Time-resolved biomarker discovery in 1H-NMR data using generalized fuzzy Hough transform alignment and parallel factor analysis.

This work addresses the subject of time-series analysis of comprehensive (1)H-NMR data of biological origin. One of the problems with toxicological and efficacy studies is the confounding of correlation between the administered drug, its metabolites and the systemic changes in molecular dynamics, i.e., the flux of drug-related molecules correlates with the molecules of system regulation. This correlation poses a problem for biomarker mining since this confounding must be untangled in order to separate true biomarker molecules from dose-related molecules. One way of achieving this goal is to perform pharmacokinetic analysis. The difference in pharmacokinetic time profiles of different molecules can aid in the elucidation of the origin of the dynamics, this can even be achieved regardless of whether the identity of the molecule is known or not. This mode of analysis is the basis for metabonomic studies of toxicology and efficacy. One major problem concerning the analysis of (1)H-NMR data generated from metabonomic studies is that of the peak positional variation and of peak overlap. These phenomena induce variance in the data, obscuring the true information content and are hence unwanted but hard to avoid. Here, we show that by using the generalized fuzzy Hough transform spectral alignment, variable selection, and parallel factor analysis, we can solve both the alignment and the confounding problem stated above. Using the outlined method, several different temporal concentration profiles can be resolved and the majority of the studied molecules and their respective fluxes can be attributed to these resolved kinetic profiles. The resolved time profiles hereby simplifies finding true biomarkers and bio-patterns for early detection of biological conditions as well as providing more detailed information about the studied biological system. The presented method represents a significant step forward in time-series analysis of biological (1)H-NMR data as it provides almost full automation of the whole data analysis process and is able to analyze over 800 unique features per sample. The method is demonstrated using a (1)H-NMR rat urine dataset from a toxicology study and is compared with a classical approach: COW alignment followed by bucketing.

Carbon-11 labeled ethionine and propionine as tumor detecting agents.

To develop 18F-fluoroalkyl derivatives of methionine (MET) as a tumor detecting agent by mean of clinical PET, a pilot study assessing the potential of their parent compounds, 11C-labeled ethionine (11C-ETH) and propionine (11C-PRO), was performed. 11C-ETH and 11C-PRO were prepared by the reaction of L-homocysteine thiolactone and corresponding 11C-alkyl iodides. After i.v. injection of a mixture of 3H-MET. 14C-ETH and 11C-PRO into mice bearing FM3A mammary carcinoma, the highest FM3A uptake was found in 14C-ETH, followed by 3H-MET and 11C-PRO, while the FM3A-to-brain and FM3A-to-muscle ratios were nearly the same for all three compounds. The FM3A uptake of 14C-ETH and 11C-PRO were nearly equal or slightly higher than the liver uptake. In the pancreas, liver, FM3A and brain tissues, incorporation of 14C-ETH into acid-precipitable materials was much lower than that of 3H-MET, whereas no incorporation of 11C-PRO was found. Brain uptake of all three compounds was significantly reduced by carrier MET-loading (5 min p.i.) or by cycloheximide treatment to inhibit protein synthesis (60 min p.i.), whereas the FM3A uptake was not affected. Incorporation of 14C-ETH into acid-precipitable materials was inhibited by the cycloheximide. The results suggest that 11C-labeled ETH has a similar potential for tumor detection by PET as 11C-MET, and that 11C-PRO has similar properties to those of other artificial amino acids. The development of 18F-fluoroalkyl derivatives of MET is of interest as the next step.

Glutathione-related detoxication functions in streptozotocin-induced diabetic rats.

In order to analyze the detoxication functions in rats with diabetes induced by streptozotocin, the authors administered to the diabetic animals two drugs, ethionine and benzo(a)pyrene, which affect mainly the liver and are metabolized through a glutathione conjugation process, and examined the changes in the content of glutathione and activities of related enzymes in the liver. In the liver of the rats with streptozotocin-induced diabetes, the total glutathione content, glutathione S-transferase activity and glutathione-insulin transhydrogenase activity were lower than those of normal rat livers, while the glutathione peroxidase activity showed high values. Although specific changes in the glutathione-related detoxication functions were observed in the rats to which ethionine or benzo(a)pyrene had been administered, these changes were not revealed under diabetic conditions. It is suggested that in diabetic rats responses to toxic stimuli are suppressed.

Methyl-deficient mammalian transfer RNA: II. Homologous methylation in vitro of liver tRNA from normal and ethionine-fed rats: ethionine effect on 5-methyl-cytidine synthesis in vivo.

Following hydroxyapatite chromatography, rat liver tRNA methylase activity was assayed with liver tRNA from normal rats and with methyl-deficient liver tRNA from ethionine-fed rats. The difference in homologous methylation between normal and methyl-deficient tRNA was maximal in certain fractions in presence of cadaverine, and much less in presence of Mg(++) or Mg(++) plus cadaverine. These methylase fractions, which contained endogenous tRNA, were used for preparative homologous methylation of added normal and methyl-deficient tRNA in presence of 30 mM cadaverine. The (14)C-methylated tRNA was digested with RNase T(2) and the resulting methylated mononucleotides were characterized and quantitated after twodimensional thinlayer chromatography and autoradiography. The major products of homologous tRNA methylation were m(5)C and m(1)A. However, the methylase fraction used here did not catalyze the formation of m(6) (2)A with m(6) (2)A-deficient tRNA as substrate.- In addition to the previously described, analytically detectable m(6) (2)A-deficiency, a partial m(5)C-deficiency was demonstrated in liver tRNA from ethionine-fed rats by measuring the methylacceptance in vitro. In presence of cadaverine, with the methylase fraction used here, methyl-deficient tRNA from ethionine-fed rats was a twofold more efficient methyl-acceptor in vitro than normal liver tRNA, while endogenous tRNA isolated from the methylase fraction was a threefold more efficient methyl-acceptor than normal liver tRNA. Homologous methylation of normal tRNA, as observed here, has not been described before.

Phosphoenolpyruvate carboxykinase of kidney

A method for the assay of phosphoenolpyruvate carboxykinase is presented, based on the enzymic determination of the phosphoenolpyruvate produced by the enzyme reaction. The subcellular distribution of phosphoenolpyruvate carboxykinase in the kidney of several animal species resembled the distribution in the liver. The rise in enzyme activity in the kidney cortex of rats made acidotic by feeding with ammonium chloride was not prevented by the administration of ethionine or actinomycin. The possibility is suggested that in the kidney acidosis causes activation of an inactive form of the enzyme already present. (AU)