POSA: Perl Objects for DNA Sequencing Data Analysis

Background  

Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines.     

Selective reversed-phase liquid chromatography method for the kinetic investigation of 3-hydroxyflavone photostability

This paper reports a fast and accurate RP-HPLC chromatographic method for the simultaneous determination of 3-hydroxyflavone (3-OH F) and its photodegradation products. Solutions (5 x 10(-5) M) in acetonitrile (ACN) of the molecule were subjected to forced degradation by exposure to artificial UV-A light source (black-light, lambda(max) 354 nm) and the changes appearing in chromatograms were monitored at selected irradiation times. A multistep gradient was optimised to achieve complete elution of all photoproducts in the shortest analysis time. UV spectra recorded by the diode array detector system (285 and 340 nm) clearly showed the structural changes in the new species formed, with respect to the parent compound. The analytical method was subjected to a validation procedure in which linearity and range, as well as specificity, precision and accuracy were determined according to ICH guidelines. Quantitative evaluation of the photochemical process was performed on the basis of the calculated kinetic parameters: photodegradation rate constant k, half-life time t(0.5), time degradation of 10% of the drug t(0.1).     

Low power microwave interaction with phospholipase C and D signal transduction pathways in myogenic cells

Ionic channel proteins are possible sites of microwave interaction at the cell membrane level. Patch-clamp data, using single channel and total current recording, indicated that low level microwave fields may modify some functional parameters of the nicotinic acetylcholine receptor in primary chick myotubes, suggesting a possible effect of microwaves on myogenic cells. Here, we investigated the biological relevance of such results, in relation to the possible involvement of intracellular signaling processes. We exposed L6-C5 myogenic cells to low power electromagnetic fields and observed the consequences on hormonal activation of phospholipases C and D. We found that increased inositol phospholipid turnover, induced by acetylcholine and arginine vasopressin activation of phospholipase C, was not modified in microwave irradiated myoblasts or myotubes. Moreover, vasopressin-dependent phospholipase D activation, assessed by measuring the [3H]-free choline release, was not modified by microwave irradiation. Our conclusions suggest that low level microwave fields do not modify signal transduction pathways activated by acetylcholine and vasopressin in L6-C5 myogenic cells.     

Biochemical basis for depressed serum retinol levels in transthyretin-deficient mice

Transthyretin (TTR) acts physiologically in the transport of retinol in the circulation. We previously reported the generation and partial characterization of TTR-deficient (TTR(-)) mice. TTR(-) mice have very low circulating levels of retinol and its specific transport protein, retinol-binding protein (RBP). We have examined the biochemical basis for the low plasma retinol-RBP levels. Cultured primary hepatocytes isolated from wild type (WT) and TTR(-) mice accumulated RBP in their media to an identical degree, suggesting that RBP was being secreted from the hepatocytes at the same rate. In vivo experiments support this conclusion. For the first 11 h after complete nephrectomy, the levels retinol and RBP rose in the circulations of WT and TTR(-) mice at nearly identical rates. However, human retinol-RBP injected intravenously was more rapidly cleared from the circulation (t(12) = 0.5 h for TTR(-) versus t(12) >6 h for WT) and accumulated faster in the kidneys of TTR(-) compared with WT mice. The rate of infiltration of the retinol-RBP complex from the circulation to tissue interstitial fluids was identical in both strains. Taken together, these data indicate that low circulating retinol-RBP levels in TTR(-) mice arise from increased renal filtration of the retinol-RBP complex.     

Activation of matrix-metalloproteinase-2 and membrane-type-1-matrix-metalloproteinase in endothelial cells and induction of vascular permeability in vivo by human immunodeficiency virus-1 Tat protein and basic fibroblast growth factor

Previous studies indicated that the Tat protein of human immunodeficiency virus type-1 (HIV-1) is a progression factor for Kaposi's sarcoma (KS). Specifically, extracellular Tat cooperates with basic fibroblast growth factor (bFGF) in promoting KS and endothelial cell growth and locomotion and in inducing KS-like lesions in vivo. Here we show that Tat and bFGF combined increase matrix-metalloproteinase-2 (MMP-2) secretion and activation in endothelial cells in an additive/synergistic manner. These effects are due to the activation of the membrane-type-1-matrix-metalloproteinase and to the induction of the membrane-bound tissue inhibitor of metalloproteinase-2 (TIMP-2) by Tat and bFGF combined, but also to Tat-mediated inhibition of both basal or bFGF-induced TIMP-1 and -2 secretion. Consistent with this, Tat and bFGF promote vascular permeability and edema in vivo that are blocked by a synthetic MMP inhibitor. Finally, high MMP-2 expression is detected in acquired immunodeficiency virus syndrome (AIDS)-KS lesions, and increased levels of MMP-2 are found in plasma from patients with AIDS-KS compared with HIV-uninfected individuals with classic KS, indicating that these mechanisms are operative in AIDS-KS. This suggests a novel pathway by which Tat can increase KS aggressiveness or induce vasculopathy in the setting of HIV-1 infection.     

KDC1, a novel carrot root hair K+ channel. Cloning, characterization, and expression in mammalian cells

Potassium is an essential nutrient which plays an important role in many aspects of plant growth and development. Plants have developed a number of highly specific mechanisms to take up potassium from the soil; these include the expression of K(+) transporters and potassium channels in root cells. Despite the fact that root epidermal and hair cells are in direct contact with the soil, the role of these tissues in K(+) uptake is not well understood. Here we report the molecular cloning and functional characterization of a novel potassium channel KDC1 which forms part of a new subfamily of plant K(in) channels. Kdc1 was isolated from carrot root RNA and in situ hybridization experiments show Kdc1 to be highly expressed in root hair cells. Expressing the KDC1 protein in Chinese hamster ovary cells identified it as a voltage and pH-dependent inwardly rectifying potassium channel. An electrophysiological analysis of carrot root hair protoplasts confirmed the biophysical properties of the Kdc1 gene product (KDC1) in the heterologous expression system. KDC1 thus represents a major K(+) uptake channel in carrot root hair cells.     

Fluorescence quenching of dipyridamole associated to peroxyl radical scavenging: a versatile probe to measure the chain breaking antioxidant activity of biomolecules

Dypiridamole is a highly efficient chain breaking antioxidant (Iuliano et al., Free Radic. Biol. Med. 18 (1995) 239-247) with an aromatic ring system responsible for an intense absorption band in the 400-480-nm region and for an intense fluorescence. Dipyridamole fluorescence is quantitatively quenched upon reaction with peroxyl radicals. In the presence of a flux of peroxyl radicals generated by thermal dissociation of azo-initiators, dipyridamole fluorescence decays linearly, showing a first-order reaction with respect to peroxyl radicals, and zero-order with respect to dipyridamole. The pH optimum for the fluorescence quenching is in the 7-8 range, from pH 7 to 6, the decay of fluorescence rapidly decreases to became negligible below pH 5.5. Dipyridamole consumption is blocked in the presence of an added chain breaking antioxidant for a time that is proportional to the antioxidant concentration. This effect is shown for ascorbic acid, trolox, vitamin E, uric acid, and N, N'-diphenyl-p-phenylenediamine. The slope of the linear correlation relative to trolox allows calculation of the bimolecular rate constant for a given molecule and peroxyl radicals. Comparison of data obtained by the dipyridamole consumption are comparable to values obtained by the oxygen consumption method.