Carcinogenic chromium(VI) induces cross-linking of vitamin C to DNA in vitro and in human lung A549 cells

Reductive activation of carcinogenic Cr(VI) is required for the induction of DNA damage and mutations. Here, we examined the formation of Cr-DNA adducts in the reactions of Cr(VI) with its dominant biological reducer, vitamin C (ascorbate). Reductive conversion of Cr(VI) to Cr(III) by ascorbate produced stable Cr-DNA adducts, of which approximately 25% constituted ascorbate-Cr(III)-DNA cross-links. No evidence was found for the involvement of Cr(V) or Cr(IV) intermediates in the formation of either binary or ternary adducts. The cross-linking reaction was consistent with the attack of DNA by transient Cr(III)-ascorbate complexes. The yield of Cr(III)-DNA adducts was similar on dsDNA and AGT, ACT, or CT oligonucleotides and was strongly inhibited by Mg(2+), suggesting predominant coordination of Cr(III) to DNA phosphate oxygens. We also detected cross-linking of ascorbate to DNA in Cr(VI)-exposed human lung A549 cells that were preincubated with dehydroascorbic acid to create normal levels of intracellular ascorbate. Ascorbate-Cr-DNA cross-links accounted for approximately 6% of the total Cr-DNA adducts in A549 cells. Shuttle-vector experiments showed that ascorbate-Cr-DNA cross-links were mutagenic in human cells. Our results demonstrate that in addition to reduction of Cr(VI) to DNA-reactive Cr(III), vitamin C contributes to the genotoxicity of Cr(VI) via a direct chemical modification of DNA. The absence of Asc in A549 and other human cultured cells indicates that cells maintained under the usual in vitro conditions lack the most important reducing agent for Cr(VI) and would primarily display slow thiol-dependent activation of Cr(VI).     

Lattice Model for QSAR Studies

A system of lattice models that takes into account the structures of molecules, their form, stereochemical features and their interaction with the enclosing space, is proposed. The local, integral and field structural parameters of molecules (more than 20 thousand per compound) are estimated within the proposed framework. An investigation of the utility of these parameters in Quantitative Structure-Activity Relationships (QSAR) has been made using several statistical methods (multiple regression analysis, partial least squares (PLS), trend-vector procedure). The efficiency of the proposed approach has been examined using a data set derived from the formation of charge-transfer complexes of monosubstituted bezens with 1,3,5-trinitrobenzene.     

Cell Type Specific Signalling by Hematopoietic Growth Factors in Neural Cells

Correct timing and spatial location of growth factor expression is critical for undisturbed brain development and functioning. In terminally differentiated cells distinct biological responses to growth factors may depend on cell type specific activation of signalling cascades. We show that the hematopoietic growth factors thrombopoietin (TPO) and granulocyte colony-stimulating factor (GCSF) exert cell type specific effects on survival, proliferation and the degree of phosphorylation of Akt1, ERK1/2 and STAT3 in rat hippocampal neurons and cortical astrocytes. In neurons, TPO induced cell death and selectively activated ERK1/2. GCSF protected neurons from TPO- and hypoxia-induced cell death via selective activation of Akt1. In astrocytes, neither TPO nor GCSF had any effect on cell viability but inhibited proliferation. This effect was accompanied by activation of ERK1/2 and inhibition of STAT3 activity. A balance between growth factors, their receptors and signalling proteins may play an important role in regulation of neural cell survival.     

Acarbose attenuates experimental non-alcoholic steatohepatitis

The alpha-glucosidase inhibitor acarbose is beneficial in the prevention of type 2 diabetes. To determine whether it attenuates the commonly associated non-alcoholic steatohepatitis (NASH), we used an experimental NASH model. Rats were fed ad libitum a nutritionally adequate high fat diet (71% of calories as fat) with or without acarbose (200 mg/1000 calories) for 3 weeks. All rats given the high fat diet only developed typical NASH whereas acarbose attenuated several of the characteristic hepatic alterations of NASH: there was less steatosis and inflammation, with a significant reduction in the mRNA of the hepatic inflammatory cytokine TNF-alpha and of its protein. There was also a decrease in the CYP2E1 mRNA and in collagen, with similar trends for CYP2E1 protein and procollagen mRNA. Because acarbose attenuates many of the hepatic alterations associated with experimental NASH, it is now indicated to determine whether it exerts similar beneficial effects in patients afflicted by this disease.     

Tracking plant physiological properties from multi-angular tower-based remote sensing

Imaging spectroscopy is a powerful technique for monitoring the biochemical constituents of vegetation and is critical for understanding the fluxes of carbon and water between the land surface and the atmosphere. However, spectral observations are subject to the sun–observer geometry and canopy structure which impose confounding effects on spectral estimates of leaf pigments. For instance, the sun–observer geometry influences the spectral brightness measured by the sensor. Likewise, when considering pigment distribution at the stand level scale, the pigment content observed from single view angles may not necessarily be representative of stand-level conditions as some constituents vary as a function of the degree of leaf illumination and are therefore not isotropic. As an alternative to mono-angle observations, multi-angular remote sensing can describe the anisotropy of surface reflectance and yield accurate information on canopy structure. These observations can also be used to describe the bi-directional reflectance distribution which then allows the modeling of reflectance independently of the observation geometry. In this paper, we demonstrate a method for estimating pigment contents of chlorophyll and carotenoids continuously over a year from tower-based, multi-angular spectro-radiometer observations. Estimates of chlorophyll and carotenoid content were derived at two flux-tower sites in western Canada. Pigment contents derived from inversion of a CR model (PROSAIL) compared well to those estimated using a semi-analytical approach (r ² = 0.90 and r ² = 0.69, P < 0.05 for both sites, respectively). Analysis of the seasonal dynamics indicated that net ecosystem productivity was strongly related to total canopy chlorophyll content at the deciduous site (r ² = 0.70, P < 0.001), but not at the coniferous site. Similarly, spectral estimates of photosynthetic light-use efficiency showed strong seasonal patterns in the deciduous stand, but not in conifers. We conclude that multi-angular, spectral observations can play a key role in explaining seasonal dynamics of fluxes of carbon and water and provide a valuable addition to flux-tower-based networks.     

Selection of control genes for quantitative RT-PCR based on microarray data

Use of internal reference gene(s) is necessary for adequate quantification of target gene expression by RT-PCR. Herein, we elaborated a strategy of control gene selection based on microarray data and illustrated it by analyzing endomyocardial biopsies with acute cardiac rejection and infection. Using order statistics and binomial distribution we evaluated the probability of finding low-varying genes by chance. For analysis, the microarray data were divided into two sample subsets. Among the first 10% of genes with the lowest standard deviations, we found 14 genes common to both subsets. After normalization using two selected genes, high correlation was observed between expression of target genes evaluated by microarray and RT-PCR, and in independent dataset by RT-PCR (r = 0.9, p < 0.001). In conclusion, we showed a simple and reliable strategy of selection and validation of control genes for RT-PCR from microarray data that can be easily applied for different experimental designs and tissues.     

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding

Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distributions and to derive rotamers, defined as the most probable conformation in a cluster. Six rotamer libraries were generated: full surface, surface noninterface, and surface interface-each for bound and unbound states. The libraries were used to calculate the probabilities of the rotamer transitions upon binding. The stability of amino acids was quantified based on the transition maps. The noninterface residues' stability was higher than that of the interface. Long side chains with three or four dihedral angles were less stable than the shorter ones. The transitions between the rotamers at the interface occurred more frequently than on the noninterface surface. Most side chains changed conformation within the same rotamer or moved to an adjacent rotamer. The highest percentage of the transitions was observed primarily between the two most occupied rotamers. The probability of the transition between rotamers increased with the decrease of the rotamer stability. The analysis revealed characteristics of the surface side-chain conformational transitions that can be utilized in flexible docking protocols.     

Accumulation of poly-(hydroxybutyrate) by a non-sulfur photosynthetic bacterium,Rhodobacter sphaeroides RV at different pH

Summary Effect of pH of culture media on intracellular accumulation of poly-(hydroxybutyrate) (PHB) by a non-sulfur photosynthetic bacterium, Rhodobacter sphaeroides strain RV was studied in pH-stat cultures. Sub-optimal pH for growth, 8.0 or 8.5 gave the higher content of PHB rather than optimal pH 7.5 for growth. These results show that growth and PHB accumulation of the bacteria can be controlled by pH of culture media.