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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    Response to Perrier and Charmantier: On the importance of time scales when studying adaptive evolution
    Bosse, Mirte ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; Mcmahon, Keith ; Poissant, Jocelyn ; Verhagen, Irene ; Groenen, Martien A.M. ; Oers, Kees Van; Sheldon, Ben C. ; Visser, Marcel E. ; Slate, Jon - \ 2019
    Evolution Letters 3 (2019)3. - ISSN 2056-3744 - p. 248 - 253.
    Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
    Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
    forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

    Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

    Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
    Clifton-Brown, John ; Harfouche, Antoine ; Casler, Michael D. ; Dylan Jones, Huw ; Macalpine, William J. ; Murphy-Bokern, Donal ; Smart, Lawrence B. ; Adler, Anneli ; Ashman, Chris ; Awty-Carroll, Danny ; Bastien, Catherine ; Bopper, Sebastian ; Botnari, Vasile ; Brancourt-Hulmel, Maryse ; Chen, Zhiyong ; Clark, Lindsay V. ; Cosentino, Salvatore ; Dalton, Sue ; Davey, Chris ; Dolstra, Oene ; Donnison, Iain ; Flavell, Richard ; Greef, Joerg ; Hanley, Steve ; Hastings, Astley ; Hertzberg, Magnus ; Hsu, Tsai Wen ; Huang, Lin S. ; Iurato, Antonella ; Jensen, Elaine ; Jin, Xiaoli ; Jørgensen, Uffe ; Kiesel, Andreas ; Kim, Do Soon ; Liu, Jianxiu ; McCalmont, Jon P. ; McMahon, Bernard G. ; Mos, Michal ; Robson, Paul ; Sacks, Erik J. ; Sandu, Anatolii ; Scalici, Giovanni ; Schwarz, Kai ; Scordia, Danilo ; Shafiei, Reza ; Shield, Ian ; Slavov, Gancho ; Stanton, Brian J. ; Swaminathan, Kankshita ; Trindade, Luisa M. - \ 2019
    Global change biology Bioenergy 11 (2019)1. - ISSN 1757-1693 - p. 118 - 151.
    bioenergy - feedstocks - lignocellulose - M. sacchariflorus - M. sinensis - Miscanthus - Panicum virgatum - perennial biomass crop - Populus spp. - Salix spp.

    Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

    Research Through Design in Landscape Architecture: a first State of the Art
    Lenzholzer, S. ; Nijhuis, Steffen ; Cortesão, J. - \ 2018
    In: Proceedings of DRS2018. - - p. 381 - 393.
    Research Through Design - Landscape Architecture
    The discussion regarding the relation of design and research in landscape architecture started somewhat later than in other design disciplines. But the past decade has shown a sharp rise of publications on ‘research through/by design(ing)’ (RTD). The literature has now reached a level of richness that enables a review of the State of the Art and a differentiation of types of contributions to the discourse. We reviewed more than 200 publications (scientific journal papers, conference papers, PhD theses, MSc theses and others) on RTD in relation to landscape architecture and closely related disciplines. The review shows that a rather small portion of the publications deals with RTD a scholarly sense. The remaining portion of scholarly publications offered a useful base for further scrutiny. We categorised the relevant literature according to types of publications and the epistemological stances taken. Based on this categorisation we identified areas that need further research and thus sketched an agenda for further research on RTD in landscape architecture.
    Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
    O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
    Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
    Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
    Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
    Variation in Reproductive Success Across Captive Populations: Methodological Differences, Potential Biases and Opportunities
    Griffith, Simon C. ; Crino, Ondi L. ; Andrew, Samuel C. ; Nomano, Fumiaki Y. ; Adkins-Regan, Elizabeth ; Alonso-Alvarez, Carlos ; Bailey, Ida E. ; Bittner, Stephanie S. ; Bolton, Peri E. ; Boner, Winnie ; Boogert, Neeltje ; Boucaud, Ingrid C.A. ; Briga, Michael ; Buchanan, Katherine L. ; Caspers, Barbara A. ; Cichoń, Mariusz ; Clayton, David F. ; Derégnaucourt, Sebastien ; Forstmeier, Wolfgang ; Guillette, Lauren M. ; Hartley, Ian R. ; Healy, Susan D. ; Hill, Davina L. ; Holveck, Marie Jeanne ; Hurley, Laura L. ; Ihle, Malika ; Tobias Krause, E. ; Mainwaring, Mark C. ; Marasco, Valeria ; Mariette, Mylene M. ; Martin-Wintle, Meghan S. ; McCowan, Luke S.C. ; McMahon, Maeve ; Monaghan, Pat ; Nager, Ruedi G. ; Naguib, Marc ; Nord, Andreas ; Potvin, Dominique A. ; Prior, Nora H. ; Riebel, Katharina ; Romero-Haro, Ana A. ; Royle, Nick J. ; Rutkowska, Joanna ; Schuett, Wiebke ; Swaddle, John P. ; Tobler, Michael ; Trompf, Larissa ; Varian-Ramos, Claire W. ; Vignal, Clémentine ; Villain, Avelyne S. ; Williams, Tony D. - \ 2017
    Ethology 123 (2017)1. - ISSN 0179-1613 - p. 1 - 29.
    captive breeding - captivity - domestication - husbandry - model species - reproductive failure - Taeniopygia guttata - zebra finch

    Our understanding of fundamental organismal biology has been disproportionately influenced by studies of a relatively small number of ‘model’ species extensively studied in captivity. Laboratory populations of model species are commonly subject to a number of forms of past and current selection that may affect experimental outcomes. Here, we examine these processes and their outcomes in one of the most widely used vertebrate species in the laboratory – the zebra finch (Taeniopygia guttata). This important model species is used for research across a broad range of fields, partly due to the ease with which it can be bred in captivity. However despite this perceived amenability, we demonstrate extensive variation in the success with which different laboratories and studies bred their subjects, and overall only 64% of all females that were given the opportunity, bred successfully in the laboratory. We identify and review several environmental, husbandry, life-history and behavioural factors that potentially contribute to this variation. The variation in reproductive success across individuals could lead to biases in experimental outcomes and drive some of the heterogeneity in research outcomes across studies. The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency.

    Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
    Bowers, Robert M. ; Kyrpides, Nikos C. ; Stepanauskas, Ramunas ; Harmon-Smith, Miranda ; Doud, Devin ; Reddy, T.B.K. ; Schulz, Frederik ; Jarett, Jessica ; Rivers, Adam R. ; Eloe-Fadrosh, Emiley A. ; Tringe, Susannah G. ; Ivanova, Natalia N. ; Copeland, Alex ; Clum, Alicia ; Becraft, Eric D. ; Malmstrom, Rex R. ; Birren, Bruce ; Podar, Mircea ; Bork, Peer ; Weinstock, George M. ; Garrity, George M. ; Dodsworth, Jeremy A. ; Yooseph, Shibu ; Sutton, Granger ; Glöckner, Frank O. ; Gilbert, Jack A. ; Nelson, William C. ; Hallam, Steven J. ; Jungbluth, Sean P. ; Ettema, Thijs J.G. ; Tighe, Scott ; Konstantinidis, Konstantinos T. ; Liu, Wen Tso ; Baker, Brett J. ; Rattei, Thomas ; Eisen, Jonathan A. ; Hedlund, Brian ; McMahon, Katherine D. ; Fierer, Noah ; Knight, Rob ; Finn, Rob ; Cochrane, Guy ; Karsch-Mizrachi, Ilene ; Tyson, Gene W. ; Rinke, Christian ; Lapidus, Alla ; Meyer, Folker ; Yilmaz, Pelin ; Parks, Donovan H. ; Eren, A.M. - \ 2017
    Nature Biotechnology 35 (2017)8. - ISSN 1087-0156 - p. 725 - 731.

    We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

    In-situ observations using tagged animals
    Roquet, F. ; Boehme, L. ; Bester, M.N. ; Bornemann, H. ; Brasseur, S.M.J.M. ; Charrassin, J.B. ; Costa, D. ; Fedak, M.A. ; Guinet, C. ; Hall, A. ; Harcourt, R. ; Hindell, M.A. ; Kovacs, K.M. ; Lea, M.A. ; Lovell, P. ; Lowther, A. ; Lyderson, C. ; Mcmahon, C. ; Picard, B. ; Reverdin, G. ; Vincent, C. - \ 2017
    - 5 p.
    Marine mammals help gather information on some of the harshest environments on the planet, through the use of miniaturized ocean sensors glued on their fur. Since 2004, hundreds of diving marine animals, mainly Antarctic and Arctic seals, have been fitted with a new generation of Argos tags developed by the Sea Mammal Research Unit of the University of St Andrews in Scotland, UK. These tags investigate the at-sea ecology of these animals while simultaneously collecting valuable oceanographic data. Some of the study species travel thousands of kilometres continuously diving to great depths (up to 2100 m). The resulting data are now freely available to the global scientific community at Despite great progress in their reliability and data accuracy, the current generation of loggers while approaching standard ARGO quality specifications have yet to match them. Yet, improvements are underway; they involve updating the technology, implementing a more systematic phase of calibration and taking benefit of the recently acquired knowledge on the dynamical response of sensors. Together these efforts are rapidly transforming animal tagging into one of the most important sources of oceanographic data in polar regions and in many coastal areas
    Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait
    Bosse, M. ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, I.C. ; Groenen, M. ; Oers, C.H.J. ; Sheldon, Ben C. ; Visser, M.E. ; Slate, Jon - \ 2017
    Wageningen University & Research
    adaptation - evolution - genomics - natural selection - bill length - birds - Parus major
    We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
    Recent natural selection causes adaptive evolution of an avian polygenic trait
    Bosse, Mirte ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, Irene ; Groenen, Martien A.M. ; Oers, Kees van; Sheldon, Ben C. ; Visser, Marcel E. ; Slate, Jon - \ 2017
    Science 358 (2017)6361. - ISSN 0036-8075 - p. 365 - 368.

    We used extensive data froma long-term study of great tits (Parusmajor) in theUnitedKingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes.We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirmthat these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.

    Overview of the PREPARE WP3: management of contaminated goods in post-accidental situation – Synthesis of European stakeholders' panels
    Charron, S. ; Lafage, S. ; Asselt, E. Van; Baptista, M. ; Bourgondiën, M. Van; Brandhoff, P. ; Cabianca, T. ; Camps, J. ; Cessac, B. ; Crouail, P. ; Durand, V. ; Gallego, E. ; Gil, O. ; Holmes, S. ; Hourdakis, C. ; Jones, K. ; Kamenopoulou, V. ; Lecomte, J.F. ; Liland, A. ; Lopes, I. ; Madruga, M.J. ; Martins, J.O. ; McMahon, C. ; Montero, M. ; Murith, C. ; Olyslaegers, G. ; Organo, C. ; Paiva, I. ; Peltonen, T. ; Portugal, L. ; Potiriadis, C. ; Prades, A. ; Reis, M. ; Rossignol, N. ; Schneider, T. ; Sala, R. ; Smith, V. ; Tafili, V. ; Teles, P. ; Tomkiv, Y. ; Trueba, C. ; Turcanu, C. ; Turtiainen, T. ; Twenhöfel, C. ; Vaz, P. ; Duranova, Tatiana ; Raskob, Wolfgang ; Schneider, Thierry - \ 2016
    Radioprotection 51 (2016). - ISSN 0033-8451 - p. S83 - S91.
    Recommendations and requirements for the management of foodstuffs including drinking water and
    feedstuffs (but not other commodities) contaminated after a nuclear accident or a radiological event have been developed by
    international bodies such as Codex Alimentarius Commission or European Union as well as by individual countries.
    However, the experience fromsevere nuclear accidents (Chernobyl,Fukushima) and less serious radiological events, shows
    that the implementation of such systems (based on criteria expressed in activity concentration) seems to be not fully suitable
    to prevent several difficulties such as, for instance, stigmatization and even rejection attitudes from consumers or retailers
    (anticipating the fears of consumers). Tofurther investigate the possible strategies and stakeholder expectations to deal with
    this sensitive issue, a study has been launchedwithin the European research projectPREPARE-WP3. The overall objective
    of this work, coordinated is to contribute to the development of strategies, guidance and tools for the management of the
    contaminated products, taking into account the views of producers, processing and retail industries and consumers. For this
    purpose, 10 stakeholder panels from different European countries have been set up. In addition, feedback experience from
    the management of contaminated goods following the Fukushima accident has been provided by Japanese stakeholders.
    This paper highlights the key topics tackled by the different European stakeholders’ panels
    Genome-wide analysis identifies 12 loci influencing human reproductive behavior
    Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
    Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
    The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
    Food Safety Regulations Applied to Traditional and Ethnic Foods
    Meulen, B.M.J. van der; Juanjuan, Sun ; Carvajal, Ricardo ; Kite, Jonathon ; Costa Dias, Thiago - \ 2016
    In: Regulating Safety in Traditional and Ethnic Foods / Prakash, Vishweshwaraiah, Martín-Belloso, Olga, Keener, Larry, Astley, Sian, Braun, Susanne, Mcmahon, Helena, Lelieveld, Huub, Waltham : Academic Press Elsevier - ISBN 9780128006054 - p. 441 - 466.
    Traditional and ethnic foods are characterized by their history. By this category, they are usually considered safe on the basis of experience within the jurisdiction where they are indigenous. Elsewhere they may face authorization requirements.

    Foods characterized by historical production methods may face challenges from modern food hygiene legislation. In some situations, exemptions apply that enable the continuation of traditional practices, despite food safety concerns.

    This chapter explores how food law addresses one or both of these issues in the United States, Australia and New Zealand, Brazil, China, and the European Union (EU). From the perspective of global harmonization, it is preferable for national systems to take account of experience elsewhere and to be flexible toward nonindustrial ways of production.
    Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades
    Bruneau, A. ; Doyle, J.J. ; Herendeen, P. ; Hughes, C. ; Kenicer, G. ; Lewis, G. ; Mackinder, B.A. ; Pennington, R.T. ; Sanderson, M.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Brown, G. ; Cardoso, D. ; Crips, M. ; Egan, A. ; Fortunato, R. ; Hawkins, J. ; Kajita, T. ; Klitgaard, B.B. ; Koenen, E. ; Lavin, M. ; Luckow, M. ; Marazzi, B. ; McMahon, M.M. ; Miller, J.T. ; Murphy, D.J. ; Ohashi, H. ; Queiroz, L.P. de; Rico, L. ; Särkinen, T. ; Schrire, B. ; Simon, M.F. ; Souza, E.R. ; Steele, K. ; Torke, B.M. ; Wieringa, J.J. ; Wijk, B.E. - \ 2013
    Taxon 62 (2013)2. - ISSN 0040-0262 - p. 217 - 248.
    swartzia leguminosae-papilionoideae - tribe millettieae leguminosae - chloroplast dna regions - southern south-america - intron spacer regions - matk coding sequence - plastid trnl-f - molecular phylogenetics - divergence times - s.l. leguminosae
    The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades
    Green infrastructure: an integrating concept for regional climate change
    Vos, C.C. ; Teeffelen, A.J.A. van - \ 2011
    The concept of Green Infrastructure (Benedict & McMahon 2002) emphasizes the importance of ensuring the provision of ecosystem goods and services for society and the value of functionally and spatially connected, healthy ecosystems. It is being recognized that Green Infrastructure can contribute to the functional connectivity of the Natura 2000 network by improving landscape permeability and thus could also add to the resilience of ecological networks to climate change (Heller & Zavaleta 2009). In return resilient ecosystems provide many benefits to society e.g. biodiversity, climate change mitigation and adaptation, water management, pest control, pollination, etc.. There is no standard definition of Green Infrastructure and the description is often broad. A broad multifunctional definition has the advantage that many coalitions can be found between nature and other land uses and functions, such as agriculture, forestry and water management. The multifunctional nature of green infrastructure, providing multiple benefits for society, will help the support for and implementation of green infrastructure. Examples of the potentials of green infrastructure as a regional planning tool are given from the CARE project (Climate Adaptation for Rural Areas, part of the Dutch Climate for Knowledge Programme). It is illustrated how the concept of multifunctional green infrastructure on the one hand is important to increase the resilience of the ecological network but at the same time provides opportunities to achieve synergy in regional climate adaptation. We show the strong potentials of the green infrastructure as a unifying concept in regional stakeholder negotiations, as it forms, as part of the ecological network, the spatial main structure for the sustainable provision of ecosystem services.
    Microbial population dynamics during startup and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge
    McMahon, K.D. ; Zheng, D. ; Stams, A.J.M. ; Mackie, R.I. ; Raskin, L. - \ 2004
    Biotechnology and Bioengineering 87 (2004)7. - ISSN 0006-3592 - p. 823 - 834.
    propionate-oxidizing bacteria - rna hybridization probes - ribosomal-rna - syntrophobacter-wolinii - pure culture - methanogenic ecosystems - oligonucleotide probes - mixing conditions - granular sludge - gen-nov
    Microbial population dynamics were investigated during start-up and during periods of overload conditions in anaerobic co-digesters treating municipal solid waste and sewage sludge. Changes in community structure were monitored using ribosomal RNA-based oligonucleotide probe hybridization to measure the abundance of syntrophic propionate-oxidizing bacteria (SPOB), saturated fatty acid-beta-oxidizing syntrophs (SFAS), and methanogens. These changes were linked to traditional performance parameters such as biogas production and volatile fatty acid (VFA) concentrations. Digesters with high levels of Archaea started up successfully. Methanosaeta concilii was the dominant aceticlastic methanogen in these systems. In contrast, digesters that experienced a difficult start-up period had lower levels of Archaea with proportionally more abundant Methanosarcina spp. Syntrophic propionate-oxidizing bacteria and saturated fatty acid-beta-oxidizing syntrophs were present at low levels in all digesters, and SPOB appeared to play a role in stabilizing propionate levels during start-up of one digester. Digesters with a history of poor performance tolerated a severe organic overload event better than digesters that had previously performed well. It is hypothesized that higher levels of SPOB and SFAS and their methanogenic partners in previously unstable digesters are responsible for this behavior. (C) 2004 Wiley Periodicals, Inc.
    Fine structure of parvocellular receptive fields in the primate fovea revealed by laser interferometry
    McMahon, Matthew J. ; Lankheet, Martin J.M. ; Lennie, Peter ; Williams, David R. - \ 2000
    Journal of Neuroscience Methods 20 (2000)5. - ISSN 0270-6474 - p. 2043 - 2053.
    Acuity - Ganglion cells - Interferometry - LGN - Parvocellular - Retinal circuitry - Spatial vision

    Optical blurring in the eye prevents conventional physiological techniques from revealing the fine structure of the small parvocellular receptive fields in the primate fovea in vivo. We explored the organization of receptive fields in macaque parvocellular lateral geniculate nucleus cells by using sinusoidal interference fringes formed directly on the retina to measure spatial frequency tuning at different orientations. Most parvocellular cells in and near the fovea respond reliably to spatial frequencies up to and beyond 100 cycles/°of visual angle, implying center input arising mainly from a single cone. Temporal frequency and contrast response characteristics were also measured at spatial frequencies up to 130 cycles/°. We compared our spatial frequency data with the frequency responses of model receptive fields that estimate the number, configuration, and weights of cones that feed the center and surround. On the basis of these comparisons, we infer possible underlying circuits. Most cells had irregular spatial frequency-response curves that imply center input from more than one cone. The measured responses are consistent with a single cone center together with weak input from nearby cones. By exposing a fine structure that cannot be discerned by conventional techniques, interferometry allows functional measurements of the early neural mechanisms in spatial vision.

    Environmental and physiological determinants of successful foraging by naive southern elephant seal pups during their first trip to sea
    Hindell, M.A. ; McConnell, B.J. ; Fedak, M.A. ; Slip, D.J. ; Burton, H.R. ; Reijnders, P.J.H. ; McMahon, C.R. - \ 1999
    Canadian Journal of Zoology 77 (1999)11. - ISSN 0008-4301 - p. 1807 - 1821.
    The ability to forage successfully during their first trip to sea is fundamental to the ultimate survival of newly weaned southern elephant seals (Mirounga leonina). However, there is considerable variation in the body mass and fat content of seal pups at weaning, which results in some individuals having larger energy and oxygen stores than others, which may confer advantages on them. The diving behaviour of 21 newly weaned seals was studied using satellite relayed data loggers. Seals were captured at Macquarie Island in December 1995 and 1996, approximately 4 weeks after weaning. Two groups of seals were specifically targeted: a heavy group from the top quartile of weaning masses (n = 6) and a light group from the lower quartile (n = 15). Most of the seals made dives in excess of 100 m depth and 5 min before final departure from the island. However, for the first 60-80 d, all of the seals exhibited behaviour quite distinct from the patterns reported for older conspecifics, and made relatively shallow (100 +/- 39 m; mean +/- SD) and short (5.7 +/- 1.23 min) dives. During this time the seals spent 74.3 +/- 12.6 of each day diving, and the depth of the dives did not follow any diurnal pattern. The diving behaviour of all seals changed abruptly whenthey started on their return to land. During this time their behaviour was more like that of adults: they made deeper (159 +/- 9 m) and longer dives (9.01 +/- 1.69 min) than previously, and the dives showed a strong diurnal pattern in depth. There is no obvious explanation for this change in behaviour, although its abrupt nature suggests that it is unlikely to have been due to physiological changes in the seals. The size of the seals at weaning was an important influence on diving behaviour. Heavy weaners made significantly deeper (130 +/- 40 m) and longer dives (7.36 +/- 0.55 min) than light weaners (88 +/- 32 m and 5.04 +/- 0.64 min, respectively). This indicates that smaller seals are constrained to some extent by their physiological capabilities, which perhaps requires some individuals to adopt different foraging strategies. VA:IBN
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