The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.

The aim of this study was to analyze the influence of moderate endurance training on a set of physiological parameters accompanying menopausal transition. One hundred sixty-eight women participated in the study. The cohort was divided into three subgroups: premenopausal, perimenopausal, and postmenopausal. A 12-week moderate intensity Nordic Walking program was administered to the cohort. The changes in body mass index (BMI), total fat mass (TF), low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglycerides (TGs), and waist circumference (WC) were assessed by means of appropriate statistical methods. Significant differences are observed in VO2max and cholesterol levels as a function of age, both ovarian and chronological. BMI, TF, LDL, HDL, TGs, and WC also fluctuate, however insignificantly, as a function of age. Administration of a 12-week Nordic Walking program results in significant changes in the parameters studied. The only exception is HDL level in postmenopausal women. Significant decreases in BMI, TF, LDL, TGs, and WC and increase in HDL in premenopausal and perimenopausal women indicate the outstanding role the appropriately chosen moderate endurance training may play in the quality of daily life in perimenopausal women.

Molecular dynamics (MD) simulations were performed to investigate the structure of a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer in liquid-crystalline (fluid) phase at 30 °C. The bilayer consists of 200 DMPC lipid molecules with nw=27.4 water molecules per lipid. The membrane was built with reference to the coordinates of a previously published 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane patch. A four-step dynamic procedure (110 ps) with Berendsen pressure rescaling (P=0 and 1 bar), applied in all three directions, was used to rapidly prepare the bilayer. This system was then subjected to two separate constant pressure and temperature simulations at 1 bar and 30 °C for ∼380 ps, using the Nosé–Hoover NPT method with periodical boundaries and Berendsen temperature and pressure rescaling method, respectively. The resultant bilayer has an area per lipid of 59.2 Å2 and a head-to-head thickness (DHH) of 36.3 Å. These values are in good agreement with the x-ray diffraction data of 59.7 Å2 and 34.4 Å, respectively, for DMPC at 30 °C with nw of 25.7 [H. I. Petrache, S. Tristram-Nagle, and J. F. Nagle, Chem. Phys. Lipids 95, 83 (1998)]. The fractions of trans and gauche bonds in the hydrocarbon chains, averaged for the last 94 ps of simulation, are 81.7% and 18.3%, respectively, suggesting a fluid phase of the membrane. The electron density profile resembles closely that measured by x-ray diffraction. Water density profile suggests a significant penetration of water molecules into the bilayer head region to as deep as the carbonyl groups, with phosphate groups being strongly hydrated.