Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain

To ascertain the role of Zn(II) as an allosteric modulator on P2X4R, QM/MM molecular dynamic simulations were performed on the WT and two P2X4R mutants suggested by previous electrophysiological data to affect Zn(II) binding. The Gibbs free energy for the reduction of the putative P2X4R Zn(II) binding site by glutathione was estimated at −22 kcal/mol. Simulations of the WT P2X4R head domain revealed a flexible coordination sphere dominated by an octahedral geometry encompassing C126, N127, C132, C149, C159 and a water molecule. The C132A mutation disrupted the metal binding site, leading to a coordination sphere with a majority of water ligands, and a displacement of the metal ion towards the solvent. The C132A/C159A mutant exhibited a tendency towards WT-like stability by incorporating the R148 backbone to the coordination sphere. Thus, the computational findings agree with previous experimental data showing Zn(II) modulation for the WT and C132A/C159A variants, but not for the C132A mutant. The results provide molecular insights into the nature of the Zn(II) modulation in P2X4R, and the effect of the C132A and C132A/C159A mutations, accounting for an elusive modulation mechanism possibly occurring in other extracellular or membrane protein.     

Estimating effective degrees of freedom in motor systems.

Studies of the degrees of freedom and "synergies" in musculoskeletal systems rely critically on algorithms to estimate the "dimension" of kinematic or neural data. Linear algorithms such as principal component analysis (PCA) are the most popular. However, many biological data (or realistic experimental data) may be better represented by nonlinear sets than linear subspaces. We evaluate the performance of PCA and compare it to two nonlinear algorithms [Isomap and our novel pointwise dimension estimation (PD-E)] using synthetic and motion capture data from a robotic arm with known kinematic dimensions, as well as motion capture data from human hands. We find that PCA can lead to more accurate dimension estimates when considering additional properties of the PCA residuals, instead of the dominant method of using a threshold of variance captured. In contrast to the single integer dimension estimates of PCA and Isomap, PD-E provides a distribution and range of estimates of fractal dimension that identify the heterogeneous geometric structure in the experimental data. A strength of the PD-E method is that it associates a distribution of dimensions to the data. Since there is no a priori reason to assume that the sets of interest have a single dimension, these distributions incorporate more information than a single summary statistic. Our preliminary findings suggest that fewer than ten DOFs are involved in some hand motion tasks. Contrary to common opinion regarding fractal dimension methods, PD-E yielded reasonable results with reasonable amounts of data. Given the complex nature of experimental and biological data, we conclude that it is necessary and feasible to complement PCA with methods that take into consideration the nonlinear properties of biological systems for a more robust estimation of their DOFs.     

On capacity planning for the GMPLS network control plane

This article presents capacity planning rules for the control plane of all-optical networks featuring GMPLS and RSVP-TE as a connection setup protocol. As per RSVP standard, a refresh message mechanism is incorporated to RSVP such that the state is periodically refreshed on a link per link basis. We provide analytical expressions for the bandwidth and buffer sizes to be provided such that no flows are torn down due to lack of refresh messages. Our findings show that small buffers (several KBytes) suffice to sustain the signaling load for as much as 400 RSVP flows per link, with the simplest RSVP refresh mechanism (neither using link bundling nor acknowledgments). On the other hand, we also find the packet drop probability per link for a given network topology for the case that the flow survival probability is larger than a given threshold. We provide numerical examples based on the COST 239 european network topology and real RSVP traffic traces from early-commercial switching equipment.

Differentiation of co-winemaking wines by their aroma composition

Co-winemaked Monastrell wines with Cabernet Sauvignon or Merlot, at different proportions have been studied for first time in terms of its odor activity value (OAV) in young wines, aging wines (after 9 months in French oak barrels) and bottled aging wines (aging wines after 6 months in the bottle). The co-winemaking wines showed a different aromatic complexity as they were fruitier and sweeter than the monovarietal ones, enhancing their aroma characteristics, being more evident at 60:40 proportion in case of Merlot for young and aging wines and Cabernet Sauvignon for bottled ones. In terms of extractable oak compounds, Monastrell–Merlot wines showed the highest values suggesting that they may need a shorter period within the barrel than Monastrell–Cabernet Sauvignon ones.     

Antimicrobial activity of sub- and supercritical CO2 extracts of the green alga Dunaliella salina

The objective of this research was to evaluate the antimicrobial activity of carbon dioxide extracts of the unicellular biflagellated green alga Dunaliella salina against Escherichia coli, Staphylococcus aureus, Candida albicans, and Aspergillus niger. The effects of different extraction pressures ranging from 185 to 442 bar and extraction temperatures ranging from 9.8 to 45.2 degrees C on the extracts' composition and consequently on their antimicrobial activities were investigated. The extracts were analyzed by gas chromatography-mass spectrometry in order to identify the compounds responsible for the antimicrobial activity detected. Fourteen different volatile compounds and several fatty acids were identified. The highest antimicrobial activity was obtained using 314 bar and 9.8 degrees C. Under these conditions, the presence of an indolic derivative that had never been reported in D. salina was detected in the extract, together with polyunsaturated fatty acids and compounds related to carotene metabolism, such as beta-ionone and neophytadiene, with known antimicrobial activity.     

Differential effect of organic cultivation on the levels of phenolics,peroxidase and capsidiol in sweet peppers

BACKGROUND: Coincident with the changes in agricultural practices from conventional to organic, changes in the nutrient composition of fresh fruits and vegetables have been identified. The levels of peroxidase, total phenolics content, and capsidiol activity in organic as compared with conventional sweet pepper fruit were examined in this study. In order to avoid interferences of environmental factors on the studied parameters, the sweet peppers were grown (organically and conventionally) in a greenhouse under the same soil and climate conditions. RESULTS: Peroxidase was partially purified using the Triton X‐114 method and both organic and conventional peppers had the same isoenzymatic form. However, peroxidase activity in organic sweet peppers was higher than in conventional ones, in both maturity stages studied. The level of total phenolics compunds was also higher in organic than in conventional sweet peppers. With respect to the capsidiol activity, expressed as inhibition of fungus growth, it was not affected by the cultivation method at the green mature stage. However, at the red mature stage, organic sweet peppers showed higher capsidiol activity than those grown under the conventional system. CONCLUSION: Sweet peppers grown under organic culture have a maturity‐related response, with high levels of phenolic compounds, and peroxidase and capsidiol activity that contribute to disease resistance in organic farming. Copyright © 2007 Society of Chemical Industry