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.     

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.     

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.     

Investigations of the pigments fromCytophaga johnsonae Cy j1

Besides carotenoids a complex of flexirubin-type pigments was isolated from the gliding bacteriumCytophaga johnsonae Cy j1 and separated into 6 components, which partly containe chlorine. In spite of the fact that these components still consist of pigment mixtures, the gross structures of 18 new flexirubin-type pigments could be deduced by spectroscopic and chemical investigations. The results open insights into biosynthesis and structural variety of the flexirubins, the novel non-isoprenoid pigments recently found inFlexibacter elegans.Non-Standard Abbreviations FT Fourier transformation - HPLC high pressure liquid chromatography - M⁺ molecular ion - M/M resolution of mass spectrometer - mu mass units - t _R retention time - TLC thin layer chromatography Part 16: Investigations on metabolites of microorganisms. Part. XV: H. Achenbach, W. Kohl, H. Reichenbach: Die Hauptpigmente vonCytophaga johnsonae. Tetrahedron Lett.1977, 1061. Part XIV: H. Achenbach, J. Witzke: Totalsynthese des Flexirubindimethylethers. Angew. Chem.89, 198 (1977); Angew. Chem. Int. Ed. Engl.16, 191 (1977)     

Protection of neonatal mice against herpes simplex virus infection: probable in vivo antibody-dependent cellular cytotoxicity

Infant mice are extremely susceptible to fatal Herpes simplex virus (HSV) infection. They are unable to produce antibody to HSV, and their leukocytes cannot mediate antibody-dependent cellular cytotoxicity (ADCC) to HSV-infected cells. In order to avoid H-2-dependent effector mechanisms and instead analyze possible in vivo ADCC, a murine model employing adoptive transfer of antibody and human leukocytes was developed. Administration of either human immune globulin or leukocytes i.p. from HSV immune or nonimmune humans could not protect infant C57BL/6 mice from fatal HSV infection. In contrast, a combination of a subneutralizing dilution of globulin and leukocytes from nonimmune or immune human donors, given one day before inoculation, was highly protective against lethal HSV infection. The cells involved included lymphocytes or monocyte-macrophages. At least 5 X 10(6) viable leukocytes (or 1 X 10(6) monocyte-macrophages) and immune serum globulin concentrations as low as 10(-8) were protective. Infected cell monolayer adsorption and DEAE column fractionation demonstrated that the protection by globulin was due to specific antiviral IgG antibody. Protection was n ot seen in animals receiving virus before immune transfer. Protection did not involve synergistic viral neutralization by antibody and cells, as shown by in vitro experiments. Animals receiving globulin and cells, unlike normal infant mice, had circulating antiviral antibody and peritoneal leukocytes able to mediate ADCC to HSV-infected cells. This is the first in vivo evidence for the role of human ADCC. This model also allows for the in vivo evaluation of the ability of cells from immunocompromised humans to curb viral infection.     

Quantitative, radial diffusion slide assay for staphylocoagulase.

A simple, quantitative radial diffusion assay for staphylocoagulase in culture fluids, using microscope slides coated with a thin layer of agar containing plasma and fibrinogen, was developed. No prior purification of the enzyme was needed, and only small quantities, 7 microliter, were required for each test. This method is particularly suitable for objectively comparing the relative amounts of coagulase produced by different cultures of Staphylococcus aureus.