Pathogen-secreted proteases activate a novel plant immune pathway.

Mitogen-activated protein kinase (MAPK) cascades play central roles in innate immune signalling networks in plants and animals. In plants, however, the molecular mechanisms of how signal perception is transduced to MAPK activation remain elusive. Here we report that pathogen-secreted proteases activate a previously unknown signalling pathway in Arabidopsis thaliana involving the Gα, Gβ, and Gγ subunits of heterotrimeric G-protein complexes, which function upstream of an MAPK cascade.

Effects of bacterial ACC deaminase on Brassica napus gene expression.

Plants in association with plant growth-promoting rhizobacteria can benefit from lower plant ethylene levels through the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. This enzyme cleaves the immediate biosynthetic precursor of ethylene, ACC. Ethylene is responsible for many aspects of plant growth and development but, under stressful conditions, it exacerbates stress symptoms.

Proteome reference map for the plant growth-promoting bacterium Pseudomonas putida UW4.

A proteome reference map containing 326 2-D gel spots representing 275 different proteins was constructed for the plant growth-promoting bacterium Pseudomonas putida UW4. Protein identifications were obtained using Q-TOF MS/MS spectra matching to homologous proteins from other Pseudomonas strains and confirmed by PMF analysis. This data set is accessible at http://world-2dpage.

Assessing the evolution of gene expression using microarray data.

Classical studies of the evolution of gene function have predominantly focused on mutations within protein coding regions. With the advent of microarrays, however, it has become possible to evaluate the transcriptional activity of a gene as an additional characteristic of function. Recent studies have revealed an equally important role for gene regulation in the retention and evolution of duplicate genes.

Comparison of small n statistical tests of differential expression applied to microarrays.

Background: DNA microarrays provide data for genome wide patterns of expression between observation classes. Microarray studies often have small samples sizes, however, due to cost constraints or specimen availability. This can lead to poor random error estimates and inaccurate statistical tests of differential expression.

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data.

Background: High-throughput systems are powerful tools for the life science research community. The complexity and volume of data from these systems, however, demand special treatment. Graphical tools are needed to evaluate many aspects of the data throughout the analysis process because plots can provide quality assessments for thousands of values simultaneously.

A methodology for global validation of microarray experiments.

Background: DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with data publicly available for mining by other investigators. Under most circumstances, validation of differential expression of genes is performed on a gene to gene basis.