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Wageningen, Netherlands

Arvas M.,VTT Technical Research Center of Finland | Haiminen N.,University of Helsinki | Smit B.,FrieslandCampina Innovation Europe | Rautio J.,PlexPress | And 11 more authors.
Gene | Year: 2010

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions.We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9. Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100. b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties. © 2010 Elsevier B.V. Source

Gao R.,Wageningen University | Van Leeuwen H.P.,Wageningen University | Temminghoff E.J.,Wageningen University | Van Valenberg H.J.,Wageningen University | And 2 more authors.
Journal of Agricultural and Food Chemistry | Year: 2010

The mean spherical approximation (MSA) theory is used to explain the impact of sugars on ion properties in milk-based systems by taking into account electrostatic interactions and volume exclusion effects. This study first focuses on the changes in Ca2+ activity and pH in a solution consisting of CaCl2, KCl, and K3citrate, as a function of sucrose concentration. MSA model calculations were compared with experimental results, and the model satisfactorily describes the ion properties. The excluded volume effects appear to account for a considerable increase in activity coefficient of the ions. This offers a sufficient explanation for the increase in Ca2+ activity and the decrease in pH in milk-based systems with added disaccharides. In addition, hydration of milk proteins seems to enhance ion pair formation in milk. All disaccharides lead to similar modification of the thermodynamic properties of milklike systems, confirming that the observed effects are primarily due to volume exclusion effects. © 2010 American Chemical Society. Source

Gao R.,Wageningen University | van Halsema F.E.D.,HaloteC Intruments BV | Temminghoff E.J.M.,Wageningen University | van Leeuwen H.P.,Wageningen University | And 3 more authors.
Food Chemistry | Year: 2010

This study aims to determine whether the dynamic ion speciation (DIS) model, as introduced in part I, can predict the ion composition in freshly prepared simulated milk ultrafiltrate (SMUF) under various conditions, e.g. pH, ionic strength and presence of various polyphosphates. Experiments were carried out in freshly prepared SMUF enriched with different salts. The model predictions were in satisfactory agreement with experimental results for all conditions. Moreover, specific ion effects were taken into account in the model, where sodium ions were not counted as equivalent to potassium ions due to differences in hydration properties. Polyphosphates, in particular sodium hexametaphosphate (SHMP), were well integrated into the DIS model with reasonable association constants and solubility products. The DIS model suggests that SHMP displays chain polyphosphate properties, which provides better understanding of its interaction with cations. The DIS model appears to be a robust and versatile tool to describe ion equilibria in SMUF. © 2010 Elsevier Ltd. All rights reserved. Source

Gao R.,Wageningen University | van Halsema F.E.D.,HaloteC Instruments BV | Temminghoff E.J.M.,Wageningen University | van Leeuwen H.P.,Wageningen University | And 4 more authors.
Food Chemistry | Year: 2010

Freshly prepared simulated milk ultrafiltrate (SMUF) is a solution that is supersaturated with respect to various calcium phosphate phases that precipitate in time. As a consequence, the ion composition of equilibrated SMUF was found to be significantly different from that of freshly prepared SMUF. This study proposes a thermodynamic ion-speciation model that is able to describe ion equilibria in SMUF. Moreover, it is also able to describe calcium phosphate precipitation in fresh SMUF on its way to equilibrium by using an apparent solubility product for CaHPO4·2H2O as a function of time. The model was validated by experiments in which CaCl2 and Na2HPO4 were added to freshly prepared SMUF. The changes in calcium activity and pH were followed and the precipitates were characterised by X-ray diffraction. The model was able to predict the observed changes. © 2010 Elsevier Ltd. All rights reserved. Source

Vissers Y.M.,Wageningen University | Snel J.,NIZO food research | Zuurendonk P.F.,FrieslandCampina Innovation Europe | Kleerebezem M.,NIZO food research | And 2 more authors.
FEMS Immunology and Medical Microbiology | Year: 2011

The objective of this study was to assess the potential immunomodulatory effect of six Lactobacillus strains on human peripheral blood mononuclear cells (hPBMC) isolated from allergic patients. hPBMC from patients allergic to birch pollen or grass pollen were cultured in vitro in the presence or absence of selective bacterial strains. Cultures were left unstimulated or stimulated with αCD3/αCD28 or Bet v 1. After 1, 4 and 8 days, cells and culture supernatants were harvested and the effect on cellular proliferation and the supernatant levels of several cytokines was assessed. All strains had the ability to repress IL-13 production but did show a differential effect on IFN-γ induction. Both strains B223 and B1697 showed a lower IFN-γ, IL-12 and TNF-α induction as compared with the other tested strains. Strain B633 showed the best proliferation-suppressive properties in αCD3/αCD28-stimulated cells. Suppression of the T-helper type 2 (Th2) cytokine induction and induction of the Th1 cytokine production by specific strains might be beneficial for allergic patients having a disturbed Th1/Th2 immune balance. Furthermore, hPBMC of patients with seasonal allergy outside the pollen season can be used to determine the immunomodulatory activities of probiotic bacteria. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved. Source

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