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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    Impact of diets with a high content of greaves-meal protein or carbohydrates on faecal characteristics, volatile fatty acids and faecal calprotectin concentrations in healthy dogs
    Hang, I. ; Heilmann, R.M. ; Grützner, N. ; Suchodolski, J.S. ; Steiner, J.M. ; Atroshi, F. ; Sankari, S. ; Kettunen, A. ; Vos, W.M. de; Zentek, J. ; Spillmann, T. - \ 2013
    BMC Veterinary Research 9 (2013). - ISSN 1746-6148 - 8 p.
    calcium-binding proteins - nutrient digestibility - intestinal inflammation - bacterial metabolites - rheumatoid-arthritis - canine calprotectin - responsive diarrhea - epithelial-cells - cystic-fibrosis - body-size
    BACKGROUND: Research suggests that dietary composition influences gastrointestinal function and bacteria-derived metabolic products in the dog colon. We previously reported that dietary composition impacts upon the faecal microbiota of healthy dogs. This study aims at evaluating the dietary influences on bacteria-derived metabolic products associated with the changes in faecal microbiota that we had previously reported. We fed high-carbohydrate starch based (HCS), [crude protein: 194 g/kg, starch: 438 g/kg], high-protein greaves-meal (HPGM), [crude protein: 609 g/kg, starch: 54 g/kg] and dry commercial (DC), [crude protein: 264 g/kg, starch: 277 g/kg] diets, and studied their effects on the metabolism of the colonic microbiota and faecal calprotectin concentrations in five Beagle dogs, allocated according to the Graeco-Latin square design. Each dietary period lasted for three weeks and was crossed-over with washout periods. Food intake, body weight, and faecal consistency scores, dry matter, pH, ammonia, volatile fatty acids (VFAs), and faecal canine calprotectin concentrations were determined. RESULTS: Faecal ammonia concentrations decreased with the HCS diet. All dogs fed the HPGM diet developed diarrhoea, which led to differences in faecal consistency scores between the diets. Faecal pH was higher with the HPGM diet. Moreover, decreases in propionic and acetic acids coupled with increases in branched-chain fatty acids and valeric acid caused changes in faecal total VFAs in dogs on the HPGM diet. Faecal canine calprotectin concentration was higher with the HPGM diet and correlated positively with valeric acid concentration. CONCLUSIONS: The HPGM diet led to diarrhoea in all dogs, and there were differences in faecal VFA profiles and faecal canine calprotectin concentrations
    Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites
    Bielecki, P. ; Komor, U. ; Bielecka, A. ; Müsken, M. ; Puchalka, J. ; Pletz, M.W. ; Ballmann, M. ; Martins Dos Santos, V.A.P. ; Weiss, S. ; Häussler, S. - \ 2013
    Environmental Microbiology 15 (2013)2. - ISSN 1462-2912 - p. 570 - 587.
    burn wound infections - biofilm formation - cystic-fibrosis - therapeutic strategies - expression - motility - mutants - protein - system - identification
    The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P.¿ aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases
    Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis
    Oberhardt, M. ; Puchalka, J. ; Martins Dos Santos, V.A.P. ; Papin, J.A. - \ 2011
    PLoS Computational Biology 7 (2011)3. - ISSN 1553-734X - 18 p.
    pseudomonas-aeruginosa pao1 - flux balance analysis - cystic-fibrosis - opportunistic pathogen - putida kt2440 - anaerobic survival - network analysis - mutant library - genes - annotation
    In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism, leading to greater understanding of observed phenotypes. These methods have been sparsely applied to comparisons between multiple organisms, however, due mainly to the existence of differences between reconstructions that are inherited from the respective reconstruction processes of the organisms to be compared. To circumvent this obstacle, we developed a novel process, termed metabolic network reconciliation, whereby non-biological differences are removed from genome-scale reconstructions while keeping the reconstructions as true as possible to the underlying biological data on which they are based. This process was applied to two organisms of great importance to disease and biotechnological applications, Pseudomonas aeruginosa and Pseudomonas putida, respectively. The result is a pair of revised genome-scale reconstructions for these organisms that can be analyzed at a systems level with confidence that differences are indicative of true biological differences (to the degree that is currently known), rather than artifacts of the reconstruction process. The reconstructions were re-validated with various experimental data after reconciliation. With the reconciled and validated reconstructions, we performed a genome-wide comparison of metabolic flexibility between P. aeruginosa and P. putida that generated significant new insight into the underlying biology of these important organisms. Through this work, we provide a novel methodology for reconciling models, present new genome-scale reconstructions of P. aeruginosa and P. putida that can be directly compared at a network level, and perform a network-wide comparison of the two species. These reconstructions provide fresh insights into the metabolic similarities and differences between these important Pseudomonads, and pave the way towards full comparative analysis of genome-scale metabolic reconstructions of multiple species
    Changes in disease gene frequency over time with differential genotype fitness and various control strategies
    Thompson, P.N. ; Heesterbeek, J.A.P. ; Arendonk, J.A.M. van - \ 2006
    Journal of Animal Science 84 (2006)10. - ISSN 0021-8812 - p. 2629 - 2635.
    uridine monophosphate synthase - holstein-friesian cattle - overlapping generations - segregation analysis - recessive genes - cystic-fibrosis - meat quality - deficiency - populations - eradication
    A spreadsheet model was constructed to describe the change in allelic frequency over time for a lethal recessive mutation in an animal population. The model allowed relative fitness to differ between genotypes, between sexes, and over time. Whereas a lethal recessive allele is naturally eliminated very slowly from a population, a small selective disadvantage of the heterozygote results in a large increase in the rate of elimination. With selective advantage of the heterozygote through linkage with a production trait or pleiotropy, the allele is never naturally eliminated but tends toward a stable equilibrium frequency. The model was used to investigate various alternative control programs based on the detection of heterozygotes by genotyping and their exclusion from breeding. The programs (genotyping males only, genotyping males and 50% of females, and genotyping all breeding animals) were modeled for various initial heterozygote frequencies, and the results were described in terms of the number of generations, number of tests, and number of culls required to reduce the heterozygote frequency to a predefined level. The model can be used to compare the feasibility and cost of various control strategies and to illustrate clearly to breeders the expected outcomes, as well as the danger of prematurely terminating a control program when there is a selective advantage of the heterozygote.
    An efficient glycosylation reaction for the synthesis of asialo GM2 analogues
    Sun, B. ; Pukin, A.V. ; Visser, G.M. ; Zuilhof, H. - \ 2006
    Tetrahedron Letters 47 (2006)41. - ISSN 0040-4039 - p. 7371 - 7374.
    cystic-fibrosis - glycosidation - oligosaccharides - tetrasaccharide - derivatives - lactose - gm(1)
    We investigated the coupling reaction of glycosyl donors N-trichloroethoxycarbonyl-galactosamine-O-trichloroacetimidate (2a) and N-p-nitrobenzyloxycarbonyl-galactosamine-O-trichloroacetimidate (2b) with the 4¿-OH of lactose derivatives (3a¿d) to synthesize key intermediates of asialo GM2 analogues, and found that the glycosylation yield with 2a was 90% or more in all investigated cases.
    Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium
    Salles, J.F. ; Samyn, E. ; Vandamme, P.A. ; Veen, J.A. van; Elsas, J.D. van - \ 2006
    Soil Biology and Biochemistry 38 (2006)4. - ISSN 0038-0717 - p. 661 - 673.
    gradient gel-electrophoresis - cepacia complex infection - land-use history - sp-nov - cystic-fibrosis - bacterial communities - microbial diversity - maize-rhizosphere - genetic diversity - genomovar-iii
    In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monoculture; arable land and arable land converted into grassland. Burkholderia isolates obtained on PCAT medium were grouped in 47 clusters using 16S ribosomal RNA gene based PCR-DGGE combined with BOX genomic fingerprinting (DGGE-BOX). The distribution of the isolates in the DGGE-BOX clusters was used to calculate the Shannon diversity index per treatment. Interestingly, we observed that the Burkholderia diversity was affected by changes in the agricultural management, since the highest diversity was observed in permanent grassland and in continuous arable land. In addition, the diversity tended to be higher in the rhizosphere than in the corresponding bulk soil. The use of species abundance models indicated that rhizosphere communities had more even distributions than communities collected from the bulk soil. Identification of isolates revealed that only 2% of these belonged to the B. cepacia complex and that the majority was assigned to either (1) new Burkholderia species or (2) Burkholderia species that had originally been isolated from soil. Isolates classified as B. hospita, B. caledonica and Burkholderia sp. LMG 22934' and `LMG 22936' were found mainly in the arable land, while isolates belonging to Burkholderia sp. `LMG 22929 and B. phytofirmans were associated with the grassland area. Another potentially new Burkholderia species, `LMG 22932'', was found in both areas, in close association with the maize rhizosphere
    Dietary flavonoids and iodine Metabolism
    Elst, J.P. van der; Smit, J.W.A. ; Romijn, H.A. ; Heide, D. van der - \ 2003
    BioFactors 19 (2003)3/4. - ISSN 0951-6433 - p. 171 - 176.
    human thyroid-carcinoma - cystic-fibrosis - symporter hnis - in-vitro - transporter - expression - cancer - epithelium - cloning - growth
    Flavonoids have inhibiting effects on the proliferation of cancer cells, including thyroidal ones. In the treatment of thyroid cancer the uptake of iodide is essential. Flavonoids are known to interfere with iodide organification ill vitro, and to cause goiter. The influence of flavonoids on iodine metabolism was studied in a human thyroid cancer cell line (FTC-133) transfected with the human sodium/iodide transporter (NIS). All flavonoids inhibited growth, and iodide uptake was decreased in most cells. NIS mRNA expression was affected during the early hours after treatment, indicating that these flavonoids can act on NIS. Pendrin mRNA expression did not change after treatment. Only myricetin increased iodide uptake. Apeginin, luteolin, kaempferol and F21388 increased the efflux of iodide, leading to a decreased retention of iodide. Instead myricetin increased the retention of iodide; this could be of use in the radioiodide treatment of thyroid cancer.
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