A Robust Water Potential Parameterisation

Abstract

We compare molecular dynamics simulation results for the properties of liquid water predicted by four novel water potential models. These models are designed as a combination of parameters taken from the dedicated but brittle TIP3P water potential, and the more flexible but less accurate parameterisations such as the Dreiding and Universal force fields. We find that a hybrid of Dreiding and TIP3P delivers the best results, yielding a density, diffusion coefficient and radial distribution function in good agreement with experiment, performing in some respects even better than the dedicated reference TIP3P model. Another Dreiding based force field predicts semi-quantitative results for the water structure and dynamics while the Universal force field based models are incapable of simulating a condensed phase of water at all, continuing to expand indefinitely. These observations are useful for selecting and designing robust water force field parameterisations that can be used for general simulation purposes.     

The ecosystem wilting point defines drought response and recovery of a Quercus-Carya forest

Soil and atmospheric droughts increasingly threaten plant survival and productivity around the world. Yet, conceptual gaps constrain our ability to predict ecosystem-scale drought impacts under climate change. Here, we introduce the ecosystem wilting point (Ψ_EWP), a property that integrates the drought response of an ecosystem's plant community across the soil–plant–atmosphere continuum. Specifically, Ψ_EWP defines a threshold below which the capacity of the root system to extract soil water and the ability of the leaves to maintain stomatal function are strongly diminished. We combined ecosystem flux and leaf water potential measurements to derive the Ψ_EWP of a Quercus-Carya forest from an “ecosystem pressure–volume (PV) curve,” which is analogous to the tissue-level technique. When community predawn leaf water potential (Ψ_pd) was above Ψ_EWP (=−2.0 MPa), the forest was highly responsive to environmental dynamics. When Ψ_pd fell below Ψ_EWP, the forest became insensitive to environmental variation and was a net source of carbon dioxide for nearly 2 months. Thus, Ψ_EWP is a threshold defining marked shifts in ecosystem functional state. Though there was rainfall-induced recovery of ecosystem gas exchange following soaking rains, a legacy of structural and physiological damage inhibited canopy photosynthetic capacity. Although over 16 growing seasons, only 10% of Ψ_pd observations fell below Ψ_EWP, the forest is commonly only 2–4 weeks of intense drought away from reaching Ψ_EWP, and thus highly reliant on frequent rainfall to replenish the soil water supply. We propose, based on a bottom-up analysis of root density profiles and soil moisture characteristic curves, that soil water acquisition capacity is the major determinant of Ψ_EWP, and species in an ecosystem require compatible leaf-level traits such as turgor loss point so that leaf wilting is coordinated with the inability to extract further water from the soil.     

Roughness of the plasma membrane as an independent morphological parameter to study RBCs: A quantitative atomic force microscopy investigation

A novel approach to the study of RBCs based on the collection of three-dimensional high-resolution AFM images and on the measure of the surface roughness of their plasma membrane is presented. The dependence of the roughness from several parameters of the imaging was investigated and a general rule for a trustful analysis and comparison has been suggested. The roughness of RBCs is a morphology-related parameter which has been shown to be characteristic of the single cells composing a sample, but independent of the overall geometric shape (discocyte or spherocyte) of the erythrocytes, thus providing extra-information with respect to a conventional morphology study. The use of the average roughness value as a label of a whole sample was tested on different kinds of samples. Analyzed data revealed that the quantitative roughness value does not change after treatment of RBCs with various commonly used fixation and staining methods while a drastic decrease occurs when studying cells with membrane-skeletal alteration both naturally occurring or artificially induced by chemical treatments. The present method provides a quantitative and powerful tool for a novel approach to the study of erythrocytes structure through an ultrastructural morphological analysis with the potential to give information, in a non-invasive way, on the RBCs function.     

Assessing the impact of episodic pollution

The increased tightening of controls on industrial and municipal wastewater discharges has resulted in steady improvements in the quality of many important rivers over recent years. However, episodic pollution, particularly from farm wastes and combined sewer overflows continues to pose a major problem, and is one of the main causes of poor quality rivers today. Despite our acknowledgement of this continuing problem, very little is known of the mechanistic basis of responses and recovery of aquatic organisms and communities exposed to intermittent pulses of common pollutants. The majority of ecotoxicological studies to date have been concerned with the effects of continuous exposure. Although such studies may provide a means of predicting the impact of episodic pollution events, a more appropriate test design would be to assess toxicity under pulsed and fluctuating exposure. Studies should also include a post-exposure observation period and should consider recovery of individuals and communities. This paper reviews the results of reported studies relevant to the investigation of episodic pollution and pays particular attention to the effects of magnitude, duration and frequency of exposure. Results of field investigations using an in situ bioassay technique are also presented to emphasize the importance of field validation of proposed water quality criteria for intermittent pollution events.     

Molecular Mechanisms of Polymyxin B-Membrane Interactions: Direct Correlation Between Surface Charge Density and Self-Promoted Transport

We have studied the interaction of the polycationic peptide antibiotic polymyxin B (PMB) with asymmetric planar bilayer membranes via electrical measurements. The bilayers were of different compositions, including those of the lipid matrices of the outer membranes of various species of Gram-negative bacteria. One leaflet, representing the bacterial inner leaflet, consisted of a phospholipid mixture (PL; phosphatidylethanolamine, -glycerol, and diphosphatidylglycerol in a molar ratio of 81:17:2). The other (outer) leaflet consisted either of lipopolysaccharide (LPS) from deep rough mutants of PMB-sensitive (Escherichia coli F515) or -resistant strains (Proteus mirabilis R45), glycosphingolipid (GSL-1) from Sphingomonas paucimobilis IAM 12576, or phospholipids (phosphatidylglycerol, diphytanoylphosphatidylcholine). In all membrane systems, the addition of PMB to the outer leaflet led to the induction of current fluctuations due to transient membrane lesions. The minimal PMB concentration required for the induction of the lesions and their size correlated with the charge of the lipid molecules. In the membrane system resembling the lipid matrix of a PMB-sensitive strain (F515 LPS/PL), the diameters of the lesions were large enough (d= 2.4 nm ± 8%) to allow PMB molecules to permeate (self-promoted transport), but in all other systems they were too small. A comparison of these phenomena with membrane effects induced by detergents (dodecyltriphenylphosphonium bromide, dodecyltrimethylammonium bromide, sodiumdodecylsulfate) revealed a detergent-like mechanism of the PMB-membrane interaction. Received: 16 September 1997/Revised: 25 November 1997     

Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.

Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the 1H, 13C, and 15N resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded 1H epsilon 2 of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 x 10(-5) s-1 at pH*7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pKa of His 156 is unperturbed at approximately 6.5, as measured from the pH dependence of the 15N- and 1H-NMR spectra of BCX. In contrast, His 149 has a pKa < 2.3, existing in the neutral N epsilon 2H tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX.     

Effects of sand bar openings on some limnological variables in a hypertrophic tropical coastal lagoon of Brazil

This study describes the spatial and temporal dynamics of several physical, chemical and biological variables in the Grussai lagoon, and their relationship to ephemeral sand bar openings and to a constant in natura waste water input. The spatial variation in pH, dissolved oxygen, electrical conductivity, total alkalinity and nutrients (e.g. soluble reactive silicate, soluble reactive phosphate and ammonium) was associated to the anoxic and nutrient rich groundwater discharge, the development of aquatic macrophytes, the biological activities of phytoplanktonic community and the marine influence. During the period when the sand bar was closed (isolated), the lagoon water was supersaturated with dissolved oxygen and exhibited high values of pH (8–10), total alkalinity (3.000–5.000 μeq l^-1), and chlorophyll a contents (60-300 μg l^-1), and had low values of dissolved nutrients (nearly undetectable). These suggest a biological processes dominance. When the sand bar was opened, there was an enrichment with dissolved inorganic nutrients (e.g. ammonium and soluble reactive phosphorus up to 120 and 5 μM, respectively) and a decrease in pH (below 8), total alkalinity (below 3.000 μeq l^-1) and dissolved oxygen during the initial second to eight days. Subsequently there was a period when the physical and chemical characteristics of seawater prevailed. The lagoon returned chemical to the pre-opening water conditions in a few days (∼ 10–20). This quick return implies highly efficient biological mechanisms. The high levels of chlorophyll a, total nitrogen and phosphorus in the water column indicate a high eutrophication stage in the Grussai lagoon during the sand bar closed periods. This revised version was published online in July 2006 with corrections to the Cover Date.     

基于传统生态智慧的江南水网空间韧性机制及实践启示

传统江南水网空间是一种典型的社会—生态系统,人文社会系统和自然生态系统之间的良性互动对于其韧性构建有着重要的积极作用。基于柯林斯等人提出的压力—冲击动态（PPD）模型,以平江府为典型代表,研究传统江南水网空间如何通过生态系统服务的桥梁搭建水网物质空间与人类社区发展之间的联系,从而厘清社会—生态系统在此过程中如何培育、优化和提升江南水网空间韧性。在此基础上,创新性地从生态系统服务供需关系的角度提出社会—生态韧性构建的生态智慧,并倡导以恢复力、适应力与变革力韧性机制培育为导向的、江南地区构建现代社区实践的若干启示,旨在引导江南水网空间实现具有韧性的社会—生态系统转型发展。     

Hydraulic architecture and water relations of Spartium junceum branches affected by a mycoplasm disease

Plant water relations, xylem anatomy and the hydraulic architecture of 1‐year‐old twigs of Spartium junceum, both healthy and affected by a phytoplasm disease, were studied. The disease causes twigs to be either shortened (witches broom disease, WBD) or flat (fasciate disease, FD). WBD twigs show a sevenfold increase in total leaf area, smaller and shorter xylem conduits, a higher stomatal conductance (g_l) and a decline of minimum leaf water potentials ( Ψ _l) below the turgor loss point. FD twigs had nearly twice the leaf area of the healthy controls as well as high g_l values and Ψ _l values below the turgor loss point. Moreover, significant differences between healthy and affected twigs in stem stomatal conductance (g_s) and in the total stem area were recorded. Affected twigs die back under drought stress, which is explained by a pronounced loss of hydraulic conductivity of the infected stems (40 and 60%) in FD and WBD as well as by the unfavourable ratio of weighted conduit radius ( Σ r⁴) to total surface area (A_t), so that the efficiency of the stem in supplying the whole transpiring area with water is strongly reduced.     

Impact of microorganisms,humidity, and temperature on the enantioselective degradation of imazethapyr in two soils

Imazethapyr (IM) is a chiral herbicide composed of an (−)‐R‐enantiomer and an (+)‐S‐enantiomer with differential herbicidal activity. In this study, the effects of microbial organisms, humidity, and temperature on the selective degradation of the (−)‐R‐ and (+)‐S‐enantiomers of IM were determined in silty loam (SL) and clay loam (CL) soil with different pH values. The (−)‐R‐enantiomer of IM was preferentially degraded in two soils under different microorganism, humidity, and temperature conditions. The average half‐lives of R‐IM ranged from 43 to 66.1 days and were significantly shorter (P <  0.05) than those of S‐IM, which ranged from 51.4 to 79.8 days. The enantiomer fraction (EF = (+)‐S‐enantiomer/((−)‐R‐enantiomer + (+)‐S‐enantiomer)) values were used to describe the enantioselectivity of degradation of IM were >0.5 (P <  0.05) in two unsterilized soils under different humidity and temperature conditions. The highest EF values were observed at unsterilized CL soil samples under 50% maximum water‐holding capacity (MWHC) and 25 °C environmental conditions. The EF values of the IM enantiomers were significantly higher (P <  0.05) in CL soils (higher pH = 5.81) and were 0.581 (unsterilized) and 0.575 (50% MWHC; 25 °C) compared with those recorded in SL soil (lower pH = 4.85). In addition, this study revealed that microbial organisms preferentially utilized the more herbicidal active IM enantiomer.