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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    A single locus confers tolerance to continuous light and allows substantial yield increase in tomato
    Vélez Ramírez, A.I. ; Ieperen, W. van; Vreugdenhil, D. ; Poppel, P.M.J.A. van; Heuvelink, E. ; Millenaar, F.F. - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723
    differential expression analysis - photosystem-ii - lycopersicon-esculentum - greenhouse tomato - dependent phosphorylation - chlorophyll fluorescence - arabidopsis-thaliana - gene-expression - air humidity - plants
    An important constraint for plant biomass production is the natural day length. Artificial light allows for longer photoperiods, but tomato plants develop a detrimental leaf injury when grown under continuous light—a still poorly understood phenomenon discovered in the 1920s. Here, we report a dominant locus on chromosome 7 of wild tomato species that confers continuous light tolerance. Genetic evidence, RNAseq data, silencing experiments and sequence analysis all point to the type III light harvesting ¿chlorophyll a/b binding protein 13 (¿CAB-13) gene as a major factor responsible for the tolerance. In Arabidopsis thaliana, this protein is thought to have a regulatory role balancing light harvesting by photosystems I and II. Introgressing the tolerance into modern tomato hybrid lines, results in up to 20% yield increase, showing that limitations for crop productivity, caused by the adaptation of plants to the terrestrial 24-h day/night cycle, can be overcome.
    Massive activation of archaeal defense genes during viral infection
    Quax, T.E.F. ; Voet, M. ; Sismeiro, O. ; Dillies, M.A. ; Jagla, B. ; Coppée, J.Y. ; Sezonov, G. ; Forterre, P. ; Oost, J. van der; Lavigne, R. ; Prangishvili, D. - \ 2013
    Journal of Virology 87 (2013)15. - ISSN 0022-538X - p. 8419 - 8428.
    differential expression analysis - turreted icosahedral virus - toxin-antitoxin systems - sulfolobus-solfataricus - cell-division - host interactions - crispr rnas - dna - prokaryotes - complex
    Archaeal viruses display unusually high genetic and morphological diversity. Studies of these viruses proved to be instrumental for the expansion of knowledge on viral diversity and evolution. The Sulfolobus islandicus rod-shaped virus 2 (SIRV2) is a model to study virus-host interactions in Archaea. It is a lytic virus that exploits a unique egress mechanism based on the formation of remarkable pyramidal structures on the host cell envelope. Using whole-transcriptome sequencing, we present here a global map defining host and viral gene expression during the infection cycle of SIRV2 in its hyperthermophilic host S. islandicus LAL14/1. This information was used, in combination with a yeast two-hybrid analysis of SIRV2 protein interactions, to advance current understanding of viral gene functions. As a consequence of SIRV2 infection, transcription of more than one-third of S. islandicus genes was differentially regulated. While expression of genes involved in cell division decreased, those genes playing a role in antiviral defense were activated on a large scale. Expression of genes belonging to toxin-antitoxin and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems was specifically pronounced. The observed different degree of activation of various CRISPR-Cas systems highlights the specialized functions they perform. The information on individual gene expression and activation of antiviral defense systems is expected to aid future studies aimed at detailed understanding of the functions and interplay of these systems in vivo
    Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes using DNA microarray and next generation sequencing technologies
    Leimena, M.M. ; Wels, M. ; Bongers, R. ; Smid, E.J. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2012
    Applied and Environmental Microbiology 78 (2012)12. - ISSN 0099-2240 - p. 4141 - 4148.
    differential expression analysis - rna-seq - gene-expression - messenger-rna - tiling arrays - count data - normalization - metabolism - platforms - bacteria
    RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. Application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase the relative abundance of mRNA and cannot employ the poly-T primed approach in cDNA synthesis. In this study, we aimed to validate the use of RNA sequencing (direct cDNA sequencing and 3' -UTR sequencing) using Lactobacillus plantarum WCFS1 as a model organism, employing its established microarray platform as a reference. Limited impact of mRNA enrichment on genome-wide transcript quantification was observed, and comparative transcriptome analyses were performed for L. plantarum WCFS1 grown in two different laboratory media. Microarray analyses and both RNA sequencing methods resulted in similar depth of analysis and generated similar fold-change ratio of differentially expressed genes. The highest overall correlation was found between microarray and direct cDNA sequencing derived transcriptomes, while the 3' -UTR sequencing derived transcriptome appeared to deviate most. Overall, a high similarity between patterns of transcript abundance and fold-change levels of differentially expressed genes was detected by all three methods, indicating that the biological conclusions drawn from the transcriptome-data were consistent between the three technologies
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