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Henrik Bjørn Nielsen

Publications and source records attributed to Henrik Bjørn Nielsen.

7 recordsLinked to original sources

Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4.

Arabidopsis MPK4 has been implicated in plant defense regulation because mpk4 knockout plants exhibit constitutive activation of salicylic acid (SA)-dependent defenses, but fail to induce jasmonic acid (JA) defense marker genes in response to JA. We show here that mpk4 mutants are also defective in defense gene induction in response to ethylene (ET), and that they are more susceptible than wild-type (WT) to Alternaria brassicicola that induces the ET/JA defense pathway(s). Both SA-repressing and ET/JA-(co)activating functions depend on MPK4 kinase activity and involve the defense regulators EDS1 and PAD4, as mutations in these genes suppress de-repression of the SA pathway and suppress the block of the ET/JA pathway in mpk4. EDS1/PAD4 thus affect SA-ET/JA signal antagonism as activators of SA but as repressors of ET/JA defenses, and MPK4 negatively regulates both of these functions. We also show that the MPK4-EDS1/PAD4 branch of ET defense signaling is independent of the ERF1 transcription factor, and use comparative microarray analysis of ctr1, ctr1/mpk4, mpk4 and WT to show that MPK4 is required for induction of a small subset of ET-regulated genes. The regulation of some, but not all, of these genes involves EDS1 and PAD4.

Alternaria↗

Distinct developmental defense activations in barley embryos identified by transcriptome profiling.

Proper embryo development is crucial for normal growth and development of barley. Numerous related aspects of this process--for example how the embryo establishes and sustains disease resistance for extended periods during dormancy--remain largely unknown. Here we report the results of microarray analyses of >22,000 genes, which together with measurements of jasmonic acid and salicylic acid during embryo development provide new information on the initiation in the developing barley embryo of at least two distinct types of developmental defense activation (DDA). Early DDA is characterized by the up-regulation of a specific set of genes around 20 days after flowering, including co-regulation of those for encoding 9-lipoxygenase and several oxylipin-generating enzymes, possibly leading to the formation of alpha-ketols. The same developmental phase includes an up-regulation of several defense genes, and indications of co-regulation of those for enzymes involved in the generation of phenylpropanoid phytoalexins. Late DDA is initiated prior to grain desiccation, around 37 days after flowering, with up-regulation of several genes encoding proteins with roles in antioxidant responses as well as a simultaneous up-regulation of several PR genes is notable. Throughout barley embryo development, there are no indications of an increased biosynthesis of either jasmonic acid or salicylic acid. Collectively, the results help explain how the proposed DDA enables protection of the developing barley embryo and grain for purposes of disease resistance.

Cell Cycle↗

OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes.

OligoWiz 2.0 is a powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management. Furthermore, we show that probes designed using OligoWiz 2.0 give rise to consistent hybridization results (http://www.cbs.dtu.dk/services/OligoWiz2).

Algorithms↗

The MAP kinase substrate MKS1 is a regulator of plant defense responses.

Arabidopsis MAP kinase 4 (MPK4) functions as a regulator of pathogen defense responses, because it is required for both repression of salicylic acid (SA)-dependent resistance and for activation of jasmonate (JA)-dependent defense gene expression. To understand MPK4 signaling mechanisms, we used yeast two-hybrid screening to identify the MPK4 substrate MKS1. Analyses of transgenic plants and genome-wide transcript profiling indicated that MKS1 is required for full SA-dependent resistance in mpk4 mutants, and that overexpression of MKS1 in wild-type plants is sufficient to activate SA-dependent resistance, but does not interfere with induction of a defense gene by JA. Further yeast two-hybrid screening revealed that MKS1 interacts with the WRKY transcription factors WRKY25 and WRKY33. WRKY25 and WRKY33 were shown to be in vitro substrates of MPK4, and a wrky33 knockout mutant was found to exhibit increased expression of the SA-related defense gene PR1. MKS1 may therefore contribute to MPK4-regulated defense activation by coupling the kinase to specific WRKY transcription factors.

Amino Acid Motifs↗

New weakly expressed cell cycle-regulated genes in yeast.

We present an approach combining bioinformatics prediction with experimental microarray validation to identify new cell cycle-regulated genes in Saccharomyces cerevisiae. We identify in the order of 100 new cell cycle-regulated genes and show by independent data that these genes in general tend to be more weakly expressed than the genes identified hitherto. Among the genes not previously suggested to be periodically expressed we find genes linked to DNA repair, cell size monitoring and transcriptional control, as well as a number of genes of unknown function. Several of the gene products are believed to be phosphorylated by Cdc28. For many of these new genes, homologues exist in Schizosaccharomyces pombe and Homo sapiens for which the expression also varies with cell cycle progression.

Cell Cycle Proteins↗

Implementation of a gene expression index calculation method based on the PDNN model.

UNLABELLED: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS, dChip, and RMA methods. A new method to estimate the gene expression value utilizing the probe sequence information named position-dependent nearest-neighbor (PDNN) has been suggested by Zhang et al. (2003). Here we describe an open source implementation of the PDNN method for the statistical language R. AVAILABILITY: The package can be downloaded from http://www.bioconductor.org/repository/devel/package/html/affypdnn.html CONTACT: hbjorn@cbs.dtu.dk.

Algorithms↗

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.

Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/.

DNA Primers↗