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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General Framing of Low-, Mid-, and High-Level Data Fusion With Examples in the Life Sciences
Smolinska, Agnieszka ; Engel, Jasper ; Szymanska, Ewa ; Buydens, Lutgarde ; Blanchet, Lionel - \ 2019
In: Data Fusion Methodology and Applications Elsevier Ltd, Academic Press (Data Handling in Science and Technology ) - ISBN 9780444639844 - p. 51 - 79.
Analytical technique - Data fusion - Gas chromatography–mass spectrometry - Kernel-based data fusion - Liquid chromatography - Microbiome data

The constant development of analytical techniques leads to an increase in the amount of information available to describe phenomena in life science. In parallel, the inherent complexity of life science makes it almost impossible to obtain a comprehensive description using only one technical modality. Therefore, it became very popular to combine several biological or technical platforms/modalities to obtain a better understanding of the underlying problems. Merging different types of measurements/platforms into a single analysis is, however, a complex topic. Combining various platforms into single analysis is defined as data fusion. We describe here different types of data fusion strategies: the well-established low-, mid-, and high-level data fusion and the more recently introduced sustainable mid-level data fusion and kernel-based data fusion. For each type, we provide a detailed description. To illustrate these various data fusion approaches, we rely on four real data sets, namely, exhaled breath data of patients with Crohn disease (CD) obtained by gas chromatography–mass spectrometry (GC-MS), 454 pyrosequencing microbiome data of patients with CD, and metabolic profiling of beer brands by GC-MS and positive and negative ion modes of liquid chromatography.

A foot-and-mouth disease SAT2 vaccine protects swine against experimental challenge with a homologous virus strain, irrespective of mild pathogenicity in this species
Mouton, Laure ; Dekker, Aldo ; Bleijenberg, Meindert ; Blanchet, Michel ; Coco-Martin, Jose ; Hudelet, Pascal ; Goutebroze, Sylvain - \ 2018
Vaccine 36 (2018)15. - ISSN 0264-410X - p. 2020 - 2024.
Challenge - Foot-and-mouth disease - Pigs - Serotype SAT - Vaccine efficacy
FMDV serotype SAT2 is most frequently associated with outbreaks in ruminants. However, the risk of it spreading from cattle to pigs cannot be excluded. To assess the efficacy of an SAT2-type FMD inactivated vaccine against homologous challenge in pigs, a suitable challenge strain adapted to pigs was produced. After two passages in two pigs each, a FMDV stock of SAT2 challenge strain was produced. This material was used to infect two groups of five pigs. The first group being vaccinated 28 days before challenge and the other one left as an unvaccinated control. Clinical signs were recorded, virus shedding was assessed on mouth swabs, and neutralising antibody titres were determined. At least 80% of the vaccinated pigs were protected against clinical disease. Furthermore, no virus shedding was observed in any of the vaccinated pigs. This study shows that experimentally inoculated pigs can become infected with a SAT2 serotype. Furthermore, vaccination offers protection against generalisation and viral excretion, confirming the potential of vaccination as an important tool in the control of FMD in pigs.
Evaluating Scenarios for Upgrading Sustainability of the Meat Supply Chain
Broek, E.M.F. van den; Verwaart, T. - \ 2014
In: Advances in Artificial Economics / Amblard, F., Miguel, F.J., Blanchet, A., Benoit, G., Heidelberg : Springer (Lecture Notes in Economics and Mathematical Systems 676) - ISBN 9783319095776
Rph22: mapping of a novel leaf rust resistance gene introgressed from the non-host Hordeum bulbosum L. into cultivated barley (Hordeum vulgare L.)
Johnston, P.A. ; Niks, R.E. ; Meiyalaghan, V. ; Blanchet, E. ; Pickering, R. - \ 2013
Theoretical and Applied Genetics 126 (2013)6. - ISSN 0040-5752 - p. 1613 - 1625.
powdery mildew resistance - near-isogenic lines - puccinia-hordei - latent period - genome - qtls - specificity - pathogens - map - identification
A resistance gene (Rph22) to barley leaf rust caused by Puccinia hordei was introgressed from the non-host species Hordeum bulbosum into cultivated barley. The H. bulbosum introgression in line ‘182Q20’ was located to chromosome 2HL using genomic in situ hybridisation (GISH). Using molecular markers it was shown to cover approximately 20 % of the genetic length of the chromosome. The introgression confers a very high level of resistance to P. hordei at the seedling stage that is not based on a hypersensitive reaction. The presence of the resistance gene increased the latency period of the leaf rust fungus and strongly reduced the infection frequency relative to the genetic background cultivar ‘Golden Promise’. An F2 population of 550 individuals was developed and used to create a genetic map of the introgressed region and to determine the map position of the underlying resistance gene(s). The resistance locus, designated Rph22, was located to the distal portion of the introgression, co-segregating with markers H35_26334 and H35_45139. Flanking markers will be used to reduce the linkage drag, including gene(s) responsible for a yield penalty, around the resistance locus and to transfer the gene into elite barley germplasm. This genetic location is also known to harbour a QTL (Rphq2) for non-hypersensitive leaf rust resistance in the barley cultivar ‘Vada’. Comparison of the ‘Vada’ and H. bulbosum resistances at this locus may lead to a better understanding of the possible association between host and non-host resistance mechanisms.
Functional characterization of NRAMP3 and NRAMP4 from the metal hyperaccumulator Thlaspi caerulescens
Oomen, R.J.F.J. ; Wu, J. ; Lelievre, F. ; Blanchet, S. ; Richaud, P. ; Barbier-Brygoo, H. ; Aarts, M.G.M. ; Thomine, S. - \ 2009
New Phytologist 181 (2009)3. - ISSN 0028-646X - p. 637 - 650.
arabidopsis-thaliana - gene encodes - heavy-metal - transporter genes - iron transport - saccharomyces-cerevisiae - expression differences - zinc transporter - cadmium - protein
The ability of metal hyperaccumulating plants to tolerate and accumulate heavy metals results from adaptations of metal homeostasis. NRAMP metal transporters were found to be highly expressed in some hyperaccumulating plant species. Here, we identified TcNRAMP3 and TcNRAMP4, the closest homologues to AtNRAMP3 and AtNRAMP4 in Thlaspi caerulescens and characterized them by expression analysis, confocal imaging and heterologous expression in yeast and Arabidopsis thaliana. TcNRAMP3 and TcNRAMP4 are expressed at higher levels than their A. thaliana homologues. When expressed in yeast TcNRAMP3 and TcNRAMP4 transport the same metals as their respective A. thaliana orthologues: iron (Fe), manganese (Mn) and cadmium (Cd) but not zinc (Zn) for NRAMP3; Fe, Mn, Cd and Zn for NRAMP4. They also localize at the vacuolar membrane in A. thaliana protoplasts. Inactivation of AtNRAMP3 and AtNRAMP4 in A. thaliana results in strong Cd and Zn hypersensitivity, which is fully rescued by TcNRAMP3 or TcNRAMP4 expression. However, metal tolerance conferred by TcNRAMP expression in nramp3nramp4 mutant does not exceed that of wild-type A. thaliana. Our data indicate that the difference between TcNRAMP3 and TcNRAMP4 and their A. thaliana orthologues does not lie in a different protein function, but probably resides in a different expression level or expression pattern
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