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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    Bepaling van het aantal nesten en het uitvliegsucces van Grote Sterns op Texel met behulp van een drone
    Spaans, B. ; Leopold, M.F. ; Plomp, M. - \ 2018
    Limosa 91 (2018)1. - ISSN 0024-3620 - p. 30 - 37.
    Sinds 1997 broedt de Grote Stern weer op Texel en sinds 2010 met duizenden paren. De hoge dichtheid aan broedende vogels in de kolonies, in combinatie met de eventueel aanwezige vegetatie, maken het lastig het aantal broedende vogels van een afstand nauwkeurig te tellen. Bezoek aan de kolonie om de nesten te tellen heeft echter langdurige verstoring tot gevolg en wordt door de beheerders niet toegestaan. Daarom rees bij ons de vraag: kunnen we met een drone opnames van boven maken teneinde de broedende vogels te tellen? Het vliegen met een drone bleek de sterns niet te verstoren en maakte zeer nauwkeurige nesttellingen mogelijk. Omdat de bijna vliegvlugge jonge sterns goed te herkennen zijn op de drone-opnames, kon later in het seizoen ook het uitvliegsucces worden bepaald.
    Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms
    Claassens, Nico J. ; Siliakus, Melvin F. ; Spaans, Sebastiaan K. ; Creutzburg, Sjoerd C.A. ; Nijsse, Bart ; Schaap, Peter J. ; Quax, Tessa E.F. ; Oost, John Van Der - \ 2017
    PLoS ONE 12 (2017)9. - ISSN 1932-6203
    High-level, recombinant production of membrane-integrated proteins in Escherichia coli is extremely relevant for many purposes, but has also been proven challenging. Here we study a combination of transcriptional fine-tuning in E. coli LEMO21(DE3) with different codon usage algorithms for heterologous production of membrane proteins. The overexpression of 6 different membrane proteins is compared for the wild-type gene codon usage variant, a commercially codon-optimized variant, and a codon-harmonized variant. We show that transcriptional fine-tuning plays a major role in improving the production of all tested proteins. Moreover, different codon usage variants significantly improved production of some of the tested proteins. However, not a single algorithm performed consistently best for the membrane-integrated production of the 6 tested proteins. In conclusion, for improving heterologous membrane protein production in E. coli, the major effect is accomplished by transcriptional tuning. In addition, further improvements may be realized by attempting different codon usage variants, such as codon harmonized variants, which can now be easily generated through our online Codon Harmonizer tool.
    Thermococcus kodakarensis : the key to affordable biohydrogen production
    Spaans, S.K. - \ 2016
    Wageningen University. Promotor(en): John van der Oost, co-promotor(en): Servé Kengen. - Wageningen : Wageningen University - ISBN 9789462577725 - 245
    thermococcus - thermococcus kodakarensis - hydrogen - bioenergy - canonical analysis - biosynthesis - nadph - archaea - microbiology - thermococcus - thermococcus kodakarensis - waterstof - bio-energie - canonische analyse - biosynthese - nadph - archaea - microbiologie
    NADPH-generating systems in bacteria and archaea
    Spaans, S.K. ; Weusthuis, R.A. ; Oost, J. van der; Kengen, S.W.M. - \ 2015
    Frontiers in Microbiology 6 (2015). - ISSN 1664-302X - 47 p.
    Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided
    The chromosome copy number of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1
    Spaans, S.K. ; Oost, J. van der; Kengen, S.W.M. - \ 2015
    Extremophiles 19 (2015)4. - ISSN 1431-0651 - p. 741 - 750.
    The euryarchaeon Thermococcus kodakarensis is a well-characterized anaerobic hyperthermophilic heterotroph and due to the availability of genetic engineering systems it has become one of the model organisms for studying Archaea. Despite this prominent role among the Euryarchaeota, no data about the ploidy level of this species is available. While polyploidy has been shown to exist in various Euryarchaeota, especially Halobacteria, the chromosome copy number of species belonging to one of the major orders within that phylum, i.e., the Thermococcales (including Thermococcus spp. and Pyrococcus spp.), has never been determined. This prompted us to investigate the chromosome copy number of T. kodakarensis. In this study, we demonstrate that T. kodakarensis is polyploid with a chromosome copy number that varies between 7 and 19 copies, depending on the growth phase. An apparent correlation between the presence of histones and polyploidy in Archaea is observed
    Flexibility in faithfulness of Dark-bellied Brent Geese, Branta b. bernicla to moulting sites
    Ebbinge, B.S. ; Prokosch, P. ; Spaans, B. ; Müskens, G.J.D.M. ; Bom, R. ; Kokorev, Y. ; Syroechkovskiy, E.E. - \ 2013
    Wildfowl 2013 (2013)3. - ISSN 0954-6324 - p. 116 - 134.
    The distribution of Dark-bellied Brent Geese Branta b. bernicla moulting on the Taimyr Peninsula, in the Russian arctic, varies between years depending on whether the birds had a successful breeding season. Counts made of moulting flocks show that major shifts in numbers occur, particularly in non-breeding years, when in line with Salomonsen’s (1968) hypothesis a higher proportion of the population moults further north. For instance, the delta of the Lower Taimyr River in the northern part of the Taimyr Peninsula held 10-times more moulting Dark-bellied Brent Geese in 1989, a non-breeding year, than it did in the good 1990 breeding season. At a more local scale, in good breeding years family groups with small goslings tend to move away from breeding islands in the Pyasina Delta, western Taimyr, to avoid gosling predation by Taimyr Gulls Larus taimyrensis which nest in colonies on the same islands, whereas in poor breeding years adult geese concentrate on these same islands to moult and avoid the mainland sites used for moulting in good breeding years. Failed breeders have greater freedom than parent birds to choose where to moult as successful breeders remain with their goslings to protect and guide them to the safest nursery and moult areas. Re-captures of ringed Darkbellied Brent Geese at a moulting site in the Pyasina Delta found that, in poor breeding years, up to one-fifth the birds had moulted at the site previously, but that the majority of ringed birds known to be still alive were not site-faithful to their moulting grounds.
    Een beschermingsplan voor de Spaanse vlag in Limburg
    Wallis de Vries, M.F. ; Groenendijk, D. ; Huigens, M.E. - \ 2013
    Natuurhistorisch Maandblad 102 (2013)8. - ISSN 0028-1107 - p. 177 - 183.
    lepidoptera - natuurbescherming - beschermingsgebieden - natura 2000 - zuid-limburg - limburg - lepidoptera - nature conservation - conservation areas - natura 2000 - zuid-limburg - limburg
    De nachtvlinder Spaans Vlag (Euplagia quadripunctaria) geniet bescherming volgens de Europese Habitatsrichtlijn. In het kader van Natura 2000 is het lastig gebleken om beschermde gebieden voor de soort aan te wijzen. Als alternatief is door de overheid besloten om een regionaal beschermingsplan voor de soort op te stellen (Wallis de Vries & Groenendijk, 2012). Daarbij is ook aanvullend onderzoek naar de larvale ecologie van deze vlinder uitgevoerd.
    A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis
    Hesselman, M.C. ; Odoni, D.I. ; Ryback, B.M. ; Groot, S. de; Heck, R.G.A. van; Keijsers, J. ; Kolkman, P. ; Nieuwenhuijse, D. ; Nuland, Y.M. ; Sebus, E. ; Spee, R. ; Vries, H. de; Wapenaar, M.T. ; Ingham, C.J. ; Schroen, K. ; Martins Dos Santos, V.A.P. ; Spaans, S.K. ; Hugenholtz, F. ; Passel, M.W.J. van - \ 2012
    PLoS ONE 7 (2012)5. - ISSN 1932-6203
    culture - microorganisms - population - resistance - membranes - bacteria - chamber - support - arrays
    Novel microbial cultivation platforms are of increasing interest to researchers in academia and industry. The development of materials with specialized chemical and geometric properties has opened up new possibilities in the study of previously unculturable microorganisms and has facilitated the design of elegant, high-throughput experimental set-ups. Within the context of the international Genetically Engineered Machine (iGEM) competition, we set out to design, manufacture, and implement a flow device that can accommodate multiple growth platforms, that is, a silicon nitride based microsieve and a porous aluminium oxide based microdish. It provides control over (co-)culturing conditions similar to a chemostat, while allowing organisms to be observed microscopically. The device was designed to be affordable, reusable, and above all, versatile. To test its functionality and general utility, we performed multiple experiments with Escherichia coli cells harboring synthetic gene circuits and were able to quantitatively study emerging expression dynamics in real-time via fluorescence microscopy. Furthermore, we demonstrated that the device provides a unique environment for the cultivation of nematodes, suggesting that the device could also prove useful in microscopy studies of multicellular microorganisms
    Foraging site selection of two subspecies of Bar-tailed Godwit Limosa lapponica: time minimizers accept greater predation danger than energy minimizers
    Duijns, S. ; Dijk, J.G.B. van; Spaans, B. ; Jukema, J. ; Boer, W.F. de; Piersma, Th. - \ 2009
    Ardea 97 (2009)1. - ISSN 0373-2266 - p. 51 - 59.
    long-distance migrant - stopover site - migration strategies - relative importance - western sandpipers - raptor predation - calidris-mauri - bird migration - large falcons - banc-darguin
    Different spatial distributions of food abundance and predators may urge birds to make a trade-off between food intake and danger. Such a trade-off might be solved in different ways in migrant birds that either follow a time-minimizing or energy-minimizing strategy; these strategies have been assigned to two subspecies of Bar-tailed Godwits Limosa lapponica that use the European Wadden Sea during northward migration. At the study area on Terschelling, we recorded feeding site selection, time budgets and intake rates (prey/min) in the period that both lapponica (energy minimizer) and taymyrensis (time minimizer) subspecies were present (late April till the end of May 2007). Prey availability (number of prey/m2) was negatively correlated to the distance from cover. Based on sightings of colour-ringed Bar-tailed Godwits, taymyrensis was foraging closer to cover, and for a higher proportion of time than lapponica (67% vs. 33%). During the high tide period taymyrensis was also foraging on inland coastal meadows. Moreover, taymyrensis was more vigilant than lapponica, whereas lapponica showed more resting and preening behaviour. Lapponica had a higher instantaneous intake rate, but taymyrensis had a higher overall intake rate and the birds were more successful in taking larger prey items than lapponica. Supposedly, due to the increased foraging time and additional foraging on the inland meadows, the time-minimizing taymyrensis achieved a higher fuel deposition rate than lapponica. Taymyrensis shifted towards food-rich areas, apparently accepting higher predation risks, whereas energy-minimizing lapponica avoided predation danger by foraging further from cover
    Triggering transitions towards sustainable development of the Dutch agricultural sector: TransForum's approach
    Veldkamp, A. ; Altvorst, A.C. Van; Eweg, R. ; Jacobsen, E. ; Kleef, A. Van; Latesteijn, H. Van; Mager, S. ; Mommaas, H. ; Smeets, P.J.A.M. ; Spaans, L. ; Trijp, J.C.M. van - \ 2009
    Agronomy for Sustainable Development 29 (2009). - ISSN 1774-0746 - p. 87 - 96.
    social-ecological systems - land-use - perspective - resilience
    TransForum is an innovation program which aims to make a substantial contribution to the transition towards more sustainable development of the Dutch agricultural sector. This article describes the scientific foundation and architecture of this program. TransForum operates on the basis of five working hypotheses which together constitute one integrated analytical framework. These hypotheses are: (1) sustainable development is a dynamic system property; (2) sustainable development needs system innovation; (3) system innovation is a non-linear learning process; (4) system innovation requires active participation of relevant key players from knowledge institutes, governmental bodies, civil society organisations and the business community; (5) the program requires transdisciplinary collaboration of all players. TransForum identifies three new innovation strategies: (1) vital clusters; (2) regional development; (3) international agro-food networks; as alternatives to the current arrangements. Innovative projects are organised in these innovation strategies. The aim of the scientific program is threefold: (1) it addresses research questions raised in the innovative projects; (2) it investigates the need for system-innovations and the way in which they can be realized; (3) it designs research projects to test the 5 main working hypotheses of the program. The scientific program is organised in four themes following a cyclic innovation process which is constantly monitored. The cycle starts with people's preferences and images, followed by studies on which inventions are required to achieve a successful innovation. Subsequently, it is investigated how to organize new innovations and transitions and finally, how citizen/consumers behaviour and preferences mobilizes sustainable development, closing the loop
    COWZ, schaalvergroting in het groot
    Keurentjes, F. ; Spaans, N. ; Velde, A. van der; Philipsen, A.P. - \ 2007
    Wageningen UR Livestock Research
    Cowmunity : Innovatie in de melkveehoudeerij
    Rienks, W.A. ; Vries, C. de; Keurentjes, F. ; Spaans, N. ; Velde, A. van der - \ 2007
    Zoetermeer : Stichting Courage - 24
    melkveehouderij - innovaties - dairy farming - innovations
    Schaalvergroting is hét adagium in de internationale melkveehouderij, om melk tegen een lagere prijs te kunnen produceren. Nederlandse melkveebedrijven lijken die trend echter niet bij te houden. Verliest de Nederlandse melkveehouderij en zuivelsector daardoor op termijn haar internationaal toonaangevende positie? In deze uitgave vindt u het resultaat van onze zoektocht, inclusief mogelijke bedrijfsconcepten, eerste ontwerpschetsen en een aantal ‘innovatieopgaven’.
    The significance of female body stores for egg laying and incubation in dark-bellied brent geese Branta bernicla bernicla
    Spaans, B. ; Hoff, C.A. van 't; Veer, W. van der; Ebbinge, B.S. - \ 2007
    Ardea 95 (2007)1. - ISSN 0373-2266 - p. 3 - 15.
    nesting success - arctic foxes - birds - behavior - goose - dynamics - nutrient - reserves - protein - eiders
    The probability of successful breeding by Brent geese in the Arctic appears to be positively correlated with the mass of females when they depart from spring staging areas in North-western Europe. To clarify the mechanism behind this relationship we investigated the significance of flown-in female body stores for breeding over six summer seasons (1990-1995) in the Pyasina Delta in Taimyr, Russia. Female Brent Geese were caught upon arrival on the breeding grounds. Changes in female body mass and the timing and duration of nest recesses were recorded via electronic weighing platforms placed under their nests. Average female body masses declined through the breeding season; from 1464 g at arrival to 1269 g after egg laying and 1066 g at hatching, which was supposed to be close to lean body mass. Thus half of the stores were used between arrival and clutch completion, the other half during incubation. All females foraged during incubation. On average they left the nest 13.1 times every 24 hours, resulting in a daily recess time of 198 min during the first 21 days of incubation. Females were less likely to leave the nest during the last three days of incubation. Leaving the nest was risky: 40% of the Brent Goose nests in the study area lost one or more eggs to gulls during absence of the female. We estimated that 52% of the energy required during incubation was derived from body stores and the rest (48%) from food intake.
    Cowmunity : zoektocht naar grensverleggende melkveehouderij in Nederland
    Rienks, W.A. ; Vries, C. de; Keurentjes, F. ; Spaans, N. ; Velde, A. van - \ 2006
    Zoetermeer : Courage (InnovatieNetwerk ) - 202
    dairy farming - large scale husbandry - sustainability - innovations - melkveehouderij - veehouderij op grote schaal - duurzaamheid (sustainability) - innovaties
    Schaalvergroting is voor melkveehouders in Nederland een belangrijke strategie voor bedrijfsontwikkeling. Schaalvergroting vindt overal in de Westerse wereld plaats waarbij circa elke 15 jaar het aantal bedrijven halveert. Bijdoorgaandeschaalvergroting lopen melkveehouders tegen grenzen van de duurzaamheid aan; bijvoorbeeld rondom arbeid, financiering en dierenwelzijn. De schaalvergroting biedt echter ook kansen door inzet van arbeidsbesparende en milieuvriendelijketechnologie. Indeze studie is een schaalsprong gemaakt waarbij vier concepten voor een grootschalig melkveebedrijf van 1000 koeien zijn uitgewerkt. Voor ieder van de concepten is gekeken naar de duurzaamheid van de bedrijfssystemen. Verslag van een project vanuit Alterra, Courage (LTO) en melkveehouders

    Cowmunity is een initiatief van stichting Courage en Alterra, Wageningen UR.
    Het project is financieel mogelijk gemaakt door: Courage/Innovatienetwerk, Samenwerkingsverband Noord-
    Nederland, Noordelijke Ontwikkelings Maatschappij, Provincie Groningen, Provincie Friesland en de EU via
    de kaderverordening Plattelandsontwikkeling.
    Transition of an abandoned Dutch agrosilvopastoral landscape to "new wilderness" by extensive grazing with free-ranging cattle and horses
    Kuiters, A.T. - \ 2005
    In: Silvopastoralism and sustainable land management. - Wallingford (UK) : CABI - ISBN 9781845930011 - p. 148 - 149.
    The Veluwezoom National Park, a former agrosilvopastoral landscape covering 4900 ha (central part of The Netherlands), was designated in 1930 as a national park after most agricultural activities had been stopped due to changed agroeconomic conditions. The area comprised a mosaic of dry grass-heaths, pastures, abandoned arable fields, scrub and coniferous and deciduous woodland. From the 1980s, transition to 'new wilderness' became the main management aim, applying large-scale extensive grazing. Free-ranging cattle and horses were introduced. It was questioned if the high habitat diversity of this semi-open landscape was maintained by extensive grazing, without additional management measures. Research has been carried out on habitat use and interaction of domestic and wild herbivore grazers, and the impact of grazing on woody regeneration dynamics. Possibilities and constraints of extensive, year-round grazing with free-ranging cattle and horses as a management option in the transition of an agrosilvopastoral landscape to 'new wilderness' are discussed
    Supply chain development for fresh products in Thailand
    Buurma, J.S. ; Saranark, J. - \ 2004
    In: Hide or Confide; The Dilemma of Transparency / Hofstede, G.J., Spaans, L., Schepers, H.E., Trienekens, J.H., Beulens, A., Reed Business Information - ISBN 9789059013742 - 248 p.
    Transparency: Perceptions, Practices and Promises
    Hofstede, G.J. ; Beulens, A.J.M. ; Spaans, L. - \ 2004
    In: The Emerging World of Chains and Networks, bridging theory and practice 's Gravenhage : Reed Business Information - ISBN 9789059019287 - p. 285 - 310.
    Hoyer, P. ; Broens, D.F. - \ 2004
    In: Tools voor samenwerking in ketens en netwerken / Batterink, M., Hoyer, P., Prof. Dr Omta, S.W.F., Spaans, L., Den Haag : Reed Business Information (The emerging world of chains and networks ) - ISBN 9789059013735 - p. 33 - 47.
    Samenwerken voor verbeterde productkwaliteit
    Vernede, R. ; Scheer, F.P. ; Batterink, M.H. - \ 2004
    In: Tools voor samenwerking in ketens en netwerken / Ir Batterink, M.H., Ir Hoyer, P.K.M., Prof. Dr Omta, S.W.F., MBA Spaans, L., Den Haag : Reed Business Information (The Emerging World of Chains and Networks ) - ISBN 9789059013735 - p. 101 - 113.
    Samenwerken voor standaardisatie
    Batterink, M.H. ; Broens, D.F. - \ 2004
    In: Tools voor samenwerking in ketens en netwerken / Ir Batterink, M.H., Ir Hoyer, P.K.M., Prof. Dr Omta, S.W.F., MBA Spaans, L., Den Haag : Reed Business Information (The Emerging World of Chains and Networks ) - ISBN 9789059013735 - p. 83 - 100.
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