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A Lipidomic Approach to Identify Cold-Induced Changes in Arabidopsis Membrane Lipid Composition
Lipidomic analysis using electrospray ionization triple quadrupole mass spectrometry can be employed to monitor lipid changes that occur during cold and freezing stress of plants. Here we describe the analysis of Arabidopsis thaliana polar glycerolipids with normal and oxidized acyl chains, sampled during cold and freezing treatments. Mass spectral data are processed using the online capabilities of LipidomeDB Data Calculation Environment. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

Profiling Methods to Identify Cold-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry
This book chapter describes the analytical procedures required for the profiling of a metabolite fraction enriched for primary metabolites. The profiling is based on routine gas chromatography coupled to mass spectrometry (GC-MS). The generic profiling method is adapted to plant material, specifically to the analysis of single leaves from plants that were exposed to temperature stress experiments. The described method is modular. The modules include a rapid sampling and metabolic inactivation protocol for samples in a wide size range, a sample extraction procedure, a chemical derivatization step that is required to make th...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

Proteomic Approaches to Identify Cold-Regulated Plasma Membrane Proteins
Plasma membrane is the primary determinant of freezing tolerance in plants because of its central role in freeze–thaw cycle. Changes in the plasma membrane proteins have been one of the major research areas in plant cold acclimation. To obtain comprehensive profiles of the plasma membrane proteomes and their changes during the cold acclimation process, a plasma membrane purification method using a dextran–polyethylene glycol two polymer system and a mass spectrometry-based shotgun proteomics method using nano-LC-MS/MS for the plasma membrane proteins are described. The proteomic results obtained are further app...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

Proteomic Approaches to Identify Cold-Regulated Soluble Proteins
DIGE (differential in-gel electrophoresis) is a modified version of the widely used 2-D gel electrophoresis (2-DE) for separation of complex protein samples. Two extracts to be compared are differentially labeled using fluorescent cyanine dyes and then separated together by 2-DE. An internal standard labeled using a third dye is included. This approach avoids the pitfalls of gel distortions frequently observed in the standard procedure, which hamper the subsequent gel image analysis. Inclusion of an internal standard improves the quantitative evaluation of the protein patterns. Using the advantages of the DIGE approach, im...
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

Three-Dimensional Reconstruction of Frozen and Thawed Plant Tissues from Microscopic Images
We present a relatively simple and less-expensive technique using pixel-based (JPEG) images of histological sections of an Arabidopsis thaliana plant and commercially available software to generate 3D reconstructions of internal structures. The technique has proven to work just as effectively for images from medical histology. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

Cryo-Scanning Electron Microscopy to Study the Freezing Behavior of Plant Tissues
A cryo-scanning electron microscope (cryo-SEM) is a valuable tool for observing bulk frozen samples to monitor freezing responses of plant tissues and cells. Here, essential processes of a cryo-SEM to observe freezing behaviors of plant tissue cells are described. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 27, 2014 Category: Biology Source Type: news

TILLING for Plant Breeding
TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 12, 2014 Category: Biology Source Type: news

The Control of Recombination in Wheat by Ph1 and Its Use in Breeding
Two meiotic processes have a major influence on the plant breeding, namely, the independent assortment of chromosomes, and recombination. The major chromosome pairing locus in hexaploid and tetraploid wheat, Ph1, has a significant effect on both these processes. This chapter reviews our current understanding of this locus and how mutants of it can be exploited for breeding purposes. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 12, 2014 Category: Biology Source Type: news

Simulated Breeding with QU-GENE Graphical User Interface
Comparing the efficiencies of breeding methods with field experiments is a costly, long-term process. QU-GENE is a highly flexible genetic and breeding simulation platform capable of simulating the performance of a range of different breeding strategies and for a continuum of genetic models ranging from simple to complex. In this chapter we describe some of the basic mechanics behind the QU-GENE user interface and give a simplified example of how it works. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 12, 2014 Category: Biology Source Type: news

Genomic Selection in Plant Breeding
Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 12, 2014 Category: Biology Source Type: news

Simultaneous Analyses of Oxidized and Reduced Forms of Photosynthetic Quinones by High-Performance Liquid Chromatography
Plastoquinones and phylloquinones are the major plant quinones localized in chloroplasts, and they act as photosynthetic electron redox mediators in thylakoid membranes. These quinones are analyzed by two processes: extraction with organic solvents and quinone assay by high-performance liquid chromatography (HPLC) analysis. Solvent choice is very important from the viewpoint of stability of the redox state in the extraction processes and during storage of plant quinones. We introduce procedures and solvents to avoid changes in the redox state of quinones, in addition to achieving high extraction efficiency. Traditional met...
Source: Springer protocols feed by Plant Sciences - May 1, 2014 Category: Biology Source Type: news

Analysis of Carotenoids and Tocopherols in Plant Matrices and Assessment of Their In Vitro Antioxidant Capacity
Carotenoids and tocopherols are lipid secondary metabolites that play essential roles in plants. They are also relevant compounds from a nutritional standpoint and attract much attention due to their proposed antioxidant properties. In this chapter, methodologies for the extraction and HPLC analysis of these compounds are described as well as a widely used protocol to assess their antioxidant capacity. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - May 1, 2014 Category: Biology Source Type: news

Metabolite Profiling of Plastidial Deoxyxylulose-5-Phosphate Pathway Intermediates by Liquid Chromatography and Mass Spectrometry
Metabolite profiling is a powerful tool that enhances our understanding of complex regulatory processes and extends to the comparative analysis of plant gene function. However, at present, there are relatively few examples of metabolite profiling being used to characterize the regulatory aspects of the plastidial deoxyxylulose-5-phosphate (DXP) pathway in plants. Since the DXP pathway is one of two pathways in plants that are essential for isoprenoid biosynthesis, it is imperative that robust analytical methods be employed for the characterization of this metabolic pathway. Recently, liquid chromatography-mass spectrometry...
Source: Springer protocols feed by Plant Sciences - May 1, 2014 Category: Biology Source Type: news

Analysis of Steroidal Alkaloids and Saponins in Solanaceae Plant Extracts Using UPLC-qTOF Mass Spectrometry
Plants of the Solanaceae family are renowned for the production of cholesterol-derived steroidal glycosides, including the nitrogen containing glycoalkaloids and steroidal saponins. In this chapter we describe the use of UPLC (Ultra Performance Liquid Chromatography) coupled with qTOF (Quadrupole Time-of-Flight) mass spectrometry for profiling of these two large classes of semipolar metabolites. The presented method includes an optimized sample preparation protocol, a procedure for high resolution chromatographic separation and metabolite detection using the TOF mass spectrometer which provides high resolution and mass acc...
Source: Springer protocols feed by Plant Sciences - May 1, 2014 Category: Biology Source Type: news

Gas Chromatography–Mass Spectrometry Method for Determination of Biogenic Volatile Organic Compounds Emitted by Plants
Gas chromatography–mass spectrometry (GC-MS) is one of the most widely used methods for analyzing the emissions of biogenic volatile organic compounds (VOCs) from plants. Preconcentration of VOCs on the cartridges filled with different adsorbents is a well-accepted method for sampling of headspace. Here, we describe a gas-chromatographic method for determination of different isoprenoids (isoprene, monoterpenes, homoterpenes, and sesquiterpenes). The technique is based on adsorption of compounds of interest on multibed adsorbent cartridges followed by thermodesorption, and detection and analysis by GC-MS. (Source: Spr...
Source: Springer protocols feed by Plant Sciences - May 1, 2014 Category: Biology Source Type: news