiveldafvoer waarbij water tijdelijk op het maaiveld wordt geborgen, met als neveneffect structurele grondwaterstandverhogingen en effecten op de landbouw. Minder effectieve maatregelen hebben een marginaal effect op de regionale hydrologie. Inundaties verdwijnen sneller met goede drainage.
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