The interpretation of nuclear magnetic resonance (NMR) experimental results for metabolomics studies requires intensive signal processing and multivariate data analysis techniques. A key step in this process is the quantification of spectral features, which is commonly accomplished by dividing an NMR spectrum into several hundred integral regions or bins. Binning attempts to minimize effects from variations in peak positions caused by sample pH, ionic strength, and composition, while reducing the dimensionality for multivariate statistical analyses. Herein we develop an improved novel spectral quantification technique, dynamic adaptive binning. With this technique, bin boundaries are determined by optimizing an objective function using a dynamic programming strategy. The objective function measures the quality of a bin configuration based on the number of peaks per bin. This technique shows a significant improvement over both traditional uniform binning and other adaptive binning techniques. This improvement is quantified via synthetic validation sets by analyzing an algorithm's ability to create bins that do not contain more than a single peak and that maximize the distance from peak to bin boundary. The validation sets are developed by characterizing the salient distributions in experimental NMR spectroscopic data. Further, dynamic adaptive binning is applied to a 1 H NMRbased experiment to monitor rat urinary metabolites to empirically demonstrate improved spectral quantification.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicits a broad spectrum of species-specific effects that have not yet been fully characterized. This study compares the temporal effects of TCDD on hepatic aqueous and lipid metabolite extracts from immature ovariectomized C57BL/6 mice and Sprague-Dawley rats using gas chromatography-mass spectrometry and nuclear magnetic resonance-based metabolomic approaches and integrates published gene expression data to identify species-specific pathways affected by treatment. TCDD elicited metabolite and gene expression changes associated with lipid metabolism and transport, choline metabolism, bile acid metabolism, glycolysis, and glycerophospholipid metabolism. Lipid metabolism is altered in mice resulting in increased hepatic triacylglycerol as well as mono- and polyunsaturated fatty acid (FA) levels. Mouse-specific changes included the induction of CD36 and other cell surface receptors as well as lipases- and FA-binding proteins consistent with hepatic triglyceride and FA accumulation. In contrast, there was minimal hepatic fat accumulation in rats and decreased CD36 expression. However, choline metabolism was altered in rats, as indicated by decreases in betaine and increases in phosphocholine with the concomitant induction of betaine-homocysteine methyltransferase and choline kinase gene expression. Results from these studies show that aryl hydrocarbon receptor-mediated differential gene expression could be linked to metabolite changes and species-specific alterations of biochemical pathways.

In many metabolomics studies, NMR spectra are divided into bins of fixed width. This spectral quantification technique, known as uniform binning, is used to reduce the number of variables for pattern recognition techniques and to mitigate effects from variations in peak positions; however, shifts in peaks near the boundaries can cause dramatic quantitative changes in adjacent bins due to non-overlapping boundaries. Here we describe a new Gaussian binning method that incorporates overlapping bins to minimize these effects. A Gaussian kernel weights the signal contribution relative to distance from bin center, and the overlap between bins is controlled by the kernel standard deviation. Sensitivity to peak shift was assessed for a series of test spectra where the offset frequency was incremented in 0.5 Hz steps. For a 4 Hz shift within a bin width of 24 Hz, the error for uniform binning increased by 150%, while the error for Gaussian binning increased by 50%. Further, using a urinary metabolomics data set (from a toxicity study) and principal component analysis (PCA), we showed that the information content in the quantified features was equivalent for Gaussian and uniform binning methods. The separation between groups in the PCA scores plot, measured by the J 2 quality metric, is as good or better for Gaussian binning versus uniform binning. The Gaussian method is shown to be robust in regards to peak shift, while still retaining the information needed by classification and multivariate statistical techniques for NMR-metabolomics data.

The relationship between cytotoxicity and kinetics of cadmium uptake was investigated in primary rat hepatocyte cultures. Primary rat hepatocytes were exposed to cadmium concentrations ranging from 1.0 to 80 micro M in albumin-free buffer or 32 to 8,000 microM in buffer containing physiological concentrations of bovine serum albumin (600 micro M) for 1 h, and cellular toxicity was observed at 23 h postexposure. Hepatocytes exposed to cadmium in the presence of albumin appeared less sensitive to cadmium toxicity when compared to cells exposed in the absence of albumin. The experimentally derived 23-h postexposure EC(50)s for hepatocytes exposed to cadmium in both presence and absence of albumin was 65.5 +/- 2.4 and 14.3 +/- 3.9 microM, respectively. A Scatchard plot of cadmium binding to albumin suggested two high-affinity binding sites. The observed uptake of cadmium by hepatocytes in the absence and presence of albumin consisted of a composite fast uptake rate and cell membrane association (Component I), and a slow, sustained uptake rate (Component II). Cadmium uptake rates in hepatocytes, based on total medium cadmium concentrations, indicated that Component II uptake rates were four times faster under albumin-free exposure conditions. However, when uptake rates were evaluated, based on the calculated equilibrium concentration of free cadmium in the exposure buffer, uptake rates in hepatocytes exposed in the presence of albumin were two times as fast. This faster cadmium uptake in the presence of albumin may result from diffusion-limited, nonequilibrium conditions occurring at the cell surface.

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