Massive settlements of the Pacific oyster, <Emphasis Type="Italic">Crassostrea gigas</Emphasis>, in Scandinavia

The Pacific oyster (Crassostrea gigas) is an important aquaculture species world-wide. Due to its wide environmental tolerance and high growth rate, it has also become a successful invader in many areas, leading to major ecosystem changes. Low water temperatures were previously believed to restrict the establishment of Pacific oysters in Scandinavia. However, recent surveys reveal that the Pacific oyster is now established in many areas in Scandinavia. We present data on the current distribution, abundance and age-structure in Denmark, Sweden and Norway. The biomass of oysters in the Danish Wadden Sea increased from 1,056 to 6,264 tonnes between 2005 and 2007. Massive settlements were observed along the Swedish west coast in 2007, with densities >400 oysters per m⁻². In Norway, populations are established on the southern coast, and specimens have been found as far north as 60°N. The potential impacts and probable causes of this recent large-scale establishment are discussed.     

A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data

A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion. It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis. Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z’s) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z’s 774.5 and 775.5 with retention time of 14.1 min. This methodology enables extraction of chemical information from large data sets (>10⁸ entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.     

ET viewer: an application for predicting and visualizing functional sites in protein structures

SUMMARY: The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures. ETV is implemented using Java to run across different operating systems using Java Web Start technology. AVAILABILITY: The ETV is available for download from our website at http://mammoth.bcm.tmc.edu/traceview/index.html. This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail.     

Satellite-based mapping of the growing season and bioclimatic zones in Fennoscandia

Aim  To test whether satellite-derived NDVI values obtained during the growing season as delimited by the onset of phenological phases can be used to map bioclimatically a large region such as Fennoscandia.
Location  Fennoscandia north of about 58° N and neighbouring parts of NW Russia.
Methods  Phenology data on birch from 15 research stations and the half-monthly GIMMS-NDVI data set with 8 × 8 km² resolution from the period 1982–2002 were used to characterize the growing season. To link surface phenology with NDVI data, new algorithms on a pixel-by-pixel basis that show high correlation with phenophases on birch were developed. Then, time-integrated values (TI NDVI) during the phenologically defined growing season were computed to produce a bioclimatological map of Fennoscandia, which was tested and correlated with growing degree days (GDD) obtained from 20 meteorological stations. The map was also compared vs. traditional bioclimatic maps, and analysed for error factors distorting NDVI values.
Results  The correlation between GDD and TI NDVI data during the phenologically defined growing season was very high. Therefore, the TI NDVI map could be presented as a bioclimatic map reflecting GDD. However, several major areas have interfering factors distorting NDVI values, such as the pixel heterogeneity caused by the altitudinal mosaic in western Norway, the mosaic of lakes in southeastern Finland, and the agriculture-dominated areas in southern Fennoscandia.
Main conclusions  TI NDVI data from the phenologically defined growing season during 1982–2002 in Fennoscandia can be processed as a bioclimatic map reflecting GDD, except for the areas distorting NDVI values by their strong ground-cover heterogeneity.     

Interaction between smoking, GSTM1 deletion and colorectal cancer: results from the GSEC study

Cigarette smoking has inconsistently been associated with an increased risk of colorectal cancer. One of the enzymes responsible for the detoxification of the carcinogenic compounds present in tobacco smoke is glutathione S-transferase-μ (GST-μ). The gene that codes for this enzyme is GSTM1. In this study, we evaluated the associations and interaction between GSTM1 deletion, smoking behaviour and the development of colorectal cancer. We performed a pooled analysis within the International Collaborative Study on Genetic Susceptibility to Environmental Carcinogens (GSEC). We selected six studies on colorectal cancer, including 1130 cases and 2519 controls, and restricted our analyses to Caucasians because the number of patients from other races was too limited. In addition we performed a meta-analysis including the studies from the GSEC database and other studies identified on MEDLINE on the same subject. The prevalence of the GSTM1 null genotype was within the range reported in other studies: 51.8% of the cases had the GSTM1 null genotype versus 56.6% of the controls. No significant association between the GSTM1 null genotype and colorectal cancer was found (odds ratio 0.92, 95% confidence interval 0.73-1.14). Our results suggest a possible positive association between lack of the GST-μ enzyme and colorectal cancer for non-smoking women (odds ratio 1.47, 95% confidence interval 0.80-2.70). There was no interaction between the effects of smoking and GSTM1 genotype on colorectal cancer risk in men and women (χ²=0.007, p=0.97). Our findings do not support an association between the GSTM1 null genotype and colorectal cancer. In addition, we did not find any modification of the smoking-induced colorectal cancer risk by GSTM1 genotype     

Inhibition of very-low-density lipoprotein secretion by chloroquine, verapamil and monensin takes place in the Golgi complex

The effects of chloroquine, verapamil and monensin on secretion of very-low-density lipoproteins (VLDLs) were studied in cultured rat hepatocytes. Maximum inhibition of VLDL-triacylglycerol secretion by 50–90% of control was reached at 200 μM chloroquine, 200 μM verapamil and 5 μM monensin, whereas no effect on cellular triacylglycerol synthesis was observed. The inhibition could be seen within 15 min and was reversible after washout of the drugs. Chloroquine and verapamil inhibited both cellular protein synthesis and protein secretion, whereas monesin reduced protein secretion without any effect on protein synthesis. Control experiments with cycloheximide revealed that intact protein synthesis was not necessary for secretion of VLDL-triacylglycerol during 2 h. Electron micrographs of cells treated with chloroquine, verapamil or monensin showed swollen Golgi cisternae containing VLDL-like particles. By morphometry, a more than 2-fold increase in volume fractions and size indices of Golgi complexes and secondary lysosomes was observed, except that monensin had no significant effect on these parameters of secondary lysosomes. These results suggest that the inhibition of VLDL secretion by chloroquine, verapamil and monensin which takes place in the Golgi complex might be due to disruption of trans-membrane proton gradients. An increase in pH of acidic Golgi vesicles may cause swelling and disturb sorting and membrane flow through this organelle.     

Characterization of a stellate cell activation-associated protein (STAP) with peroxidase activity found in rat hepatic stellate cells

A proteome approach for the molecular analysis of the activation of rat stellate cell, a liver-specific pericyte, led to the discovery of a novel protein named STAP (stellate cell activation-associated protein). We cloned STAP cDNA. STAP is a cytoplasmic protein with molecular weight of 21,496 and shows about 40% amino acid sequence homology with myoglobin. STAP was dramatically induced in in vivo activated stellate cells isolated from fibrotic liver and in stellate cells undergoing in vitro activation during primary culture. This induction was seen together with that of other activation-associated molecules, such as smooth muscle alpha-actin, PDGF receptor-beta, and neural cell adhesion molecule. The expression of STAP protein and mRNA was augmented time dependently in thioacetamide-induced fibrotic liver. Immunoelectron microscopy and proteome analysis detected STAP in stellate cells but not in other hepatic constituent cells. Biochemical characterization of recombinant rat STAP revealed that STAP is a heme protein exhibiting peroxidase activity toward hydrogen peroxide and linoleic acid hydroperoxide. These results indicate that STAP is a novel endogenous peroxidase catabolizing hydrogen peroxide and lipid hydroperoxides, both of which have been reported to trigger stellate cell activation and consequently promote progression of liver fibrosis. STAP could thus play a role as an antifibrotic scavenger of peroxides in the liver.     

Calcium-dependent association of annexins with lipid bilayers modifies gramicidin A channel parameters

In order to examine whether calcium-dependent binding of annexin to acidic phospholipids could change the lipid bilayer environment sufficiently to perturb channel-mediated transmembrane ion-transport, gramicidin A channel activity in planar lipid bilayers was investigated in the presence of calcium and annexins II, III or V. The experiments were performed with membranes consisting of phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine in 300 mM KCl solution buffered to pH 7.4 and with either 0.1 or 1 mM calcium added to the solution. Annexin (1 microM) was subsequently applied to the cis side of the membrane. All three annexins (II, III and V) when tested at 1 mM calcium decreased the gramicidin single-channel conductance. Annexins II and III increased the mean lifetime of the channels whereas annexin V seemed to have no influence on the mean lifetime. Since the lifetime of gramicidin A channels is a function of the rate constant for dissociation of the gramicidin dimer, which is dependent on the physical properties of the lipid phase, binding of annexins II and III seems to stabilize the gramicidin channel owing to a change of the bilayer structure.