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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    Using citizen science data to inform the relative sensitivity of waterbirds to natural versus human-dominated landscapes in China
    Duan, Houlang ; Xia, Shaoxia ; Yu, Xiubo ; Liu, Yu ; Teng, Jiakun ; Dou, Yuehan - \ 2020
    Ecology and Evolution 10 (2020)14. - ISSN 2045-7758 - p. 7233 - 7241.
    China - functional group - human-dominated landscapes - natural landscapes - sensitivity - waterbirds

    Habitat loss is widely regarded as one of the most destructive factors threatening native biodiversity. Because migratory waterbirds include some of the most globally endangered species, information on their sensitivity to landscape would benefit their conservation. While citizen science data on waterbird species occurrence are subjected to various biases, their appropriate interpretation can provide information of benefit to species conservation. We apply a bootstrapping procedure to citizen science data to reduce sampling biases and report the relative sensitivity of waterbird species to natural versus human-dominated landscapes. Analyses are performed on 30,491 data records for 69 waterbird species referred to five functional groups observed in China between 2000 and 2018. Of these taxa, 30 species (43.5%) are significantly associated with natural landscapes, more so for cranes, geese, and ducks than for shorebirds and herons. The relationship between land association and the threat status of waterbirds is significant when the range size of species is considered as the mediator, and the higher the land association, the higher the threat status. Sensitive species significantly associated with natural landscapes are eight times more likely to be classified as National Protected Species (NPS) Classes I or II than less sensitive species significantly associated with human-dominated landscapes. We demonstrate the potential for citizen science data to assist in conservation planning in the context of landscape changes. Our methods might assist others to obtain information to help relieve species decline and extinction.

    An economic approach to non-animal toxicity testing for skin sensitisation
    Leontaridou, Maria - \ 2017
    Wageningen University. Promotor(en): E.C. van Ierland, co-promotor(en): S.G.M. Gabbert; R. Landsiedel. - Wageningen : Wageningen University - ISBN 9789463431361 - 151
    animal testing alternatives - toxicity - testing - sensitivity - sensitivity analysis - bayesian theory - alternatieven voor dierproeven - toxiciteit - testen - gevoeligheid - gevoeligheidsanalyse - bayesiaanse theorie

    Chemicals applied in products, such as food products, pharmaceuticals or cosmetics, create great benefits in society while posing risks to human health and the quality of the environment. To control those risks, it is mandatory to perform risk assessments of chemicals which require information on their hazardous properties. To meet these information requirements without sacrificing large numbers of animal tests, many non-animal testing methods and strategies have become available. Given the increasing needs for assessing chemicals’ risks, toxicity testing has become costly in terms of testing costs, time and animal welfare.

    Focusing on skin sensitisation as a case study, this thesis aims at introducing an economic approach towards the optimisation of toxicity testing strategies. Chapter 2 surveys the current status of non-animal toxicity testing strategies assessing skin sensitisation and compares criteria suggested in the toxicological literature with the conceptual and informational criteria introduced in this chapter for increasing resource-efficiency in the development of testing strategies. Chapter 3 extends to the development of a Bayesian Value-of-Information model for the optimisation of non-animal toxicity testing strategies. This optimisation model is applied to construct optimal non-animal toxicity testing strategies for the assessment of skin sensitisation potential.

    Chapter 4 focuses on the precision of testing methods and the impact of limited precision on the evaluation of test results. The borderline range of testing methods is quantified and applied as an additional evaluation measure in the prediction models of testing methods to identify substances as positive and negative (for substances yielding clear-cut test results), or as discordant (for substances yielding test results within the borderline range). Chapter 5 addresses the uncertainties underlying the predictive accuracy metrics for non-animal testing methods due to their limited precision, the sample size and composition of the samples of chemicals used to estimate the predictive capacity of testing methods. Chapters 4 and 5 focus on non-animal testing methods for the assessment of skin sensitisation potential.

    This thesis concludes that introducing the economic perspective into the construction of toxicity testing strategies is necessary to develop the means by which resource-efficiency in toxicity testing is achieved. Furthermore, the evaluation of testing methods should consider both predictivity and precision limitations such that decision makers can draw robust conclusions on the hazardous properties of chemicals.

    EU-approved rapid tests might underestimate bovine spongiform encephalopathy infection in goats
    Meloni, Daniela ; Bozzetta, Elena ; Langeveld, Jan P.M. ; Groschup, Martin H. ; Goldmann, Wilfred ; Andrèoletti, Olivier ; Lantier, Isabelle ; Keulen, Lucien Van; Bossers, Alex ; Pitardi, Danilo ; Nonno, Romolo ; Sklaviadis, Theodoros ; Ingravalle, Francesco ; Peletto, Simone ; Colussi, Silvia ; Acutis, Pier Luigi - \ 2017
    Journal of Veterinary Diagnostic Investigation 29 (2017)2. - ISSN 1040-6387 - p. 232 - 236.
    Bovine spongiform encephalopathy - diagnosis - EU - goats - rapid tests - scrapie - sensitivity - surveillance
    We report the diagnostic sensitivity of 3 EU-approved rapid tests (ELISAs; 1 from IDEXX and 2 from Bio-Rad) for the detection of transmissible spongiform encephalopathy diseases in goats. Ninety-eight goat brainstem samples were tested. All the rapid tests had 100% specificity and ≥80% sensitivity, with the IDEXX test significantly more sensitive than the 2 Bio-Rad tests. All tests detected 100% of samples from goats with clinical scrapie, but missed 8% (IDEXX) to 33% (Bio-Rad SG) of samples from preclinical goats. Importantly, only IDEXX picked up all samples from clinical bovine spongiform encephalopathy (BSE)-infected goats, whereas the other 2 rapid tests missed 15% (Bio-Rad SG) to 25% (Bio-Rad SAP). These results show that a fraction of preclinical scrapie infections are likely missed by EU surveillance, with sensitivity of detection strongly dependent on the choice of the rapid test. Moreover, a significant proportion of clinical BSE infections are underestimated by using either Bio-Rad test. Assuming that the same sensitivity on preclinical goats would also occur in BSE-infected goats, our data suggest that IDEXX is likely the most sensitive test for detecting preclinical field cases of BSE infection in goats, although with an 8% failure rate. These results raise some concerns about the reliability of current EU surveillance figures on BSE infection in goats.
    The origin, versatility and distribution of azole fungicide resistance in the banana black Sigatoka pathogen Pseudocercospora fijiensis
    Chong Aguirre, Pablo A. - \ 2016
    Wageningen University. Promotor(en): Gert Kema; Pedro Crous. - Wageningen : Wageningen University - ISBN 9789462578791 - 289
    pseudocercospora - plant pathogenic fungi - fungicides - pesticide resistance - defence mechanisms - genetic diversity - genetic mapping - sensitivity - musa - bananas - fungal diseases - disease control - pseudocercospora - plantenziekteverwekkende schimmels - fungiciden - resistentie tegen pesticiden - verdedigingsmechanismen - genetische diversiteit - genetische kartering - gevoeligheid - musa - bananen - schimmelziekten - ziektebestrijding

    Pseudocercospora fijiensis causes black Sigatoka disease of banana. It is one of the most damaging threats of the crop requiring excessive fungicide applications for disease control as the major export “Cavendish” clones are highly susceptible. The consequence of this practice is the reduced efficacy of disease management strategies due to increasing levels of fungicide resistance. In this thesis the history and current practices of black Sigatoka disease management as well as the underlying mechanisms of fungicide resistance to a major group of fungicides are described. We discovered that both target site mutations and promotor insertions are crucial for modulating sensitivity. The more insertions, the higher the expression of the gene and the more resistant the strain. Using this information, we advocate modern monitoring techniques and improved disease control strategies as well as the urgent need for innovative banana breeding to develop resistant varieties for a sustainable global banana production.

    Species interactions and chemical stress combined effects of intraspecific and interspecific interactions and pyrene n Daphnia magna populations dynamics
    Viaene, K.P.J. ; Laender, F. de; Rico, A. ; Brink, P.J. van den; Guardo, A. Di; Morselli, M. ; Janssen, C.R. - \ 2015
    Environmental Toxicology and Chemistry 34 (2015)8. - ISSN 0730-7268 - p. 1751 - 1759.
    ecological risk-assessment - competition delays recovery - dry-weight estimate - modeling approach - exposure - sensitivity - water - ecotoxicology - contaminants - zooplankton
    Species interactions are often suggested as an important factor when assessing the effects of chemicals on higher levels of biological organization. Nevertheless, the contribution of intraspecific and interspecific interactions to chemical effects on populations is often overlooked. In the present study, Daphnia magna populations were initiated with different levels of intraspecific competition, interspecific competition, and predation and exposed to pyrene pulses. Generalized linear models were used to test which of these factors significantly explained population size and structure at different time points. Pyrene had a negative effect on total population densities, with effects being more pronounced on smaller D. magna individuals. Among all species interactions tested, predation had the largest negative effect on population densities. Predation and high initial intraspecific competition were shown to interact antagonistically with pyrene exposure. This was attributed to differences in population structure before pyrene exposure and pyrene-induced reductions in predation pressure by Chaoborus sp. larvae. The present study provides empirical evidence that species interactions within and between populations can alter the response of aquatic populations to chemical exposure. Therefore, such interactions are important factors to be considered in ecological risk assessments. Environ Toxicol Chem 2015;34:1751-1759. (c) 2015 SETAC
    Genetic and Non-Genetic Inheritance of Natural Antibodies Binding Keyhole Limpet Hemocyanin in a Purebred Layer Chicken Line
    Berghof, T.V.L. ; Klein, S.A.S. van der; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Bovenhuis, H. - \ 2015
    PLoS ONE 10 (2015)6. - ISSN 1932-6203 - 13 p.
    laying hens - immune-responses - parameters - iga - survival - isotypes - associations - sensitivity - disease - cells
    Natural antibodies (NAb) are defined as antibodies present in individuals without known antigenic challenge. Levels of NAb binding keyhole limpet hemocyanin (KLH) in chickens were earlier shown to be heritable, and to be associated with survival. Selective breeding may thus provide a strategy to improve natural disease resistance. We phenotyped 3,689 white purebred laying chickens for KLH binding NAb of different isotypes around 16 weeks of age. Heritabilities of 0.12 for the titers of total antibodies (IgT), 0.14 for IgM, 0.10 for IgA, and 0.07 for IgG were estimated. We also estimated high, positive genetic, and moderate to high, positive phenotypic correlations of IgT, IgM, IgA, and IgG, suggesting that selective breeding for NAb can be done on all antibody isotypes simultaneously. In addition, a relatively substantial non-genetic maternal environmental effect of 0.06 was detected for IgM, which may reflect a transgenerational effect. This suggests that not only the genes of the mother, but also the maternal environment affects the immune system of the offspring. Breaking strength and early eggshell whiteness of the mother’s eggs were predictive for IgM levels in the offspring, and partly explained the observed maternal environmental effects. The present results confirm that NAb are heritable, however maternal effects should be taken into account.
    Cumulative ozone effect on canopy stomatal resistance and the impact on boundary layer dynamics and CO2 assimilation at the diurnal scale: A case study for grassland in the Netherlands
    Super, I. ; Vilà-Guerau De Arellano, J. ; Krol, M.C. - \ 2015
    Journal of Geophysical Research: Biogeosciences 120 (2015). - ISSN 2169-8953 - p. 1348 - 1365.
    climate-change - soil-moisture - vegetation - exposure - drought - yield - l. - conductance - sensitivity - atmosphere
    Biological, chemical, and dynamical processes occurring at the surface strongly interact at diurnal scales. Therefore, this study examines the seasonal ozone impact on stomatal resistance, surface energy balance, boundary layer dynamics, and CO2 assimilation at this (sub)diurnal scale under changing conditions. We combine a seasonal canopy resistance module with a surface-boundary layer model that solves the diurnal evolution of dynamical and chemical variables in a well-mixed, convective boundary layer. The model is constrained with observations from Cabauw (Netherlands) for the dry year 2003, representing a well-mixed boundary layer at midlatitudes over water-stressed grassland. To quantify the ozone impact, the Cumulative Uptake of Ozone is calculated over a growing season, which gives an estimate of the reduction in stomatal aperture and photosynthesis. From a sensitivity analysis with mixed-layer temperature and soil moisture content we conclude that drought is the dominant factor that determines the surface energy partitioning and limits CO2 assimilation. Although drought causes stomatal closure, the results indicate that ozone damage, nevertheless, occurs. A second sensitivity analysis with CO2 and ozone shows that ozone damage causes an increase in stomatal resistance of up to 40% under high ozone levels and that CO2-induced stomatal closure limits ozone damage. The impact on boundary layer development through the effect of CO2 and ozone on the stomatal resistance is much smaller. At the diurnal scale soil moisture influences the surface energy partitioning, which affects the entrainment of ozone-rich air. Due to ozone damage, the CO2 assimilation flux is reduced by about 15%.
    QTL analysis for stomatal functioning in tetraploid Rosa x hybrida grown at high relative air humidity and its implications on postharvest longevity
    Carvalho, D.R.A. ; Koning, C.F.S. ; Fanourakis, D. ; Vasconcelos, M.W. ; Carvalho, S.M.P. ; Heuvelink, E. ; Krens, F.A. ; Maliepaard, C.A. - \ 2015
    Molecular Breeding 35 (2015). - ISSN 1380-3743 - 11 p.
    marker-assisted selection - water relations - cut roses - in-vitro - traits - environments - conductance - sensitivity - improvement - resistance
    High relative air humidity (RH = 85 %) during leaf development disturbs stomatal functioning leading to excessive water loss in conditions of high evaporative demand, resulting in severe reduction in postharvest longevity. In roses, this effect depends on the genotype, opening the possibility for breeding cultivars with more responsive stomata. In this study, we aim at identifying genomic regions associated with the control of water loss following growth at high RH. The F1 generation (108 offspring) and the two parents (P540 and P867) of a tetraploid cut rose population grown at high (85 %) RH were phenotyped for stomatal control to water loss by assessing the relative water content after 4 h of leaflet desiccation (RWC_4 h). The RWC_4 h varied between 7 and 62 % across the 110 studied individuals, with parents P540 and P867 showing 51 and 20 % RWC_4 h, respectively. Based on these data, a quantitative trait locus (QTL) analysis was performed. The impact of the identified QTLs on postharvest longevity of ten selected offspring was further evaluated. Three QTLs were identified: two major [positioned on linkage group 5 of the integrated consensus map (ICM 5) of both parents and on ICM 2 of the parent P867] and one putative minor (mapped to ICM 6 of both parents), explaining 32 % of the variability in the RWC_4 h. Low RWC_4 h was found to be a good proxy for eliminating the offspring with short vase life. This study constitutes a first step toward identifying the most likely regions for genes of interest controlling stomatal functioning in high RH-grown plants.
    Long-term decline of Amazon carbon the sink
    Brienen, R.J.W. ; Phillips, O.L. ; Feldpausch, T. ; Gloor, E. ; Baker, T.R. ; Arets, E.J.M.M. ; Pena Claros, M. ; Poorter, L. - \ 2015
    Nature 519 (2015). - ISSN 0028-0836 - p. 344 - 348.
    tropical rain-forests - experimental drought - wood productivity - tree mortality - turnover rates - sensitivity - biomass - growth - plots - co2
    Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades1, 2, with a substantial fraction of this sink probably located in the tropics3, particularly in the Amazon4. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity5. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale1, 2, and is contrary to expectations based on models6.
    Studying the movement behaviour of benthic macroinvertebrates with automated video tracking
    Augusiak, J.A. ; Brink, P.J. van den - \ 2015
    Ecology and Evolution 5 (2015)8. - ISSN 2045-7758 - p. 1563 - 1575.
    laboratory experiments - stream invertebrates - ecosystem function - dispersal - sensitivity - directions - landscapes - dimension - paradigm - ecology
    Quantifying and understanding movement is critical for a wide range of questions in basic and applied ecology. Movement ecology is also fostered by technological advances that allow automated tracking for a wide range of animal species. However, for aquatic macroinvertebrates, such detailed methods do not yet exist. We developed a video tracking method for two different species of benthic macroinvertebrates, the crawling isopod Asellus aquaticus and the swimming fresh water amphipod Gammarus pulex. We tested the effects of different light sources and marking techniques on their movement behavior to establish the possibilities and limitations of the experimental protocol and to ensure that the basic handling of test specimens would not bias conclusions drawn from movement path analyses. To demonstrate the versatility of our method, we studied the influence of varying population densities on different movement parameters related to resting behavior, directionality, and step lengths. We found that our method allows studying species with different modes of dispersal and under different conditions. For example, we found that gammarids spend more time moving at higher population densities, while asellids rest more under similar conditions. At the same time, in response to higher densities, gammarids mostly decreased average step lengths, whereas asellids did not. Gammarids, however, were also more sensitive to general handling and marking than asellids. Our protocol for marking and video tracking can be easily adopted for other species of aquatic macroinvertebrates or testing conditions, for example, presence or absence of food sources, shelter, or predator cues. Nevertheless, limitations with regard to the marking protocol, material, and a species’ physical build need to be considered and tested before a wider application, particularly for swimming species. Data obtained with this approach can deepen the understanding of population dynamics on larger spatial scales and of the effects of different management strategies on a species’ dispersal potential.
    Genetic relations between natural antibodies binding keyhole limpet hemocyanin and production traits in a purebred layer chicken line
    Klein, S.A.S. van der; Berghof, T.V.L. ; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Bovenhuis, H. - \ 2015
    Poultry Science 94 (2015)5. - ISSN 0032-5791 - p. 875 - 882.
    red-blood-cells - sheep erythrocytes - laying hens - immune-response - selection experiments - parameters - survival - isotypes - responsiveness - sensitivity
    Natural antibodies (NAb) are an important component of the first line of immune defense. Selective breeding for enhanced NAb levels in chickens may improve general disease resistance. It is unknown what the consequences of selection for NAb will be on the productive performance of laying hens. In this paper we describe the genetic relations between NAb titers binding keyhole limpet hemocyanin at 19 wk age and production traits in a white purebred leghorn chicken line observed in several time periods. A linear animal model was used to estimate (co)variance components, heritabilities, and correlations. Negative genetic correlations were found between egg weight and NAb titers, and between egg breaking strength and NAb titers. Positive genetic correlations were found between the feed conversion ratio (consumed feed/egg mass produced) and NAb titers, and egg production and NAb titers. Negative phenotypic correlations were found between body weight and NAb titers, between egg weight and NAb titers, and between egg breaking strength and NAb titers. Positive phenotypic correlations were found between egg production and NAb titers, and feed conversion ratio and NAb titers. In general, phenotypic correlations were more often significant, but less pronounced than genetic correlations. Other production traits were not found to be significant related to NAb titers. These findings suggest that there is a genetic tradeoff between levels of immunity and some production traits, although the underlying mechanism(s) remain(s) unclear. The results suggest possible consequences for production efficiency as a result of selective breeding for improved general disease resistance by natural antibodies.
    Detection of Single-Nucleotide Polymorphisms in Plasmodium falciparum by PCR Primer Extension and Lateral Flow Immunoassay
    Moers, A.P.H.A. ; Hallett, R.L. ; Borrow, R. ; Schallig, H.D.F.H. ; Sutherland, C.J. ; Amerongen, A. van - \ 2015
    Antimicrobial Agents and Chemotherapy 59 (2015)1. - ISSN 0066-4804 - p. 365 - 371.
    real-time pcr - carbon nanoparticles - malaria - dna - chloroquine - assay - amplification - sensitivity - resistance - travelers
    The resistance of Plasmodium falciparum to some antimalarial drugs is linked to single-nucleotide polymorphisms (SNPs). Currently, there are no methods for the identification of resistant parasites that are sufficiently simple, cheap, and fast enough to be performed at point-of-care, i.e., in local hospitals where drugs are prescribed. Primer extension methods (PEXT) were developed to identify 4 SNPs in P. falciparum positioned at amino acids 86, 184, and 1246 of the P. falciparum multidrug resistance 1 gene (pfmdr1) and amino acid 76 of the chloroquine resistance transporter gene (pfcrt). The PEXT products were visualized by a nucleic acid lateral flow immunoassay (NALFIA) with carbon nanoparticles as the detection labels. PCR-PEXT-NALFIAs showed good correlation to the reference methods, quantitative PCR (qPCR) or direct amplicon sequence analysis, in an initial open-label evaluation with 17 field samples. The tests were further evaluated in a blind study design in a set of 150 patient isolates. High specificities of 98 to 100% were found for all 4 PCR-PEXT genotyping assays. The sensitivities ranged from 75% to 100% when all PEXT-positive tests were considered. A number of samples with a low parasite density were successfully characterized by the reference methods but failed to generate a result in the PCR-PEXT-NALFIA, particularly those samples with microscopy-negative subpatent infections. This proof-of principle study validates the use of PCR-PEXT-NALFIA for the detection of resistance-associated mutations in P. falciparum, particularly for microscopy-positive infections. Although it requires a standard thermal cycler, the procedure is cheap and rapid and thus a potentially valuable tool for point-of-care detection in developing countries
    Mechanistic modelling of toxicokinetic processess within Mytiophyllum
    Heine, S. ; Schmitt, W. ; Schaffer, A. ; Gorlitz, G. ; Buresova, H. ; Arts, G. ; Preuss, T.G. - \ 2015
    Chemosphere 120 (2015). - ISSN 0045-6535 - p. 292 - 298.
    partition-coefficients - cuticular membranes - risk-assessment - aquatic macrophytes - water permeability - plant cuticles - sensitivity - diffusion - chemicals - linuron
    Effects of chemicals are, in most cases, caused by internal concentrations within organisms which rely on uptake and elimination kinetics. These processes might be key components for assessing the effects of time-variable exposure of chemicals which regularly occur in aquatic systems. However, the knowledge of toxicokinetic patterns caused by time-variable exposure is limited, and gaining such information is complex. In this work, a previously developed mechanistic growth model of Myriophyllum spicatum is coupled with a newly developed toxicokinetic part, providing a model that is able to predict uptake and elimination of chemicals, as well as distribution processes between plant compartments (leaves, stems, roots) of M. spicatum. It is shown, that toxicokinetic patterns, at least for most of the investigated chemicals, can be calculated in agreement with experimental observations, by only calibrating two chemical- specific parameters, the cuticular permeability and a plant/water partition coefficient. Through the model-based determination of the cuticular permeabilities of Isoproturon, Iofensulfuron, Fluridone, Imazamox and Penoxsulam, their toxicokinetic pattern can be described with the model approach. For the use of the model for predicting toxicokinetics of other chemicals, where experimental data is not available, equations are presented that are based on the log (Poct/wat) of a chemical and estimate parameters that are necessary to run the model. In general, a method is presented to analyze time-variable exposure of chemicals more in detail without conducting time and labour intensive experiments.
    The Challenge of Forecasting the Onset and Development of Radiation Fog Using Mesoscale Atmospheric Models
    Steeneveld, G.J. ; Ronda, R.J. ; Holtslag, A.A.M. - \ 2015
    Boundary-Layer Meteorology 154 (2015)2. - ISSN 0006-8314 - p. 265 - 289.
    boundary-layer - climate models - prediction - resolution - weather - system - parameterization - detrainment - sensitivity - simulation
    The numerical weather prediction of radiation fog is challenging, as many models typically show large biases for the timing of the onset and dispersal of the fog, as well as for its depth and liquid water content. To understand the role of physical processes, i.e. turbulence, radiation, land-surface coupling, and microphysics, we evaluate the HARMONIE and Weather Research and Forecasting (WRF) mesoscale models for two contrasting warm fog episodes at the relatively flat terrain around the Cabauw tower facility in the Netherlands. One case involves a radiation fog that arose in calm anticyclonic conditions, and the second is a radiation fog that developed just after a cold front passage. The WRF model represents the radiation fog well, while the HARMONIE model forecasts a stratus lowering fog layer in the first case and hardly any fog in the second case. Permutations of parametrization schemes for boundary-layer mixing, radiation and microphysics, each for two levels of complexity, have been evaluated within the WRF model. It appears that the boundary-layer formulation is critical for forecasting the fog onset, while for fog dispersal the choice of the microphysical scheme is a key element, where a double-moment scheme outperforms any of the single-moment schemes. Finally, the WRF model results appear to be relatively insensitive to horizontal grid spacing, but nesting deteriorates the modelled fog formation. Increasing the domain size leads to a more scattered character of the simulated fog. Model results with one-way or two-way nesting show approximately comparable results.
    Identification of changes in hydrological drought characteristics from a multi-GCM driven ensemble constrained by observed discharge
    Huijgevoort, M.H.J. van; Lanen, H.A.J. van; Teuling, A.J. ; Uijlenhoet, R. - \ 2014
    Journal of Hydrology 512 (2014). - ISSN 0022-1694 - p. 421 - 434.
    environment simulator jules - climate-change - global-scale - ocean circulation - model description - water-resources - river runoff - impact - sensitivity - projections
    Drought severity and related socio-economic impacts are expected to increase due to climate change. To better adapt to these impacts, more knowledge on changes in future hydrological drought characteristics (e.g. frequency, duration) is needed rather than only knowledge on changes in meteorological or soil moisture drought characteristics. In this study, effects of climate change on droughts in several river basins across the globe were investigated. Downscaled and bias-corrected data from three General Circulation Models (GCMs) for the A2 emission scenario were used as forcing for large-scale models. Results from five large-scale hydrological models (GHMs) run within the EU-WATCH project were used to identify low flows and hydrological drought characteristics in the control period (1971–2000) and the future period (2071–2100). Low flows were defined by the monthly 20th percentile from discharge (Q20). The variable threshold level method was applied to determine hydrological drought characteristics. The climatology of normalized Q20 from model results for the control period was compared with the climatology of normalized Q20 from observed discharge of the Global Runoff Data Centre. An observation-constrained selection of model combinations (GHM and GCM) was made based on this comparison. Prior to the assessment of future change, the selected model combinations were evaluated against observations in the period 2001–2010 for a number of river basins. The majority of the combinations (82%) that performed sufficiently in the control period, also performed sufficiently in the period 2001–2010. With the selected model combinations, future changes in drought for each river basin were identified. In cold climates, model combinations projected a regime shift and increase in low flows between the control period and future period. Arid climates were found to become even drier in the future by all model combinations. Agreement between the combinations on future low flows was low in humid climates. Changes in hydrological drought characteristics relative to the control period did not correspond to changes in low flows in all river basins. In most basins (around 65%), drought duration and deficit were projected to increase by the majority of the selected model combinations, while a decrease in low flows was projected in less basins (around 51%). Even if low discharge (monthly Q20) was not projected to decrease for each month, droughts became more severe, for example in some basins in cold climates. This is partly caused by the use of the threshold of the control period to determine drought events in the future, which led to unintended droughts in terms of expected impacts. It is important to consider both low discharge and hydrological drought characteristics to anticipate on changes in droughts for implementation of correct adaptation measures to safeguard future water resources.
    The effect of spatial soil variation on the hydrology of a semi-arid Rocky Mountains catchment
    Diek, S. ; Temme, A.J.A.M. ; Teuling, A.J. - \ 2014
    Geoderma 235-236 (2014). - ISSN 0016-7061 - p. 113 - 126.
    pedotransfer functions - front range - temporal stability - water-retention - colorado - sensitivity - parameters - dynamics - models - flow
    Soil properties can exhibit strong spatial variability, even at the small catchment scale. However, the hydrological implications of actual variability remain widely unknown since the required data are not easily collected. This is especially true for observations of covariation between local soil properties and local hydrological ¿uxes (e.g. evapotranspiration and drainage) and/or vegetation. We studied the impact of soil variation on the discharge of an incised catchment in the Colorado Rocky Mountains. Soil variation was determined by ¿eld and laboratory work on 100 soil pro¿les in the catchment. Soils were found to have substantially variable properties but had on average sandy texture, weak structure and limited depth to bedrock. Observed soil properties were translated into hydraulic properties using pedotransfer functions and then used in a 1D hydrological model based on Richards' equation to quantify the effect on hydrological ¿uxes. Hydrological model results indicated that the ef-fect of soil variation on the variation of hydrological model outputs was larger than the effects of variation in to-pographic in¿uenced parameters. Dependent on the hydrological model output, variation in soil hydraulic parameters is more important than the variation in soil depth and vice versa. Spatial variation of hydrological characteristics is underestimated when spatial variation of the soil information is unknown. As a consequence, knowledge on the spatial variation of input data is important for policy and water-management in order to in-clude spatial variation in the prediction of dry season stream¿ow in semi-arid catchments.
    Effects of climate and nutrient load on the water quality of shallow lakes assessed through ensemble runs by PCLake
    Nielsen, A. ; Trolle, D. ; Bjerring, R. - \ 2014
    Ecological Applications 24 (2014)8. - ISSN 1051-0761 - p. 1926 - 1944.
    ecosystem model pclake - danish lakes - phosphorus - state - eutrophication - restoration - equifinality - uncertainty - sensitivity - management
    Complex ecological models are used to predict the consequences of anticipated future changes in climate and nutrient loading for lake water quality. These models may, however, suffer from nonuniqueness in that various sets of model parameter values may yield equally satisfactory representations of the system being modeled, but when applied in future scenarios these sets of values may divert considerably in their simulated outcomes. Compilation of an ensemble of model runs allows us to account for simulation variability arising from model parameter estimates. Thus, we propose a new approach for aquatic ecological models creating a more robust prediction of future water quality. We used our ensemble approach in an application of the widely used PCLake model for Danish shallow Lake Arreskov, which during the past two decades has demonstrated frequent shifts between turbid and clear water states. Despite marked variability, the span of our ensemble runs encapsulated 70–90% of the observed variation in lake water quality. The model exercise demonstrates that future warming and increased nutrient loading lead to lower probability of a clear water, vegetation-rich state and greater likelihood of cyanobacteria dominance. In a 6.0°C warming scenario, for instance, the current nutrient loading of nitrogen and phosphorus must be reduced by about 75% to maintain the present ecological state of Lake Arreskov, but even in a near-future 2.0°C warming scenario, a higher probability of a turbid, cyanobacteria-dominated state is predicted. As managers may wish to determine the probability of achieving a certain ecological state, our proposed ensemble approach facilitates new ways of communicating future stressor impacts.
    Evaluation and Selection of Indicators for Land Degradation and Desertification Monitoring: Types of Degradation, Causes, and Implications for Management
    Kairis, O. ; Kosmas, C. ; Karavitis, C. ; Ritsema, C.J. ; Salvati, L. ; Acikalin, S. ; Alcala, M. ; Alfama, P. ; Atlhopheng, J. ; Barrera, J. ; Belgacem, A. ; Sole-Benet, A. ; Brito, J. ; Chaker, M. ; Chanda, R. ; Coelho, C. ; Darkoh, M. ; Diamantis, I. ; Ermolaeva, O. ; Fassouli, V. ; Fei, W. ; Feng, J. ; Fernandez, F. ; Ferreira, A. ; Gokceoglu, C. ; Gonzalez, D. ; Gungor, H. ; Hessel, R. ; Juying, J. ; Khatteli, H. ; Khitrov, N. ; Kounalaki, A. ; Laouina, A. ; Lollino, P. ; Lopes, M. ; Magole, L. ; Medina, L. ; Mendoza, M. ; Morais, P. ; Mulale, K. ; Ocakoglu, F. ; Ouessar, M. ; Ovalle, C. ; Perez, C. ; Perkins, J. ; Pliakas, F. ; Polemio, M. ; Pozo, A. ; Prat, C. ; Qinke, Y. ; Ramos, A. ; Ramos, J. ; Riquelme, J. ; Romanenkov, V. ; Rui, L. ; Santaloia, F. ; Sebego, R. ; Sghaier, M. ; Silva, N. ; Sizemskaya, M. ; Soares, J. ; Sonmez, H. ; Taamallah, H. ; Tezcan, L. ; Torri, D. ; Ungaro, F. ; Valente, S. ; Vente, J. de; Zagal, E. ; Zeiliguer, A. ; Zhonging, W. ; Ziogas, A. - \ 2014
    Environmental Management 54 (2014)5. - ISSN 0364-152X - p. 971 - 982.
    region ne spain - tillage erosion - soil displacement - translocation - vulnerability - sensitivity - performance - vegetation - systems - impact
    Indicator-based approaches are often used to monitor land degradation and desertification from the global to the very local scale. However, there is still little agreement on which indicators may best reflect both status and trends of these phenomena. In this study, various processes of land degradation and desertification have been analyzed in 17 study sites around the world using a wide set of biophysical and socioeconomic indicators. The database described earlier in this issue by Kosmas and others (Environ Manage, 2013) for defining desertification risk was further analyzed to define the most important indicators related to the following degradation processes: water erosion in various land uses, tillage erosion, soil salinization, water stress, forest fires, and overgrazing. A correlation analysis was applied to the selected indicators in order to identify the most important variables contributing to each land degradation process. The analysis indicates that the most important indicators are: (i) rain seasonality affecting water erosion, water stress, and forest fires, (ii) slope gradient affecting water erosion, tillage erosion and water stress, and (iii) water scarcity soil salinization, water stress, and forest fires. Implementation of existing regulations or policies concerned with resources development and environmental sustainability was identified as the most important indicator of land protection.
    Graded behavioral responses and habituation to sound in the common cuttlefish, Sepia officinalis
    Samson, J.E. ; Mooney, T.A. ; Gussekloo, S.W.S. ; Hanlon, R.T. - \ 2014
    Journal of Experimental Biology 217 (2014)24. - ISSN 0022-0949 - p. 4347 - 4355.
    equal-loudness contours - acoustic startle - water movements - squid - cephalopods - fish - predators - sensitization - lolliguncula - sensitivity
    Sound is a widely available and vital cue in aquatic environments yet most bioacoustic research has focused on marine vertebrates, leaving sound detection in invertebrates poorly understood. Cephalopods are an ecologically key taxon that likely use sound and may be impacted by increasing anthropogenic ocean noise, but little is known regarding their behavioral responses or adaptations to sound stimuli. These experiments identify the acoustic range and levels that elicit a wide range of secondary defense behaviors such as inking, jetting, and rapid coloration change. Secondarily, it was found that cuttlefish habituate to certain sound stimuli. The present study examined the behavioral responses of 22 cuttlefish (Sepia officinalis) to pure-tone pips ranging from 80-1000 Hz with sound pressure levels of 85–188 dB re 1 µPa rms and particle accelerations of 0-17.1 m.s-2. Cuttlefish escape responses (inking, jetting) were observed between frequencies of 80-300 Hz and at sound levels above 140 dB re 1 µPa rms and 0.01 m.s-2 (0.74 m.s-2 for inking responses). Body patterning changes and fin movements were observed at all frequencies and sound levels. Response intensity was dependent upon stimulus amplitude and frequency, suggesting that cuttlefish also possess loudness perception with a maximum sensitivity around 150 Hz. Cuttlefish habituated to repeated 200 Hz tone pips, at two sound intensities. Total response inhibition was not reached, however, and a basal response remained present in most animals. The graded responses provide a loudness sensitivity curve and suggest an ecological function for sound-use in cephalopods.
    Optimising and Evaluating the Characteristics of a Multiple Antigen ELISA for Detection of Mycobacterium bovis Infection in a Badger Vaccine Field Trial
    Aznar, I. ; Frankena, K. ; More, S.J. ; Whelan, C. ; Martin, W. ; Gormley, E. ; Corner, L.A.L. ; Murphy, D. ; Jong, M.C.M. de - \ 2014
    PLoS ONE 9 (2014)7. - ISSN 1932-6203
    gamma-interferon assay - meles-meles - endobronchial inoculation - experimental tuberculosis - protective immunity - cattle herds - bcg - sensitivity - challenge - pathology
    A long-term research programme has been underway in Ireland to evaluate the usefulness of badger vaccination as part of the national bTB (bovine tuberculosis) control strategy. This culminated in a field trial which commenced in county Kilkenny in 2009 to determine the effects of badger vaccination on Mycobacterium bovis transmission in badgers under field conditions. In the present study, we sought to optimise the characteristics of a multiplex chemiluminescent assay for detection of M. bovis infection in live badgers. Our goal was to maximise specificity, and therefore statistical power, during evaluation of the badger vaccine trial data. In addition, we also aimed to explore the effects of vaccination on test characteristics. For the test optimisation, we ran a stepwise logistic regression with analytical weights on the converted Relative Light Units (RLU) obtained from testing blood samples from 215 badgers captured as part of culling operations by the national Department of Agriculture, Food and the Marine (DAFM). The optimised test was applied to two other datasets obtained from two captive badger studies (Study 1 and Study 2), and the sensitivity and specificity of the test was attained separately for vaccinated and non-vaccinated badgers. During optimisation, test sensitivity was maximised (30.77%), while retaining specificity at 99.99%. When the optimised test was then applied to the captive badger studies data, we observed that test characteristics did not vary greatly between vaccinated and non-vaccinated badgers. However, a different time lag between infection and a positive test result was observed in vaccinated and non-vaccinated badgers. We propose that the optimized multiplex immunoassay be used to analyse the vaccine trial data. In relation to the difference in the time lag observed for vaccinated and non-vaccinated badgers, we also present a strategy to enable the test to be used during trial evaluation.
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