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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    Automated identification of animal species in camera trap images
    Yu, X. ; Wang, J. ; Kays, R. ; Jansen, P.A. ; Wang, T. ; Huang, T. - \ 2013
    EURASIP Journal on Image and Video Processing 2013 (2013). - ISSN 1687-5281 - 10 p.
    Image sensors are increasingly being used in biodiversity monitoring, with each study generating many thousands or millions of pictures. Efficiently identifying the species captured by each image is a critical challenge for the advancement of this field. Here, we present an automated species identification method for wildlife pictures captured by remote camera traps. Our process starts with images that are cropped out of the background. We then use improved sparse coding spatial pyramid matching (ScSPM), which extracts dense SIFT descriptor and cell-structured LBP (cLBP) as the local features, that generates global feature via weighted sparse coding and max pooling using multi-scale pyramid kernel, and classifies the images by a linear support vector machine algorithm. Weighted sparse coding is used to enforce both sparsity and locality of encoding in feature space. We tested the method on a dataset with over 7,000 camera trap images of 18 species from two different field cites, and achieved an average classification accuracy of 82%. Our analysis demonstrates that the combination of SIFT and cLBP can serve as a useful technique for animal species recognition in real, complex scenarios.
    An evaluation of WRF's ability to reproduce the surface wind over complex terrain based on typical circulation patterns.
    Jiménez, P.A. ; Dudhia, J. ; González-Rouco, J.F. ; Montávez, J.P. ; Garcia-Bustamante, E. ; Navarro, J. ; Vilà-Guerau de Arellano, J. ; Munoz-Roldán, A. - \ 2013
    Journal of Geophysical Research: Atmospheres 118 (2013)14. - ISSN 2169-897X - p. 7651 - 7669.
    regional climate model - cluster-analysis - quality-assurance - mesoscale model - united-states - variability - validation - reanalysis - classification - simulation
    [1] The performance of the Weather Research and Forecasting (WRF) model to reproduce the surface wind circulations over complex terrain is examined. The atmospheric evolution is simulated using two versions of the WRF model during an over 13¿year period (1992 to 2005) over a complex terrain region located in the northeast of the Iberian Peninsula. A high horizontal resolution of 2km is used to provide an accurate representation of the terrain features. The multiyear evaluation focuses on the analysis of the accuracy displayed by the WRF simulations to reproduce the wind field of the six typical wind patterns (WPs) identified over the area in a previous observational work. Each pattern contains a high number of days which allows one to reach solid conclusions regarding the model performance. The accuracy of the simulations to reproduce the wind field under representative synoptic situations, or pressure patterns (PPs), of the Iberian Peninsula is also inspected in order to diagnose errors as a function of the large-scale situation. The evaluation is accomplished using daily averages in order to inspect the ability of WRF to reproduce the surface flow as a result of the interaction between the synoptic scale and the regional topography. Results indicate that model errors can originate from problems in the initial and lateral boundary conditions, misrepresentations at the synoptic scale, or the realism of the topographic features.
    Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
    Szitenberg, A. ; Becking, L.E. ; Vargas, S. ; Fernandez, J. ; Santodomingo, N. - \ 2013
    Molecular Phylogenetics and Evolution 67 (2013)2. - ISSN 1055-7903 - p. 509 - 519.
    multiple sequence alignment - antarctic sponges - mixed models - mitochondrial - tree - dna - classification - astrophorida - evolution - alloclada
    Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1–D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
    Hydrological drought across the world: impact of climate and physical catchment structure
    Lanen, H.A.J. van; Wanders, N. ; Tallaksen, L.M. ; Loon, A.F. van - \ 2013
    Hydrology and Earth System Sciences 17 (2013)5. - ISSN 1027-5606 - p. 1715 - 1732.
    water availability - european runoff - united-states - groundwater - flow - model - simulations - trends - classification - propagation
    Large-scale hydrological drought studies have demonstrated spatial and temporal patterns in observed trends, and considerable difference exists among global hydrological models in their ability to reproduce these patterns. In this study a controlled modeling experiment has been set up to systematically explore the role of climate and physical catchment structure (soils and groundwater systems) to better understand underlying drought-generating mechanisms. Daily climate data (1958-2001) of 1495 grid cells across the world were selected that represent Koppen-Geiger major climate types. These data were fed into a conceptual hydrological model. Nine realizations of physical catchment structure were defined for each grid cell, i.e., three soils with different soil moisture supply capacity and three groundwater systems (quickly, intermediately and slowly responding). Hydrological drought characteristics (number, duration and standardized deficit volume) were identified from time series of daily discharge. Summary statistics showed that the equatorial and temperate climate types (A-and C-climates) had about twice as many drought events as the arid and polar types (B-and E-climates), and the durations of more extreme droughts were about half the length. Selected soils under permanent grassland were found to have a minor effect on hydrological drought characteristics, whereas groundwater systems had major impact. Groundwater systems strongly controlled the hydrological drought characteristics of all climate types, but particularly those of the wetter A-, C-and D-climates because of higher recharge. The median number of droughts for quickly responding groundwater systems was about three times higher than for slowly responding systems. Groundwater systems substantially affected the duration, particularly of the more extreme drought events. Bivariate probability distributions of drought duration and standardized deficit for combinations of Koppen-Geiger climate, soil and groundwater system showed that the responsiveness of the groundwater system is as important as climate for hydrological drought development. This urges for an improvement of subsurface modules in global hydrological models to be more useful for water resources assessments. A foreseen higher spatial resolution in large-scale models would enable a better hydrogeological parameterization and thus inclusion of lateral flow.
    Soil maps of The Netherlands
    Hartemink, A.E. ; Sonneveld, M.P.W. - \ 2013
    Geoderma 204-205 (2013). - ISSN 0016-7061 - p. 1 - 9.
    water-table - seasonal fluctuation - survey information - classification - evaluate
    The Netherlands has a long history of soil research. Over the past 150 years, seven national soil maps have been produced at scales ranging from 1:50,000 to 1:1,000,000. The maps were based on different conceptual models which reflected advances in soil science as well as societal demands. There are four phases in the development of soil mapping in The Netherlands. The first three are: (i) the geological phase (1837–1937), (ii) the physiographic phase (1937–1962) and (iii) the morphometric phase (1962–1995). The earliest soil maps, made in the mid-1800s, were largely based on surface geology. In 1950 the first national soil map was published based on physiographic soil mapping. From the 1960s onwards, mapping followed a pedogenetic–morphometric approach and these maps have been widely used in land use planning, hydrologic studies, re-allotments, and agricultural land evaluations. An increase in environmental awareness with the need to assess environmental impacts and developments in information technology induced the digital soil information phase (1995–present). New technologies have improved the collection, storage, analysis and presentation of soil geographic information. It is concluded that initial soil mapping in The Netherlands had a strong agricultural focus but that the current maps are used in a wide range of applications.
    Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
    Kourmpetis, Y.A.I. ; Dijk, A.D.J. van; Braak, C.J.F. ter - \ 2013
    Algorithms for Molecular Biology 8 (2013)1. - ISSN 1748-7188
    arabidopsis-thaliana - integration - annotation - regression - network - classification - association - terms - tool
    Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one.We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project
    A high-resolution and harmonized model approach for reconstructing and analysing historic land changes in Europe
    Fuchs, R. ; Herold, M. ; Verburg, P.H. ; Clevers, J.G.P.W. - \ 2013
    Biogeosciences 10 (2013). - ISSN 1726-4170 - p. 1543 - 1559.
    mediterranean landscapes - atmospheric co2 - cover changes - future - carbon - maps - classification - emissions - centuries
    Human-induced land use changes are nowadays the second largest contributor to atmospheric carbon dioxide after fossil fuel combustion. Existing historic land change reconstructions on the European scale do not sufficiently meet the requirements of greenhouse gas (GHG) and climate assessments, due to insufficient spatial and thematic detail and the consideration of various land change types. This paper investigates if the combination of different data sources, more detailed modelling techniques, and the integration of land conversion types allow us to create accurate, high-resolution historic land change data for Europe suited for the needs of GHG and climate assessments. We validated our reconstruction with historic aerial photographs from 1950 and 1990 for 73 sample sites across Europe and compared it with other land reconstructions like Klein Goldewijk et al. (2010, 2011), Ramankutty and Foley (1999), Pongratz et al. (2008) and Hurtt et al. (2006). The results indicate that almost 700 000 km2 (15.5%) of land cover in Europe has changed over the period 1950–2010, an area similar to France. In Southern Europe the relative amount was almost 3.5% higher than average (19%). Based on the results the specific types of conversion, hot-spots of change and their relation to political decisions and socio-economic transitions were studied. The analysis indicates that the main drivers of land change over the studied period were urbanization, the reforestation program resulting from the timber shortage after the Second World War, the fall of the Iron Curtain, the Common Agricultural Policy and accompanying afforestation actions of the EU. Compared to existing land cover reconstructions, the new method considers the harmonization of different datasets by achieving a high spatial resolution and regional detail with a full coverage of different land categories. These characteristics allow the data to be used to support and improve ongoing GHG inventories and climate research
    Mapping land cover gradients through analysis of hyper-temporal NDVI imagery
    Ali, A. ; Bie, C.A.J.M. de; Skidmore, A.K. ; Scarrott, R.G. ; Hamad, A. ; Venus, V. ; Lymberakis, P. - \ 2013
    International Journal of applied Earth Observation and Geoinformation 23 (2013). - ISSN 0303-2434 - p. 301 - 312.
    multitemporal modis images - remotely-sensed imagery - time-series - fuzzy-sets - species composition - accuracy assessment - neural-networks - classification - vegetation - boundaries
    The green cover of the earth exhibits various spatial gradients that represent gradual changes in space of vegetation density and/or in species composition. To date, land cover mapping methods differentiate at best, mapping units with different cover densities and/or species compositions, but typically fail to express such differences as gradients. Present interpretation techniques still make insufficient use of freely available spatial-temporal Earth Observation (EO) data that allow detection of existing land cover gradients. This study explores the use of hyper-temporal NDVI imagery to detect and delineate land cover gradients analyzing the temporal behavior of NDVI values. MODIS-Terra MVC-images (250 m, 16-day) of Crete, Greece, from February 2000 to July 2009 are used. The analysis approach uses an ISODATA unsupervised classification in combination with a Hierarchical Clustering Analysis (HCA). Clustering of class-specific temporal NDVI profiles through HCA resulted in the identification of gradients in landcover vegetation growth patterns. The detected gradients were arranged in a relational diagram, and mapped. Three groups of NDVI-classes were evaluated by correlating their class-specific annual average NDVI values with the field data (tree, shrub, grass, bare soil, stone, litter fraction covers). Multiple regression analysis showed that within each NDVI group, the fraction cover data were linearly related with the NDVI data, while NDVI groups were significantly different with respect to tree cover (adj. R 2 = 0.96), shrub cover (adj. R 2 = 0.83), grass cover (adj. R 2 = 0.71), bare soil (adj. R 2 = 0.88), stone cover (adj. R 2 = 0.83) and litter cover (adj. R 2 = 0.69) fractions. Similarly, the mean Sorenson dissimilarity values were found high and significant at confidence interval of 95% in all pairs of three NDVI groups. The study demonstrates that hyper-temporal NDVI imagery can successfully detect and map land cover gradients. The results may improve land cover assessment and aid in agricultural and ecological studies.
    Use of agro-climatic zones to upscale simulated crop yield potential
    Wart, J. van; Bussel, L.G.J. van; Wolf, J. ; Licker, R. ; Grassini, P. ; Nelson, A. ; Boogaard, H.L. ; Gerber, J. ; Mueller, N.D. ; Claessens, L.F.G. ; Ittersum, M.K. van; Cassman, K.G. - \ 2013
    Field Crops Research 143 (2013). - ISSN 0378-4290 - p. 44 - 55.
    global land areas - climate-change - agroecological zones - management - impacts - classification - agriculture - patterns - system - world
    Yield gap analysis, which evaluates magnitude and variability of difference between crop yield potential (Yp) or water limited yield potential (Yw) and actual farm yields, provides a measure of untapped food production capacity. Reliable location-specific estimates of yield gaps, either derived from research plots or simulation models, are available only for a limited number of locations and crops due to cost and time required for field studies or for obtaining data on long-term weather, crop rotations and management practices, and soil properties. Given these constraints, we compare global agro-climatic zonation schemes for suitability to up-scale location-specific estimates of Yp and Yw, which are the basis for estimating yield gaps at regional, national, and global scales. Six global climate zonation schemes were evaluated for climatic homogeneity within delineated climate zones (CZs) and coverage of crop area. An efficient CZ scheme should strike an effective balance between zone size and number of zones required to cover a large portion of harvested area of major food crops. Climate heterogeneity was very large in CZ schemes with less than 100 zones. Of the other four schemes, the Global Yield Gap Atlas Extrapolation Domain (GYGA-ED) approach, based on a matrix of three categorical variables (growing degree days, aridity index, temperature seasonality) to delineate CZs for harvested area of all major food crops, achieved reasonable balance between number of CZs to cover 80% of global crop area and climate homogeneity within zones. While CZ schemes derived from two climate-related categorical variables require a similar number of zones to cover 80% of crop area, within-zone heterogeneity is substantially greater than for the GYGA-ED for most weather variables that are sensitive drivers of crop production. Some CZ schemes are crop-specific, which limits utility for up-scaling location-specific evaluation of yield gaps in regions with crop rotations rather than single crop species.
    A proposal for including humus forms in the World Reference Base for soil resources (WRB-FAO)
    Jabiol, B. ; Zanella, A. ; Ponge, J.F. ; Sarton, G. ; Englisch, M. ; Delft, S.P.J. van; Waal, R.W. de; Claire-Le Bayon, R. - \ 2013
    Geoderma 192 (2013). - ISSN 0016-7061 - p. 286 - 294.
    earthworm invasion - organic-matter - forest - classification - vegetation - france
    The morpho-functional classification of humus forms proposed in a previous issue by Zanella and collaborators for Europe has been extended and modified, without any change in diagnostic horizons, in order to embrace a wide array of humus forms at worldwide level and to complete and make more effective the World Reference Base for Soil Resources. For that purpose 31 Humus Form Reference Groups (HFRGs) and a set of prefix and suffix qualifiers are proposed, following the rules erected for the WRB. An exhaustive classification key, respecting the principles of WRB, is suggested and examples of classification are given for some already well known humus forms.
    Environmental stratifications as the basis for national, European and global ecological monitoring
    Metzger, M.J. ; Brus, D.J. ; Bunce, R.G.H. ; Carey, P.D. ; Goncalves, J. ; Honrado, J. ; Jongman, R.H.G. ; Trabucco, A. ; Zomer, R. - \ 2013
    Ecological Indicators 33 (2013). - ISSN 1470-160X - p. 26 - 35.
    conterminous united-states - countryside survey - observing system - temporal trend - biodiversity - classification - design - earth - land - landscapes
    There is growing urgency for integration and coordination of global environmental and ecological data and indicators required to respond to the ‘grand challenges’ the planet is facing, including climate change and biodiversity decline. A consistent stratification of land into relatively homogenous strata provides a valuable spatial framework for comparison and analysis of ecological and environmental data across large heterogeneous areas. We discuss how statistical stratification can be used to design national, European and global biodiversity observation networks. The value of strategic ecological survey based on stratified samples is first illustrated using the United Kingdom (UK) Countryside Survey, a national monitoring programme that has measured ecological change in the UK countryside for the last 35 years. We then present a design for a European-wide sampling design for monitoring common habitats, and discuss ways of extending these approaches globally, supported by the recently developed Global Environmental Stratification. The latter provides a robust spatial analytical framework for the identification of gaps in current monitoring efforts, and systematic design of new complementary monitoring and research. Examples from Portugal and the transboundary Kailash Sacred Landscape in the Himalayas illustrate the potential use of this stratification, which has been identified as a focal geospatial dataset within the Group on Earth Observation Biodiversity Observation Network (GEO BON).
    Remote sensing image processing
    Camps-Valls, Gustavo ; Tuia, Devis ; Gómez-Chova, Luis ; Jiménez, Sandra ; Malo, Jesús - \ 2012
    Morgan and Claypool Publishers (Synthesis Lectures on Image, Video, and Multimedia Processing ) - ISBN 9781608458196 - 194 p.
    biophysical parameter - classification - computer vision - Earth observation - feature selection and extraction - image statistics - machine learning - manifold learning - morphology - pattern recognition - regression - remote sensing - retrieval - segmentation - spectral signature - spectroscopy - statistical learning - unmixing - vision science

    Earth observation is the field of science concerned with the problem of monitoring and modeling the processes on the Earth surface and their interaction with the atmosphere.The Earth is continuously monitored with advanced optical and radar sensors.The images are analyzed and processed to deliver useful products to individual users, agencies and public administrations.To deal with these problems, remote sensing image processing is nowadays a mature research area, and the techniques developed in the field allow many real-life applications with great societal value.For instance, urban monitoring, fire detection or flood prediction can have a great impact on economical and environmental issues. To attain such objectives, the remote sensing community has turned into a multidisciplinary field of science that embraces physics, signal theory, computer science, electronics and communications. From a machine learning and signal/image processing point of view, all the applications are tackled under specific formalisms, such as classification and clustering, regression and function approximation, data coding, restoration and enhancement, source unmixing, data fusion or feature selection and extraction. This book covers some of the fields in a comprehensive way.

    Freshwater resources management in coastal zones in different climates
    Blom-Zandstra, Greet - \ 2012
    water quality - fresh water - classification - quality standards - marine areas - freshwater ecology - drinking water
    Taxonomic revision of Myrosma (Marantaceae)
    Vieira, S. ; Maas, P.J.M. ; Borchsenius, F. - \ 2012
    Blumea 57 (2012)2. - ISSN 0006-5196 - p. 125 - 130.
    central-american marantaceae - classification - phylogeny
    Myrosma is a genus of rosulate herbs characterized by a compact and strongly monosymmetric inflorescence with conspicuous, white to pale green, mostly membranous bracts, in the axil of which is a single flower pair. The genus is widely distributed throughout Central Brazil, northern South America, and the Caribbean region. It occurs mostly in savannah environments but can also be found in humid and shaded habitats. We present a taxonomic revision of Myrosma recognizing a single species, Myrosma cannifolia L.f. A complete description of that species is provided with notes on its ecology, distribution, and variation. Three species and one variety are reduced into synonymy and four names are lectotypified. A complete nomenclatural account for all combinations including the name Myrosma is given.
    Phytoplankton species predictability increases towards warmer regions
    Kruk, C. ; Segura, A.M. ; Peeters, E.T.H.M. ; Huszar, V.L.M. ; Costa, L.S. ; Kosten, S. ; Lacerot, G. ; Scheffer, M. - \ 2012
    Limnology and Oceanography 57 (2012)4. - ISSN 0024-3590 - p. 1126 - 1135.
    latitudinal diversity gradient - fresh-water phytoplankton - multispecies competition - community - plankton - classification - biodiversity - disturbance - limitation - dispersal
    We explored systematic patterns in predictability of phytoplankton species from 83 lakes over a gradient ranging from subpolar to tropical regions in South America. We estimated the explained variance (proxy of predictability) of the presence and biomass (estimated as biovolume) of species using multiple regressions from commonly measured environmental variables such as nutrient levels, light, mixing depth, temperature, and zooplankton biomass. Both the presence and biomass of species occurring at least in 10 lakes were quite well predicted from the environmental variables, with average values of 35% and 58%, respectively. Predictability was not systematically related to phylogenetic affiliation or particular functional groups as defined by morphology. However, biomass predictability decreased with increasing occurrence, and improved with larger species size (maximum linear dimension). Species that were predictable in terms of biomass (R-2 >= 0.5, p
    Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: The case of TEM beta-lactamases
    Abriata, L.A. ; Salverda, M.L.M. ; Tomatis, P.E. - \ 2012
    FEBS Letters 586 (2012)19. - ISSN 0014-5793 - p. 3330 - 3335.
    antibiotic-resistance - directed evolution - natural evolution - chemical-properties - global suppressor - in-vitro - enterobacteriaceae - classification - prediction - pathways
    A dataset of TEM lactamase variants with different substrate and inhibition profiles was compiled and analyzed. Trends show that loops are the main evolvable regions in these enzymes, gradually accumulating mutations to generate increasingly complex functions. Notably, many mutations present in evolved enzymes are also found in simpler variants, probably originating functional promiscuity. Following a function-stability tradeoff, the increase in functional complexity driven by accumulation of mutations fosters the incorporation of other stability-restoring substitutions, although our analysis suggests they might not be as "global" as generally accepted and seem instead specific to different networks of protein sites. Finally, we show how this dataset can be used to model functional changes in TEMs based on the physicochemical properties of the amino acids.
    Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection
    Mauroy, A. ; Poel, W.H.M. van der; Honing-Hakze, R.W. van der; Thys, C. ; Thiry, E. - \ 2012
    BMC Veterinary Research 8 (2012). - ISSN 1746-6148 - 11 p.
    virus-like particles - genetic diversity - enteric caliciviruses - epidemiology - noroviruses - recombination - pigs - classification - europe - assays
    Background: Sapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine. Results: The method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences). Conclusions: A rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.
    The Rubetum taxandriae ass. nov. (Lonicero-Rubion silvatici, Lonicero-Rubetea plicati), a new bramble association from the Belgian and Dutch Campine
    Haveman, R. ; Ronde, I. de; Weeda, E.J. - \ 2012
    Tuexenia 32 (2012). - ISSN 0722-494X - p. 55 - 65.
    Bramble scrubs are among the least known and understood vegetation types in Europe. In the Dutch National Vegetation Overview, three associations belonging to the Lonicero-Rubion silvatici were distinguished, viz. the Rubetum grati, Rubetum silvatici, and Rubetum pedemontani. During several vegetation mapping projects and Rubus excursions, a distinct type of bramble scrub was recorded repeatedly in the Campine in the province Noord-Brabant in the southern part of the Netherlands. In this paper, this scrub is described as a new association, the Rubetum taxandriae Haveman, de Ronde & Weeda, with R. taxandriae, R. campaniensis, and R. baronicus as character species, and R. insectifolius as regional character species. Variation, ecology and distribution of this new association are given and discussed, and two subassociations are distinguished. The differences with the Rubetum silvatici, to which this community was believed to belong, are discussed. Based on an earlier analysis of the centres of diversity of the genus Rubus in the Netherlands, it is supposed that the Rubetum silvatici in its circumscription in the Dutch National Vegetation Overview can be divided in more regionally distributed communities, partly as subassociations of the Rubetum silvatici, partly as independent associations.
    Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
    Spring, S. ; Visser, M. ; Lu, M. ; Copeland, A. ; Lapidus, A. ; Lucas, S. ; Cheng, J.F. ; Han, C. ; Tapia, R. ; Goodwin, L.A. ; Pitluck, S. ; Ivanova, N. ; Land, M. ; Hauser, L. ; Larimer, F. ; Rohde, M. ; Göker, M. ; Detter, J.C. ; Kyrpides, N. ; Woyke, T. ; Schaap, P.J. ; Plugge, C.M. ; Muyzer, G. ; Kuever, J. ; Pereira, I.A.C. ; Parshina, S.N. ; Bernier-Latmani, R. ; Stams, A.J.M. ; Klenk, H.P. - \ 2012
    Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
    bacterial names - classification - hydrogenases - database - archaea - system - site - tool
    Strain DLT (= DSM 2154 = ATCC 23193 = NCIMB 8452) is the type strain of the species Desulfotomaculum ruminis [1], one out of current-ly 30 species with validly published names in the paraphyletic genus Desulfotomaculum [2,3]. Strain DLT was initially isolated by G. S. Coleman in the 1950s from the rumen of hay-fed sheep [4]. Dissimilatory reduction of sulfate to sulfide in the rumen was first demonstrated by Lewis [5], who dosed fistulated sheep with sulfate and deter-mined the amount of sulfide produced. As high amounts of sulfide may be toxic to animals, bacte-rial sulfate-reduction in ruminants was a concern due to the presence of sulfate in grass and hay. D. ruminis represented the first pure culture of a sul-fate-reducing bacterium isolated from the rumen. The genus name was derived from the Latin words 'de', from, ‘sulfur’, sulfur, and 'tomaculum', a kind of sausage, meaning 'a sausage-shaped sul-fate reducer' [2,6]. The species epithet is derived from the Latin word 'rumen', throat, first stomach (rumen) of a ruminant, meaning of a rumen [1,2]. Here, we present a summary classification and a set of features for D. ruminis strain DLT, together with the description of the complete genomic se-quencing and annotation. The complete genome sequence of strain DLT will provide valuable in-formation for defining a more adequate descrip-tion of the currently paraphyletic genus Desulfotomaculum
    Structural and mechanistic insight into N-glycan processing by endo-a-mannosidase
    Thompson, A.J. ; Williams, R.J. ; Hakki, Z. ; Alonzi, D.S. ; Wennekes, T. ; Gloster, T.M. ; Songsrirote, K. ; Thomas-Oates, E. ; Wrodnigg, T.M. ; Spreitz, J. ; Stütz, A.E. ; Butters, T.D. ; Williams, S.J. ; Davies, G.J. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)3. - ISSN 0027-8424 - p. 781 - 786.
    asparagine-linked oligosaccharides - glucosidase-ii-deficient - glycoprotein-biosynthesis - endomannosidase pathway - endoplasmic-reticulum - glycoside hydrolases - quality-control - inhibitors - cells - classification
    N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-a-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-a-mannosidase. Structures solved at resolutions 1.7–2.1 Å reveal a (ß/a)8 barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc1/3Man9GlcNAc2 yields Glc1/3-Man. Using the bespoke substrate a-Glc-1,3-a-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-a-mannosidase inhibitor a-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, a-Glc-1,3-isofagomine, and with the reducing-end product a-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
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