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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Greenhouse gas emissions in the Netherlands 1990-2017 : National inventory report 2019
Ruyssenaars, P.G. ; Coenen, P.W.H.G. ; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Dröge, R. ; Geilenkirchen, G. ; Hoen, M. 't; Honig, E. ; Huet, B. van; Huis, E.P. van; Koch, W.W.R. ; Lagerwerf, L.L. ; Molder, R.A. te; Montfoort, J.A. ; Peek, C.J. ; Vonk, J. ; Zanten, M.C. van - \ 2019
RIVM - 420 p.
Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Diversiteit en krielonderzoek : bij de traditionele Nederlandse hoenderrassen
Bortoluzzi, C. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Boer, Henk de; Taks, A. ; Kroon, Piet ; Hoving, A.H. - \ 2018
Kleindier magazine 132 (2018)6. - p. 11 - 13.
Recent onderzoek heeft aangetoond dat de ‘nieuwe’ krielrassen, de verkrielde vorm van de grote hoenderrassen,genetische variatie toevoegt aan de Nederlandse hoenderrassen en oorspronkelijke krielrassen. Door het kruisenmet dieren van verschillende rassen van niet-Nederlandseoorsprong worden nieuwe kenmerken vastgelegd enworden nieuwe rassen gevormd met een andere genetische diversiteit. Binnen de rassen is deze diversiteit laag,vanwege intensieve selectie op specifieke eigenschappenen door paringen tussen verwante dieren. Dit vergroot dekans op erfelijke aandoeningen en minder vitaal nageslacht. Volgend op dit onderzoek starten Wageningen University en Research, Animal Breeding en Genomics en Centrum voor Genetische Bronnen Nederland samen met de speciaalclubs een pilot om per paring informatie vannakomelingen te verzamelen. Deze informatie zal worden gebruikt om verstandig fokken voor de toekomst beter mogelijk te maken. Voor dit pilotonderzoek zijn vier rassen gekozen: de Eikenburger kriel, een ras met veel inteelt,de Nederlandse Uilebaard, een ras met lage inteelt en het Twents hoen en de Lakenvelder, die genetisch gezien op afstand staan van de andere Nederlandse rassen.
Regels industriekip nekken oer-Hollandse Chaamse Hoen
Candel, Jeroen - \ 2018
Greenhouse gas emissions in the Netherlands 1990-2016 : National Inventory Report 2018
Coenen, P.W.H.G. ; Zanten, M.C. van; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Berghe, A.C.W.M. van den; Huis, E.P. van; Geilenkirchen, G. ; Hoen, M. 't; Hoogsteen, M. ; Molder, R. te; Dröge, R. ; Montfoort, J.A. ; Peek, C.J. ; Vonk, J. ; Dellaert, S. ; Koch, W.W.R. - \ 2018
Bilthoven : National Institute for Public Health and the Environment (RIVM report 2018-0006) - 406
DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood
Tobi, Elmar W. ; Slieker, Roderick C. ; Luijk, René ; Dekkers, Koen F. ; Stein, Aryeh D. ; Xu, Kate M. ; Slagboom, P.E. ; Zwet, Erik W. Van; Lumey, L.H. ; Heijmans, Bastiaan T. ; T'Hoen, Peter A. ; Pool, René ; Greevenbroek, Marleen M. Van; Stehouwer, Coen D. ; Kallen, Carla J. Van Der; Schalkwijk, Casper G. ; Wijmenga, Cisca ; Zhernakova, Sasha ; Tigchelaar, Ettje F. ; Beekman, Marian ; Deelen, Joris ; Heemst, Diana Van; Veldink, Jan H. ; Berg, Leonard H. Van Den; Duijn, Cornelia M. Van; Hofman, Albert ; Uitterlinden, André G. ; Jhamai, P.M. ; Verbiest, Michael ; Verkerk, Marijn ; Breggen, Ruud Van Der; Rooij, Jeroen Van; Lakenberg, Nico ; Mei, Hailiang ; Bot, Jan ; Zhernakova, Dasha V. ; Hof, Peter Van 't; Deelen, Patrick ; Nooren, Irene ; Moed, Matthijs ; Vermaat, Martijn ; Jan Bonder, Marc ; Dijk, Freerk Van; Arindrarto, Wibowo ; Kielbasa, Szymon M. ; Swertz, Morris A. ; Isaacs, Aaron ; Franke, Lude - \ 2018
Science Advances 4 (2018)1. - ISSN 2375-2548
Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342, 596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formalmediation analysis.DNAm mediated the association of prenatal famine exposure with adult BMI and TG but not with glucose. DNAm at PIM3 (cg09349128), a gene involved in energy metabolism, mediated 13.4% [95% confidence interval (CI), 5 to 28%] of the association between famine exposure and BMI. DNAm at six CpGs, including TXNIP (cg19693031), influencing b cell function, and ABCG1 (cg07397296), affecting lipid metabolism, together mediated 80% (95% CI, 38.5 to 100%) of the association between famine exposure and TG. Analyses restricted to those exposed to famine during early gestation identified additional CpGs mediating the relationship with TG near PFKFB3 (glycolysis) and METTL8 (adipogenesis). DNAm at the CpGs involved was associated with gene expression in an external data set and correlated with DNAm levels in fat depots in additional postmortem data. Our data are consistent with the hypothesis that epigenetic mechanisms mediate the influence of transient adverse environmental factors in early life on long-termmetabolic health. The specific mechanism awaits elucidation.
Veel vraag naar hoen met een verhaal : variatie in pluimveerassen
Hoving, A.H. ; Buiter, R. ; Hiemstra, S.J. - \ 2017
Centrum voor Genetische Bronnen Nederland - 2 p.
Deze leaflets laten in een oogopslag zien hoe het met de populatiestatus en risicoclassificatie van de Nederlandse rassen landbouwhuisdieren is
De kip, van orakelhoen tot produktiekip: een historisch perspectief (herziene versie)
Pistorius, R. ; Hiemstra, S.J. ; Hoving, A.H. - \ 2017
poultry
Het Nederlandse hoen (of kip, waarmee we meestal hetzelfde dier bedoelen) staat symbool voor onze eeuwenlange verbondenheid met de kleinschalige landbouw. Al naar gelang de tijdgeest komt het tamme hoen in veel gedaanten voor: van onopvallende scharrelaar bij kleine boeren tot adellijk pronkstuk, en van zinnebeeld van 'vleselijk genot' tot productiekip. Deze brochure biedt een kort overzicht van de rol van de verschillende hoenderrassen in de landbouwgeschiedenis, en van de rijke diversiteit aan rassen en kleurslagen.
The FAIR Guiding Principles for scientific data management and stewardship : Comment
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2016
Scientific Data 3 (2016). - ISSN 2052-4463

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Ontwikkeling pluimveehouderij met focus op dierenwelzijn - Dierenwelzijn in beeld
Ruis, M.A.W. - \ 2016
You Tube
pluimvee - dierlijke productie - dierenwelzijn - diergedrag - huisvesting, dieren - diervoeding - diergezondheid - dierethiek - domesticatie - kippen - pluimveehouderij - lesmaterialen - poultry - animal production - animal welfare - animal behaviour - animal housing - animal nutrition - animal health - animal ethics - domestication - fowls - poultry farming - teaching materials
De hedendaagse kip is ontstaan uit vier wilde rassen. Het Bankivahoen uit Zuid-Oost Azie is hiervan de belangrijkste. Vanaf 1.500 vóór Christus verspreidde het hoen zich door heel Zuid-Oost Azië, China en Japan. In Noordwest Europa is de kip vermoedelijk rond 200 voor Christus geïntroduceerd door de Grieken en Romeinen. In de jaren ’50 van de vorige eeuw werd in Nederland op grote schaal geïnvesteerd in innovaties en verschenen de grote broedmachines en de eerste volautomatische legbatterijen. Ook kwamen begin jaren ’50 verschillende ‘merken’ hybride kippen - kruisingen van zuivere lijnen of rassen - op de markt. Hieruit ontstonden de hoogproductieve leghennen en vleeskuikens.

Halverwege de jaren ’60 dringt in de maatschappij het besef door dat er weinig oog is voor het welzijn van kippen. Decennia later heeft dit geleid tot een aantal veranderingen en verboden. Vanaf 2012 is het in heel Europa verboden om leghennen in legbatterijen te houden, en het aantal vleeskuikens per vierkante meter is in Europa aan banden gelegd. Een ander voorbeeld is de aankomende plicht om leghennen, en vermeerderingsdieren voor de vleessector, met hele snavels te houden. De pluimveesector is de uitdaging aangegaan om vlees en eieren duurzamer te produceren.
Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
Gerven, L.P.A. van; Brederveld, R.J. ; Klein, J.J.M. de; DeAngelis, D.L. ; Downing, A.S. ; Faber, M. ; Gerla, D.J. ; Hoen, J. 't; Janse, J.H. ; Janssen, A.B.G. ; Jeuken, Michel ; Kooi, B.W. ; Kuiper, J.J. ; Lischke, B. ; Liu, Sien ; Petzoldt, Thomas ; Schep, S.A. ; Teurlincx, Sven ; Thiange, C. ; Trolle, D. ; Nes, E.H. van; Mooij, W.M. - \ 2015
Fundamental and Applied Limnology 186 (2015)1-2. - ISSN 1863-9135 - p. 5 - 20.
Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches. PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework – including runtime performance – can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
Efficiëntere bemestingsstrategie mogelijke opslossing Lyprauta in potorchidee : gezonde plant toont minder schade van potworm
Rodenburg, J. ; Kruidhof, H.M. - \ 2015
Onder Glas 12 (2015)2. - p. 29 - 31.
orchidaceae - phalaenopsis - plantenplagen - potplanten - insectenplagen - effecten - bemesting - landbouwkundig onderzoek - mestgiften - glastuinbouw - plant pests - pot plants - insect pests - effects - fertilizer application - agricultural research - dressings - greenhouse horticulture
Zijn potwormen in orchidee misschien minder schadelijk dan altijd werd gedacht? Adviseur René ‘t Hoen denkt van wel. Hij claimt dat ondanks de aanwezigheid van potwormen, een gezonde plant zonder problemen kan uitgroeien tot een prima verkoopbaar product. Dit zou betekenen dat de teeltstrategie belangrijker is dan bestrijding van de schadelijke muggenlarven. Tegelijkertijd vindt hij dat zijn waarnemingen moeten worden gestaafd door onderzoek. Er is namelijk nog zeer weinig bekend over de biologie van potwormen.
Serving many at once: How a database approach can create unity in dynamical ecosystem modelling
Mooij, W.M. ; Brederveld, R.J. ; Klein, J.J.M. de; DeAngelis, D.L. ; Downing, A.S. ; Faber, M. ; Gerla, D.J. ; Hipsey, M.R. ; Hoen, J. 't; Janse, J.H. ; Janssen, A.B.G. ; Jeuken, M. ; Kooi, B.W. ; Lischke, B. ; Petzoldt, T. ; Postma, L. ; Schep, S.A. ; Scholten, H. ; Teurlincx, S. ; Thiange, C. ; Trolle, D. ; Dam, A.A. van; Gerven, L.P.A. van; Nes, E.H. van; Kuiper, J.J. - \ 2014
Environmental Modelling & Software 61 (2014). - ISSN 1364-8152 - p. 266 - 273.
shallow lakes - simulation - eutrophication - management - package - pclake
Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. © 2014 The Authors.
An atlas of over 90.000 conserved noncoding sequences provides insight into crucifer regulatory regions
Haudry, A. ; Platts, A.E. ; Vello, E. ; Hoen, D.R. ; Leclerq, M. ; Williamson, R.J. ; Forczek, E. ; Joly-Lopez, Z. ; Steffen, J.G. ; Hazzouri, K.M. ; Dewar, K. ; Stinchcombe, J.R. ; Schoen, D.J. ; Wang, X. ; Schmutz, J. ; Town, C.D. ; Edger, P.P. ; Pires, J.C. ; Schumaker, K.S. ; Jarvis, D.E. ; Mandakova, T. ; Lysak, M. ; Bergh, E. van den; Schranz, M.E. ; Harrison, P.M. - \ 2013
Nature Genetics 45 (2013). - ISSN 1061-4036 - p. 891 - 898.
arabidopsis-thaliana - human genome - dna elements - ultraconserved elements - brassica-oleracea - gene-expression - evolution - drosophila - size - annotation
Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
A community-based framework for aquatic ecosystem models
Trolle, D. ; Hamilton, D.P. ; Hipsey, M.R. ; Bolding, K. ; Bruggeman, J. ; Mooij, W.M. ; Janse, J.H. ; Nielsen, A. ; Jeppesen, E. ; Elliott, J.A. ; Makler-Pick, V. ; Petzoldt, T. ; Rinke, K. ; Flindt, M.R. ; Arhonditsis, G.B. ; Gal, G. ; Bjerring, R. ; Tominaga, K. ; Hoen, J. 't; Downing, A.S. ; Marques, D.M. ; Fragoso, C.R. ; Sondergaard, M. ; Hanson, P.C. - \ 2012
Hydrobiologia 683 (2012)1. - ISSN 0018-8158 - p. 25 - 34.
climate-change - lake kinneret - phytoplankton - management - fish
Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid 're-inventing the wheel', thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework.
Challenges and opportunities for integrating lake ecosystem modelling approaches
Mooij, W.M. ; Trolle, D. ; Jeppesen, E. ; Arhonditsis, G. ; Belolipetsky, P.V. ; Chitamwebwa, D.B.R. ; Degermendzhy, A.G. ; DeAngelis, D.L. ; Domis, L.N.D. ; Downing, A.S. ; Elliott, J.A. ; Fragoso, C.R. ; Gaedke, U. ; Genova, S.N. ; Gulati, R.D. ; Hakanson, L. ; Hamilton, D.P. ; Hipsey, M.R. ; Hoen, J. 't; Hulsmann, S. ; Los, F.H. ; Makler-Pick, V. ; Petzoldt, T. ; Prokopkin, I.G. ; Rinke, K. ; Schep, S.A. ; Tominaga, K. ; Dam, A.A. van; Nes, E.H. van; Wells, S.A. ; Janse, J.H. - \ 2010
Aquatic Ecology 44 (2010)3. - ISSN 1386-2588 - p. 633 - 667.
fresh-water ecosystems - of-the-art - daphnia population-dynamics - trophic state indicators - predator-prey system - causes regime shifts - library salmo-oo - shallow lakes - climate-change - submerged macrophytes
A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.
Conservering van sperma van de Nederlandse zeldzame kippenrassen
Zuidberg, C.A. ; Woelders, H. ; Sulkers, H. ; Boks, A. ; Hiemstra, S.J. - \ 2009
Wageningen : CGN / Stichting DLO (CGN Rapport 263) - 25
kippen - ex-situ conservering - genenbanken - kippenrassen - zeldzame rassen - cryopreservering - sperma - hanen - fowls - ex situ conservation - gene banks - fowl breeds - rare breeds - cryopreservation - semen - cocks
Na de eerste drie „inhaalslagen‟ in 2003, 2005 en 2007 is weer een project opgezet om te komen tot het verzamelen van genetisch materiaal van een aantal hanen van zeldzame kippenrassen (inhaalslag 4). Het doel van het project is om (de genetische variatie van) deze (kleine) rassen veilig te stellen in de genenbank. Met de financiële middelen van 2009 kon voor de vierde maal worden gestart met een aantal hanen van rassen, die in 2003, 2005 en 2007 niet voldoende aan bod waren gekomen. In een evaluatie met de Stichting Zeldzame Huisdierrassen en rekening houdend met de reeds aanwezige genenbank collecties zijn zestien rassen geselecteerd waarvan genetisch materiaal is gecryo-conserveerd, te weten het Hollandse Kriel (11), Eikenburger Kriel (5), Sabelpoot Krielen (10), Fries Hoen (2), Hollands Kuifhoen (6), Assendelfter Hoen (6), Drents Hoen (3), Groninger Meeuw (5), Noordhollands Hoen (6), Twents Hoen (3), Chaams Hoen (3), Welsumer (2), Lakenvelder (2), Nederlandse Uilenbaard (2), Barnevelder (4) en het Hollands Hoen (3). Van deze 16 rassen zijn totaal 73 hanen aangevoerd. Vier hanen zijn in de eerste dagen reeds gesneuveld. Van één Eikenburger Kriel haan kon geen sperma worden verkregen. Met de aanvulling van het sperma van de hanen van voornoemde rassen zou de doelstelling kunnen worden bereikt, om van elk ras ca. 800 doses sperma in opslag te hebben van minimaal 10 hanen. In totaal zijn in deze vierde inhaalslag 5534 doses sperma ingevroren en in de genenbank weggezet. De Eikenburger Kriel haalde deze aantallen niet vanwege de te geringe spermaproductie (ruim 200 doses!). Van het Drents Hoen, de Assendelfter Hoen en de Schijndelaar benaderen de aantallen doses sperma de 800.
Relative power and sample size analysis on gene expression profiling data
Iterson, M. van; Hoen, P.A.C. 't; Pedotti, P. ; Hooiveld, G.J.E.J. ; Dunnen, J.T. den; Ommen, G.J.B. van; Boer, J.M. ; Menezes, R.X. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164
false discovery rate - control maqc project - microarray data - dna microarray
Background - With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental. Results - Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARa agonists were administered to wild-type and PPARa-null mice. Our analysis confirms the hierarchy of PPARa-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampal dC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms. Conclusion - Power and sample size analysis based on pilot data give valuable information on the performance of the experiment and can thereby guide further decisions on experimental design. Solexa/Illumina deep sequencing is the technology of choice if interest lies in genes expressed in the low-intensity range. Researchers can get guidance on experimental design using our approach on their own pilot data implemented as a BioConductor package, SSPA http://bioconductor.org/packages/release/bioc/html/SSPA.html
Het Globe Programma: Module Bodem
Hulst, L. van; Speijers, C. ; Goede, R.G.M. de; Delft, B. van; Dirven, L. van; Hartemink, A. ; Meijberg, W. ; Hoeven, N. van der; Hoen, J. 't; Haan, I. de - \ 2007
Utrecht : Globe Nederland - 204 p.
Gemiddeld 5% hogere productie haalbaar met aanpassing teeltmethode: Oud-tomatenteler Koos 't Hoen: "Groei waait de kas uit" (o.a.interview Peter van Weel)
Arkesteijn, Marleen ; Weel, P.A. van - \ 2007
Onder Glas 4 (2007)9. - p. 104 - 105.
kassen - tomaten - cultuurmethoden - klimaatregeling - milieubeheersing - plantenontwikkeling - glastuinbouw - productiegroei - groenten - greenhouses - tomatoes - cultural methods - air conditioning - environmental control - plant development - greenhouse horticulture - production growth - vegetables
Oud-tomatenteler Koos 't Hoen stelt dat de tomatenproductie gemiddeld met 5% omhoog kan door aanpassingen door te voeren in de teeltmethode. Hij ontwikkelde een theorie om de kwaliteit en productie van tuinbouwgewassen te verbeteren. Door de luchtramen aan het einde van de dag zoveel mogelijk dicht te laten en de temepratuur in de kas, afhankelijk van de lichtsom te laten oplopen. Dit werkt bevordelijk voor productie en kwaliteit. Onderzoekers Jan Voogt en Peter van Weel kunnen zich vinden in de aanpak van de methode, maar wijzen een hogere RV en Co2 gehalte aan als oorzaak voor de productieverhoging
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