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ABSTRACT European river basin authorities are responsible for the implementation of the new river basin management plans in accordance with the European Water Framework Directive. This paper presents a new methodology framework and approach to define and evaluate environmental flow regimes in the realistic complexities that exist with multiple water resource needs at a basin scale. This approach links river basin simulation models and habitat time series analysis to generate ranges of environmental flows (e-flows), which are evaluated by using habitat, hydropower production and reliability of water supply criteria to produce best possible alternatives. With the use of these tools, the effects of the proposed e-flows have been assessed to help in the consultation process. The possible effects analysed are impacts on water supply reliability, hydropower production and aquatic habitat. After public agreements, a heuristic optimization process was applied to maximize e-flows and habitat indicators, while maintaining a legal level of reliability for water resource demands. The final optimal e-flows were considered for the river basin management plans of the Duero river basin. This paper demonstrates the importance of considering quantitative hydrologic and ecological aspects of e-flows at the basin scale in addressing complex water resource systems. This approach merges standard methods such as physical habitat simulations and time series analyses for evaluating alternatives, with recent methods to simulate and optimize water management alternatives in river networks. It can be integrated with or used to complement other frameworks for e-flow assessments such as the In-stream Flow Incremental Methodology and Ecological Limits of Hydrologic Alteration. Copyright © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

We have computed the pKa’s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin $ \alpha$ -hemolysin, by using two types of input structures, namely the crystal structure of the heptameric $ \alpha$ -hemolysin and a set of over four hundred snapshots from a 4.38ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pKa of a given residue to small changes in the local structure. The calculated pKa are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements. [ABSTRACT FROM AUTHOR]

Nonstructural protein 2B of foot-and-mouth disease (FMD) virus (FMDV) is comprised of a small, hydrophobic, 154-amino-acid protein. Structurefunction analyses demonstrated that FMDV 2B is an ion channel-forming protein. Infrared spectroscopy measurements using partially overlapping peptides that spanned regions between amino acids 28 and 147 demonstrated the adoption of helical conformations in two putative transmembrane regions between residues 60 and 78 and between residues 119 and 147 and a third transmembrane region between residues 79 and 106, adopting a mainly extended structure. Using synthetic peptides, ion channel activity measurements in planar lipid bilayers and imaging of single giant unilamellar vesicles (GUVs) revealed the existence of two sequences endowed with membrane-porating activity: one spanning FMDV 2B residues 55 to 82 and the other spanning the C-terminal region of 2B from residues 99 to 147. Mapping the latter sequence identified residues 119 to 147 as being responsible for the activity. Experiments to assess the degree of insertion of the synthetic peptides in bilayers and the inclination angle adopted by each peptide regarding the membrane plane normal confirm that residues 55 to 82 and 119 to 147 of 2B actively insert as transmembrane helices. Using reverse genetics, a panel of 13 FMD recombinant mutant viruses was designed, which harbored nonconservative as well as alanine substitutions in critical amino acid residues in the area between amino acid residues 28 and 147. Alterations to any of these structures interfered with pore channel activity and the capacity of the protein to permeabilize the endoplasmic reticulum (ER) to calcium and were lethal for virus replication. Thus, FMDV 2B emerges as the first member of the viroporin family containing two distinct pore domains. [ABSTRACT FROM AUTHOR]