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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    Lateral root formation involving cell division in both pericycle, cortex and endodermis is a common and ancestral trait in seed plants
    Xiao, Ting Ting ; Velzen, Robin van; Kulikova, Olga ; Franken, Carolien ; Bisseling, Ton - \ 2019
    Development 146 (2019)20. - ISSN 0950-1991
    Endodermis - Lateral root development - Medicago - Primordium - Quiescent centre - Stem cells

    Studies on the model plant Arabidopsis have led to the common view that lateral roots are exclusively formed from pericycle cells and that the latter are unique in their ability to be reprogrammed into stem cells. By analysing lateral root formation in an evolutionary context, we show that lateral root primordium formation in which cortex, endodermis and pericycle are mitotically activated, is a common and ancestral trait in seed plants, whereas the exclusive involvement of pericycle evolved in the Brassicaceae. Furthermore, the endodermis can also be reprogrammed into stem cells in some species.

    Non-diazotrophic Bradyrhizobium spp. genome sequencing and assembly
    Schneijderberg, M.A. ; Schmitz, Lucas ; Cheng, X. ; Polman, Sharon ; Franken, C. ; Geurts, R. ; Bisseling, A.H.J. - \ 2018
    PRJNA417035 - SAMN07975002 - SAMN08687197 - SAMN08687198 - SAMN08687199 - Bradyrhizobium
    This study provides evidence that both diazotrophic and non-diazotrophic Bradyrhizobium spp. colonize the root endophytic compartment of a wide variety of plant species, including the model species Arabidopsis thaliana. This suggests that plant roots form a major ecological niche of Bradyrhizobium spp., which might be ancestral to the evolution of the nodulation and nitrogen-fixation trait in this genus.
    Referenties en maatlatten voor natuurlijke watertypen voor de Kaderrichtlijn Water 2021-2027
    Altenburg, W. ; Arts, G. ; Baretta-Bekker, J.G. ; Berg, M.S. van den; Broek Broek, T. van den; Buskens, R. ; Bijkerk, R. ; Coops, H.C. ; Dam, H. van; Ee, G. van; Evers, C.H.M. ; Franken, R. ; Higler, B. ; Ietswaart, T. ; Jaarsma, N. ; Jong, D.J. de; Joosten, A.M.T. ; Klinge, M. ; Knoben, R.A.E. ; Kranenbarg, J. ; Loon, W.M.G.M. van; Noordhuis, R. ; Pot, R. ; Twisk, F. ; Verdonschot, P.F.M. ; Vlek, H. ; Backx, J.J.G.M. ; Beers, M. ; Buijse, A.D. ; Duursema, G. ; Fagel, M. ; Leeuw, J. de; Molen, J. van der; Nijboer, R.C. ; Postma, J. ; Vriese, T. ; Duijts, R. ; Hartholt, J.G. ; Jager, Z. ; Stikvoort, E.C. ; Walvoort, D. - \ 2018
    Amersfoort : Stowa (Stowa rapport 2018-49) - ISBN 9789057738135 - 481
    Eigenschappen verankeren - hoe gevaarlijk is inteelt?
    Buis-Franken, Yvonne ; Schurink, A. - \ 2018
    Balans van de Leefomgeving 2018 : Nederland duurzaam vernieuwen
    Egmond, Petra van; Elzenga, Hans ; Buitelaar, Edwin ; Eerdt, Martha van; Eskinasi, Martijn ; Franken, Ron ; Gaalen, Frank van; Hanemaaijer, Aldert ; Hilbers, Hans ; Hollander, Guus de; Nijland, Hans ; Ritsema van Eck, Jan ; Ros, Jan ; Schilder, Frans ; Spoon, Martijn ; Uitbeijerse, Gabrielle ; Wouden, Ries van der; Vonk, Marijke ; Vugteveen, Pim ; Goossen, Martijn ; Blom, Wim ; Bredenoord, Hendrien ; Brink, Thelma van den; Evers, David ; Doren, Didi van; Grinsven, Hans van; Hinsberg, Arjen van; Muilwijk, Hanneke ; Oorschot, Mark van; Peeters, Jeroen ; Puijenbroek, Peter van; Raspe, Otto ; Rijn, Frank van; Schijndel, Marian van; Sluis, Sietske van der; Sorel, Niels ; Timmerhuis, Jacqueline ; Verwest, Femke ; Westhoek, Henk ; Sanders, Marlies ; Dirkx, Joep - \ 2018
    Den Haag : Planbureau voor de Leefomgeving - 284
    In situ hybridization method for localization of mRNA molecules in medicago tissue sections
    Kulikova, Olga ; Franken, Carolien ; Bisseling, Ton - \ 2018
    In: Functional Genomics in Medicago truncatula Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493986323 - p. 145 - 159.
    Alkaline phosphatase (AP) - Amplifier - Branched DNA - Preamplifier - RNA in situ probe sets - ViewRNA™ ISH Tissue Assays

    Here we describe an in situ hybridization (ISH) method using Invitrogen™ ViewRNA™ ISH Tissue Assay (ThermoFisher Scientific) optimized for Medicago root and nodules sections. The method is based on branched (b)DNA signal amplification technology originally developed for use in microplate format and further adapted for detection of (m)RNAs in mammalian tissue sections. Signal amplification is achieved via a series of sequential hybridizations of linking sequences which are anchored to complementary sequences present on specific oligonucleotide probes. The typical (m)RNA probe set contains ~20 synthetic adjacent oligonucleotide pairs. Each probe is composed of a 20bp primary sequence designed to target sequence of interest and a secondary extended sequence serving as a template for hybridization of a preamplifier oligonucleotide. The preamplifier forms a stable hybrid only if it hybridizes to two adjacent probes. By this principle, background is reduced. Other regions on the preamplifier are designed to hybridize to multiple bDNA amplifier molecules that create a branched structure. Finally, alkaline phosphatase (AP)-labeled oligonucleotides, which are complementary to bDNA amplifier sequences, bind to the bDNA molecule by hybridization. By adding Fast Red substrate, red punctuated precipitates are formed that can be detected by light bright and/or fluorescent microscope. ThermoFisher Scientific (https://www.thermofisher.com/nl/en/home.html) designs and synthesizes probe sets for a gene of interest and Invitrogen™ ViewRNA™ ISH Tissue Assay kits include all components required for pretreatment of plant tissues, hybridization and signal amplification.

    A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana
    Schneijderberg, Martinus ; Schmitz, Lucas ; Cheng, Xu ; Polman, Sharon ; Franken, Carolien ; Geurts, Rene ; Bisseling, Ton - \ 2018
    BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
    Arabidopsis - Bradyrhizobium - Endophytic compartment - Root colonization
    Background: Diazotrophic Bradyrhizobium spp. are well known for their ability to trigger nodule formation on a variety of legume species. In nodules, Bradyrhizobium utilizes plant-derived carbohydrates in exchange for fixed nitrogen. The genes essential for the nodulation and nitrogen-fixation trait are clustered in a genomic region, which is known as the 'symbiotic island'. Recently, novel non-diazotrophic Bradyrhizobium spp. have been found to be highly abundant in soils, suggesting that these species can also have a 'free-living' life history. However, whether non-diazotrophic Bradyrhizobium spp. can live in association with plants remains elusive. Results: In this study, we show that Bradyrhizobium spp. are common root endophytes of non-legume plant species - including Arabidopsis thaliana (Arabidopsis) - grown in an ecological setting. From a single Arabidopsis root, four Bradyrhizobium sp. strains (designated MOS001 to MOS004) were isolated. Comparative genome analysis revealed that these strains were genetically and functionally highly diverse, but did not harbour the nodulation and the nitrogen fixation gene clusters. Comparative colonization experiments, with MOS strains and nitrogen-fixing symbiotic strains, revealed that all tested Bradyrhizobium spp. can colonize the root endophytic compartment of Arabidopsis. Conclusion: This study provides evidence that both diazotrophic and non-diazotrophic Bradyrhizobium spp. colonize the root endophytic compartment of a wide variety of plant species, including the model species Arabidopsis. This demonstrates that plant roots form a major ecological niche for Bradyrhizobium spp., which might be ancestral to the evolution of the nodulation and nitrogen-fixation trait in this genus.
    Graphical Illustration of Interaction Effects in Binary Choice Models : A Note
    Franken, Jason R.V. ; Pennings, Joost M.E. ; Garcia, Philip - \ 2018
    Journal of Agricultural Economics 69 (2018)3. - ISSN 0021-857X - p. 852 - 858.
    Asset specificity - Binary choice models - Contracts - Transaction costs economics - Uncertainty
    Graphing procedures for evaluating power or interaction terms in binary logit and probit models are illustrated in an application to hog producers' decisions based on transaction cost economics' hypothesised positive effect of the interaction of uncertainty and asset specificity on contract use. Results support the hypothesis, particularly for producers that are otherwise on the cusp (near the 50/50 probability) of choosing either contract or spot transactions based on their responses for other variables. Such insights may not be drawn without use of the demonstrated graphing procedures.
    Risk attitudes and the structure of decision-making : Evidence from the Illinois hog industry
    Franken, Jason R.V. ; Pennings, Joost M.E. ; Garcia, Philip - \ 2017
    Agricultural Economics 48 (2017)1. - ISSN 0169-5150 - p. 41 - 50.
    Contracting - D81 - Q13 - Risk attitude - Risk behavior - Structural equation modeling

    Research offers mixed evidence about the risk management decision-making process of producers. Whether producers' characteristics drive behavior directly or through risk attitude remains a puzzle. We assess whether managerial/firm characteristics directly affect choices or if their influence occurs indirectly through impacts on risk attitude. The findings, which support indirect effects, indicate that failure to represent relationships between risk attitude, other characteristics, and behavior appropriately can mask the effect of risk attitude. A more complete understanding of the structure of decision-making may assist economists, policymakers, and industry stakeholders in designing and targeting mechanisms to manage or transfer risk.

    Referenties en maatlatten voor natuurlijke watertypen voor de kaderrichtlijn water 2015-2021 ; 2e dr.
    Altenburg, W. ; Arts, G. ; Baretta-Bekker, J.G. ; Berg, M.S. van den; Broek, T. van den; Buskens, R. ; Bijkerk, R. ; Coops, H.C. ; Dam, H. van; Ee, G. van; Evers, C.H.M. ; Franken, R. ; Higler, B. ; Ietswaart, T. ; Jaarsma, N. ; Jong, D.J. de; Joosten, A.M.T. ; Klinge, M. ; Knoben, R.A.E. ; Kranenbarg, J. ; Loon, W.M.G.M. van; Noordhuis, R. ; Pot, R. ; Twisk, F. ; Verdonschot, P.F.M. ; Vlek, H. ; Wolfstein, K. ; Backx, J.J.G.M. ; Beers, M. ; Buijse, A.D. ; Duursema, G. ; Fagel, M. ; Leeuw, J. de; Molen, J. van der; Nijboer, R.C. ; Postma, J. ; Vriese, T. ; Molen, D.T. van der; Herpen, F.C.J. van; Nieuwerburgh, L.L.J. van - \ 2016
    Amersfoort : Stowa (Stowa rapport 2012-31) - 466
    In het najaar van 2012 werd een geactualiseerde versie van het document Referenties en maatlatten voor natuurlijke watertypen voor de Kaderrichtlijn Water 2015-2021 vastgesteld. Uit het gebruik van deze maatlatten en het programmeren van de Aquokit Biologie (webservice voor toetsen van ecologische kwaliteit met deze maatlatten ontwikkeld door het InformatieHuis Water) bleek dat er correcties en verduidelijkingen nodig waren om te zorgen voor een juiste en consistente toepassing van de maatlatten. Deze correcties en verduidelijkingen zijn doorgevoerd in deze tweede druk. In bijlage 14 is een overzicht opgenomen van de aanpassingen in de maatlat ten opzichte van de eerst druk.
    Graphical Illustration of Interaction Effects in Binary Choice Models
    Franken, J.R.V. ; Pennings, J.M.E. ; Garcia, P. - \ 2016
    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.

    Meerwaarde ecosysteemdiensten voor Deltaprogramma
    Franken, Ron ; Meulen, Suzanne van der; Kwakernaak, C. ; Bos, Maaike ; Lenselink, Gerda ; Hartgers, E.M. - \ 2016
    Milieu : opinieblad van de Vereniging van Milieuprofessionals 22 (2016)3. - ISSN 1873-5436 - p. 12 - 14.
    waterbeheer - hoogwaterbeheersing - veiligheid - biodiversiteit - ecosysteemdiensten - dijken - regionale planning - natuurbeheer - water management - flood control - safety - biodiversity - ecosystem services - dykes - regional planning - nature management
    Het PBL verkent de mogelijkheden om natuur een rol te laten spelen in de uitvoering van het Deltaprogramma om onze waterveiligheid te waarborgen. Dit gebeurt met oog voor de meerwaarde voor de biodiversiteit. Kennis wordt opgedaan in twee praktijkprojecten: de verbetering van de zeedijk tussen Eemshaven en Delfzijl en de aanleg van een hoogwatergeul bij Varik-Heesselt.
    Waterkwaliteit nu en in de toekomst : Eindrapport ex ante evaluatie van de Nederlandse plannen voor de Kaderrichtlijn Water : beleidsstudie
    Gaalen, F. van; Tiktak, A. ; Franken, Ron ; Boekel, E.M.P.M. van; Puijenbroek, P. ; Muilwijk, Hanneke ; Grinsven, H. van; Rougoor, C. ; Salm, C. van der; Groenendijk, P. ; Cleij, P. ; Roovaart, Joost van den - \ 2016
    Planbureau voor de Leefomgeving (PBL-publicatie / Planbureau voor de Leefomgeving 1727) - 54
    waterkwaliteit - kaderrichtlijn water - oppervlaktewater - oppervlaktewaterkwaliteit - waterbeheer - pesticiden - stroomgebieden - water quality - water framework directive - surface water - surface water quality - water management - pesticides - watersheds
    De Nederlandse stroomgebiedbeheerplannen voor de periode 2016-2021 zijn in december 2015 vastgesteld. Het PBL heeft op verzoek van het ministerie van Infrastructuur en Milieu (IenM) op basis van metingen en modelberekeningen geëvalueerd of de voorgestelde maatregelen in de plannen en het vijfde nitraatactieprogramma afdoende zijn om de gestelde doelen voor 2027 te halen. Het voorliggende rapport is een vervolg op de in mei 2015 door het PBL gepubliceerde tussentijdse rapportage (PBL 2015). Nieuw in dit eindrapport zijn onder andere de onderdelen verontreinigende stoffen en rijkswateren, waarvoor destijds nog geen gegevens beschikbaar waren. Ook nieuw zijn de resultaten van een analyse waarin op basis van meetgegevens de toestand en trend in het verleden zijn bepaald.
    Development and application of a protocol to evaluate herd welfare in Dutch dairy farms
    Metz, J.H.M. ; Dijkstra, T. ; Franken, P. ; Frankena, K. - \ 2015
    Livestock Science 180 (2015). - ISSN 1871-1413 - p. 183 - 193.
    A protocol was developed and applied in a field survey to incorporate evaluation of herd welfare into the existing quality assurance program in Dutch dairy farming. Welfare was derived from the state of the biological needs of cows. Welfare targets and critical control points were selected according to HACCP principles, while restriction was to dairy herds with loose-cubicle housing (>90% of Dutch herds). The feasibility for measurement of the protocol was tested in a pilot study with 52 preselected, medium-sized herds for time needed for the observations (set at ~1 h to 2 h ), robustness of parameters (threshold of 80% true cases for repeated scores), and opinions from inspectors and farmers, which were variable but positive on average. The final protocol consisted of 16 animal-based and 14 environment-based parameters. From a random sample of 240 dairy herds (1% of Dutch farms), 164 herds (12,267 cows) with median herd size of 67 cows (SD=38) participated in the field survey, on a voluntary basis. The time needed for scoring averaged 78 min (SD=22) per herd. Animal-based parameters included leg disorders, normal and abnormal locomotion, external lesions, skin and teat problems, poor body condition, and fearfulness of the herd. Herd prevalence averaged highest for abnormal locomotion (43.8%), swollen hocks and knees (25.2%), dermatophytosis (24.2%), scabies (20.1%), and filthiness (17.4%). However, herd prevalence was lowest (96% of herds). Overall, our results indicate various directions for welfare improvement in practice, both at the individual farm and sector level.
    Octopus life history relative to age, in a multi-geared developmental fishery
    Leporati, S.C. ; Hart, A.M. ; Larsen, R. ; Franken, L.E. ; Graaf, M. de - \ 2015
    Fisheries Research 165 (2015). - ISSN 0165-7836 - p. 28 - 41.
    tetricus mollusca-cephalopoda - cadiz sw spain - vulgaris cuvier - reproductive-biology - female octopus - common octopus - food-intake - growth - temperature - pallidus
    The ability to obtain broad-scale age information for an exploited octopus population enables the identification of essential life history information, such as age at maturity, recruitment pulses and seasonal effects on growth. This study uses stylet weight (reduced internal shell) as a proxy to age 3494 Octopus (cf) tetricus, the target species of a rapidly developing octopus fishery in Western Australia. Samples were collected during 2008–2012 using passive shelter pots and active trigger traps. Both males and females were found to have similar maximum ages at 1.5 years, with males reaching maturity at 243 days compared to 379 days for females. The two gear types selected for different parts of the population, with shelter pots catching mostly octopus 1 kg total weight, of which 75% of the total catch were mature males. This variation in catch composition coupled with the inshore (shelter pot) and offshore (trigger trap) depth profiles of the gear types suggests offshore migration may be occurring. Back-calculated hatch months revealed six-monthly recruitment pulses and a positive relationship with ascending sea surface temperature and growth up to 22 °C.
    Kustbescherming
    Henkens, R.J.H.G. ; Loon-Steensma, J.M. van; Franken, Ron ; Tol, Sandy ; Knegt, B. de - \ 2014
    In: Graadmeter Diensten van Natuur. Vraag, aanbod, gebruik en trend van goederen en diensten uit ecosystemen in Nederland In: de Knegt, B. (ed). / Knegt, de, B, Wageningen : WOT Natuur & Milieu - p. 113 - 121.
    Measuring the effect of risk attitude on marketing behavior
    Franken, J.R.V. ; Pennings, J.M.E. ; Garcia, P. - \ 2014
    Agricultural Economics 45 (2014)5. - ISSN 0169-5150 - p. 525 - 535.
    farmers subjective probabilities - econometric estimation - production contracts - northern thailand - preference - aversion - perceptions - decisions - construct - india
    Despite extensive study, researchers continue to search for consistent and reliable measures of risk preferences to explain market behavior. We find that a measure, combining experiments rooted in expected utility theory and measures derived from surveys, explains spot and contractual sales, but does not exhibit substantially greater explanatory power than its underlying components. Survey-based measures are generally more significant indicators of marketing choices, but experimental measures reveal how risk attitudes vary over a range of probable outcomes, which is important in light of increased commodity price volatility. Given recently identified limitations on the applicability of expected utility theory, we suggest that researchers include survey methods to obtain low-cost supplemental measures.
    An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings
    Marsch-Martinez, N. ; Franken, J. ; Gonzalez-Aguilera, K.L. ; Folter, S. de; Angenent, G.C. ; Alvarez-Buylla, E.R. - \ 2013
    Plant Methods 9 (2013). - ISSN 1746-4811
    ft protein - shoot - transport - cotyledon - movement - plants - rnas - root
    Background: Grafting procedures are an excellent tool to study long range signalling processes within a plant. In the last decade, suitable flat-surface grafting procedures for young Arabidopsis seedlings using a collar to support the graft have been developed, allowing the study of long-range signals from a molecular perspective. Results: In the modification presented here, scion and stock are put together on the medium without supporting elements, while cotyledons are removed from the scion, resulting in increased grafting success that can reach up to 100%. At the same time, the protocol enables to process as many as 36 seedlings per hour, which combined with the high success percentage represents increased efficiency per time unit. Conclusions: Growing cotyledons usually push the scion and the rootstock away in the absence of a supporting element. Removing them at the grafting step greatly improved success rate and reduced post-grafting manipulations.
    Bio-energie en bodemkwaliteit : : terugwinning van nutriënten en organische stof bij kleinschalige bio-energie systemen in ontwikkelingslanden
    Bonten, L.T.C. ; Wosten, J.H.M. ; Rijssenbeek, W.L.M.M. ; Franken, Y.J. - \ 2012
    Bodem 22 (2012)5. - ISSN 0925-1650 - p. 24 - 26.
    bodemkwaliteit - duurzaamheid (sustainability) - landbouwproductie - brandstofgewassen - nutriëntenstromen - ontwikkelingslanden - bio-energie - biobased economy - soil quality - sustainability - agricultural production - fuel crops - nutrient flows - developing countries - bioenergy - biobased economy
    Bio-energie kan een bijdrage leveren aan een duurzamere energievoorziening. Grootschalige export van biomassa voor energieproductie, uit vooral tropische landen, gaat echter gepaard met de export van nutriënten en organische stof, en heeft uitputting van de bodem tot gevolg. Bij lokale productie van bio-energie kunnen nutriënten en organische stof wellicht teruggewonnen worden.
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