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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    Scenario processes for socio-environmental systems analysis of futures : A review of recent efforts and a salient research agenda for supporting decision making
    Elsawah, Sondoss ; Hamilton, Serena H. ; Jakeman, Anthony J. ; Rothman, Dale ; Schweizer, Vanessa ; Trutnevyte, Evelina ; Carlsen, Henrik ; Drakes, Crystal ; Frame, Bob ; Fu, Baihua ; Guivarch, Celine ; Haasnoot, Marjolijn ; Kemp-Benedict, Eric ; Kok, Kasper ; Kosow, Hannah ; Ryan, Mike ; Delden, Hedwig van - \ 2020
    Science of the Total Environment 729 (2020). - ISSN 0048-9697
    Consistency - Cross-sectoral - Diversity - Policy - Stakeholders - Story-and-simulation - Uncertainty

    This paper reviews the latest research on scenarios including the processes and products for socio-environmental systems (SES) analysis, modeling and decision making. A group of scenario researchers and practitioners participated in a workshop to discuss consolidation of existing research on the development and use of scenario analysis in exploring and understanding the interplay between human and environmental systems. This paper presents an extended overview of the workshop discussions and follow-up review work. It is structured around the essential challenges that are crucial to progress support of decision making and learning with respect to our highly uncertain socio-environmental futures. It identifies a practical research agenda where challenges are grouped according to the process stage at which they are most significant: before, during, and after the creation of the scenarios as products. These challenges for SES include: enhancing the role of stakeholder and public engagement in the co-development of scenarios, linking scenarios across multiple geographical, sectoral and temporal scales, improving the links between the qualitative and quantitative aspects of scenario analysis, addressing uncertainties especially surprise, addressing scenario diversity and their consistency together, communicating scenarios including visualization methods, and linking scenarios to decision making.

    Physical activity and risks of breast and colorectal cancer : a Mendelian randomisation analysis
    Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Martin, Richard M. ; Lewis, Sarah J. ; Kazmi, Nabila ; Robinson, Timothy M. ; Albanes, Demetrius ; Aleksandrova, Krasimira ; Berndt, Sonja I. ; Timothy Bishop, D. ; Brenner, Hermann ; Buchanan, Daniel D. ; Bueno-de-Mesquita, Bas ; Campbell, Peter T. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Ellingjord-Dale, Merete ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Giovannucci, Edward ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harlid, Sophia ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hopper, John L. ; Hsu, Li ; María Huerta, José ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Vecchia, Carlo La; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Lindor, Noralane M. ; Lynch, Brigid ; Markowitz, Sanford D. ; Masala, Giovanna ; May, Anne M. ; Milne, Roger ; Monninkhof, Evelyn ; Moreno, Lorena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Perduca, Vittorio ; Pharoah, Paul D.P. ; Platz, Elizabeth A. ; Potter, John D. ; Rennert, Gad ; Riboli, Elio ; Sánchez, Maria Jose ; Schmit, Stephanie L. ; Schoen, Robert E. ; Severi, Gianluca ; Sieri, Sabina ; Slattery, Martha L. ; Song, Mingyang ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Travis, Ruth C. ; Trichopoulou, Antonia ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Vodicka, Pavel ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Peters, Ulrike ; Gunter, Marc J. ; Murphy, Neil - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Physical activity has been associated with lower risks of breast and colorectal cancer in epidemiological studies; however, it is unknown if these associations are causal or confounded. In two-sample Mendelian randomisation analyses, using summary genetic data from the UK Biobank and GWA consortia, we found that a one standard deviation increment in average acceleration was associated with lower risks of breast cancer (odds ratio [OR]: 0.51, 95% confidence interval [CI]: 0.27 to 0.98, P-value = 0.04) and colorectal cancer (OR: 0.66, 95% CI: 0.48 to 0.90, P-value = 0.01). We found similar magnitude inverse associations for estrogen positive (ER+ve) breast cancer and for colon cancer. Our results support a potentially causal relationship between higher physical activity levels and lower risks of breast cancer and colorectal cancer. Based on these data, the promotion of physical activity is probably an effective strategy in the primary prevention of these commonly diagnosed cancers.

    Hazardous Chemicals in Plastics in Marine Environments : International Pellet Watch
    Yamashita, Rei ; Tanaka, Kosuke ; Yeo, Bee Geok ; Takada, Hideshige ; Franeker, Jan A. van; Dalton, Megan ; Dale, Eric - \ 2019
    In: Hazardous Chemicals Associated with Plastics in the Marine Environment Springer Verlag (Handbook of Environmental Chemistry ) - ISBN 9783319955667 - p. 163 - 183.
    Additives - Equilibrium - Open ocean - Pellets - Sorption

    Marine plastic debris, including microplastics <5Â mm, contain additives as well as hydrophobic chemicals sorbed from surrounding seawater. A volunteer-based global monitoring programme entitled International Pellet Watch (IPW) is utilizing the sorptive nature of plastics, more specifically of beached polyethylene (PE) pellets, in order to measure persistent organic pollutants (POPs) throughout the world. Spatial patterns of polychlorinated biphenyls (PCBs) and organochlorine pesticides have been revealed. Original data of IPW show large piece-to-piece variability in PCB concentrations in pellets collected at each location. This is explained by the combination of slow sorption/desorption and large variabilities of speed and route of floating plastics. The sporadically high concentrations of POPs, both sorbed chemicals and hydrophobic additives, are frequently observed in pellets and the other microplastics in open ocean and remote islands. This poses a chemical threat to marine ecosystems in remote areas.

    Genetic association analysis of candidate loci under selection with size in the South African abalone
    Dale-Kuys, Ruth ; Vervalle, Jessica ; Roodt-Wilding, Rouvay ; Rhode, Clint - \ 2017
    Aquaculture International 25 (2017)3. - ISSN 0967-6120 - p. 1197 - 1214.
    Association studies - Domestication - Growth rate - Haliotis midae - Marker assisted selection - Quantitative trait loci - Signatures of selection

    The abalone, Haliotis midae, is an important aquaculture species in South Africa and the largest generator of revenue for the mariculture sector. Despite domestication of this species still being in the initial stages, significant differentiation has been observed between wild and cultured populations. The genetic consequences of founder effects have been well documented in many aquaculture species; however, the effects of selection remain under-investigated. Previous studies in this species identified several loci thought to be under divergent selection between wild and cultured populations. The aim of this study was therefore to investigate the influence of artificial selection on genetic variation by determining whether these candidate loci are associated with larger size (primary production trait) in a commercial F1 population. Thirteen microsatellite markers, putatively identified as being under directional selection, were chosen for association analysis. Various statistical tests were used to detect significant genotype-phenotype associations within a family-bias corrected population cohort and two family cohorts. Two loci demonstrated significant evidence for association with size, with both loci possessing alleles that correlated significantly with either increased or decreased size. As size is currently the only trait actively selected for in terms of production, the current results suggest that natural selection for adaptation to the novel aquaculture environment is the predominant selective force shaping genetic variation during the initial stages of domestication in abalone. Furthermore, whilst it is currently unclear as to whether these loci represent causative variants for size traits, they may be useful in future molecular-assisted breeding programmes for H. midae.

    Transgenic Cavendish bananas with resistance to Fusarium wilt tropical race 4
    Dale, James ; James, Anthony ; Paul, Jean Yves ; Khanna, Harjeet ; Smith, Mark ; Peraza-Echeverria, Santy ; Garcia-Bastidas, Fernando ; Kema, Gert ; Waterhouse, Peter ; Mengersen, Kerrie ; Harding, Robert - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723
    Banana (Musa spp.) is a staple food for more than 400 million people. Over 40% of world production and virtually all the export trade is based on Cavendish banana. However, Cavendish banana is under threat from a virulent fungus, Fusarium oxysporum f. sp. cubense tropical race 4 (TR4) for which no acceptable resistant replacement has been identified. Here we report the identification of transgenic Cavendish with resistance to TR4. In our 3-year field trial, two lines of transgenic Cavendish, one transformed with RGA2, a gene isolated from a TR4-resistant diploid banana, and the other with a nematode-derived gene, Ced9, remain disease free. Transgene expression in the RGA2 lines is strongly correlated with resistance. Endogenous RGA2 homologs are also present in Cavendish but are expressed tenfold lower than that in our most resistant transgenic line. The expression of these homologs can potentially be elevated through gene editing, to provide non-transgenic resistance.
    Bio-based chemicals: general discussion
    Bitter, Harry ; Clark, James ; Rothenberg, Gadi ; Matharu, Avtar ; Crestini, Claudia ; Argyropoulos, Dimitris ; Cabrera-Rodríguez, Carlos I. ; Dale, Bruce E. ; Stevens, Christian ; Marrocchi, Assunta ; Graca, Ines ; Luo, Hui ; Pant, Deepak ; Wilson, Karen ; Zijlstra, Douwe Sjirk ; Gschwend, Florence ; Mu, Xindong ; Zhou, Long ; Hu, Changwei ; Lapkin, Alexei ; Mascal, Mark ; Budarin, Vitaliy ; Hunt, Andrew ; Waldron, Keith ; Zhang, Fang ; Zhenova, Anna ; Samec, Joseph ; Huber, George ; Coma, Marta ; Huang, Xiaoming ; Bomtempo, José-Vitor - \ 2017
    Faraday Discussions 202 (2017). - ISSN 1359-6640 - p. 227 - 245.
    The roads ahead : Narratives for shared socioeconomic pathways describing world futures in the 21st century
    O'Neill, Brian C. ; Kriegler, Elmar ; Ebi, Kristie L. ; Kemp-Benedict, Eric ; Riahi, Keywan ; Rothman, Dale S. ; Ruijven, Bas J. van; Vuuren, Detlef P. van; Birkmann, Joern ; Kok, Kasper - \ 2017
    Global environmental change : human and policy dimensions 42 (2017). - ISSN 0959-3780 - p. 169 - 180.
    Adaptation - Climate change - Mitigation - Narratives - Scenarios - Shared socioeconomic pathways

    Long-term scenarios play an important role in research on global environmental change. The climate change research community is developing new scenarios integrating future changes in climate and society to investigate climate impacts as well as options for mitigation and adaptation. One component of these new scenarios is a set of alternative futures of societal development known as the shared socioeconomic pathways (SSPs). The conceptual framework for the design and use of the SSPs calls for the development of global pathways describing the future evolution of key aspects of society that would together imply a range of challenges for mitigating and adapting to climate change. Here we present one component of these pathways: the SSP narratives, a set of five qualitative descriptions of future changes in demographics, human development, economy and lifestyle, policies and institutions, technology, and environment and natural resources. We describe the methods used to develop the narratives as well as how these pathways are hypothesized to produce particular combinations of challenges to mitigation and adaptation. Development of the narratives drew on expert opinion to (1) identify key determinants of these challenges that were essential to incorporate in the narratives and (2) combine these elements in the narratives in a manner consistent with scholarship on their inter-relationships. The narratives are intended as a description of plausible future conditions at the level of large world regions that can serve as a basis for integrated scenarios of emissions and land use, as well as climate impact, adaptation and vulnerability analyses.

    Evaluating agricultural trade-offs in the age of sustainable development
    Kanter, David R. ; Musumba, Mark ; Wood, Sylvia L.R. ; Palm, Cheryl ; Antle, John ; Balvanera, Patricia ; Dale, Virginia H. ; Havlik, Petr ; Kline, Keith L. ; Scholes, R.J. ; Thornton, Philip ; Tittonell, Pablo ; Andelman, Sandy - \ 2016
    Agricultural Systems 163 (2016). - ISSN 0308-521X - p. 73 - 88.
    A vibrant, resilient and productive agricultural sector is fundamental to achieving the Sustainable Development Goals. Bringing about such a transformation requires optimizing a range of agronomic, environmental and socioeconomic outcomes from agricultural systems – from crop yields, to biodiversity, to human nutrition. However, these outcomes are not independent of each other – they interact in both positive and negative ways, creating the potential for synergies and trade-offs. Consequently, transforming the agricultural sector for the age of sustainable development requires tracking these interactions, assessing if objectives are being achieved and allowing for adaptive management within the diverse agricultural systems that make up global agriculture. This paper reviews the field of agricultural trade-off analysis, which has emerged to better understand these interactions – from field to farm, region to continent. Taking a “cradle-to-grave” approach, we distill agricultural trade-off analysis into four steps: 1) characterizing the decision setting and identifying the context-specific indicators needed to assess agricultural sustainability, 2) selecting the methods for generating indicator values across different scales, 3) deciding on the means of evaluating and communicating the trade-off options with stakeholders and decision-makers, and 4) improving uptake of trade-off analysis outputs by decision-makers. Given the breadth of the Sustainable Development Goals and the importance of agriculture to many of them, we assess notions of human well-being beyond income or direct health concerns (e.g. related to gender, equality, nutrition), as well as diverse environmental indicators ranging from soil health to biodiversity to climate forcing. Looking forward, areas of future work include integrating the four steps into a single modeling platform and connecting tools across scales and disciplines to facilitate trade-off analysis. Likewise, enhancing the policy relevance of agricultural trade-off analysis requires improving scientist-stakeholder engagement in the research process. Only then can this field proactively address trade-off issues that are integral to sustainably intensifying local and global agriculture – a critical step toward successfully implementing the Sustainable Development Goals.
    Human autoreactive T cells recognize CD1b and phospholipids
    Rhijn, Ildiko Van; Berlo, Twan Van; Hilmenyuk, Tamara ; Cheng, Tan Yun ; Wolf, Benjamin J. ; Tatituri, Raju V.V. ; Uldrich, Adam P. ; Napolitani, Giorgio ; Cerundolo, Vincenzo ; Altman, John D. ; Willemsen, Peter ; Huang, Shouxiong ; Rossjohn, Jamie ; Besra, Gurdyal S. ; Brenner, M.B. ; Godfrey, Dale I. ; Moody, D.B. - \ 2016
    Proceedings of the National Academy of Sciences of the United States of America 113 (2016)2. - ISSN 0027-8424 - p. 380 - 385.
    CD1b - Dendritic cell - Lipid antigen - Self-antigen - T cell

    In contrast with the common detection of T cells that recognize MHC, CD1a, CD1c, or CD1d proteins, CD1b autoreactive T cells have been difficult to isolate in humans. Here we report the development of polyvalent complexes of CD1b proteins and carbohydrate backbones (dextramers) and their use in identifying CD1b autoreactive T cells from human donors. Activation is mediated by αβ T-cell receptors (TCRs) binding to CD1b-phospholipid complexes, which is sufficient to activate autoreactive responses to CD1b-expressing cells. Using mass spectrometry and T-cell responses to scan through the major classes of phospholipids, we identified phosphatidylglycerol (PG) as the immunodominant lipid antigen. T cells did not discriminate the chemical differences that distinguish mammalian PG from bacterial PG. Whereas most models of T-cell recognition emphasize TCR discrimination of differing self and foreign structures, CD1b autoreactive T cells recognize lipids with dual self and foreign origin. PG is rare in the cellular membranes that carry CD1b proteins. However, bacteria and mitochondria are rich in PG, so these data point to a more general mechanism of immune detection of infection- or stressassociated lipids.

    Input and service provision supply methods in mixed crop-livestock production systems in South-Ethiopia: Improvement options from a dairy perspective
    Terefe, T. ; Lee, J. van der - \ 2015
    - 7 p.
    This study was conducted in the Dale and Shebedino districts of southern Ethiopia during the period October 2014 to January 2015. It investigates dairy-related input and service provision in mixed crop-livestock production systems. Data were collected from 120 dairy producers, six focus group discussions, and six key informant interviews. Concentrate feed, improved forage seed, heifers, breeding services, and veterinary services, &drug supply appeared to be the main dairy inputs and services used by the farmers. In Dale district, concentrate feed and breeding serviceswere the main input and servicesobtained by dairy farmers, whilethe farmers in Shebedino district more frequently use improved forage seed and veterinary vaccinesand drugs. The Agriculture office is the main source of dairy inputs and services in Shebedino district. In Dale district, private actors like cooperatives, companies, and NGOs are the main service providers. Theyplay a vital role by providing feed, veterinary drugs, animal health care, and milk processing, and serve as an important market outlet for milk and dairy products in this district. The major shortcomings of input supply and service provision in the two districts included poor support for husbandry system improvement, fragmented livestock development operations, lack of a value chain approach, inefficient and ineffective AI services, shortage in distribution of improved dairy animals and forage seed, limited private sector involvement, and poor organization of farmers for input supply and service provision.Dairy related input supply and service provision in the studied areas could be improved by organizing farmers into small and medium-scale commercial dairy enterprises through the involvement and support of private sector and national and international development partners.
    Smallholder Dairy Production: Analysis of Development Constraints in the Dairy Value Chain of Southern Ethiopia
    Weldesilassie, T. ; Oosting, S.J. ; Lee, J. van der - \ 2014
    In: Book of Abstracts of the 6th All Africa Conference on Animal Agriculture. - - p. 39 - 40.
    This study analyses development constraints of smallholder dairy production system in the Dale and Shebedino districts of Southern Ethiopia. Data were collected from 120 dairy producers, six focus group discussions and six key informant interviews. Two major dairy production systems were identified based on major agricultural activities: the coffee-based dairy production system and the enset-coffee-based dairy production system. Coffee-based dairy producers owned less local breed dairy cows and earned higher income as compared to farmers in enset-coffee-based dairy production systems, which generated relatively more income from off-farm activities. Access to farm resources, inputs and services were the major dairy development constraints in the two districts. Farmers in the districts had limited access to credit, veterinary services, artificial insemination (AI), and markets in the dairy value chain. Rapid urbanization, rising income, and population growth were creating market opportunities for dairy products in the area. Market was found to be the driving force of dairy development. In response to increasing demand for dairy products, most of the dairy producers were willing to expand their dairy farming. Sustainable dairy development can be achieved through improving access to key resources, inputs and services in the dairy production value chain and markets
    Protease digestion from wheat stillage within a dry grind ethanol facility
    Bals, B. ; Brehmer, B. ; Dale, B. ; Sanders, J.P.M. - \ 2011
    Biotechnology Progress 27 (2011)2. - ISSN 8756-7938 - p. 428 - 434.
    distillers grains - extraction - proteins - optimization - hydrolysis - solubles - alcohol - options - water
    As the current starch based ethanol market increases at its rapid pace, finding new markets for the primary coproduct, distiller's grains, has gained considerable interest. One possibility is to isolate the protein-rich fraction for use as precursors to biochemicals and bioplastics, further decreasing fossil fuel consumption. This research focuses on enzymatic extraction of protein peptides from wheat heavy stillage using commercially available proteases. The energy saved due to this process ranged from ~1.5 to 3.0 GJ/ton wheat stillage compared to fossil fuel-based chemicals. Using Protex 6L (Genencor), ~57% of the protein in the stillage was soluble 24 h after protease addition at 0.1% w/w loading. Of these proteins, ~32% were already soluble, indicating the importance of using wet heavy stillage as the feedstock rather than dried distiller's grains. Peptide size was less than 6 kDa. Further improvements in protein removal may be obtained through a fed batch addition of protease and improved protease cocktails
    Genome sequence of the pea aphid Acyrthosiphon pisum
    Richards, Stephen ; Gibbs, Richard A. ; Gerardo, Nicole M. ; Moran, Nancy ; Nakabachi, Atsushi ; Stern, David ; Tagu, Denis ; Wilson, Alex C.C. ; Muzny, Donna ; Kovar, Christie ; Cree, Andy ; Chacko, Joseph ; Chandrabose, Mimi N. ; Dao, Marvin Diep ; Dinh, Huyen H. ; Gabisi, Ramatu Ayiesha ; Hines, Sandra ; Hume, Jennifer ; Jhangian, Shalini N. ; Joshi, Vandita ; Lewis, Lora R. ; Liu, Yih Shin ; Lopez, John ; Morgan, Margaret B. ; Nguyen, Ngoc Bich ; Okwuonu, Geoffrey O. ; Ruiz, San Juana ; Santibanez, Jireh ; Wright, Rita A. ; Fowler, Gerald R. ; Hitchens, Matthew E. ; Lozado, Ryan J. ; Moen, Charles ; Steffen, David ; Warren, James T. ; Zhang, Jingkun ; Nazareth, Lynne V. ; Chavez, Dean ; Davis, Clay ; Lee, Sandra L. ; Patel, Bella Mayurkumar ; Pu, Ling Ling ; Bell, Stephanie N. ; Johnson, Angela Jolivet ; Vattathil, Selina ; Williams, Rex L. ; Shigenobu, Shuji ; Dang, Phat M. ; Morioka, Mizue ; Fukatsu, Takema ; Kudo, Toshiaki ; Miyagishima, Shin Ya ; Jiang, Huaiyang ; Worley, Kim C. ; Legeai, Fabrice ; Gauthier, Jean Pierre ; Collin, Olivier ; Zhang, Lan ; Chen, Hsiu Chuan ; Ermolaeva, Olga ; Hlavina, Wratko ; Kapustin, Yuri ; Kiryutin, Boris ; Kitts, Paul ; Maglott, Donna ; Murphy, Terence ; Pruitt, Kim ; Sapojnikov, Victor ; Souvorov, Alexandre ; Thibaud-Nissen, Françoise ; Câmara, Francisco ; Guigó, Roderic ; Stanke, Mario ; Solovyev, Victor ; Kosarev, Peter ; Gilbert, Don ; Gabaldón, Toni ; Huerta-Cepas, Jaime ; Marcet-Houben, Marina ; Pignatelli, Miguel ; Moya, Andrés ; Rispe, Claude ; Ollivier, Morgane ; Quesneville, Hadi ; Permal, Emmanuelle ; Llorens, Carlos ; Futami, Ricardo ; Hedges, Dale ; Robertson, Hugh M. ; Alioto, Tyler ; Mariotti, Marco ; Nikoh, Naruo ; McCutcheon, John P. ; Burke, Gaelen ; Kamins, Alexandra ; Latorre, Amparo ; Ashton, Peter ; Calevro, Federica ; Charles, Hubert ; Colella, Stefano ; Douglas, Angela E. ; Jander, Georg ; Jones, Derek H. ; Febvay, Gérard ; Kamphuis, Lars G. ; Kushlan, Philip F. ; Macdonald, Sandy ; Ramsey, John ; Schwartz, Julia ; Seah, Stuart ; Thomas, Gavin ; Vellozo, Augusto ; Cass, Bodil ; Degnan, Patrick ; Hurwitz, Bonnie ; Leonardo, Teresa ; Koga, Ryuichi ; Altincicek, Boran ; Anselme, Caroline ; Atamian, Hagop ; Barribeau, Seth M. ; Vos, Martin De; Duncan, Elizabeth ; Evans, Jay ; Ghanim, Murad ; Heddi, Abdelaziz ; Kaloshian, Isgouhi ; Vincent-Monegat, Carole ; Parker, Ben J. ; Pérez-Brocal, Vicente ; Rahbé, Yvan ; Spragg, Chelsea J. ; Tamames, Javier ; Tamarit, Daniel ; Tamborindeguy, Cecilia ; Vilcinskas, Andreas ; Bickel, Ryan D. ; Brisson, Jennifer A. ; Butts, Thomas ; Chang, Chun Che ; Christiaens, Olivier ; Davis, Gregory K. ; Duncan, Elizabeth ; Ferrier, David ; Iga, Masatoshi ; Janssen, Ralf ; Lu, Hsiao Ling ; McGregor, Alistair ; Miura, Toru ; Smagghe, Guy ; Smith, James ; Zee, Maurijn Van Der; Velarde, Rodrigo ; Wilson, Megan ; Dearden, Peter ; Edwards, Owain R. ; Gordon, Karl ; Hilgarth, Roland S. ; Rider, Stanley Dean ; Srinivasan, Dayalan ; Walsh, Thomas K. ; Ishikawa, Asano ; Jaubert-Possamai, Stéphanie ; Fenton, Brian ; Huang, Wenting ; Rizk, Guillaume ; Lavenier, Dominique ; Nicolas, Jacques ; Smadja, Carole ; Zhou, Jing Jiang ; Vieira, Filipe G. ; He, Xiao Li ; Liu, Renhu ; Rozas, Julio ; Field, Linda M. ; Campbell, Peter ; Carolan, James C. ; Fitzroy, Carol I.J. ; Reardon, Karen T. ; Reeck, Gerald R. ; Singh, Karam ; Wilkinson, Thomas L. ; Huybrechts, Jurgen ; Abdel-Latief, Mohatmed ; Robichon, Alain ; Veenstra, Jan A. ; Hauser, Frank ; Cazzamali, Giuseppe ; Schneider, Martina ; Williamson, Michael ; Stafflinger, Elisabeth ; Hansen, Karina K. ; Grimmelikhuijzen, Cornelis J.P. ; Price, Daniel R.G. ; Caillaud, Marina ; Fleet, Eric Van; Ren, Qinghu ; Gatehouse, John A. ; Brault, Véronique ; Monsion, Baptiste ; Diaz, Jason ; Hunnicutt, Laura ; Ju, Ho Jong ; Pechuan, Ximo ; Aguilar, José ; Cortés, Teresa ; Ortiz-Rivas, Benjamín ; Martínez-Torres, David ; Dombrovsky, Aviv ; Dale, Richard P. ; Davies, T.G.E. ; Williamson, Martin S. ; Jones, Andrew ; Sattelle, David ; Williamson, Sally ; Wolstenholme, Adrian ; Cottret, Ludovic ; Sagot, Marie France ; Heckel, David G. ; Hunter, Wayne - \ 2010
    PloS Biology 8 (2010)2. - ISSN 1544-9173

    Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

    Over een fascinatie voor een fascinatie
    Waal, R.M. de - \ 2010
    Topos : periodiek over landschapsarchitectuur, ruimtelijke planning en sociaal-ruimtelijke analyse 20 (2010). - ISSN 1572-302X - p. 60 - 63.
    landschap - perceptie - landscape - perception
    Volgens Van Dale is fascineren 'zeer sterk boeien'. Mijn landschappen hebben een dergelijke uitwerking op mensen. Maar waarom worden mensen eigenlijk zo geboeid door deze op het eerste gezicht negetieve ingrepen op het landschap? En wie zijn deze mensen? En waarom boeit deze fascinatie van anderen de auteur, als landschapsarchitect?
    Sensitivity to long-term climate change of subpermafrost groundwater systems in Svalbard
    Haldorsen, S. ; Heim, M. ; Dale, A. ; Landvik, J.Y. ; Ploeg, M.J. van der; Leijnse, A. ; Salvigsen, O. ; Ove Hagen, J. ; Banks, D. - \ 2010
    Quaternary Research 73 (2010)2. - ISSN 0033-5894 - p. 393 - 402.
    troll thermal springs - ice-sheet - northwestern spitsbergen - travertine formation - western spitsbergen - glacial maximum - mass-balance - north slope - hydrochemistry - bockfjorden
    Deep subpermafrost aquifers are highly climate-dependent, with the permafrost as an aquitard preventing groundwater recharge and discharge. A study from the high-arctic island of Spitsbergen, Svalbard, shows that during a glacial to interglacial phase, both the permafrost and the glacier regime will respond to climatic changes, and a glacier-fed groundwater flow system will vary accordingly. A full glaciation results in the melting of permafrost, and groundwater can flow through pores and fracture systems in the rocks and sediments below the temperate zones of glaciers. These groundwater flow systems will mainly be localized to fjords and valleys and form low-lying terrestrial springs when the relative sea level drops during deglaciation due to glacio-isostatic rise. During an interglaciation, permafrost develops and thickens and the groundwater recharge and discharge areas will thereby be gradually reduced to a minimum reached at the warmest part of an interglaciation. An already frozen spring system cannot reopen before the permafrost melts. Only groundwater springs related to permanently warm-based glacial ice will persist into the next glaciation. During a new glaciation, flow systems that terminated during the previous interglaciation may become revitalized if overridden by warm-based ice causing permafrost thawing.
    Identifying future research needs in landscape genetics: Where to from here?
    Balkenhol, N. ; Gugerli, F. ; Cushman, S.A. ; Waits, L.P. ; Coulon, A. ; Arntzen, J.W. ; Holderegger, R. ; Wagner, H.H. ; Arens, P.F.P. ; Campagne, P. ; Dale, V.H. ; Nicieza, A.G. ; Smulders, M.J.M. ; Tedesco, E. ; Wang, H. ; Wasserman, T. - \ 2009
    Landscape Ecology 24 (2009)4. - ISSN 0921-2973 - p. 455 - 463.
    population-structure - habitat fragmentation - environmental-factors - sympatric speciation - spatial-analysis - circuit-theory - diversity - ecology - connectivity - conservation
    Landscape genetics is an emerging interdisciplinary field that combines methods and concepts from population genetics, landscape ecology, and spatial statistics. The interest in landscape genetics is steadily increasing, and the field is evolving rapidly. We here outline four major challenges for future landscape genetic research that were identified during an international landscape genetics workshop. These challenges include (1) the identification of appropriate spatial and temporal scales; (2) current analytical limitations; (3) the expansion of the current focus in landscape genetics; and (4) interdisciplinary communication and education. Addressing these research challenges will greatly improve landscape genetic applications, and positively contribute to the future growth of this promising field
    Improving the corn-ethanol industry: studying protein separation techniques to obtain higher value added product options for distillers grains
    Brehmer, B. ; Bals, B. ; Sanders, J.P.M. ; Dale, B. - \ 2008
    Biotechnology and Bioengineering 101 (2008)1. - ISSN 0006-3592 - p. 49 - 61.
    enzymatic-hydrolysis - pretreatment - biomass - energy - stover
    Currently in America the biofuel ethanol is primarily being produced by the dry grind technique to obtain the starch contained in the corn grains and subsequently subjected to fermentation. This so-called 1st generation technology has two setbacks; first the lingering debate whether its life cycle contributes to a reduction of fossil fuels and the animal feed sectors future supply/demand imbalance caused by the co-product dry distillers grains (DDGS). Additional utilization of the cellulosic components and separation of the proteins for use as chemical precursors have the potential to alleviate both setbacks. Several different corn feedstock layouts were treated with 2nd generation ammonia fiber expansion (AFEX) pre-treatment technology and tested for protein separation options (protease solubilization). The resulting system has the potential to greatly improve ethanol yields with lower bioprocessing energy costs and satisfy a significant portion of the organic chemical industry.
    Applying Knowledge Engineering and Ontology Engineering to construct a Knowledge Base for Early Warning and Proactive Control
    Li, Y. ; Kramer, M.R. ; Beulens, A.J.M. ; Vorst, J.G.A.J. van der - \ 2008
    In: WMSCI 2008.The 12th World Multi-Conference on Systemics, Cybernetics and Informatics. - Orlando : International Institute of Informatics and Systemics - ISBN 9781934272305 - p. 146 - 151.
    Characterization and distribution of mating type genes in the Dothistroma needle blight pathogens
    Groenewald, M. ; Barnes, I. ; Bradshaw, R.E. ; Brown, A.V. ; Dale, A. ; Groenewald, J.Z. ; Lewis, K.J. ; Wingfield, B.D. ; Wingfield, M.J. ; Crous, P.W. - \ 2007
    Phytopathology 97 (2007)7. - ISSN 0031-949X - p. 825 - 834.
    pinus-radiata - scirrhia-pini - mycosphaerella-graminicola - dna-sequences - novo-ulmi - protein - cloning - cercospora - locus - idiomorphs
    Dothistroma septosporum and D. pini are the two causal agents of Dothistroma needle blight of Pinus spp. in natural forests and plantations. Degenerate primers amplified portions of mating type genes (MAT1-1-1 and MAT1-2) and chromosome walking was applied to obtain the full-length genes in both species. The mating-type-specific primers designed in this study could distinguish between the morphologically similar D. pini and D. septosporum and between the different mating types of these species. Screening of isolates from global collections of D. septosporum showed that only MAT2 isolates are present in Australian and New Zealand collections, where only the asexual form of the fungus has been found. In contrast, both mating types of D. septosporum were present in collections from Canada and Europe, where the sexual state is known. Intriguingly, collections from South Africa and the United Kingdom, where the sexual state of the fungus is unknown, included both mating types. In D. pini, for which no teleomorph is known, both mating types were present in collections from the United States. These results provided new insights into the biology and global distribution of two of the world's most important pine pathogens and should facilitate management of the diseases caused by these fungi.
    Dutch force pace on new regulations for closed systems and develop nutrient sensors
    Dale, S. ; Gieling, Th.H. - \ 1999
    The Commercial Greenhouse Grower (1999)March. - p. 13 - 13.
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