GeneCAT—novel webtools that combine BLAST and co-expression analyses

The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughput Map-O-Matic tool matches co-expression pattern of multiple query genes to genes present in user-defined subdatabases, and can therefore be used for gene mapping in forward genetic screens. Third, Rosetta combines co-expression analysis with BLAST and can be used to find ‘true’ gene orthologs in the plant model organisms Arabidopsis thaliana and Hordeum vulgare (Barley). GeneCAT is equipped with expression data for the model plant A. thaliana, and first to introduce co-expression mining tools for the monocot Barley. GeneCAT is available at http://genecat.mpg.d

Rhamnogalacturonan I in Solanum tuberosum tubers contains complex arabinogalactan structures

A rhamnogalacturonan I polysaccharide was isolated from potato (Solanum tuberosum cv. Posmo) tuber cell walls and characterised by enzymatic digestion with an endo-β-1 → 4-galactanase and an endo-α-1 → 5-arabinanase, individually or in combination. The reaction products were separated using size-exclusion chromatography and further analysed for monosaccharide composition and presence of epitopes using the LM5 anti-β-1 → 4-galactan and LM6 anti-α-1 → 5-arabinan monoclonal antibodies. The analyses point to distinct structural features of potato tuber rhamnogalacturonan I, such as the abundance of β-1 → 4-galactan side chains that are poorly substituted with short arabinose-containing side chains, the presence of α-1 → 5-arabinan side chains substituted with β-1 → 4-galactan oligomers (degree of polymerisation >4), and the presence of α-1 → 5-arabinans that resist enzymatic degradation. A synergy between the enzymes was observed towards the degradation of arabinans but not towards the degradation of galactans. The effect of the enzymes on isolated RG I is discussed in relation to documented effects of enzymes heterologously expressed in potato tubers. In addition, a novel and rapid method for the determination of the monosaccharide and uronic acid composition of cell wall polysaccharides using high-performance anion exchange chromatography with pulsed amperometric detection is described. A rhamnogalacturonan I polysaccharide from potato tuber cell walls and isolated and characterised by enzymatic digestion with different pectinases. In addition, a novel and rapid method for the determination of common cell wall monosaccharides using high-performance anion exchange chromatography with pulsed amperometric detection is described