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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    Unveiling soil degradation and desertification risk in the Mediterranean basin: a data mining analysis of the relationships between biophysical and socioeconomic factors in agro-forest landscapes
    Salvati, L. ; Kosmas, C. ; Kairis, O. ; Karavitis, C. ; Hessel, R. ; Ritsema, C.J. - \ 2015
    Journal of Environmental Planning and Management 58 (2015)10. - ISSN 0964-0568 - p. 1789 - 1803.
    land-use change - abandonment - erosion - vulnerability - performance - indicators - region - europe - system - spain
    Soil degradation and desertification processes in the Mediterranean basin reflect the interplay between environmental and socioeconomic drivers. An approach to evaluate comparatively the multiple relationships between biophysical variables and socioeconomic factors is illustrated in the present study using the data collected from 586 field sites located in five Mediterranean areas (Spain, Greece, Turkey, Tunisia and Morocco). A total of 47 variables were chosen to illustrate land-use, farm characteristics, population pressure, tourism development, rainfall regime, water availability, soil properties and vegetation cover, among others. A data mining approach incorporating non-parametric inference, principal component analysis and hierarchical clustering was developed to identify candidate syndromes of soil degradation and desertification risk. While field sites in the same study area showed a substantial similarity, the multivariate relationship among variables diverged among study areas. Data mining techniques proved to be a practical tool to identify spatial determinants of soil degradation and desertification risk. Our findings identify the contrasting spatial patterns for biophysical and socioeconomic variables, in turn associated with different responses to land degradation.
    Changes in agricultural land use affecting future soil redistribution patterns: A case study in southern tuscany (ITALY)
    Debolini, M. ; Schoorl, J.M. ; Temme, A.J.A.M. ; Galli, M. ; Bonari, E. - \ 2015
    Land Degradation and Development 26 (2015)6. - ISSN 1085-3278 - p. 574 - 586.
    ne spain - landscape evolution - driving forces - sediment yield - erosion - model - management - region - abandonment - catchment
    Land-use changes (LUCs) can be defined as the result of the direct action of the stakeholders in a particular area and natural or human driving forces. LUCs can influence various processes within the landscape and can have an impact on landscape functions. An analysis of the impact of LUCs on landscape processes can help to focus future rural policies. LUCs in Mediterranean areas particularly affect landscape functions because of their agro-pedoclimatical characteristics. The aims of this work are as follows: (i) to characterise LUCs in the last 11¿years in a typical Mediterranean area, the Trasubbie river basin (southern Tuscany, Italy); (ii) to extrapolate these changes and create spatially explicit LUC scenarios for the near future; and (iii) to simulate how and where the predicted LUCs may affect soil redistribution. We carried out an analysis of LUCs within the study area and used the trends to propose alternative scenarios for 2013. For these years, we spatially allocated land use (using the Conversions of Land Use and its Effects model) and used a landscape process model (landscape process modelling at multi-dimensions and scales) to assess soil redistribution patterns. Land use in the study area changed almost linearly between 1996 and 2007, with cereals and annual fodder crops decreasing, and vineyards, perennial pastures and land abandonment increasing. Our LUC scenario extrapolates these dynamics to make predictions for 2013. A comparison of LAPSUS results between LUC and baseline scenarios for 2013 showed an increase in terms of net soil loss and total erosion, and a decrease in terms of sediment delivery ratio.
    Risk perception and management in smallholder dairy farming in Tigray, Northern Ethiopia
    Gebreegziabher, K. ; Tadesse Woeldesenbet, T. - \ 2014
    Journal of Risk Research 17 (2014)3. - ISSN 1366-9877 - p. 367 - 381.
    tick-borne diseases - kenya highlands - cattle - tanzania - systems - prevalence - economics - adoption - farmers - region
    Empirical studies on smallholder dairy farmers' risk perceptions and management strategies have still received little attention in agricultural research of developing countries. This study focuses on farmers' risk perception and management strategies of smallholder dairy farms in urban and peri-urban areas of Tigray in northern Ethiopia. Based on data collected from a sample of 304 smallholder dairy farm households, we used descriptive statistics for analyzing farmers' risk attitude and factor analysis for analyzing and classifying risk sources and management strategies. The majority of dairy farmers considered themselves risk takers towards farm decision that may have a positive impact on technology adoption. Factor analysis identified technological, price/market, production, financial, human, and institutional factor as major sources of risks. In addition, factor analysis indicates that disease reduction, diversification, financial management, and market network are perceived as the most effective risk management strategies. Our findings indicate that perceptions of risk and management strategies are farmer-specific; therefore, policy-makers need to consider tailor-made strategies that would address farmers' individual motives to manage risks and shocks.
    A cost-effective approach for improving the quality of soil sealing change detection from Landsat imagery
    Smiraglia, D. ; Rinaldo, S. ; Ceccarelli, T. ; Bajocco, S. ; Salvati, L. ; Ricotta, C. ; Perini, L. - \ 2014
    European Journal of Remote Sensing 47 (2014). - ISSN 2279-7254 - p. 805 - 819.
    urban - modis - tm - transformation - segmentation - phenology - sprawl - region - ndvi - area
    The aim of this study is to develop a cost-effective approach for soil sealing change detection integrating radiometric analysis, multi-resolution segmentation and object-based classifiers in two study areas in Italy: Campania region and Veneto region. The integrated approach uses multi-temporal satellite images and CORINE Land Cover (CLC) maps. A good overall accuracy was obtained for the soil sealing maps produced. The results show an improvement in terms of size of the minimum mapping unit and of the changed object (1,44 ha in both cases) in respect to the CLC. The approach proves to be cost-effective given the data which are provided at low or no cost and as well as the level of automation achievable.
    Combining multi-dimensional scaling and cluster analysis to describe the diversity of rural households
    Pacini, G.C. ; Colucci, D. ; Baudron, F. ; Righi, E. ; Corbeels, M. ; Tittonell, P.A. ; Stefanini, F.M. - \ 2014
    Experimental Agriculture 50 (2014)3. - ISSN 0014-4797 - p. 376 - 397.
    farms - management - heterogeneity - assemblages - typologies - indicators - region - spain
    Capturing agricultural heterogeneity through the analysis of farm typologies is key with regard to the design of sustainable policies and to the adoptability of new technologies. An optimal balance needs to be found between, on the one hand, the requirement to consider local stakeholder and expert knowledge for typology identification, and on the other hand, the need to identify typologies that transcend the local boundaries of single studies and can be used for comparisons. In this paper, we propose a method that supports expert-driven identification of farm typologies, while at the same time keeping the characteristics of objectivity and reproducibility of statistical tools. The method uses a range of multivariate analysis techniques and it is based on a protocol that favours the use of stakeholder and expert knowledge in the process of typology identification by means of visualization of farm groups and relevant statistics. Results of two studies in Zimbabwe and Kenya are shown. Findings obtained with the method proposed are contrasted with those obtained through a parametric method based on latent class analysis. The method is compared to alternative approaches with regard to stakeholder-orientation and statistical reliability.
    Impacts of climate change on net primary productivity of grasslands in Inner Mongolia
    Li, Q. ; Tuo Debao, ; Zhang, L. ; Wei, X. ; Wei, Y. ; Yang, N. ; Xu, Y. ; Anten, N.P.R. ; Pan, X. - \ 2014
    The Rangeland Journal 36 (2014)5. - ISSN 1036-9872 - p. 493 - 503.
    below-ground biomass - classification-system - china - ecosystems - temperate - diversity - forests - region - model
    Net primary productivity (NPP) of grasslands is a key variable for characterising carbon cycles in grassland ecosystems. The prediction of NPP in Inner Mongolia is important for adaptation to future climate change, food security and sustainable use of the grassland resources. The output from two models, potentially suitable for simulating NPP in response to climate change, was tested against observed aboveground forage mass of dry matter at eight sites in Inner Mongolia from 1995 to 2005. The Classification Indices-Based Model (CIBM) showed an acceptable agreement with field measurements. The impact of climate change on the NPP of grasslands was subsequently analysed by CIBM using future climate projections from a Global Circulation Model based on three greenhouse gas emission scenarios: A2 (medium-high emission), A1B (medium emission) and B2 (medium-low emission) differing in assumptions about patterns of global social and economic development. Generally, significant increases in NPP, compared with the baseline NPP of 3.6 tonnes ha–1 for 1961–90, were predicted. The magnitude of the increase in NPP depended on the emission scenario, as well as on the time frame and region considered. Overall the predicted NPP stimulation increased with the level of emissions assumed, being 4.8 tonnes ha–1 in the A2 scenario, 4.3 tonnes ha–1 in the B2 scenario and 4.5 tonnes ha–1 in the A1B scenario in the 2080s (2071–2100). The increase in NPP in response to climate change differed between regions and there was an interaction with emission scenario. For the A2 and the B2 emission scenarios, the western region of Inner Mongolia was predicted to exhibit the strongest NPP increases, but, under the A1B scenario for the 2050s, the south-eastern region exhibited the greatest increase in NPP. It is concluded that the productivity of grassland in Inner Mongolia is likely to increase in response to climate change but these predicted effects are sensitive to emission scenarios and differ regionally. This will provide opportunities but also challenges for herders and policy makers in adapting to this change.
    Diversity of Plasmids Encoding Virulence and Resistance Functions in Salmonella enterica subsp. enterica Serovar Typhimurium Monophasic Variant 4,[5],12:i:- Strains Circulating in Europe.
    Garcia, P. ; Hopkins, K.L. ; García, V. ; Beutlich, J. ; Mendoza, M.C. ; Threlfall, J. ; Mevius, D.J. ; Helmuth, R. ; Rodicio, M.R. ; Guerra, B. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203
    antimicrobial resistance - multidrug-resistance - spanish clone - health-risk - determinants - serotype - region - genes
    Plasmids encoding resistance and virulence properties in multidrug resistant (MDR) Salmonella enterica (S.) serovar Typhimurium monophasic variant 4,[5],12:i:- isolates recovered from pigs and humans (2006-2008) in Europe were characterised. The isolates were selected based on the detection by PCR-amplification of S. Typhimurium virulence plasmid pSLT genes and were analysed by multi-locus sequence typing (MLST). The resistance genes present in the isolates and the association of these genes with integrons, transposons and insertion sequences were characterised by PCR-sequencing, and their plasmid location was determined by alkaline lysis and by S1-nuclease pulsed-field gel electrophoresis (PFGE) Southern-blot hybridisation. Plasmids were further analysed by replicon typing, plasmid MLST and conjugation experiments. The 10 S. 4,[5],12,i:- selected isolates belonged to ST19. Each isolate carried a large plasmid in which MDR with pSLT-associated virulence genes were located. After analysis, eight different plasmids of three incompatibility groups (IncA/C, IncR and IncF) were detected. Two IncA/C plasmids represented novel variants within the plasmid family of the S. 4,[5],12:i:- Spanish clone, and carried an empty class 1 integron with a conventional qacE¿1-sul1 3' conserved segment or an In-sul3 type III with estX-psp-aadA2-cmlA1-aadA1-qacH variable region linked to tnpA440-sul3, part of Tn2, Tn21 and Tn1721 transposons, and ISCR2. Four newly described IncR plasmids contained the resistance genes within In-sul3 type I (dfrA12-orfF-aadA2-cmlA1-aadA1-qacH/tnpA440-sul3) and part of Tn10 [tet(B)]. Two pSLT-derivatives with FIIs-ST1+FIB-ST17 replicons carried cmlA1-[aadA1-aadA2]-sul3-dfrA12 and blaTEM-1 genes linked to an In-sul3 type I integron and to Tn2, respectively. In conclusion, three emerging European clones of S. 4,[5],12:i:- harboured MDR plasmids encoding additional virulence functions that could contribute significantly to their evolutionary success.
    The role of knowledge in greening flood protection. Lessons from the Dutch case study future Afsluitdijk
    Janssen, S.K.H. ; Mol, A.P.J. ; Tatenhove, J. van; Otter, H.S. - \ 2014
    Ocean & Coastal Management 95 (2014). - ISSN 0964-5691 - p. 219 - 232.
    water management - sustainable development - policy - science - information - netherlands - dynamics - projects - search - region
    Greening flood protection (GFP) is an upcoming approach in coastal protection knowledge and policy. The central notion of this multifunctional concept is that natural processes, nature development and the dynamics of ecosystems are taken into account in realising flood protection. In practice, implementation of GFP is faced with multiple barriers, of which some are strongly related to knowledge. In this paper we aim to further our understanding of the realisation of GFP in projects by focussing on the role of knowledge and specifically looking at the interaction between knowledge related to different policy fields. We analyse under what conditions knowledge can enable GFP in projects. We apply a conceptual framework of knowledge arrangements (KAs)ddrawing attention to the policy fields and the knowledge based on the Dutch flood protection project Future Afsluitdijk. While the project aimed at more than just flood protection, this was not achieved. The case serves as an illustrative example of the struggle to organise knowledge processes for an integrated, greening flood protection design. We identify four main lessons on the role of knowledge: (1) knowledge development should take place at close distance to the policy process and include intensive interaction, (2) multiple design iterations are needed, (3) integration at policy level requires structural embedding to endure, and (4) tools are required that allow for an integrated assessment. Interestingly, the failure of integration between KAs within the project led to the development and re-organisation of the nature domain. As a result nature actors managed to pursue their goals, but in a different arena.
    Human–dog interactions and behavioural responses of village dogs in coastal villages in Michoacán, Mexico
    Ruiz Izaguirre, E. ; Eilers, C.H.A.M. ; Bokkers, E.A.M. ; Ortolani, A. ; Ortega-Pacheco, A. ; Boer, I.J.M. de - \ 2014
    Applied Animal Behaviour Science 154 (2014). - ISSN 0168-1591 - p. 57 - 65.
    canis-familiaris - domestic dogs - population - bites - perceptions - attitudes - victims - disease - region - areas
    In Mexican villages, most households keep dogs that roam freely. Therefore, socialisation of village dogs occurs in a different context than that of companion dogs in developed countries. The objectives of this study were: (1) to assess village dogs’ behavioural responses towards familiar and unfamiliar humans, (2) to compare body condition of dogs living in a village with a seasonal trade in international tourism (IT-village) with dogs living in a village located in the vicinity of a sea-turtle nesting site (STN-village), and (3) to identify whether dog characteristics influence dog behaviour and body condition. Two coastal villages in Michoacán, Mexico, were selected as case study sites. Fifty-nine dogs were initially visited, 35 of which were repeatedly visited during the high and low seasons for international tourism and sea-turtle nesting. Caregivers were interviewed regarding human–dog interactions, and dogs were behaviourally tested and rated for body condition. Behavioural indicators were: (1) the dog's qualitative response to a caregiver's call and (2) the dog's willingness to approach an unfamiliar human. Additionally, a dog census per village was conducted to ascertain the dog population structure. Dogs were kept by over 60% of households in both villages. Body condition was optimal for 68% of the dogs. In the low season, dogs in the STN-village had better body condition than dogs in IT-village (P = 0.007). Dog characteristics that influenced behavioural responses were: sex, age, and whether the dog played with humans. The most common response to the caregiver's call was tail wagging, shown by 83% of male dogs and 50% of female dogs (P = 0.021). About 70% of the pups approached the unfamiliar human completely, whereas only 24% of the juveniles (P = 0.040) and 26% of the adults did so (P = 0.026). Human–dog play was reported to occur mainly with children (77%). The percentage of dogs that played with humans was higher in dogs responding with tail wagging (82%) than in dogs showing the rest of the response categories (withdrawal, baring teeth, and other) (50%) (P = 0.012). Human–dog play was reported for 85% of the male dogs compared to 55% of the female dogs (P = 0.036). This study showed that village dogs were socialised to familiar humans but were not attracted to unfamiliar humans. Village dogs maintained their body condition in the low season. Child–dog play may have a role in shaping village dog social behaviour towards humans.
    Comparative analysis of policies to deal with wildfire risk
    Carreiras, M. ; Ferreira, A.D.J. ; Valente, S. ; Fleskens, L. ; Gonzales-Pelayo, O. ; Rubio, J.L. ; Stoof, C.R. ; Coelho, C.O.A. ; Ferreira, C.S.S. ; Ritsema, C.J. - \ 2014
    Land Degradation and Development 25 (2014)1. - ISSN 1085-3278 - p. 92 - 103.
    public-participation - forest owners - fire regimes - management - portugal - perspective - examples - impacts - system - region
    Fires are the main driver of land degradation in forest areas in Mediterranean sub-humid regions and are likely to increase as a result of climate and other global changes. To prevent deleterious processes induced by fire, several policies and strategies have been implemented at national and regional scales. We perform a comparative study of policies and strategies of Portuguese and Spanish (Comunitat Valenciana) cases in order to assess the differences between them and identify their roles in forest fire prevention and in combating and mitigating impacts. To this end, we analyse the sustainability objectives stated in the legislation of each country to identify the strategies used to deal with forest fires and the extent to which they are integrated to achieve the sustainability objectives they pursue. The comparative analysis includes an assessment of sustainability, evaluated by the explicitness of the objectives, and identification of how the lines of action contribute to reach these objectives. We found different levels of complexity and that the adoption or rejection of some of the techniques is closely related to the tradition and the experience of local communities. This analysis highlights the importance of local characteristics and the stakeholders, involvement in designing effective strategies to reduce fire risk
    Worldwide Sustainability Hotspots in Potato Cultivation. 2. Areas with Improvement Opportunities
    Evert, F.K. van; Ruijter, F.J. de; Conijn, J.G. ; Rutgers, B. ; Haverkort, A.J. - \ 2013
    Potato Research 56 (2013)4. - ISSN 0014-3065 - p. 355 - 368.
    farming systems - multiyear assessment - unilevers progress - soil-erosion - nitrogen - biodiversity - indicators - australia - region - crops
    Agriculture has a large impact on the environment and retailers increasingly stimulate their suppliers to reduce the environmental impact of agricultural production. The environmental impact resulting from producing a commodity can be measured with a life cycle analysis (LCA) but performing an LCA is costly and time-consuming. In the first paper of this series a practical and general method to identify hotspot areas in crop production on a global scale was developed. The method was implemented for potatoes. The objective of the work reported here was to evaluate the tool and to identify improvement opportunities for each of seven indicators: yield, erosion risk, nitrogen surplus, depletion of water reserves, biocide use, carbon footprint, and impact on biodiversity. The tool produces realistic outputs that can be used to target improvement efforts and thus improves the use efficiency of limited resources. The tool can be expanded to produce similar results for other crops; methods to improve the resolution of the tool are discussed.
    Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
    Esteve-Codina, A. ; Paudel, Y. ; Ferretti, L. ; Megens, H.J.W.C. ; Groenen, M. - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164
    copy number variation - meat quality traits - positive selection - next-generation - snp discovery - evolution - gene - samples - region - interleukin-2
    Background In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data. Results A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism. Conclusions This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families.
    The System Nobody Sees: Irrigated Wetland Management and Alpaca Herding in the Peruvian Andes
    Verzijl, A. ; Guerrero Quispe, S. - \ 2013
    Mountain Research and Development 33 (2013)3. - ISSN 0276-4741 - p. 280 - 293.
    high-altitude wetlands - climate-change - water - resources - services - region
    Increasingly, attention in regional, national, and international water governance arenas has focused on high-altitude wetlands. However, existing local water management practices in these wetlands are often overlooked. This article looks at the irrigation activities of alpaca herders in the community of Ccarhuancho in the Central Andes of Peru. For more than two centuries, they have been constructing small-scale irrigation canals to maintain and expand the local wetlands, called bofedales. The seminomadic character of alpaca herders complicates irrigated wetland activities, such as operation and maintenance. Climate change and human and animal population pressure have increased not only the importance of these irrigation systems but also of local conflicts and communal decision making. Local irrigation activities in Ccarhuancho go unnoticed in broader water governance arenas because of its remoteness, limits to what popular new analytical tools can measure, a general undervaluation of wetlands, and a tendency of the canals to merge over time with the surrounding bofedales, making them less visible. Nevertheless, these man-made systems account for 40% of the wetlands in the study area and risk being seriously degraded or destroyed without local water management. With climatic changes affecting existing natural wetlands, the local herders were the first to recognize and respond to these changes and to defend the wetlands against degradation. Their efforts are, however, largely overlooked, even though such local water governance practices are crucial for the success of regional and national water governance in the Andes and other mountain areas. (Note: The title of this paper is an adaptation of Netting's [1974] paper “The system nobody knows” about small-scale irrigation in the Swiss Alps.)
    Measuring the neighbourhood effect to calibrate land use models
    Vliet, J. van; Naus, N. ; Lammeren, R.J.A. van; Bregt, A.K. ; Hurkens, J. ; Delden, H. van - \ 2013
    Computers, Environment and Urban Systems 41 (2013). - ISSN 0198-9715 - p. 55 - 64.
    cellular-automata - spatial externalities - urban-growth - rules - simulation - patterns - region - form
    Many spatially explicit land use models include the neighbourhood effect as a driver of land use changes. The neighbourhood effect includes the inertia of land uses over time, the conversion from one land use to another, and the attraction or repulsion of surrounding land uses. The neighbourhood effect is expressed in the neighbourhood rules, but calibration of the neighbourhood rules is not straightforward. This paper aims to characterise the neighbourhood effect of observed land use changes and use this information to improve the calibration of land use models. We measured the over- and underrepresentation of land uses in the neighbourhood of observed land use changes using a modified version of the enrichment factor. Enrichment factors of observed land use changes in Germany between 1990 and 2000 indicate that the neighbourhood effect exists. This suggests that it is appropriate to use neighbourhood rules to simulate urban land use changes. Observed enrichment factors were used to calibrate a land use model for Germany from 1990 to 2000 and the obtained neighbourhood rules were validated independently from 2000 to 2006. The results show that both the allocation accuracy and the pattern accuracy of the land use model improved for the calibration period, as well as for the independent validation period. This indicates that enrichment factors can be used to improve the calibration of the neighbourhood rules in land use models
    Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding
    Ghahramanzadeh, R. ; Esselink, G. ; Kodde, L.P. ; Duistermaat, H. ; Valkenburg, J.L.C.H. van; Marashi, S.H. ; Smulders, M.J.M. ; Wiel, C.C.M. van de - \ 2013
    Molecular Ecology Resources 13 (2013)1. - ISSN 1755-098X - p. 21 - 31.
    land plants - identifications - alignment - region - gap
    Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.
    Two instruments based on differential optical absorption spectroscopy (DOAS) to measure accurate ammonia concentrations in the atmosphere
    Volten, H. ; Bergwerff, J.B. ; Haaima, M. ; Lolkema, D.E. ; Berkhout, A.J.C. ; Hoff, G.R. ; Potma, C.J.M. ; Wichink Kruit, R.J. ; Pul, W.A.J. van; Swart, D.P.J. - \ 2012
    Atmospheric Measurement Techniques 5 (2012)2. - ISSN 1867-1381 - p. 413 - 427.
    cross-sections - herzberg continuum - region - ultraviolet - nm - temperature - spectrum - fluxes - so2 - nh3
    We present two Differential Optical Absorption Spectroscopy (DOAS) instruments built at RIVM: the RIVM DOAS and the miniDOAS. Both instruments provide virtually interference-free measurements of NH3 concentrations in the atmosphere, since they measure over an open path, without suffering from inlet problems or interference problems by ammonium aerosols dissociating on tubes or filters. They measure concentrations up to at least 200 mu g m(-3), have a fast response, low maintenance demands, and a high up-time. The RIVM DOAS has a high accuracy of typically 0.15 mu g m(-3) for ammonia for 5-min averages and over a total light path of 100 m. The miniDOAS has been developed for application in measurement networks such as the Dutch National Air Quality Monitoring Network (LML). Compared to the RIVM DOAS it has a similar accuracy, but is significantly reduced in size, costs, and handling complexity. The RIVM DOAS and miniDOAS results showed excellent agreement (R-2 = 0.996) during a field measurement campaign in Vredepeel, the Netherlands. This measurement site is located in an agricultural area and is characterized by highly variable, but on average high ammonia concentrations in the air. The RIVM-DOAS and miniDOAS results were compared to the results of the AMOR instrument, a continuous-flow wet denuder system, which is currently used in the LML. Averaged over longer time spans of typically a day, the (mini) DOAS and AMOR results agree reasonably well, although an off-set of the AMOR values compared to the (mini) DOAS results exists. On short time scales, the (mini) DOAS shows a faster response and does not show the memory effects due to inlet tubing and transport of absorption fluids encountered by the AMOR. Due to its high accuracy, high uptime, low maintenance and its open path, the (mini) DOAS shows a good potential for flux measurements by using two (or more) systems in a gradient set-up and applying the aerodynamic gradient technique.
    Short communication: A new bovine milk-protein variant: a-lactalbumin variant D.
    Visker, M.H.P.W. ; Heck, J.M. ; Valenberg, H.J.F. van; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2012
    Journal of Dairy Science 95 (2012)4. - ISSN 0022-0302 - p. 2165 - 2169.
    single-base polymorphisms - lactose synthetase - production traits - region - gene - cows - sequence - synthase - cattle
    Capillary zone electrophoresis of 1,948 Holstein-Friesian cows suggested the presence of an unknown protein variant of α-lactalbumin (α-LA) in the milk of 1 cow. Sequencing genomic DNA of this cow showed a polymorphism in the α-LA gene (LAA) that appears to be responsible for this protein variant. This single nucleotide polymorphism g.600G > T was located in exon 2 of LAA and causes the amino acid change 65Gln > His in the α-LA protein. This α-LA protein variant is a new protein variant and should be called α-LA protein variant D. This amino acid change is not expected to affect protein function. Genomic DNA of 156 bulls of various dairy cattle breeds was screened to examine the presence of the new α-LA protein variant D. Single nucleotide polymorphism g.600G > T, responsible for α-LA protein variant D, was not found in any of the 156 bulls. However, 10 other polymorphisms in the coding and promoter regions of LAA were detected that were used to construct haplotypes.
    Methicillin resistant coagulase-negative staphylococci on pig farms and as a reservoir of heterogeneous staphylococcal casette chromosome mec elements
    Tulinski, P. ; Fluit, A.C. ; Wagenaar, J.A. ; Mevius, D.J. ; Vijver, L.P.L. van de; Duim, B. - \ 2012
    Applied and Environmental Microbiology 78 (2012)2. - ISSN 0099-2240 - p. 299 - 304.
    aureus - sccmec - strains - susceptibility - identification - diversity - evolution - region - sentry - pcr
    Methicillin-resistant Staphylococcus aureus (MRSA) likely originated by acquisition of the staphylococcal cassette chromosome mec (SCCmec) from coagulase-negative staphylococci (CNS). However, it is unknown whether the same SCCmec types are present in MRSA and CNS that reside in the same niche. Here we describe a study to determine the presence of a potential mecA reservoir among CNS recovered from 10 pig farms. The 44 strains belonged to 10 different Staphylococcus species. All S. aureus strains belonged to sequence type 398 (ST398), with SCCmec types V and IVa. Type IVc, as well as types III and VI, novel subtypes of type IV, and not-typeable types, were found in CNS. S. aureus, S. epidermidis, and S. haemolyticus shared SCCmec type V. The presence of SCCmec type IVc in several staphylococcal species isolated from one pig farm is noteworthy, suggesting exchange of this SCCmec type in CNS, but the general distribution of this SCCmec type still has to be established. In conclusion, this study shows that SCCmec types among staphylococcal species on pig farms are heterogeneous. On two farms, more than one recovered staphylococcal species harbored the same SCCmec type. We conclude that staphylococci on pig farms act as a reservoir of heterogeneous SCCmec elements. These staphylococci may act as a source for transfer of SCCmec to S. aureus.
    State updating of a distributed hydrological model with Ensemble Kalman Filtering: effects of updating frequency and observation network density on forecast accuracy
    Rakovec, O. ; Weerts, A.H. ; Hazenberg, P. ; Torfs, P.J.J.F. ; Uijlenhoet, R. - \ 2012
    Hydrology and Earth System Sciences 16 (2012)9. - ISSN 1027-5606 - p. 3435 - 3449.
    rainfall-runoff model - sensed soil-moisture - data assimilation - discharge predictions - ourthe catchment - improvement - streamflow - system - region - scale
    This paper presents a study on the optimal setup for discharge assimilation within a spatially distributed hydrological model. The Ensemble Kalman filter (EnKF) is employed to update the grid-based distributed states of such an hourly spatially distributed version of the HBV-96 model. By using a physically based model for the routing, the time delay and attenuation are modelled more realistically. The discharge and states at a given time step are assumed to be dependent on the previous time step only (Markov property). Synthetic and real world experiments are carried out for the Upper Ourthe (1600 km(2)), a relatively quickly responding catchment in the Belgian Ardennes. We assess the impact on the forecasted discharge of (1) various sets of the spatially distributed discharge gauges and (2) the filtering frequency. The results show that the hydrological forecast at the catchment outlet is improved by assimilating interior gauges. This augmentation of the observation vector improves the forecast more than increasing the updating frequency. In terms of the model states, the EnKF procedure is found to mainly change the pdfs of the two routing model storages, even when the uncertainty in the discharge simulations is smaller than the defined observation uncertainty.
    Generating spatial precipitation ensembles: impact of temporal correlation structure
    Rakovec, O. ; Hazenberg, P. ; Torfs, P.J.J.F. ; Weerts, A.H. ; Uijlenhoet, R. - \ 2012
    Hydrology and Earth System Sciences 16 (2012)9. - ISSN 1027-5606 - p. 3419 - 3434.
    distributed hydrological model - radar rainfall estimation - ourthe catchment - real - bias - assimilation - resolution - region
    Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km x 10 km resolution. Uncertainty analyses in the simulated fields focus on (1) the number of previous simulation hours on which the new simulation is conditioned, (2) the advection speed of the rainfall event, (3) the size of the catchment considered, and (4) the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds > 20 km h(-1), no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50 %, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation framework and can be used as an improvement over currently used simplistic approaches to perturb the interpolated point or spatially distributed precipitation estimates.
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