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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    Global plant trait relationships extend to the climatic extremes of the tundra biome
    Thomas, H.J.D. ; Bjorkman, A.D. ; Myers-Smith, I.H. ; Elmendorf, S.C. ; Kattge, J. ; Diaz, S. ; Vellend, M. ; Blok, D. ; Cornelissen, J.H.C. ; Forbes, B.C. ; Henry, G.H.R. ; Hollister, R.D. ; Normand, S. ; Prevéy, J.S. ; Rixen, C. ; Schaepman-Strub, G. ; Wilmking, M. ; Wipf, S. ; Cornwell, W.K. ; Beck, P.S.A. ; Georges, D. ; Goetz, S.J. ; Guay, K.C. ; Rüger, N. ; Soudzilovskaia, N.A. ; Spasojevic, M.J. ; Alatalo, J.M. ; Alexander, H.D. ; Anadon-Rosell, A. ; Angers-Blondin, S. ; Beest, M. te; Berner, L.T. ; Björk, R.G. ; Buchwal, A. ; Buras, A. ; Carbognani, M. ; Christie, K.S. ; Collier, L.S. ; Cooper, E.J. ; Elberling, B. ; Eskelinen, A. ; Frei, E.R. ; Grau, O. ; Grogan, P. ; Hallinger, M. ; Heijmans, M.M.P.D. ; Hermanutz, L. ; Hudson, J.M.G. ; Johnstone, J.F. ; Hülber, K. ; Iturrate-Garcia, M. ; Iversen, C.M. ; Jaroszynska, F. ; Kaarlejarvi, E. ; Kulonen, A. ; Lamarque, L.J. ; Lantz, T.C. ; Lévesque, E. ; Little, C.J. ; Michelsen, A. ; Milbau, A. ; Nabe-Nielsen, J. ; Nielsen, S.S. ; Ninot, J.M. ; Oberbauer, S.F. ; Olofsson, J. ; Onipchenko, V.G. ; Petraglia, A. ; Rumpf, S.B. ; Shetti, R. ; Speed, J.D.M. ; Suding, K.N. ; Tape, K.D. ; Tomaselli, M. ; Trant, A.J. ; Treier, U.A. ; Tremblay, M. ; Venn, S.E. ; Vowles, T. ; Weijers, S. ; Wookey, P.A. ; Zamin, T.J. ; Bahn, M. ; Blonder, B. ; Bodegom, P.M. van; Bond-Lamberty, B. ; Campetella, G. ; Cerabolini, B.E.L. ; Chapin, F.S. ; Craine, J.M. ; Dainese, M. ; Green, W.A. ; Jansen, S. ; Kleyer, M. ; Manning, P. ; Niinemets, ; Onoda, Y. ; Ozinga, W.A. ; Peñuelas, J. ; Poschlod, P. ; Reich, P.B. ; Sandel, B. ; Schamp, B.S. ; Sheremetiev, S.N. ; Vries, F.T. de - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.

    The landscape of soil carbon data: Emerging questions, synergies and databases
    Malhotra, Avni ; Todd-Brown, Katherine ; Nave, Lucas E. ; Batjes, Niels H. ; Holmquist, James R. ; Hoyt, Alison M. ; Iversen, Colleen M. ; Jackson, Robert B. ; Lajtha, Kate ; Lawrence, Corey ; Vindušková, Olga ; Wieder, William ; Williams, Mathew ; Hugelius, Gustaf ; Harden, Jennifer - \ 2019
    Progress in Physical Geography 43 (2019)5. - ISSN 0309-1333 - p. 707 - 719.
    long-term ecological research - model–data integration - root traits - Soil carbon data - soil carbon stabilization - soil chronosequence - soil database - soil radiocarbon - wetland carbon

    Soil carbon has been measured for over a century in applications ranging from understanding biogeochemical processes in natural ecosystems to quantifying the productivity and health of managed systems. Consolidating diverse soil carbon datasets is increasingly important to maximize their value, particularly with growing anthropogenic and climate change pressures. In this progress report, we describe recent advances in soil carbon data led by the International Soil Carbon Network and other networks. We highlight priority areas of research requiring soil carbon data, including (a) quantifying boreal, arctic and wetland carbon stocks, (b) understanding the timescales of soil carbon persistence using radiocarbon and chronosequence studies, (c) synthesizing long-term and experimental data to inform carbon stock vulnerability to global change, (d) quantifying root influences on soil carbon and (e) identifying gaps in model–data integration. We also describe the landscape of soil datasets currently available, highlighting their strengths, weaknesses and synergies. Now more than ever, integrated soil data are needed to inform climate mitigation, land management and agricultural practices. This report will aid new data users in navigating various soil databases and encourage scientists to make their measurements publicly available and to join forces to find soil-related solutions.

    Enhanced nutrient supply and intestinal microbiota development in very low birth weight infants
    Blakstad, Elin W. ; Korpela, Katri ; Lee, Sindre ; Nakstad, Britt ; Moltu, Sissel J. ; Strømmen, Kenneth ; Rønnestad, Arild E. ; Brække, Kristin ; Iversen, Per O. ; Vos, Willem M. de; Drevon, Christian A. - \ 2019
    Pediatric Research 86 (2019). - ISSN 0031-3998 - p. 323 - 332.

    Background: Promoting a healthy intestinal microbiota may have positive effects on short- and long-term outcomes in very low birth weight (VLBW; BW < 1500 g) infants. Nutrient supply influences the intestinal microbiota. Methods: Fifty VLBW infants were randomized to an intervention group receiving enhanced nutrient supply or a control group. Fecal samples from 45 infants collected between birth and discharge were analyzed using 16S ribosomal RNA (rRNA) amplicon sequencing. Results: There was considerable individual variation in microbiota development. Microbial richness decreased towards discharge in the controls compared to the intervention group. In the intervention group, there was a greater increase in diversity among moderately/very preterm (MVP, gestational age ≥ 28 weeks) infants and a steeper decrease in relative Staphylococcus abundance in extremely preterm (EP, gestational age < 28 weeks) infants as compared to controls. Relative Bifidobacterium abundance tended to increase more in MVP controls compared to the intervention group. Abundance of pathogens was not increased in the intervention group. Higher relative Bifidobacterium abundance was associated with improved weight gain. Conclusion: Nutrition may affect richness, diversity, and microbiota composition. There was no increase in relative abundance of pathogens among infants receiving enhanced nutrient supply. Favorable microbiota development was associated with improved weight gain.

    Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome
    Thomas, H.J.D. ; Myers-Smith, I.H. ; Bjorkman, A.D. ; Elmendorf, S.C. ; Blok, D. ; Cornelissen, J.H.C. ; Forbes, B.C. ; Hollister, R.D. ; Normand, S. ; Prevéy, J.S. ; Rixen, C. ; Schaepman-Strub, G. ; Wilmking, M. ; Wipf, S. ; Cornwell, W. ; Kattge, J. ; Goetz, S.J. ; Guay, K.C. ; Alatalo, J.M. ; Anadon-Rosell, A. ; Angers-Blondin, S. ; Berner, L.T. ; Björk, R.G. ; Buchwal, A. ; Buras, A. ; Carbognani, M. ; Christie, K. ; Siegwart Collier, L. ; Cooper, E.J. ; Eskelinen, A. ; Frei, E.R. ; Grau, O. ; Grogan, P. ; Hallinger, M. ; Heijman, M.M.P.D. ; Hermanutz, L. ; Hudson, J.M.G. ; Hülber, K. ; Iturrate-Garcia, M. ; Iversen, C.M. ; Jaroszynska, F. ; Johnstone, J.F. ; Kaarlejärvi, E. ; Kulonen, A. ; Lamarque, L.J. ; Lévesque, E. ; Beest, M. Te; Vries, F.T. de; Ozinga, W.A. ; Bodegom, P.M. van - \ 2019
    Global Ecology and Biogeography 28 (2019)2. - ISSN 1466-822X - p. 78 - 95.
    cluster analysis - community composition - ecosystem function - plant functional groups - plant functional types - plant traits - tundra biome - vegetation change

    Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits. Location: Tundra biome. Time period: Data collected between 1964 and 2016. Major taxa studied: 295 tundra vascular plant species. Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits. Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression. Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra ecosystem change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insight into ecological prediction and modelling.

    Tundra Trait Team : A database of plant traits spanning the tundra biome
    Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Thomas, Haydn J.D. ; Alatalo, Juha M. ; Alexander, Heather ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Bai, Yang ; Baruah, Gaurav ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Blok, Daan ; Bruelheide, Helge ; Buchwal, Agata ; Buras, Allan ; Carbognani, Michele ; Christie, Katherine ; Collier, Laura S. ; Cooper, Elisabeth J. ; Cornelissen, J.H.C. ; Dickinson, Katharine J.M. ; Dullinger, Stefan ; Elberling, Bo ; Eskelinen, Anu ; Forbes, Bruce C. ; Frei, Esther R. ; Iturrate-Garcia, Maitane ; Good, Megan K. ; Grau, Oriol ; Green, Peter ; Greve, Michelle ; Grogan, Paul ; Haider, Sylvia ; Hájek, Tomáš ; Hallinger, Martin ; Happonen, Konsta ; Harper, Karen A. ; Heijmans, Monique M.P.D. ; Henry, Gregory H.R. ; Hermanutz, Luise ; Hewitt, Rebecca E. ; Hollister, Robert D. ; Hudson, James ; Hülber, Karl ; Iversen, Colleen M. ; Jaroszynska, Francesca ; Jiménez-Alfaro, Borja - \ 2018
    Global Ecology and Biogeography 27 (2018)12. - ISSN 1466-822X - p. 1402 - 1411.
    alpine - Arctic - plant functional traits - tundra

    Motivation: The Tundra Trait Team (TTT) database includes field-based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade-offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters. Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (> 1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density. Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub-Antarctic Marion Island. More than 99% of observations are georeferenced. Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods. Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species. Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release.

    Microbiota development in preterm and term infants
    Korpela, Katri ; Blakstad, Elin W. ; Moltu, Sissel J. ; Strømmen, Kenneth ; Nakstad, Britt ; Rønnestad, Arild E. ; Brække, Kristin ; Iversen, Per O. ; Drevon, Christian A. ; Vos, W.M. de - \ 2018
    Wageningen University
    PRJEB26802 - PRJEB26802 - ERP108820
    Microbiota development in (pre)term infants receiving various durations of postpartum antibiotic treatment. Determined through 16S rRNA gene amplicon sequencing (MiSeq, Illumina)
    Intestinal microbiota development and gestational age in preterm neonates
    Korpela, Katri ; Blakstad, Elin W. ; Moltu, Sissel J. ; Strømmen, Kenneth ; Nakstad, Britt ; Rønnestad, Arild E. ; Brække, Kristin ; Iversen, Per O. ; Drevon, Christian A. ; Vos, Willem de - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322 - 9 p.

    The intestinal microbiota is an important contributor to the health of preterm infants, and may be destabilized by a number of environmental factors and treatment modalities. How to promote the development of a healthy microbiota in preterm infants is largely unknown. We collected fecal samples from 45 breastfed preterm very low birth weight (birth weight < 1500 g) infants from birth until 60 days postnatal age to characterize the intestinal microbiota development during the first weeks of life in preterm infants. Fecal microbiota composition was determined by 16S rRNA amplicon sequencing. The main driver of microbiota development was gestational age; antibiotic use had strong but temporary effects and birth mode had little influence. Microbiota development proceeded in four phases indicated by the dominance of Staphylococcus, Enterococcus, Enterobacter, and finally Bifidobacterium. The Enterococcus phase was only observed among the extremely premature infants and appeared to delay the microbiota succession. The results indicate that hospitalized preterm infants receiving breast milk may develop a normal microbiota resembling that of term infants.

    Reprint of “In response to Tomás, D. et al. (2017). Validation of test portion pooling for Salmonella spp. detection in foods. International Journal of Food Microbiology, 245: 13–21”
    Joosten, Han ; Iversen, Carol - \ 2018
    International Journal of Food Microbiology 270 (2018). - ISSN 0168-1605 - p. 52 - 53.
    In response to Tomás, D. et al. (2017). Validation of test portion pooling for Salmonella spp. detection in foods. International Journal of Food Microbiology, 245: 13-21
    Joosten, Han ; Iversen, Carol - \ 2017
    International Journal of Food Microbiology 262 (2017). - ISSN 0168-1605 - p. 1 - 2.
    Heritability of the backtest response in piglets and its genetic correlations with production traits
    Iversen, M.W. ; Bolhuis, J.E. ; Camerlink, I. ; Ursinus, W.W. ; Reimert, I. ; Duijvesteijn, N. - \ 2017
    Animal 11 (2017)4. - ISSN 1751-7311 - p. 556 - 563.
    backtest - genetic correlations - heritability - pigs - production traits
    The backtest response of a pig gives an indication of its coping style, that is, its preferred strategy to cope with stressful situations, which may in turn be related to production traits. The objective of this study was therefore to estimate the heritability of the backtest response and estimate genetic correlations with production traits (birth weight, growth, fat depth and loin depth). The backtest was performed by placing the piglet on its back for 60 s and the number of struggles (NrS) and vocalizations (NrV), and the latency to struggle and vocalize (LV) was recorded. In total, 992 piglets were subjected to the backtest. Heritability estimates for backtest traits were statistically moderate (although high for behavioral traits), with LV having the highest heritability estimate (0.56±0.10, P<0.001) and NrS having the lowest estimate (0.37±0.09, P<0.001). Backtest traits also had high genetic correlations with each other, with vocalization traits (NrV and LV) having the highest (−0.94±0.03, P<0.001), and NrS with NrV the lowest correlation (0.70±0.09, P<0.001). No significant correlations were found between backtest traits and production traits, but correlations between NrS and birth weight (−0.38±0.25), and NrV and loin depth (−0.28±0.19) approached significance (P=0.07). More research into genotype-by-environment interactions may be needed to assess possible connections between backtest traits and production traits, as this may depend on the circumstances (environment, experiences, etc.). In conclusion, heritability estimates of backtest traits are high and it would therefore be possible to select for them. The high genetic correlations between backtest traits indicate that it may be possible to only consider one or two traits for characterization and selection purposes. There were no significant genetic correlations found between backtest traits and production traits, although some of the correlations approached significance and hence warrant further research.
    The Alaska Arctic Vegetation Archive (AVA-AK)
    Walker, Donald A. ; Breen, Amy L. ; Druckenmiller, Lisa A. ; Wirth, Lisa W. ; Fisher, Will ; Raynolds, Martha K. ; Šibík, Jozef ; Walker, Marilyn D. ; Hennekens, Stephan ; Boggs, Keith ; Boucher, Tina ; Buchhorn, Marcel ; Bültmann, Helga ; Cooper, David J. ; Daniëls, Fred J.A. ; Davidson, Scott J. ; Ebersole, James J. ; Elmendorf, Sara C. ; Epstein, Howard E. ; Gould, William A. ; Hollister, Robert D. ; Iversen, Colleen M. ; Jorgenson, M.T. ; Kade, Anja ; Lee, Michael T. ; MacKenzie, William H. ; Peet, Robert K. ; Peirce, Jana L. ; Schickhoff, Udo ; Sloan, Victoria L. ; Talbot, Stephen S. ; Tweedie, Craig E. ; Villarreal, Sandra ; Webber, Patrick J. ; Zona, Donatella - \ 2016
    Phytocoenologia 46 (2016)2. - ISSN 0340-269X - p. 221 - 229.
    Circumpolar - Cluster analysis - Database - Tundra - Turboveg - Vegetation classification

    The Alaska Arctic Vegetation Archive (AVA-AK, GIVD-ID: NA-US-014) is a free, publically available database archive of vegetation-plot data from the Arctic tundra region of northern Alaska. The archive currently contains 24 datasets with 3,026 non-overlapping plots. Of these, 74% have geolocation data with 25-m or better precision. Species cover data and header data are stored in a Turboveg database. A standardized Pan Arctic Species List provides a consistent nomenclature for vascular plants, bryophytes, and lichens in the archive. A web-based online Alaska Arctic Geoecological Atlas (AGA-AK) allows viewing and downloading the species data in a variety of formats, and provides access to a wide variety of ancillary data. We conducted a preliminary cluster analysis of the first 16 datasets (1,613 plots) to examine how the spectrum of derived clusters is related to the suite of datasets, habitat types, and environmental gradients. We present the contents of the archive, assess its strengths and weaknesses, and provide three supplementary files that include the data dictionary, a list of habitat types, an overview of the datasets, and details of the cluster analysis.

    Changes in perceptions and motivators that influence the implementation of on-farm Salmonella control measures by pig farmers in England
    Marier, Elizabeth ; Piers Smith, Richard ; Ellis-Iversen, Johanne ; Watson, Eamon ; Armstrong, Derek ; Hogeveen, Henk ; Cook, Alasdair J.C. - \ 2016
    Preventive Veterinary Medicine 133 (2016). - ISSN 0167-5877 - p. 22 - 30.
    Disease control - Motivators - Pig - Salmonella - Social epidemiology

    This study presents British farmers’ perception of, and barriers to, implementing Salmonella control on pig farms. Four farms that had implemented interventions and their 33 close contacts (known to the intervention farmers) took part in interviews before (phase 1) and after (phase 2) intervention trials to assess the difference in perception over time. Their results were compared against those from nine randomly selected control farms. The hypothesis was that farms implementing interventions whether or not successful, would influence their close contacts’ opinion over time. Based on a ‘pathway to disease control’ model, three intrinsic factors known to influence motivation – attitudes, social norms and self-efficacy – were evaluated. Farmers mentioned that successful interventions on a farm would attract their attention. The use of an appropriate communication strategy is therefore recommended to stimulate farmers’ intent to implement control measures. Both before and after the intervention trials, all farmers had a positive attitude towards Salmonella control and felt that their peers and authorities were supportive of controlling Salmonella on farms. In phase 2, however, farmers were more likely to want to share the burden of control with other stakeholders along the food chain and their belief in self-efficacy had weakened. Whilst social norms were not associated with an intention to take action on control, a positive attitude towards Salmonella control and a belief in self-efficacy were more likely to result in an intent to control. In phase 2, farmers with an intent to implement an intervention appeared to have a greater, but not significant positive belief in self-efficacy (p = 0.108). This study confirmed that farmers recognised their responsibility for controlling Salmonella in pork – even though their confidence in their ability to control Salmonella decreased over time – and believed that responsibility should be shared with the rest of the production chain. It showed that farmers trusted their veterinarian as a source of advice to guide them during the process of implementing change, though an increase in farms’ Salmonella seroprevalence score (Zoonosis National Control Programme (ZNCP) score) especially for those with a low ZNCP score was also likely to influence their behaviour. Getting concrete feedback from customers or a tangible benefit from their action was a strong incentive especially for farms with a ZNCP score higher than 50%. The study also revealed a need to validate which measures are effective as farmers did not perceive that the current advised interventions were worth the additional effort.

    Belowground plant biomass of different tundra vegetation types and its relationship with local temperature
    Wang, Peng ; Heijmans, M.M.P.D. ; Mommer, L. ; Ruijven, J. van; Maximov, T.C. ; Berendse, F. - \ 2014
    IntroductionClimate warming in the Arctic is much faster than the global average (IPCC, 2013). This rapid climate warming increases aboveground productivity of tundra vegetation (Epstein et al., 2012, Hudson & Henry, 2009, Verbyla, 2008), and also shifts vegetation composition in tundra ecosystems, as deciduous shrub expansion has been observed in many tundra areas (Callaghan et al., 2011, Frost & Epstein, 2014, Myers-Smith et al., 2011). However, the effects of climate warming on belowground parts of tundra vegetation are still largely unknown. Since belowground parts account for the major part of plant biomass in tundra ecosystems (Poorter et al., 2012), it is important for us to understand the potential warming effects on plant belowground parts, particularly fine roots, which is the active part for nutrient and water uptake. Moreover, roots of different plant functional types (PFTs) can significantly differ in morphology, physiology, phenology, rooting depth, and root life span (Bardgett et al., 2014, Iversen et al., 2015). Therefore, warming effects on plant roots may be different among functional types, and the potentially different responses of PFTs’ roots may play an important role in vegetation shifts in tundra. Here, we aimed to study seasonal changes and vertical distribution of root biomass across a vegetation gradient at a Siberian tundra site, focusing on the differences between graminoids and dwarf shrubs, also we aimed to elucidate the relationships of aboveground and belowground biomass with ambient temperature over a broad climate gradient, using data from 36 field studies across the tundra biome.
    Application of the CALIOP layer product to evaluate the vertical distribution of aerosols estimated by global models: AeroCom phase I results
    Koffi, B. ; Schulz, M. ; Breon, F.M. ; Griesfeller, J. ; Winker, D. ; Balkanski, Y. ; Bauer, S. ; Berntsen, T. ; Chin, M.A. ; Collins, W.D. ; Dentener, F. ; Diehl, T. ; Easter, R. ; Ghan, S. ; Ginoux, P. ; Gong, S.L. ; Horowitz, L.W. ; Iversen, T. ; Kirkevag, A. ; Koch, D. ; Krol, M.C. ; Myhre, G. ; Stier, P. ; Takemura, T. - \ 2012
    Journal of Geophysical Research: Atmospheres 117 (2012). - ISSN 2169-897X
    general-circulation model - sun photometer measurements - optical-properties - satellite-observations - goddard-institute - north-atlantic - calipso lidar - gocart model - mineral dust - emission inventories
    The CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) layer product is used for a multimodel evaluation of the vertical distribution of aerosols. Annual and seasonal aerosol extinction profiles are analyzed over 13 sub-continental regions representative of industrial, dust, and biomass burning pollution, from CALIOP 2007-2009 observations and from AeroCom (Aerosol Comparisons between Observations and Models) 2000 simulations. An extinction mean height diagnostic (Z(alpha)) is defined to quantitatively assess the models' performance. It is calculated over the 0-6 km and 0-10 km altitude ranges by weighting the altitude of each 100 m altitude layer by its aerosol extinction coefficient. The mean extinction profiles derived from CALIOP layer products provide consistent regional and seasonal specificities and a low inter-annual variability. While the outputs from most models are significantly correlated with the observed Z(alpha) climatologies, some do better than others, and 2 of the 12 models perform particularly well in all seasons. Over industrial and maritime regions, most models show higher Z(alpha) than observed by CALIOP, whereas over the African and Chinese dust source regions, Za is underestimated during Northern Hemisphere Spring and Summer. The positive model bias in Z(alpha) is mainly due to an overestimate of the extinction above 6 km. Potential CALIOP and model limitations, and methodological factors that might contribute to the differences are discussed.
    Predicting phosphorus losses with the PLEASE model on a local scale in Denmark and the Netherlands
    Salm, C. van der; Dupas, R. ; Grant, R. ; Heckrath, G. ; Iversen, B.V. ; Kronvang, B. ; Schoumans, O.F. - \ 2011
    Journal of Environmental Quality 40 (2011)5. - ISSN 0047-2425 - p. 1617 - 1626.
    united-states - soil - uncertainties - pathways - drainage - surface - europe - areas
    To reduce P losses from agricultural soils to surface water, mitigation options have to be implemented at a local scale. For a cost-effective implementation of these measures, an instrument to identify critical areas for P leaching is indispensable. In many countries, P-index methods are used to identify areas at risk for P losses to surface water. In flat areas, where losses by leaching are dominant, these methods have their limitations because leaching is often not described in detail. PLEASE is a simple mechanistic model designed to simulate P losses by leaching at the field scale using a limited amount of local field data. In this study, PLEASE was applied to 17 lowland sites in Denmark and 14 lowland sites in the Netherlands. Results showed that the simple model simulated measured fluxes and concentrations in water from pipe drains, suction cups, and groundwater quite well. The modeling efficiency ranged from 0.92 for modeling total-P fluxes to 0.36 for modeling concentrations in groundwater. Poor results were obtained for heavy clay soils and eutrophic peat soils, where fluxes and concentrations were strongly underestimated by the model. The poor performance for the heavy clay soil can be explained by the transport of P through macropores to the drain pipes and the underestimation of overland flow on this heavy-textured soil. In the eutrophic peat soils, fluxes were underestimated due to the release of P from deep soil layers.
    Towards the production of genetically modified strawberries which are acceptable to consumers
    Schaart, J.G. ; Kjellsen, T.D. ; Heggem, R. ; Iversen, T.H. ; Schouten, H.J. ; Krens, F.A. - \ 2011
    Genes, Genomes and Genomics 5 (2011)Sp.issue 1. - ISSN 1749-0383 - p. 102 - 107.
    This manuscript discusses different aspects that are relevant to genetically modified strawberry plants with improved characteristics and ‘acceptable’ to consumers and growers of strawberry. It starts with a consumer acceptance survey, held in Norway, Denmark and the UK, studying public perception of genetic modification in general and specifically of genetically modified strawberries with altered properties. This study revealed that genetically modified plants are better accepted by consumers if only genes from the species itself are used for the genetic modification. Subsequently, the results of a functional analysis of the strawberry polygalacturonase inhibiting protein gene (FaPGIP) are described. This indicates that this gene is a possible candidate to induce resistance to Botrytis cinerea when upregulated in strawberry fruits. For this analysis, the FaPGIP gene was overexpressed in transgenic strawberry plants using the cauliflower mosaic virus 35S (CaMV35S) promoter. This showed that FaPGIP overexpression led to resistance to Botrytis in transgenic leaves. For the generation of intragenic (i.e. genetically modification using native genetic elements only) strawberry plants, a transformation vector was constructed in which FaPGIP was combined with a strawberry fruit-specific promoter and terminator that were isolated from a strawberry expansin gene (FaExp2). This vector also included elements that allow the elimination of (foreign) selectable marker genes after genetically modified plant lines have been established. Using this vector, genetically modified strawberry plants were produced that contained only genes from the species itself, and therefore these plants were called intragenic, rather than transgenic. Unfortunately, further evaluations of the intragenic strawberry plants could not demonstrate any enhanced level of resistance to Botrytis in fruits.
    Perceptions, circumstances and motivators that influence implementation of zoonotic control programs on cattle farms
    Ellis-Iversen, J. ; Cook, A.J. ; Watson, E. ; Nielen, M. ; Larkin, L. ; Wooldridge, M. ; Hogeveen, H. - \ 2010
    Preventive Veterinary Medicine 93 (2010)4. - ISSN 0167-5877 - p. 276 - 285.
    management - schemes - england - model
    The implementation of disease control programs on farms requires an act of behavioral change. This study presents a theoretical framework from behavioral science, combined with basic epidemiological principles to investigate and explain the control of zoonotic agents on cattle farms. A pathway to disease control model was adapted from existing models in behavioral science and humanmedicine. Field data was used to demonstrate the validity of the model to identify and explain motivational factors for implementation of disease control programs among English and Welsh cattle farmers. The field data consisted of interviews conducted with 43 farmers, which were analyzed to investigate the farmers’perception of responsibility for safe cattle produce as well as the intrinsic and extrinsic barriers that inhibited the implementation of a zoonotic control program on their farms. The model was used to illustrate barriers affecting the implementation process and to classify farmers according to their current level of zoonotic control at each stage within the model. Ordinal multivariable logistic regression was used to identify the motivators associated with different levels of implementation. Younger farmers and/or larger herds were more likely to place financial responsibility upon the industry rather than government and all but two farmers accepted a social responsibility for food safety within cattle production. In general, attitudes towards zoonotic control were positive, but approximately half the farmers showed no intent to control and were inhibited by nonsupportive social norms and/or a lack of belief in self-efficacy. The remaining farmers showed intent to control, but had not implemented any structured control program due to external barriers including lack of knowledge and both cultural and economic pressure from society and industry. The farmers with no intent to adopt controlmeasures identified their private veterinarian as the preferred motivator, whereas consumer-demand and financial rewards or penalties were significantly associated with farmers who intended to control.
    Barriers and motivators for zoonotic control on cattle farms
    Ellis-Iversen, J. ; Hogeveen, H. - \ 2009
    In: Meeting of the Society for Veterinary Epidemiology and Preventive Medicin. - - p. 177 - 178.
    Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis
    Holden, M.T.G. ; Hauser, H. ; Sanders, M. ; Hoa Ngo, Thi ; Cherevach, I. ; Cronin, A. ; Goodhead, I. ; Mungall, K. ; Quail, M.A. ; Price, C. ; Rabbinowitsch, E. ; Sharp, S. ; Croucher, N. ; Chieu, Tran Bich ; Nguyen, Thi Hoang Mai ; To, Song Diep ; Nguyen, Tran Chinh ; Kehoe, M. ; Leigh, J.A. ; Ward, P.N. ; Dowson, C.G. ; Whatmore, A.M. ; Chanter, N. ; Iversen, P. ; Gottschalk, M. ; Slater, J.D. ; Smith, H.E. ; Spratt, B.G. ; Jianguo, Xu ; Changyun, Ye ; Bentley, S. ; Barrell, B.G. ; Schultsz, C. ; Maskell, D.J. ; Parkhill, J. - \ 2009
    PLoS ONE (2009). - ISSN 1932-6203 - 7 p.
    Background - Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings - The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ~40% of the ~2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ~90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance - The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.
    Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter
    Jorgensen, T.R. ; vanKuyk, P.A. ; Poulsen, B.R. ; Ruijter, G.J.G. ; Visser, J. ; Iversen, J.J.L. - \ 2007
    Microbiology 153 (2007)6. - ISSN 1350-0872 - p. 1963 - 1973.
    saccharomyces-cerevisiae - sugar-transport - candida-utilis - neurospora-crassa - hexose transport - nidulans - kinetics - genes - yeast - cultivations
    This is a study of high-affinity glucose uptake in Aspergillus niger and the effect of disruption of a high-affinity monosaccharide-transporter gene, mstA. The substrate saturation constant (K-s) of a reference strain was about 15 mu M in glucose-limited chemostat culture. Disruption of mstA resulted in a two- to fivefold reduction in affinity for glucose and led to expression of a low-affinity glucose transport gene, mstC, at high dilution rate. The effect of mstA disruption was more subtle at low and intermediate dilution rates, pointing to some degree of functional redundancy in the high-affinity uptake system of A. niger. The mstA disruptant and a reference strain were cultivated in glucose-limited chemostat cultures at low, intermediate and high dilution rate (D=0.07 h(-1), 0.14 h(-1) and 0.20 h(-1)). Mycelium harvested from steady-state cultures was subjected to glucose uptake assays, and analysed for expression of mstA and two other transporter genes, mstC and mstF The capacity for glucose uptake (V-max) of both strains was significantly reduced at low dilution rate. The glucose uptake assays revealed complex uptake kinetics. This impeded accurate determination of maximum specific uptake rates (V-max) and apparent affinity constants (K-m(app)) at intermediate and high dilution rate. Two high-affinity glucose transporter genes, mstA and mstF, were expressed at all three dilution rates in chemostat cultures, in contrast to batch culture, where only mstC was expressed. Expression patterns of the three transporter genes suggested differential regulation and functionality of their products.
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