State-of-the art data normalization methods improve NMR-based metabolomic analysis

Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples.

     

Defective production of anti-herpes simplex virus antibody by neonatal mice. Reconstitution with Ia+ macrophages and T helper lymphocytes from nonimmune adult syngeneic mice

Both neonatal humans and mice are exquisitely susceptible to severe HSV infection. We have now documented a profound defect in the ability of neonatal C57BL/6 mice to produce anti-HSV ADCC antibody. This ability is acquired over the first 2 to 4 wk of life. Reconstitution of neonatal mice by i.p. injection of peritoneal cells from adult nonimmune syngeneic mice both affords dose-dependent protection against lethal HSV infection and reconstitutes the antibody-production defect. By cell-separation techniques (adherence, nylon wool column purification, B cell panning) and cell ablation techniques (silica treatment, irradiation, anti-T cell, anti-Ia, anti-Lyt-1.2 and anti-Lyt-2.2 monoclonal antibodies plus complement treatment) the subpopulations involved in the antibody production reconstitution of neonatal mice by adult cells were identified. These include both an Ia+, radioresistant, adherent, silica-sensitive macrophage population and a nylon wool column-purified, radiosensitive, anti-T, anti-Lyt-1.2-sensitive helper T cell population. The latter cell may be substituted for by concanavalin A-stimulated lymphokine-containing spleen cell supernatants or human recombinant IL 2. In addition to reconstitution of ADCC antibody production, the same cell populations, or cells plus lymphokine-containing supernatants or IL 2, protected the newborn mice from lethal HSV infection. Further characterization of this system and of soluble replacement factors has implications for therapy or immunoprophylaxis of human neonates with, or at risk of, HSV infection.     

Synthesis of 3 beta-hydroxy-5 alpha-cholest-8-en-7-one and 3 beta-hydroxy-5 alpha-cholest-8-en-11-one: evaluation as potential hypocholesterolemic agents

An efficient procedure for the chemical synthesis of 3 beta-hydroxy-5 alpha-cholest-8-en-7-one and 3 beta-hydroxy-5 alpha-cholest-8-en-11-one is described. These ketosterols have been shown to have possible significant hypocholesterolemic effects when fed to normal rats at a level of 0.15% in a laboratory chow diet. The diets containing the steroids caused significant decreases in food consumption which were associated with decreases in the rate of gain in body weight.     

Site of natural N enrichment of soybean nodules

Soybean (Glycine max L. Merrill) nodules are usually more enriched in ¹⁵N than other tissues. We show that both bacteroids and nodule cortex are considerably more enriched in ¹⁵N than nodule cytosol, with bacteroids being slightly more enriched than the cortex. Hence, ¹⁵N enrichment occurs in cells of both plant and bacterial origin.     

Changes in the Water Balance and Photosynthesis of Onion, Bean and Cotton Plants under Saline Conditions

The osmotic concentration (osmotic potential) of onion leaf sap did not adjust to chloride salinity, and consequently water potential, turgor, stomatal aperture and transpiration were reduced. Although osmotic concentration of bean and cotton leaf sap did adjust to a saline root medium and turgor was no less in the salinized plants than in the controls, stomata of the salinized plants remained only partly open and transpiration was reduced. Net photosynthesis of onion plants was reduced by salinity (this effect being much enhanced in a hot dry atmosphere) but it could be rapidly raised to the level of the controls by inducing elevated leaf turgor. Stomatal closure was initially responsible for most of the ～30 % reduction in photosynthesis of salinized beans. This was due to interference with CO₂ diffusion and could be overcome by raising the CO₂ concentration in the air. At a later stage of growth, salinity affected the light reaction of bean photosynthesis, and elevation of the air CO₂ had little effect. Closure of stomata of salinized cotton plants had only a relatively small effect on net photosynthesis. Light intensity and CO₂ concentration experiments showed that salinity was reducing the photosynthesis of cotton leaves mainly by affecting the light reaction of photosynthesis. It is concluded that chloride salinity does affect the water balance and rate of photosynthesis of plants and that the nature and degree of the effects will depend upon climatic conditions and may be very different between plant species and in the same species at different periods of growth.     

Teaching of Fertility Regulation in Medical Schools: A Survey in the United States and Canada, 1964

Fertility regulation is taught didactically in 82 of 94 medical school departments of obstetrics and gynecology in the United States and Canada, but students are given clinical experience in only 59 medical schools, according to a survey conducted in 1964 by a committee of the American Public Health Association. Legal prohibitions impeded teaching in 1964 in two States and in all of Canada. Nearly all schools teach that help with fertility regulation should be offered for medical and socioeconomic stress, and most teach that it should be offered routinely in premarital counselling and in the postpartum period, but only two-thirds teach that this help should be given to unmarried adults and only one-third teach that any person requesting help with fertility regulation should receive it.     

Activities of the pentose phosphate pathway and enzymes of proline metabolism in legume root nodules

Based on localization and high activities of pyrroline-5-carboxylate reductase and proline dehydrogenase activities in soybean nodules, we previously suggested two major roles for pyrroline-5-carboxylate reductase in addition to the production of the considerable quantity of proline needed for biosynthesis; namely, transfer of energy to the location of biological N₂ fixation, and production of NADP⁺ to drive the pentose phosphate pathway. The latter produces ribose-5-phosphate which can be used in de novo purine synthesis required for synthesis of ureides, the major form in which biologically fixed N₂ is transported from soybean root nodules to the plant shoot. In this paper, we report rapid induction (in soybean nodules) and exceptionally high activities (in nodules of eight species of N₂-fixing plants) of pentose phosphate pathway and pyrroline-5-carboxylate reductase. There was a marked increase in proline dehydrogenase activity during soybean (Glycine max) ontogeny. The magnitude of proline dehydrogenase activity in bacteroids of soybean nodules was sufficiently high during most of the time course to supply a significant fraction of the energy requirement for N₂ fixation. Proline dehydrogenase activity in bacteroids from nodules of other species was also high. These observations support the above hypothesis. However, comparison of pentose phosphate pathway and pyrroline-5-carboxylate reductase activities of ureide versus amide-exporting nodules offers no support. The hypothesis predicts that pyrroline-5-carboxylate and pentose phosphate pathway activities should be higher in ureide-exporting nodules than in amide-exporting nodules. This predicted distinction was not observed in the results of in vitro assays of these activities.