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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    We will mail you new results for this query: keywords==cdna microarray data
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Aging Uncouples Heritability and Expression-QTL in Caenorhabditis elegans
Viñuela Rodriguez, A. ; Snoek, L.B. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2012
G3 : Genes Genomes Genetics 2 (2012)5. - ISSN 2160-1836 - p. 597 - 605.
quantitative trait loci - cdna microarray data - life-history traits - gene-expression - c-elegans - age - arabidopsis - genomics - normalization - plasticity
The number and distribution of gene expression QTL (eQTL) represent the genetic architecture of many complex traits, including common human diseases. We previously reported that the heritable eQTL patterns are highly dynamic with age in an N2 × CB4856 recombinant inbred population of the nematode Caenorhabditis elegans. In particular, we showed that the number of eQTL decreased with age. Here, we investigated the reason for this decrease by combining gene expression profiles at three ages in the wild types N2 and CB4856 with the reported expression profiles of the RIL population. We determined heritability and transgression (when gene expression levels in the RILs are more extreme than the parents) and investigated their relation with eQTL changes with age. Transgressive segregation was widespread but depended on physiological age. The percentage of genes with an eQTL increased with a higher heritability in young worms. However, for old worms this percentage hardly increased. Using a single marker approach, we found that almost 20% of genes with heritability >0.9 had an eQTL in developing worms. Surprisingly, only 10% was found in old worms. Using a multimarker approach, this percentage increased to almost 30% for both age groups. Comparison of the single marker to a multiple marker eQTL mapping indicated that heritable regulation of gene expression becomes more polygenic in aging worms due to multiple loci and possible epistatic interactions. We conclude that linkage studies should account for the relation between increased polygenic regulation and diminished effects at older ages.
Gene Expression Modifications by Temperature-Toxicants Interactions in Caenorhabditis elegans
Vinuela Rodriguez, A. ; Snoek, L.B. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2011
PLoS One 6 (2011)9. - ISSN 1932-6203 - 11 p.
zebrafish-danio-rerio - cdna microarray data - organophosphorus pesticides - developmental neurotoxicity - chemical-mixtures - binary-mixtures - heat-stress - c-elegans - toxicity - chlorpyrifos
Although organophosphorus pesticides (OP) share a common mode of action, there is increased awareness that they elicit a diverse range of gene expression responses. As yet however, there is no clear understanding of these responses and how they interact with ambient environmental conditions. In the present study, we investigated genome-wide gene expression profiles in the nematode Caenorhabditis elegans exposed to two OP, chlorpyrifos and diazinon, in single and combined treatments at different temperatures. Our results show that chlorpyrifos and diazinon induced expression of different genes and that temperature affected the response of detoxification genes to the pesticides. The analysis of transcriptional responses to a combination of chlorpyrifos and diazinon shows interactions between toxicants that affect gene expression. Furthermore, our combined analysis of the transcriptional responses to OP at different temperatures suggests that the combination of OP and high temperatures affect detoxification genes and modified the toxic levels of the pesticides
Proteomics and Transcriptomics Characterization of Bile Stress Response in Probiotic Lactobacillus rhamnosus GG
Koskenniemi, K. ; Laakso, K. ; Koponen, J. ; Kankainen, M. ; Greco, D. ; Auvinen, P. ; Savikoki, K. ; Vos, W.M. de; Varmanen, P. - \ 2011
Molecular and Cellular Proteomics 10 (2011)2. - ISSN 1535-9476 - 18 p.
surface-associated proteins - gram-positive bacteria - cationic antimicrobial peptides - placebo-controlled trial - long-term consumption - animalis subsp lactis - cdna microarray data - staphylococcus-aureus - lactococcus-lactis - gene-expression
Lactobacillus rhamnosus GG (GG) is a widely used and intensively studied probiotic bacterium. Although the health benefits of strain GG are well documented, the systematic exploration of mechanisms by which this strain exerts probiotic effects in the host has only recently been initiated. The ability to survive the harsh conditions of the gastrointestinal tract, including gastric juice containing bile salts, is one of the vital characteristics that enables a probiotic bacterium to transiently colonize the host. Here we used gene expression profiling at the transcriptome and proteome levels to investigate the cellular response of strain GG toward bile under defined bioreactor conditions. The analyses revealed that in response to growth of strain GG in the presence of 0.2% ox gall the transcript levels of 316 genes changed significantly (p <0.01, t test), and 42 proteins, including both intracellular and surface-exposed proteins (i.e. surfome), were differentially abundant (p <0.01, t test in total proteome analysis; p <0.05, t test in surfome analysis). Protein abundance changes correlated with transcriptome level changes for 14 of these proteins. The identified proteins suggest diverse and specific changes in general stress responses as well as in cell envelope-related functions, including in pathways affecting fatty acid composition, cell surface charge, and thickness of the exopolysaccharide layer. These changes are likely to strengthen the cell envelope against bile-induced stress and signal the GG cells of gut entrance. Notably, the surfome analyses demonstrated significant reduction in the abundance of a protein catalyzing the synthesis of exopolysaccharides, whereas a protein dedicated for active removal of bile compounds from the cells was up-regulated. These findings suggest a role for these proteins in facilitating the well founded interaction of strain GG with the host mucus in the presence of sublethal doses of bile. The significance of these findings in terms of the functionality of a probiotic bacterium is discussed
Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes
Jafrezic, F. ; Koning, D.J. de; Boettcher, P. ; Bonnet, A. ; Buitenhuis, B. ; Closset, R. ; Dejean, S. ; Delmas, C. ; Detilleux, J.C. ; Dovc, P. ; Duval, M. ; Foulley, J.L. ; Hedegaard, J. ; Hoprnshoj, H. ; Hulsegge, B. ; Janss, L. ; Jensen, K. ; Jiang, L. ; Lavric, M. ; Cao Le, K.A. ; Lund, M.S. ; Malinverni, R. ; Marot, G. ; Nie, H. ; Petzl, W. ; Pool, M.H. ; Robert-Granie, C. ; Cristobal, M. ; Schothorst, E.M. van; Schuberth, H.J. ; Sorensen, P. ; Stella, A. ; Tosser-klopp, G. ; Waddington, D. ; Watson, M. ; Yang, M. ; Zerbe, H. ; Seyfert, H.M. - \ 2007
Genetics, Selection, Evolution 39 (2007). - ISSN 0999-193X - p. 633 - 650.
cdna microarray data - mixed-model
A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies
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