Computational protocol: Abscisic acid effects on activity and expression of barley (Hordeum vulgare) plastidial glucose-6-phosphate dehydrogenase

Similar protocols

Protocol publication

[…] The protein sequence of the root barley (H. vulgare) plastidial P2-G6PDH was retrieved from the NCBI database (http://www.ncbi.nlm.nih.gov) and used to search against other genomes using BlastP or tblastn. All the sequences are available at the following websites: for A. thaliana (http://www.arabidopsis.org/), Oryza sativa (http://rice.plantbiology.msu.edu/), Sorghum bicolor (http://genome.jgipsf.org/Sorbi1/Sorbi1.home.html), N. tabacum (http://www.ncbi.nlm.nih.gov), Populus trichocarpa (http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html), Solanum tuberosum (http://www.ncbi.nlm.nih.gov), Triticum aestivum (http://www.ncbi.nlm.nih.gov), and Spinacia oleracea (http://www.ncbi.nlm.nih.gov). All protein accession numbers used in this article can be found in these databases.The amino acid alignments were performed using ClustalW (www.ebi.ac.uk/Tools/clustalw2/index.html) and the phylogenetic tree was constructed using the Neighbor–Joining tree algorithm in MEGA version 4 ().Supplemental data files available at JXB online contain all the protein sequences indexed in this study including the accession numbers. [...] The amplified products were resolved on a 1.5% agarose gel, and the DNA was visualized by ethidium bromide, using an UV transilluminator, and images were acquired by a camera. Each gel photo was processed using Image J (NIH) to obtain a threshold black and white pixel map. The spots were quantified as arbitrary units (pixel) in an Excel worksheet, and used to construct a graph using the Sigmaplot (Jandel) software. The experiment shown is representative of three experiments which showed the same general behaviour; the average values and the standard errors are given in the chart below the gel photos in the figures. […]

Pipeline specifications

Software tools BLASTP, TBLASTN, Clustal W, MEGA, SigmaPlot
Applications Miscellaneous, Phylogenetics, Amino acid sequence alignment
Organisms Hordeum vulgare
Chemicals Abscisic Acid, Glucose-6-Phosphate