The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

In-vitro study of the spontaneous calcification of PHEMA-based hydrogels in simulated body fluid

In-vitro calcification of poly(2-hydroxyethyl methacrylate) (PHEMA)-based hydrogels in simulated body fluid (SBF) under a steady/batch system without agitation or stirring the solutions has been investigated. It was noted that the formation of calcium phosphate (CaP) deposits primarily proceeded through spontaneous precipitation. The CaP deposits were found both on the surface and inside the hydrogels. It appears that the effect of chemical structure or reducing the relative number of oxygen atoms in the copolymers on the degree of calcification was only important at the early stage of calcification. The morphology of the CaP deposits was observed to be spherical aggregates with a thickness of the CaP layer less than 0.5 mu m. Additionally, the CaP deposits were found to be poorly crystalline or to have nano-size crystals, or to exist mostly as an amorphous phase. Characterization of the CaP phases in the deposits revealed that the deposits were comprised mainly of whitlockite [Ca9MgH(PO4)(7)] type apatite and DCPD (CaHPO4 center dot 2H(2)O) as the precursors of hydroxyapatite [Ca-10(PO4)(6)(OH)(2)]. The presence of carbonate in the deposits was also detected during the calcification of PHEMA based hydrogels in SBF solution.

Summer dormancy in Festuca arundinacea Schreb.; the influence of season of sowing and a simulated mid-summer storm on two contrasting cultivars

Due to the shortage of information on summer dormancy in tall fescue (Festuca arundinacea, syn. Lolium arundinaceum), we tested the response of 2 cultivars of differing dormancy expression and growth stage to a range of summer moisture conditions, including full irrigation, drought, and a simulated mid-summer storm and analysed whether traits associated with summer dormancy conferred better survival under severe field drought. Autumn-sown reproductive and younger, spring-sown plants of 2 cultivars, claimed to exhibit contrasting summer dormancy, were established and then tested in summer 2002 under either long drought, drought+ simulated mid-summer storm, or full irrigation. The autumn-sown reproductive plants of cv. Flecha exhibited traits that can be associated with partial summer dormancy since under summer irrigation they reduced aerial growth significantly and exhibited earlier herbage senescence. Moreover, cv. Flecha used 35% less soil water over the first summer. However, the water status of leaf bases of young vegetative tillers of both cultivars was similar under irrigation and also throughout most of the drought (leaf potential and water content maintained over -4MPa and at approx. 1 g H2O/g DM, respectively). The summer-active cv. Demeter did not stop leaf elongation even in drought and produced twice as much biomass as Flecha under irrigation. Cultivar Demeter responded to the simulated storm with a decline in dehydrin expression in leaf bases, whereas no decline occurred in Flecha, presumably because it remained partially dormant. The younger, spring-sown swards of both cultivars had similar biomass production under summer irrigation but whereas Demeter regrew in response to the simulated storm, cv. Flecha did not, indicating that dormancy, although only partially expressed, was reinforced by summer drought. In all trials, cv. Flecha out-yielded Demeter in autumn regrowth. In particular, the severe drought in 2003 caused a 25% loss of the basal cover in cv. Demeter, whereas Flecha fully maintained its sward allowing it to produce a higher post-drought autumn yield. This work links summer dormancy with higher persistence over long, dry summers.

Systematic inflammatory responses to maximal versus submaximal lengthening contractions of the elbow flexors

We compared changes in markers of muscle damage and systemic inflammation after submaximal and maximal lengthening muscle contractions of the elbow flexors. Using a cross-over design, 10 healthy young men not involved in resistance training completed a submaximal trial (10 sets of 60 lengthening contractions at 10% maximum isometric strength, 1 min rest between sets), followed by a maximal trial (10 sets of three lengthening contractions at 100% maximum isometric strength, 3 min rest between sets). Lengthening contractions were performed on an isokinetic dynamometer. Opposite arms were used for the submaximal and maximal trials, and the trials were separated by a minimum of two weeks. Blood was sampled before, immediately after, 1 h, 3 h, and 1-4 d after each trial. Total leukocyte and neutrophil numbers, and the serum concentration of soluble tumor necrosis factor-alpha receptor 1 were elevated after both trials (P < 0.01), but there were no differences between the trials. Serum IL-6 concentration was elevated 3 h after the submaximal contractions (P < 0.01). The concentrations of serum tumor necrosis factor-alpha, IL-1 receptor antagonist, IL-10, granulocyte-colony stimulating factor and plasma C-reactive protein remained unchanged following both trials. Maximum isometric strength and range of motion decreased significantly (P < 0.001) after both trials, and were lower from 1-4 days after the maximal contractions compared to the submaximal contractions. Plasma myoglobin concentration and creatine kinase activity, muscle soreness and upper arm circumference all increased after both trials (P < 0.01), but were not significantly different between the trials. Therefore, there were no differences in markers of systemic inflammation, despite evidence of greater muscle damage following maximal versus submaximal lengthening contractions of the elbow flexors.

The effect of music on monitoring a simulated anaesthetised patient with sonfication

The idea of sonifying anaesthetised patients’ vital signs is gaining acceptance, but some anaesthetists are concerned about additional noise in the operating theatre. We tested the effect of ambient music (jazz, classical and rock) on participants’ ability to monitor a simulated anaesthetised patient with sonification and visual monitors. Participants liked working with ambient music when workload was low. Participants preferred rock music, but reported working better with classical. Ambient music has less effect on participants’ ability to monitor the simulated patient than a distractor task does. We discuss practical implications of these findings.