Haystack, a web-based tool for metabolomics research.

BACKGROUND: Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multiple samples to diagnose phenotypic differences and elucidate relevant features. However, a significant limitation in LCMS-based metabolomics is the high-throughput data processing required for robust statistical analysis and data modeling for large numbers of samples with hundreds of unique chemical species. RESULTS: To address this problem, we developed Haystack, a web-based tool designed to visualize, parse, filter, and extract significant features from LCMS datasets rapidly and efficiently. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data processing options. Total ion chromatograms (TICs) and base peak chromatograms (BPCs) are automatically displayed, along with time-resolved mass spectra and extracted ion chromatograms (EICs) over any mass range. Output files in the common .csv format can be saved for further statistical analysis or customized graphing. Haystack's core function is a flexible binning procedure that converts the mass dimension of the chromatogram into a set of interval variables that can uniquely identify a sample. Binned mass data can be analyzed by exploratory methods such as principal component analysis (PCA) to model class assignment and identify discriminatory features. The validity of this approach is demonstrated by comparison of a dataset from plants grown at two light conditions with manual and automated peak detection methods. Haystack successfully predicted class assignment based on PCA and cluster analysis, and identified discriminatory features based on analysis of EICs of significant bins. CONCLUSION: Haystack, a new online tool for rapid processing and analysis of LCMS-based metabolomics data is described. It offers users a range of data visualization options and supports non-biased differential profiling studies through a unique and flexible binning function that provides an alternative to conventional peak deconvolution analysis methods.

Variations in bran carotenoid levels within and between rice subgroups.

Rice (Oryza sativa L.) is a major grain in the human diet and carotenoids are valuable antioxidants. However, little is known about varietal differences in the carotenoid contents of the rice bran. The objective of this study is to determine the relative differences in bran carotenoid levels among all the five subgroups of rice. Measurements were made by a recently described, rapid non-destructive fluorescence quenching method. Confirmation by high performance liquid chromatography (HPLC) after solvent extraction of the bran indicated that the major carotenoid was lutein. Our data showed that carotenoid levels were stable over 10 years of storage. Tropical japonica rice, the most consumed subgroup in the United States, tended to have the lowest levels of carotenoids in the bran while temperate japonicas had the highest. These differences in carotenoid content may open up new opportunities for identifying or breeding rice varieties with higher nutritional value.

Plant phenolic antioxidant and prooxidant activities: phenolics-induced oxidative damage mediated by metals in plants.

Plant phenolic compounds such as flavonoids and lignin precursors are important constituents of the human diet. These dietary phytophenolics have been recognized largely as beneficial antioxidants that can scavenge harmful active oxygen species including O(2)(.-), H(2)O(2), .OH, and (1)O(2). Here we review our current understanding of the antioxidant and prooxidant actions of phenolics in plant cells. In plant systems, phytophenolics can act as antioxidants by donating electrons to guaiacol-type peroxidases (GuPXs) for the detoxification of H(2)O(2) produced under stress conditions. As a result of such enzymatic as well as non-enzymatic antioxidant reactions, phenoxyl radicals are formed as the primary oxidized products. Until recently, phenoxyl radicals had been difficult to detect by static electron spin resonance (ESR) because they rapidly change to non-radical products. Application of Zn exerts spin-stabilizing effects on phenoxyl radicals that enables us to analyze the formation and decay kinetics of the radicals. The ESR signals of phenoxyl radicals are eliminated by monodehydroascorbate radical (MDA) reductase, suggesting that phenoxyl radicals, like the ascorbate radical, are enzymatically recycled to parent phenolics. Thus, phenolics in plant cells can form an antioxidant system equivalent to that of ascorbate. In contrast to their antioxidant activity, phytophenolics also have the potential to act as prooxidants under certain conditions. For example, flavonoids and dihydroxycinnamic acids can nick DNA via the production of radicals in the presence of Cu and O(2). Phenoxyl radicals can also initiate lipid peroxidation. Recently, Al, Zn, Ca, Mg and Cd have been found to stimulate phenoxyl radical-induced lipid peroxidation. We discuss the mechanism of phenoxyl radical prooxidant activity in terms of lifetime prolongation by spin-stabilizing agents.

Seasonal differences in xanthophyll cycle characteristics and antioxidants in Mahonia repens growing in different light environments.

We investigated differences between summer and winter in photosynthesis, xanthophyll cycle-dependent energy dissipation, and antioxidant systems in populations of Mahonia repens (Lindley) Don growing in the eastern foothills of the Colorado Rocky Mountains in deep shade, full exposure, and under a single-layered canopy of Pinus ponderosa (partially shaded). In summer, increasing growth irradiance (from deep shade to partial shade to full exposure) was associated with increased xanthophyll cycle-dependent energy dissipation in PSII and an increased capacity to detoxify reactive reduced oxygen species, as measured by increases in the activities of ascorbate peroxidase, superoxide scavenging, glutathione reductase, and monodehydroascorbate reductase, as well as increases in leaf ascorbate and glutathione content. Leaves of exposed and partially shaded plants exhibited decreased capacities for photosynthetic O2 evolution in winter compared to summer, while in the deeply shaded plants this parameter did not differ seasonally. Seasonal differences in the levels of antioxidants generally exhibited an inverse response to photosynthesis, being higher in winter compared to summer in the exposed and partially shaded populations, but remaining unchanged in the deeply shaded population. In addition, total pool size and conversion state of the xanthophyll cycle were higher in winter than in summer in all populations. These trends suggest that both xanthophyll cycle-dependent energy dissipation in PSII and the capacity to detoxify reactive reduced oxygen species responded to the level of excess light absorption.