PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

Pretranslational regulation of the expression of the lipoprotein lipase (EC 3.1, l.34) gene by dietary fatty acids in the rat

Although there have been a number of studies of effects of diet and hormones on lipoprotein lipase (EC 3.1.1.34; LPL) activity and levels of LPL mRNA (Raynolds et al. 1990), there have been no studies which have investigated effects of different dietary fatty acids on LPL gene expression. In the present study male Wistar Albino rats were pair-fed diets containing 50 g fat/kg of different fatty acid composition for 2 weeks. The diets fed were (1) a mixed oil (450 g saturated fatty acids, 420 g monounsaturated fatty acids, 130 g polyunsaturated fatty acids/kg; n 8), (2) maize oil (n 8), or (3) fish oil (n 8). Animals were killed, RNA was extracted from liver and perirenal and epididymal fat pads, and analysed by ‘Northern methodology’. Samples were hybridized to a human cDNA probe for LPL (Gotoda et al. 1989). Two transcripts were identified in epididymai and perirenal adipose tissue which were approximately 3·7 and 1·7 kb in size. The results suggested that (1) fish oil-fed animals had significantly greater production of LPL mRNA in epididymai adipose tissue compared with maize oil-fed animals (P < 0·05), (2) maize oil-fed animals had significantly greater production of LPL mRNA in perirenal fat compared with the other dietary groups (P < 0·05), (3) expression in the liver was not significant. Rats fed on a fish oil diet had significantly reduced plasma triacylglycerol concentrations compared with the mixed-oil group (P < 0·05), but there were no significant differences in plasma cholesterol. The differences in LPL could not be explained directly by the changes in plasma immunoreactive-insulin and glucose-dependent insulinotrophic polypeptide levels in the three groups.

Simulating the effects of mid- to upper-tropospheric clouds on microwave emissions in EC-Earth using COSP

In this work, the Cloud Feedback Model Intercomparison (CFMIP) Observation Simulation Package (COSP) is expanded to include scattering and emission effects of clouds and precipitation at passive microwave frequencies. This represents an advancement over the official version of COSP (version 1.4.0) in which only clear-sky brightness temperatures are simulated. To highlight the potential utility of this new microwave simulator, COSP results generated using the climate model EC-Earth's version 3 atmosphere as input are compared with Microwave Humidity Sounder (MHS) channel (190.311 GHz) observations. Specifically, simulated seasonal brightness temperatures (TB) are contrasted with MHS observations for the period December 2005 to November 2006 to identify possible biases in EC-Earth's cloud and atmosphere fields. The EC-Earth's atmosphere closely reproduces the microwave signature of many of the major large-scale and regional scale features of the atmosphere and surface. Moreover, greater than 60 % of the simulated TB are within 3 K of the NOAA-18 observations. However, COSP is unable to simulate sufficiently low TB in areas of frequent deep convection. Within the Tropics, the model's atmosphere can yield an underestimation of TB by nearly 30 K for cloudy areas in the ITCZ. Possible reasons for this discrepancy include both incorrect amount of cloud ice water in the model simulations and incorrect ice particle scattering assumptions used in the COSP microwave forward model. These multiple sources of error highlight the non-unique nature of the simulated satellite measurements, a problem exacerbated by the fact that EC-Earth lacks detailed micro-physical parameters necessary for accurate forward model calculations. Such issues limit the robustness of our evaluation and suggest a general note of caution when making COSP-satellite observation evaluations.