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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Fresh Water Lens Persistence and Root Zone Salinization Hazard Under Temperate Climate
Stofberg, Sija F. ; Oude Essink, G.H.P. ; Pauw, Pieter S. ; Louw, Perry G.B. de; Leijnse, Anton ; Zee, Sjoerd E.A.T.M. van der - \ 2017
Water Resources Management 31 (2017)2. - ISSN 0920-4741 - p. 689 - 702.
Fresh water lens - Root zone salinization - Salinity - Simple model - salinization - fresh water - models - water supply - coastal areas - zoutgehalte - verzilting - zoet water - modellen - watervoorziening - kustgebieden

In low lying deltaic areas in temperate climates, groundwater can be brackish to saline at shallow depth, even with a yearly rainfall excess. For primary production in horticulture, agriculture, and terrestrial nature areas, the fresh water availability may be restricted to so-called fresh water lenses: relatively thin pockets of fresh groundwater floating on top of saline groundwater. The persistence of such fresh water lenses, as well as the quantity and quality of surface water is expected to be under pressure due to climate change, as summer droughts may intensify in North-West Europe. Better understanding through modelling of these fresh water resources may help anticipate the impact of salinity on primary production. We use a simple model to determine in which circumstances fresh water lenses may disappear during summer droughts, as that could give rise to enhanced root zone salinity. With a more involved combination of expert judgement and numerical simulations, it is possible to give an appraisal of the hazard that fresh water lenses disappear for the Dutch coastal regions. For such situations, we derive an analytical tool for anticipating the resulting salinization of the root zone, which agrees well with numerical simulations. The provided tools give a basis to quantify which lenses are in hazard of disappearing periodically, as well as an impression in which coastal areas this hazard is largest. Accordingly, these results and the followed procedure may assist water management decisions and prioritization strategies leading to a secure/robust fresh water supply on a national to regional scale.

The TOXSWA model version 3.3 for pesticide behaviour in small surface waters : description of processes
Horst, M.M.S. ter; Beltman, W.H.J. ; Berg, F. van den - \ 2016
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 84) - 72
pesticides - surface water - models - modeling - aquatic ecosystems - drainage - runoff - pesticiden - oppervlaktewater - modellen - modelleren - aquatische ecosystemen - oppervlakkige afvoer
In the European Union (EU) the risk of plant protection products to aquatic organisms is assessed accordingto regulation 1107/2009. For this assessment the FOCUS Surface Water Scenarios have been developed. TheTOXSWA model is included in the FOCUS Surface Water Software tools to calculate the exposureconcentration in the water systems defined in those scenarios. At the national level the TOXSWA model isused to assess the exposure concentration in the water system defined in national scenarios. In this report adescription is given of the hydrology in the Dutch and EU water body systems and the fate of pesticides andtheir metabolites in water and sediment. The pesticide can enter the system by spray drift and/or drainageand run-off. The transport in the water system is described by advection, dispersion and diffusion. Theexchange at the water-sediment interface is described based on advection/diffusion. Other processes aresorption, volatilisation at the water – air interface and transformation in both the water layer and thesediment. The formation and transformation of metabolites in both compartments are described. The reportpresents an outlook on the improvements in the next version as well as on future developments.
Recreatiemodel AVANAR 2.0 nader beschreven en toegelicht : achtergronddocumentatie voor Status A
Vries, S. de; Staritsky, I. - \ 2016
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 80) - 44
recreatie - openluchtrecreatie - modellen - natuur - aanbodsevenwicht - recreation - outdoor recreation - models - nature - supply balance
This report contains supplementary technical documentation on the recreation model AVANAR, version 2.0.AVANAR is an abbreviation of the Dutch study on ‘Reconciling supply of & demand for nature as recreationalspace’. This report was set out to gain the A-status with respect to modelling. A short description is given inthis report together with more information on those features that have not been described earlier or only in afragmented manner. As for the latter, technical details described elsewhere have been brought together,several new tests of version 2.0 of the model are reported and earlier validation studies have beensummarized. For other features, like the argumentation of the choices made, the text refers to relevantearlier publications about AVANAR
D3.5 Formalized stepwise approach for implementing logistical concepts using BeWhere and LocaGIStics : S2Biom Project Grant Agreement No. 608622
Annevelink, E. ; Elbersen, B. ; Leduc, S. ; Staritsky, I.G. - \ 2016
S2Biom - 41 p.
biomassa - modellen - databanken - hulpbronnengebruik - biobased economy - duurzaamheid (sustainability) - europa - logistiek - biomass - models - databases - resource utilization - sustainability - europe - logistics
This deliverable describes a formaliz
logistical concepts in the practical
chains and for assessing thei
BeWhere and LocaGIStics. It describes
these two logistical assessment tools
interlinked so that LocaGIStics can further refine and detail the outcomes of the
BeWhere model and that the BeWhere model can use the outcome of the
LocaGIStics model to modify their calculations if needed.
The BeWhere model supports the development of EU
develop an optimal network of biomass delivery chains
techno-economic spatial model that enables the optimal design and allocation of
biomass delivery chains (at national level) based on the minimizatio
emissions of the full supply chain taking account economies of scale, in order to meet
certain demand.
LocaGIStics is a regional assessment tool for biomass delivery chains. This tool can
support the user to design optimal biomass deliver
level and analyze in a comparative way (for different biomass delivery chains) the
spatial implications and the environmental and economic performance. It will take
account of the biomass cost
options and novel logistical concepts.
formalized stepwise approach for implementing optimal
design of national and regional
their economic and GHG performance
. the functionality of and the relation between
tools. BeWhere and LocaGIStics are closely
ked EU-wide and national strategies to
chains. The basis of this tool is a
delivery chains and networks at regional
cost-supply, the conversion and pre-treatment technology
D3.4 + D3.6: Cover report Results logistical case studies : S2Biom Project Grant Agreement n°608622
Annevelink, E. ; Gabrielle, B. ; Carozzi, M. ; Garcia Galindo, D. ; Espatolero, S. ; Izquierdo, M. ; Väätäinen, K. ; Anttila, P. ; Staritsky, I.G. ; Vanmeulebrouk, B. ; Elbersen, B. ; Leduc, S. - \ 2016
S2Biom - 23 p.
biobased economy - europa - databanken - modellen - duurzaamheid (sustainability) - hulpbronnengebruik - biomassa - logistiek - europe - databases - models - sustainability - resource utilization - biomass - logistics
The S2Biom project - Delivery of sustainable supply of non-food biomass to support a “resource-efficient” Bioeconomy in Europe - supports the sustainable delivery of nonfood biomass feedstock at local, regional and pan European level through developing strategies, and roadmaps that will be informed by a “computerized and easy to use” toolset (and respective databases) with updated harmonized datasets at local, regional, national and pan European level for EU28, Western Balkans, Moldova, Turkey and Ukraine. A case based approach was followed, where optimal logistical concepts (conceptual designs) were matched with the specific regional situation. This was done in three logistical case studies that were performed: 1. Small-scale power production with straw and Miscanthus in the Burgundy region (France); 2. Large-scale power production with straw and with residual woody biomass in the Aragon region (Spain); 3. Advanced wood logistics in the Province of Central Finland.
D3.4 + D3.6: Annex 1 Results logistical case study Burgundy : S2Biom Project Grant Agreement n°608622
Annevelink, E. ; Gabrielle, B. ; Carozzi, M. ; Staritsky, I.G. ; Vanmeulebrouk, B. ; Elbersen, B. ; Leduc, S. - \ 2016
S2Biom - 48 p.
biobased economy - biomass - sustainability - resource utilization - europe - databases - models - logistics - biomassa - duurzaamheid (sustainability) - hulpbronnengebruik - europa - databanken - modellen - logistiek
The S2Biom project - Delivery of sustainable supply of non-food biomass to support a “resource-efficient” Bioeconomy in Europe - supports the sustainable delivery of nonfood biomass feedstock at local, regional and pan European level through developing strategies, and roadmaps that will be informed by a “computerized and easy to use” toolset (and respective databases) with updated harmonized datasets at local, regional, national and pan European level for EU28, Western Balkans, Moldova, Turkey and Ukraine. In the S2Biom project the logistical case study in Burgundy was the first that was performed. In this report the assessment methods for the logistical case study are described in Chapter 2. This is followed by the set-up of the Burgundy case study in Chapter 3. In Chapter 4 the type of data needed and in Chapter 5 the actual data used are described. Then the results are presented that were obtained by the BeWhere (Chapter 6) and by the LocaGIStics model (Chapter 7). Conclusions and recommendations are given in Chapter 8.
Ontwikkeling van een rekentool om de ammoniakemissie uit vleeskuikenstallen te kunnen voorspellen
Aarnink, Andre ; Harn, Jan van; Banken, Klaas ; Ogink, Nico - \ 2016
Wageningen : Wageningen Livestock Research (Livestock Research rapport 990) - 73
vleeskuikens - ammoniakemissie - modellen - pluimveehouderij - broilers - ammonia emission - models - poultry farming
Arctic climate change and decadal variability
Linden, Eveline C. van der - \ 2016
Wageningen University. Promotor(en): Wilco Hazeleger, co-promotor(en): R. Bintanja. - Wageningen : Wageningen University - ISBN 9789462579453 - 197
climatic change - arctic regions - global warming - temperature - models - carbon dioxide - sea water - barents sea - klimaatverandering - arctische gebieden - opwarming van de aarde - temperatuur - modellen - kooldioxide - zeewater - barentszzee

High northern latitudes exhibit enhanced near-surface warming in a climate with increasing greenhouse gases compared to other parts of the globe, indicating an amplified climate response to external forcing. Decadal to multidecadal variability sometimes enhances and at other times reduces the long-term trends. Therefore, the influence of internal variability should be taken into account when externally forced climate signals are assessed.
This thesis contributes to our understanding of Arctic climate projections by clarifying the role of coupled ocean-sea-ice-atmosphere processes on the long-term trends and decadal variability of the Arctic climate system. Important mechanisms linked to the location of the sea ice margin and ocean heat transports into the Arctic have been identified and were shown to have a substantial effect on the Arctic's response to climate change.

Calculation of exposure concentrations for NL standard scenarios by the TOXSWA model : use of FOCUS_TOXSWA 4.4.3 software for plant protection products and their metabolitesin Dutch risk assessment for aquatic ecosystems
Beltman, W.H.J. ; Vink, C. ; Poot, A. - \ 2016
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOT Natuur & Milieu) (WOt-technical report 77) - 46
pesticides - models - exposure - exposure assessment - surface water - netherlands - pesticiden - modellen - blootstelling - blootstellingsbepaling - oppervlaktewater - nederland
TOXSWA calculates exposure concentrations of plant protection products in water and in sediment and is
used in risk assessment studies of aquatic organisms. Replacement of the TOXSWA 1.2 software by the more
recent FOCUS_TOXSWA software for use with the NL standard scenarios was investigated. The impact of the
replacement on the calculated exposure concentrations of parent compounds and of metabolites was
determined. For parent substances the calculated exposure concentrations of the two TOXSWA versions were
equivalent. Due to a different way to simulate metabolites, the differences in exposure concentrations
calculated by the two versions can be large. For the simulation of metabolite substances two approaches are
given to handle situations where the formation fraction is not known.
Sustaining reservoir use through sediment trapping in NW Ethiopia
Getahun, Mulatie Mekonnen - \ 2016
Wageningen University. Promotor(en): Leo Stroosnijder, co-promotor(en): Saskia Keesstra; Jantiene Baartman. - Wageningen : Wageningen University - ISBN 9789462579101 - 132
sediment - soil conservation - reservoirs - dams - models - ethiopia - sediment - bodembescherming - reservoirs - dammen - modellen - ethiopië

To increase crop production and improve food self-sufficiency, rain-fed agriculture need to be supplemented with irrigated agriculture. To this end, a large number of reservoirs had been constructed in Ethiopia. However, reservoirs are suffering from sedimentation. This study was conducted in Minizr catchment, NW Ethiopia to (1) quantify the sediment entering Koga reservoir, (2) to assess the functioning and effectiveness of the existing man-made sediment trapping (ST) measures and natural sediment sinks, and (3) to design a possible solution to tackle the problem. Results of three years (2013-2015) field data show that 38% of the transported sediment was trapped within the Minizr catchment. Although considerable efforts were made to trap the sediment within the catchment through implementing various ST measures, lack of an integrated ST approach causes the remaining 62% of the sediment load still entering Koga reservoir.

River export of nutrients to the coastal waters of China: the MARINA model to assess sources, effects and solutions
Strokal, Maryna - \ 2016
Wageningen University. Promotor(en): Carolien Kroeze, co-promotor(en): S. Luan; Lin Ma. - Wageningen : Wageningen University - ISBN 9789462579729 - 226
cum laude - nutrients - rivers - coastal water - models - eutrophication - coastal areas - water pollution - china - voedingsstoffen - rivieren - kustwateren - modellen - eutrofiëring - kustgebieden - waterverontreiniging - china

Rivers export increasing amounts of nitrogen (N) and phosphorus (P) to the coastal waters of China. This causes eutrophication problems that can damage living organisms when oxygen levels drop and threaten human health through toxic algae. We know that these problems result from human activities on land such as agriculture and urbanization. However, the relative importance of these human activities for river export of nutrients to Chinese seas is not well studied. There are two important issues that need further investigation: the relative importance of upstream pollution on downstream impacts and the relative importance of typical sources of nutrients in Chinese rivers that are often ignored in existing modeling studies.

My PhD thesis, therefore, aims to better understand trends in river export of nutrients to the coastal waters of China by source from sub-basins, and the associated coastal eutrophication. To this end, I developed the MARINA model: Model to Assess River Inputs of Nutrients to seAs. For this, I used the existing Global NEWS-2 model (Nutrient Export from WaterSheds) as a starting point.

I formulated five sub-objectives to achieve the main objective:

To analyze the original Global NEWS-2 model for river export of nutrients and the associated coastal eutrophication (Chapter 2);

To develop a sub-basin scale modeling approach to account for impacts of upstream human activities on downstream water pollution, taking the Pearl River as an example (Chapter 3);

To quantify the relative share of manure point sources to nutrient inputs to rivers at the sub-basin scale (Chapter 4);

To quantify the relative share of sources to river export of nutrients at the sub-basin scale (Chapter 5);

To explore optimistic futures to reduce river export of nutrients and coastal eutrophication in China (Chapter 6).

The study area includes rivers draining roughly 40% of China. This includes the most densely populated areas, and areas with intensive economic activities. The rivers include the Yangtze (Changjiang), Yellow (Huanghe), Pearl, Huai, Hai and Liao. In the MARINA model, the drainage areas of the large Yangtze, Yellow and Pearl rivers are divided into up-, middle- and downstream sub-basins. The principle of the sub-basin approach of MARINA is that nutrients from human activities are transported by tributaries to outlets of sub-basins and then to the river mouth (coastal waters) through the main channel. The model takes into account nutrients that are partly lost or retained during transport towards the river mouth. The model quantifies river export of nutrients by source from sub-basins for 1970, 2000 and 2050.

The main six findings of the MARINA results for China are:

Finding 1: Dissolved N and P export by Chinese rivers increased by a factor of 2-8 between 1970 and 2000;

Finding 2: The potential for coastal eutrophication was low in 1970 and high in 2000 in China;

Finding 3: Most dissolved N and P in Chinese seas is from middlestream and downstream human activities;

Finding 4: Manure point sources are responsible for 20-80% of dissolved N and P in Chinese rivers;

Finding 5: In the future, river export of nutrients may increase in the Global Orchestration (GO) scenario of the Millennium Ecosystem Assessment. Current policy plans (CP scenario) may not sufficient to avoid this increase;

Finding 6: In optimistic scenarios (OPT-1 and OPT-2), the potential for coastal eutrophication is low in 2050, mainly as a result of assumed full implementation of: (1) high recycling rates of animal manure (OPT-1 and OPT-2), and (2) high efficiencies of nutrient removal in sewage systems (OPT-2, see Figure 1).

Figure 1. Illustration of future scenarios for coastal water quality in China. GO is Global Orchestration of the Millennium Ecosystem Assessment and assumes environmental actions that are either absent or ineffective in reducing water pollution. CP is based on GO, but incorporates the “Zero Growth in Synthetic Fertilizers after 2020” policy. OPT-1 and OP-2 are optimistic scenarios that assume high nutrient use efficiencies in agriculture (OPT-1, OPT-2) and sewage (OPT-2).

My PhD thesis reveals novel insights for effective environmental policies in China. It shows the importance of manure point sources in water pollution by nutrients. Clearly, managing this source will likely reduce coastal eutrophication in the future. Furthermore, the implementation of advanced technologies is essential when dealing with urban pollution. My PhD thesis may also be useful for other world regions with similar environmental problems as in China. The new, sub-basin scale MARINA model is rather transparent and thus can be applied to other large, data-poor basins that may benefit from the allocation of effective management options. With this I hope to contribute to future availability of sufficiently clean water for next generations, not only in China, but also in other world regions.

In vitro assays for hazard identification of nanoparticles
Kloet, Samantha K. - \ 2016
Wageningen University. Promotor(en): Ivonne Rietjens; Jochem Louisse; Nico van den Brink. - Wageningen : Wageningen University - ISBN 9789462579415 - 213
nanotechnology - particles - in vitro - models - hazards - toxicity - toxicokinetics - nanotechnologie - deeltjes - in vitro - modellen - gevaren - toxiciteit - toxicokinetiek

The production of nanoparticles (NPs) has increased in the last decades and the number of products in which NPs are being incorporated is still growing. The rapid increase of nanotechnology has several benefits for society, yet there is an increasing concern that exposure to NPs may result in significant adverse health effects. Since NPs are incorporated in a variety of consumer products, it is likely that the general population will be exposed to NPs. It would be desirable that the safety and risk assessment of NPs could be largely based on studies using in vitro models instead of in vivo models as this would reduce the use of test animals, costs and time required to test the large numbers of NPs. The aim of the present thesis was to investigate the potential of in vitro testing strategies to detect hazards of NPs, focusing on toxicokinetic as well as toxicodynamic endpoints. Toxicokinetic studies focused on translocation of NPs in in vitro models of the placental barrier, while toxicodynamic studies were directed at two endpoints that represent potential hazards of NPs that have not yet been well characterized including: developmental toxicity and immunotoxicity.

In the present thesis different types of NPs were used. Polystyrene nanoparticles (PS-NPs) were selected because of their commercial availability, with high quality and a wide variety of available physicochemical properties like surface charge, and fluorescent labeling enabling easy detection in toxicokinetic (translocation) studies. Several metal (oxide) NPs were selected as well, of which some are possible constituents of food additives like TiO2, Fe2O3, SiO2 and Ag. Other metal oxide NPs that were selected were Mn­2O3, CuO, Cr2O3, CoO and NiO to which we may be exposed via products like paints, catalysts, construction materials, coatings and batteries.

Placental translocation of NPs was studied as an important toxicokinetic aspect, since part of the toxicodynamic studies of the present thesis were directed at developmental toxicity testing of NPs. In order to obtain insight in toxicity and translocation of NPs across the placental barrier, cytotoxicity and translocation was studied for one positively and two negatively charged PS-NPs of 50 nm in an in vitro model of the placenta. In this study it appeared that in spite of similar size, surface charge and type of proteins in the protein corona, the differently charged NPs displayed a remarkable difference in cytotoxicity, with only the PS-NPs with an original positive charge inducing cytotoxicity. Translocation of PS-NPs appeared not to be related to PS-NP charge alone. A remarkable difference in translocation was found between the two 50 nm negatively charged PS-NPs that were obtained from different manufacturers. Since none of the characterized parameters, including size, surface charge and protein corona revealed remarkable differences between the two negatively charged NPs, the difference may originate from the chemical groups on the surface of the NPs generating the negative charge. The general conclusion from this study was that the in vitro BeWo b30 model can be used as a fast method to get an initial qualitative impression about the capacity of NPs to translocate across the placental barrier and to set priorities for further in vivo studies on translocation of NPs to the fetus.

The same PS-NPs as tested for placental translocation were investigated whether they are able to cause in vitro developmental toxicity in the ES-D3 cell differentiation assay of the embryonic stem cell test (EST) focusing also on the effect that charge may have. The study showed that the two negatively charged PS-NPs did not show any effect in the ES-D3 cell differentiation assay up to the highest concentration tested while the positively charged PS-NP showed a concentration-dependent inhibition of ES-D3 cell differentiation. However, effect concentrations in the ES-D3 cell differentiation assay were close to cytotoxic concentrations, which indicated that the inhibition of the ES-D3 cell differentiation may be due to cytotoxic effects of the positively charged PS-NPs. This indicated that the inhibition of the ES-D3 cell differentiation by the positively charged PS-NPs may be caused by non-specific effects. Although the experiments on placental translocation of the present thesis showed that positively charged PS-NPs are more toxic than negatively charged PS-NPs, it appeared that this may not be generalizable to other NPs. This follows from the fact that in SiO2, Ag and TiO2 NPs that were reported in other studies to inhibit ES-D3 cell differentiation were negatively charged, while the negatively charged PS-NPs of the present study did not affect ES-D3 cell differentiation. Although the limited data available indicate that charge, size and coating of NPs may be important characteristics that determine the developmental toxicity potential of NPs, more (systematic) studies are needed to assess how physicochemical characteristics of NPs relate to their developmental toxicity. This information may help to prioritize NPs for in vitro and in vivo developmental toxicity testing.

In addition, toxic effects of a series of metal (oxide) NPs were tested in macrophage RAW264.7 cells in order to obtain insight in effect of these NPs on cells of the innate immune response. In these macrophage RAW264.7 cells the effects of the metal (oxide) NPs were characterized on cell viability, TNF-α production and mitochondria-related parameters like production of reactive oxygen species (ROS), mitochondrial permeability transition pore (MPTP) opening, and intracellular ATP levels. Altogether, results obtained showed no or limited effects of the NP formulations of metal (oxide) food additives on cell viability, ROS production, MPTP opening, ATP levels and TNF-α production in RAW264.7 macrophages. Effects were only observed at high concentrations that may not be physiologically relevant, indicating that related adverse effects upon exposure to the respective NPs in vivo may be limited.

Taken together, the present thesis provided further evidence of the influence of physicochemical properties of NPs in driving toxicity in in vitro models. However, the determination of the fate and toxicity of NPs using in vitro or in vivo models is a challenge that needs further evaluation. A combination of several factors likely play a role in determining the outcome of exposure including factors like NP core material and presence and type of coating agents resulting in various physicochemical properties (size, charge, etc.). This appears to hamper conclusive evaluation of the role of physicochemical characteristics of NPs in their potential hazards and risks so far. The results obtained do show however that in vitro assays can detect differences in potential hazards posed by NPs. Therefore it is concluded that the results of the work presented in this thesis will contribute to the further development and use of non-animal based testing strategies for safety testing of NPs providing insight into selected potential hazards of the tested NPs.

Characterisation of Lactobacillus plantarum single and multi-strain biofilms
Fernández Ramírez, Mónica D. - \ 2016
Wageningen University. Promotor(en): Tjakko Abee; E.J. Smid, co-promotor(en): Masja Nierop Groot. - Wageningen : Wageningen University - ISBN 9789462579217 - 169
lactobacillus plantarum - biofilms - food spoilage - models - environmental factors - lactobacillus plantarum - biofilms - voedselbederf - modellen - milieufactoren

Biofilms consist of microorganisms attached to a surface and embedded in a protective matrix of extracellular polymeric substances. Within a biofilm, micro-organisms are protected from harsh environmental conditions including those resulting from cleaning and disinfecting agents leading to food safety and quality issues after dispersal of life biofilm cells and subsequent contamination of foods. In this thesis, single and multi-strain biofilm formation by Lactobacillus plantarum isolates was characterised including the model strain L. plantarum WCFS1 and food spoilage isolates. Analysis of the L. plantarum single strain biofilm formation showed a role for proteins and/or proteinaceous material in surface colonization and extracellular DNA as components of the biofilm matrix. The relevance of lysis for the build-up of the biofilm matrix with eDNA was demonstrated using L. plantarum WCFS1 mutants affected in the production of cell wall polysaccharides resulting in altered cell surface composition and mutants lacking cell wall lytic enzymes that showed decreased cell lysis. Dual and multi-strain biofilms were studied using quantitative PCR and next generation sequencing based on detection of strain specific alleles in competitive planktonic and surface-attached biofilm growth models. In multi-strain cultures, the performance of individual strains generally correlated with their performance in pure culture, and relative strain abundance in multi-strain static biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The next generation sequencing approach provided additional insights in the performance of twelve individual L. plantarum strains in static and dynamic flow competitive biofilm models and showed that environmental stresses such as absence of Mn(II) and increased temperature affected not only the relative abundance of each strain both in planktonic and static biofilm growth but also the release of eDNA. The strains dominating the biofilms in static conditions were not the same as those dominating in biofilms developed in dynamic flowing conditions. The genome content of the dominating strains was explored to identify genetic factors that potentially contribute to strain specific competitive-biofilm forming capacity under dynamic flowing conditions, providing leads for further research. All the single, dual and multi-strain biofilms contained a considerable number of viable L. plantarum cells, representing a potential source of contamination. The developed tools and insights obtained in L. plantarum biofilm formation capacity may assist development of strategies to prevent (re)contamination from biofilms in food processing environments.

Select strengths and biases of models in representing the Arctic winter boundary layer over sea ice : the Larcform 1 single column model intercomparison
Pithan, Felix ; Ackerman, Andrew ; Angevine, Wayne M. ; Hartung, Kerstin ; Ickes, Luisa ; Kelley, Maxwell ; Medeiros, Brian ; Sandu, Irina ; Steeneveld, Gert Jan ; Sterk, H.A.M. - \ 2016
Journal of Advances in Modeling Earth Systems 8 (2016)3. - ISSN 1942-2466 - p. 1345 - 1357.
Arctic - boundary-layer - intercomparison - inversion - mixed-phase clouds - models

Weather and climate models struggle to represent lower tropospheric temperature and moisture profiles and surface fluxes in Arctic winter, partly because they lack or misrepresent physical processes that are specific to high latitudes. Observations have revealed two preferred states of the Arctic winter boundary layer. In the cloudy state, cloud liquid water limits surface radiative cooling, and temperature inversions are weak and elevated. In the radiatively clear state, strong surface radiative cooling leads to the build-up of surface-based temperature inversions. Many large-scale models lack the cloudy state, and some substantially underestimate inversion strength in the clear state. Here, the transformation from a moist to a cold dry air mass is modeled using an idealized Lagrangian perspective. The trajectory includes both boundary layer states, and the single-column experiment is the first Lagrangian Arctic air formation experiment (Larcform 1) organized within GEWEX GASS (Global atmospheric system studies). The intercomparison reproduces the typical biases of large-scale models: some models lack the cloudy state of the boundary layer due to the representation of mixed-phase microphysics or to the interaction between micro- and macrophysics. In some models, high emissivities of ice clouds or the lack of an insulating snow layer prevent the build-up of surface-based inversions in the radiatively clear state. Models substantially disagree on the amount of cloud liquid water in the cloudy state and on turbulent heat fluxes under clear skies. Observations of air mass transformations including both boundary layer states would allow for a tighter constraint of model behavior.

De Wageningen Lowland Runoff Simulator (WALRUS): een snel neerslag-afvoermodel speciaal voor laaglandstroomgebieden
Brauer, C.C. ; Torfs, P.J.J.F. ; Teuling, A.J. ; Uijlenhoet, R. - \ 2016
Stromingen : vakblad voor hydrologen 22 (2016)1. - ISSN 1382-6069 - p. 7 - 18.
neerslag - hydrologie van stroomgebieden - modellen - afvoerwater - laaglandgebieden - stroomgebieden - grondwater - oppervlaktewater - kwel - reservoirs - droogte - risicoanalyse - precipitation - catchment hydrology - models - effluents - lowland areas - watersheds - groundwater - surface water - seepage - drought - risk analysis
De Wageningen Lowland Runoff Simulator (WALRUS) is een nieuw neerslag-afvoermodel dat het gat moet vullen tussen complexe, ruimtelijk gedistribueerde modellen die vaak gebruikt worden in laaglandstroomgebieden en simpele, ruimtelijk geïntegreerde, parametrische modellen die voornamelijk zijn ontwikkeld voor hellende stroomgebieden. WALRUS houdt expliciet rekening met hydrologische processen die belangrijk zijn in laaglandgebieden, in het bijzonder (1) de koppeling tussen grondwater en onverzadigde zone, (2) vochttoestandafhankelijke stroomroutes, (3) grondwater-oppervlaktewaterterugkoppeling en (4) kwel, wegzijging en het inlaten of wegpompen van oppervlaktewater. WALRUS bestaat uit een gekoppeld reservoir voor grondwater en onverzadigde zone, een reservoir voor snelle stroomroutes en een oppervlaktewaterreservoir. Het is geschikt voor operationele toepassingen omdat het efficiënt rekent en numeriek stabiel is. In de vrij toegankelijke modelcode zijn standaardrelaties geïmplementeerd, zodat er slechts vier parameters overblijven die gekalibreerd hoeven te worden. Het model is geschikt voor het operationeel simuleren van hoogwater en droogte ten behoeve van risico-analyses en scenario-analyses, voor het ontwerpen van infrastructuur en voor het aanvullen van ontbrekende gegevens in afvoermeetreeksen
Oil slick fate in 3D : predicting the influence of (natural and chemical) dispersion on oil slick fate
Zeinstra-Helfrich, Marieke - \ 2016
Wageningen University. Promotor(en): Tinka Murk, co-promotor(en): W. Koops. - Wageningen : Wageningen University - ISBN 9789462579279 - 174
oil spills - pollution - adverse effects - oils - dispersion - models - thickness - olieverontreinigingen - verontreiniging - nadelige gevolgen - oliën - dispersie - modellen - dikte
Making eco logic and models work : an integrative approach to lake ecosystem modelling
Kuiper, Jan Jurjen - \ 2016
Wageningen University. Promotor(en): W.M. Mooij, co-promotor(en): J.H. Janse; Jeroen de Klein. - Wageningen : Wageningen University - ISBN 9789462579446 - 192
ecology - models - ecosystems - modeling - aquatic ecology - water management - water quality - databases - ecologie - modellen - ecosystemen - modelleren - aquatische ecologie - waterbeheer - waterkwaliteit - databanken

Dynamical ecosystem models are important tools that can help ecologists understand complex systems, and turn understanding into predictions of how these systems respond to external changes. This thesis revolves around PCLake, an integrated ecosystem model of shallow lakes that is used by both scientists and water quality managers to understand and predict eutrophication effects in shallow lake ecosystems. Shallow lakes provide some of the clearest examples of alternative stable states in natural systems. PCLake can be used to calculate the critical nutrient loading, that is, the nutrient loading where an abrupt regime shift occurs from a clear aquatic plant dominated state to a turbid phytoplankton dominated state, or vice versa. Four different aspects of modelling with PCLake are addressed in this thesis: (1) making the model better accessible for the modelling community, (2) improving the model, (3) developing scientific theory, and (4) exploring new applications for water quality management.

Following a general introduction to the thesis in chapter 1, the Database Approach To Modelling (DATM) is introduced in chapter 2. DATM is invented to make dynamic models more accessible. The idea of DATM is that the mathematical equations of a model are stored in a database independently of program language and software specific information. From the database, the information can be automatically translated, augmented and compiled into working model code of various different modelling frameworks (software programs).

In chapter 3 the weak link between ecosystem models and real ecosystems is discussed in relation to model calibration and improvement. In a previous stage PCLake has been calibrated using data of more than 40 lakes to obtain a best overall fit, which has greatly increased the scope of the model by making it suitable for more generalized studies on temperate shallow lakes. However, because of this calibration, adding missing functional components to the model at a later stage does not automatically increase the validity of the model, as it may bring the model ‘out of balance’. This is exemplified by adding filter feeding zoobenthos to PCLake, which were previously ignored.

In chapter 4, the relation between food-web theory and alternative stable states theory is scrutinized. Both theoretical paradigms are highly influential in modern ecology as they help scientists understand how stability emerges in complex natural ecosystems. Unfortunately, they developed independently and it is largely unclear how the resilience of a food web relates to the stability of the complete ecosystem. For this study PCLake was used as a virtual reality from which ‘empirical’ information is sampled to parameterize a food web model, following traditional food web methods. This allowed calculating the stability of the food web along a gradient of environmental change, knowing that the complete ecosystem shows a regime shift once the critical nutrient loading is exceeded.

In chapter 5 the question is asked to what extent models of a different form can be used to describe the same natural phenomenon, and hence, how these models can be used for a better understanding of such natural phenomena. Using three classical extensions of the famous Lotka-Volterra equations, which unlike PCLake can be fully mathematically understood, we analyze the consequence of changing a system with a sophisticated functional response term (e.g. Holling type II or III) into a system with a simpler functional response term while maintaining equilibrium densities and material fluxes. These results give new insight into when empirical data can be linked to mathematical models to estimate the stability properties of real ecosystems.

Although PCLake is predominantly applied in the context of ecosystem restoration of turbid phytoplankton dominated lakes, chapter 6 focusses on the clear water state after the reestablishment of aquatic plant dominance as occured. Dense stands of aquatic plants easily cause nuisance, and hence the removal of aquatic plants is an emerging management issue. Yet, because aquatic plants play an important role in stabilizing the clear water state, the removal of plant biomass can potentially trigger a critical transition back to the turbid water state. Currently there is only limited empirical and theoretical understanding of how harvesting of aquatic plants affects ecosystem functioning, which frustrates effective and efficient ecosystem management. With PCLake the impact of harvesting is evaluated, in terms of reducing nuisance and ecosystem stability, for a wide range of external nutrient loadings, mowing intensities and timings. Additionally, the model is used to estimate how much phosphorus is removed from the system during harvesting.

In chapter 7 I discuss the added value of taking an integrative approach to modelling, and discuss the integrated nature of the studies presented in this thesis. It’s also important to note that these studies were part of a larger research project with the overall aim of increasing the usefulness and the validity of PCLake and its twin model PCDitch, and to enhance the confidence in the models among water quality managers. A synopsis of the overarching collaborative research project on PCLake and PCDitch is presented in chapter 8.

Utilization of complete chloroplast genomes for phylogenetic studies
Ramlee, Shairul Izan Binti - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Rene Smulders; Theo Borm. - Wageningen : Wageningen University - ISBN 9789462579354 - 186
phylogenetics - genomes - chloroplasts - models - solanum - orchidaceae - phylogenomics - dna sequencing - fylogenetica - genomen - chloroplasten - modellen - solanum - orchidaceae - phylogenomica - dna-sequencing

Chloroplast DNA sequence polymorphisms are a primary source of data in many plant phylogenetic studies. The chloroplast genome is relatively conserved in its evolution making it an ideal molecule to retain phylogenetic signals. The chloroplast genome is also largely, but not completely, free from other evolutionary processes such as gene duplication, concerted evolution, pseudogene formation and genome rearrangements. The conservation of the chloroplast genome sequence allows designing primers targeting regions conserved well beyond species boundaries, and amplification of these targets.

The small size together with their high copy number in leaf cells greatly facilitates chloroplast genome sequencing. In this thesis, chloroplast phylogenomics was conducted using complete chloroplast DNA genomes obtained by a newly developed method of de novo assembly. The method was not only cost-effective but also has the potential to extract a wealth of useful information of thousands of chloroplast genomes from Whole Genome Shotgun (WGS) data. We used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. This pipeline includes steps aimed at optimizing assemblies and filling gaps that are left due to coverage variation in the WGS dataset. The pipeline enabled successful de novo assembly across a range of nuclear genome sizes, from Solanum lycopersicon (tomato, 0.9 Gb) to Paphiopedilum heryanum (slipper orchid, 35 Gb).

The pipeline is suitable for studying structural variation in the chloroplast genome, as opposed to the common procedure of read mapping against a reference genome. To support the putative rearrangements, a flexible assembly quality comparison tool was created that combines and visualizes read mapping and alignment results in a two-dimensional plot. We have evaluated the ability of this tool using the de novo assemblies of S. lycopersicon and P. henryanum chloroplasts. The results show that not only we can immediately select the best of two options, but also determine the location of specific artefacts.

In order to explore and evaluate the utility of complete chloroplast phylogenomics, tomato and Paphiopedilum spp were used to conduct phylogenetic inferences based on the complete chloroplast genome. In total 84 tomato chloroplast genomes within the section Lycopersicon were assembled and phylogenetic trees produced. The analyses revealed that next to the chloroplast regions and spacers traditionally used for phylogenetics, additional regions of protein coding and non-coding DNA may be exploited for intraspecific phylogenetic studies. In particular, more than 50% of all phylogenetically relevant information could be included by just using four genes (ycf1, ndhF, ndhA, and ndhH), of which 34% in ycf1 alone. The topology of the phylogenetic tree inferred from ycf1 was the same as that of trees based on all other protein coding genes, although with lower bootstrap values. The phylogenetic analyses based on 32 complete Paphiopedilum spp. chloroplast genomes confirmed the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum. The division of five sections of subgenus Paphiopedilum was also recovered. The de novo assemblies revealed several structural rearrangements including gene loss and inversion. In addition, the chloroplast genome of Paphiopedilum has experienced extreme IR expansion that has included part of or the entire SSC region, resulting in larger IR regions than commonly observed among monocots.

In conclusion, WGS data offer opportunities to generate partial or entire chloroplast genomes for phylogenetic studies. Species discrimination can be achieved already with partial data (subsets of genes), but evolutionarily young lineages may require more informative characters. Therefore, it is expected that many complete chloroplast genomes will be produced in the years to come. While generating these genomes, the urge for de novo assembly of chloroplast genomes rather than mapping against reference genomes is adamant in order to also uncover structural rearrangements in chloroplast genome.

Improving the knowledge basis for advice on North Sea horse mackerel : developing new methods to get insight on stock boundaries and abundance
Brunel, Thomas ; Farrell, Edward D. ; Kotterman, Michiel ; Kwadijk, Christiaan ; Verkempynck, Ruben ; Chen, Chun ; Miller, David - \ 2016
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C092/16) - 57
trachurus trachurus - fish stocks - fisheries - models - visstand - visserij - modellen
The North Sea horse mackerel stock is currently classified by ICES as a data poor stock, for which the catch advice is based on the trend in an abundance index. The development of an analytical stock assessment, necessary to give more accurate advice, is hampered by a number of limitations on the input data, among which the most important are the poor quality of catch-at-age data and the absence of a targeted survey for North Sea horse mackerel. The aim of this project was to study possibilities to improve the data quality used for an analytical stock assessment model.
Improving communication and validation of ecological models : a case study on the dispersal of aquatic macroinvertebrates
Augusiak, Jacqueline A. - \ 2016
Wageningen University. Promotor(en): Paul van den Brink, co-promotor(en): V. Grimm. - Wageningen : Wageningen University - ISBN 9789462579378 - 192
macroinvertebrates - aquatic invertebrates - ecological modeling - ecology - models - dispersal - environmental policy - macroinvertebraten - waterinvertebraten - ecologische modellering - ecologie - modellen - verspreiding - milieubeleid

In recent years, ecological effect models have been put forward as tools for supporting environmental decision-making. Often they are the only way to take the relevant spatial and temporal scales and the multitude of processes characteristic to ecological systems into account. Particularly for environmental risk assessments of pesticides the potential benefits of including modelling studies were recognized and a dialogue between different stakeholder groups was opened. Representatives from academia, pesticide-producing industries, and regulators are nowadays discussing their needs, possibilities, and ways of implementation for improving the use and usefulness of such models. However, it quickly became evident that not all involved parties possess the same background knowledge in regards to modelling terminology and model quality understanding. Proper communication of a given model's structure, robustness, and soundness is crucial to render a model of real use to the decision-making. Doubts about a model's quality and mode of operation may lead to an immediate rejection of the conclusions drawn from its estimations.

In this thesis, we addressed this point of concern, and performed a literature review focusing on aspects surrounding quality assessments, validation, and communication of models. "Validation" was identified as a catch-all term, which is thus useless for any practical purpose. Based on the review, we developed a framework that splits the seemingly blurry process into associated components and introduce the term ‘evaludation’, a fusion of ‘evaluation’ and ‘validation’, to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) ‘data evaluation’ for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) ‘conceptual model evaluation’ for examining the simplifying assumptions underlying a model's design; (iii) ‘implementation verification’ for testing the model's implementation in equations and as a computer programme; (iv) ‘model output verification’ for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) ‘model analysis’ for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) ‘model output corroboration’ for comparing model output to new data and patterns that were not used for model development and parameterisation.

In a subsequent step, we used the evaludation framework to re-evaluate and adjust the documentation framework TRACE (TRAnsparent and Comprehensive Eco- logical modelling; Schmolke et al. 2010), a general framework for documenting a model's rationale, design, and testing. TRACE documents should provide convincing evidence that a model was thoughtfully designed, correctly implemented, thoroughly tested, well understood, and appropriately used for its intended purpose. TRACE documents link the science underlying a model to its application, thereby also linking modellers and model users, for example stakeholders, decision makers, and developers of policies. TRACE thus becomes a tool for planning, documenting, and assessing model evaludation, which includes understanding the rationale behind a model and its envisaged use.

To provide an example of the measures that can be taken to increase general trust in a model's design and output, we chose MASTEP (Metapopulation model for Assessing Spatial and Temporal Effects of Pesticides) for a case study. MASTEP is an individual-based model used to describe the effects on and recovery of the water louse Asellus aquaticus after exposure to an insecticide in pond, ditch, and stream scenarios. The model includes processes of mortality of A. aquaticus, life history, random walk between cells and density dependence of population regulation. One of the submodels receiving particular criticism was the random walk procedure and the uncertainty attached to the parameters used. The parameters were estimated based on experimental studies performed under very limiting conditions.

We designed and performed experiments to derive more precise parameters and to better understand the movement behaviour of this freshwater isopod. The experimental procedure that we developed employed video tracking of marked individuals that were introduced alone or as part of a group of unmarked individuals into arenas of approximately 1m2 in size. We recorded the paths of the marked individuals under a set of different conditions, i.e. presence or absence of food or shelter, population density, and after sublethal exposure to chlorpyrifos and imidacloprid. Based on the experimental findings, we refined the movement modelling procedure used in MASTEP to derive more realistic dispersal estimates, with which we revisited a modelling study performed previously by Galic et al. (2012). In this study, the effects of pesticide application timing on population dynamics and recovery times were tested and compared to outcomes from previous versions. It was furthermore possible to integrate an increased level of environmental complexity that could not be addressed before due to a lack of data. Compared to former versions of the population model, recovery times did not change significantly when the same movement parameters were applied to all simulated individuals. This indicates that the previous assumptions already yielded robust estimations. Accounting for life stage dependent movement restraints, though, delayed recovery when exposure occurred shortly before a reproduction cycle. Based on these findings, it was concluded that an increase of ever more realism and environmental complexity in modelling studies needs to be done carefully on a case-by-case basis. Increased realism in models can introduce an unwarranted increase in model complexity and uncertainty, which is not always supporting an improved credibility level of a model.

Despite the need for basic ecological research for more comprehensive ecological models, we further argue that a modelling study in general can benefit greatly from an improved plan that considers communication needs from the start. Considering such needs early on can help develop a time- and cost-saving strategy for model testing and data collection, while providing a thorough understanding of a model's underlying mechanisms across several layers of stakeholder groups.

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