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Quantifying Cell Shape and Gene Expression in the Shoot Apical Meristem Using MorphoGraphX
Confocal microscopy is a technique widely used to live-image plant tissue. Cells can be visualized by using fluorescent probes that mark the cell wall or plasma membrane. This enables the confocal microscope to be used as a 3D scanner with submicron precision. Here we present a protocol using the 3D image processing software MorphoGraphX ( http://www.MorphoGraphX.org ) to extract the surface geometry and cell shapes in the shoot apex. By segmenting cells over consecutive time points, precise growth maps of the shoot apex can be produced. It is also possible to tag a protein of...
Source: Springer protocols feed by Plant Sciences - October 19, 2013 Category: Biology Source Type: news

Transcriptome Coexpression Analysis Using ATTED-II for Integrated Transcriptomic/Metabolomic Analysis
Transcriptome coexpression analysis is an excellent tool for predicting the physiological functions of genes. It is based on the “guilt-by-association” principle. Generally, genes involved in certain metabolic processes are coordinately regulated. In other words, coexpressed genes tend to be involved in common or closely related biological processes. Genes of which the metabolic functions have been identified are preselected as “guide” genes and are used to check the transcriptome coexpression fidelity to the pathway and to determine the threshold value of correlation coefficients to be used for sub...
Source: Springer protocols feed by Plant Sciences - April 28, 2013 Category: Biology Source Type: news

Analysis of RNA-Seq Data with TopHat and Cufflinks for Genome-Wide Expression Analysis of Jasmonate-Treated Plants and Plant Cultures
The recent development of various deep sequencing techniques has led to the most powerful transcript profiling method available to date, RNA sequencing or RNA-Seq. Besides the identification of new genes and new splice variants of known genes, RNA-Seq allows to compare the whole transcriptome of any organism under two or more experimental conditions, such as before and after jasmonate treatment. However, the vast amounts of data generated during RNA-Seq experiments require complex computational methods for read mapping and expression quantification. Here, we describe a detailed protocol for the analysis of deep sequencing ...
Source: Springer protocols feed by Plant Sciences - April 28, 2013 Category: Biology Source Type: news

cDNA-AFLP-Based Transcript Profiling for Genome-Wide Expression Analysis of Jasmonate-Treated Plants and Plant Cultures
cDNA-AFLP is a commonly used, robust, and reproducible tool for genome-wide expression analysis in any species, without requirement of prior sequence knowledge. Quantitative expression data are generated by gel-based visualization of cDNA-AFLP fingerprints obtained by selective PCR amplification of subsets of restriction fragments from a double-stranded cDNA template. Differences in gene expression levels across the samples are reflected in different band intensities on the high-resolution polyacrylamide gels. The differentially expressed genes can be identified by direct sequencing of re-amplified cDNA-AFLP tags purified ...
Source: Springer protocols feed by Plant Sciences - April 28, 2013 Category: Biology Source Type: news

Metabolite Profiling of Plant Tissues by Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Plants accumulate an overwhelming variety of secondary metabolites that play important roles in defense and interaction of the plant with its environment. To investigate the dynamics of plant secondary metabolism, large-scale untargeted metabolite profiling (metabolomics) is mandatory. Here, we describe a detailed protocol for untargeted metabolite profiling in which methanol extracts of jasmonate-treated plant tissues are analyzed by reversed-phase liquid chromatography coupled to negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (MS). By means of dedicated integration and al...
Source: Springer protocols feed by Plant Sciences - April 28, 2013 Category: Biology Source Type: news