Comment on ``Piecewise potential vorticity inversion: Elementary tests''

Egger (2008) constructs some idealised experiments to test the usefulness of piecewise potential vorticity inversion (PPVI) in the diagnosis of Rossby wave dynamics and baroclinic development. He concludes that, ``PPVI does not help us to understand the dynamics of linear Rossby waves. It provides local tendencies of the streamfunction which are unrelated to the true ones. The same way, the motion of baroclinic waves in shear flow cannot be understood by using PPVI. Moreover, the effect of boundary temperatures as determined by PPVI is unrelated to the flow evolution.'' He goes further in arguing that we should not consider velocities as ``induced'' by PV anomalies defined by carving up the global domain. However, these conclusions partly reflect the limitations of his idealised experiments and the manner in which the PV components were partitioned from one another.

A high-order arbitrarily unstructured finite-volume model of the global atmosphere: tests solving the shallow-water equations

Simulations of the global atmosphere for weather and climate forecasting require fast and accurate solutions and so operational models use high-order finite differences on regular structured grids. This precludes the use of local refinement; techniques allowing local refinement are either expensive (eg. high-order finite element techniques) or have reduced accuracy at changes in resolution (eg. unstructured finite-volume with linear differencing). We present solutions of the shallow-water equations for westerly flow over a mid-latitude mountain from a finite-volume model written using OpenFOAM. A second/third-order accurate differencing scheme is applied on arbitrarily unstructured meshes made up of various shapes and refinement patterns. The results are as accurate as equivalent resolution spectral methods. Using lower order differencing reduces accuracy at a refinement pattern which allows errors from refinement of the mountain to accumulate and reduces the global accuracy over a 15 day simulation. We have therefore introduced a scheme which fits a 2D cubic polynomial approximately on a stencil around each cell. Using this scheme means that refinement of the mountain improves the accuracy after a 15 day simulation. This is a more severe test of local mesh refinement for global simulations than has been presented but a realistic test if these techniques are to be used operationally. These efficient, high-order schemes may make it possible for local mesh refinement to be used by weather and climate forecast models.

Does speciation impact on Cu uptake by, and toxicity to, the earthworm Eisenia fetida?

Eisenia fetida were exposed to different concentrations (0.009, 0.049 and 0. 125 mg L-1) of Cu in an aqueous medium. Cu speciation was manipulated through the addition of different concentrations (0. 15, 0.35 and 50 mg L-1) of EDTA. Cu speciation (as labile and non-labile pools) was determined using Differential Pulse Anodic Stripping Voltammetry. Labile Cu includes free Cu ions together with weak inorganic Cu complexes and a small fraction of easily dissociable organic complexes. Metal uptake and earthworm mortality increased with total Cu concentration in the EDTA free solutions. In the presence of EDTA both metal uptake and mortality decreased. These experiments demonstrate that Cu speciation governs uptake and consequent toxicity of Cu to E. fetida. (c) 2007 Elsevier Masson SAS. All rights reserved.

Effect of organic complexation on the toxicity of Cu to the earthworm Eisenia fetida

The relationship between Cu speciation in solution and mortality and tissue Cu concentrations in Eisenia fetida was investigated. E. fetida were exposed to solutions containing 0.009, 0.049 and 0.125 mg Cu L-1 and 0, 0.15, 0.35 and 50 mg EDTA L-1. Mortalities of 100, 60, 50 and 25% were recorded in the 0.125 mg Cu L-1 solutions containing 0, 0.15, 0.35 and 50 mg EDTA L-1, respectively. Similarly tissue body burden decreased with increasing EDTA concentration. Complexation capacity of the solution increased with EDTA concentration. In the 0.125 mg Cu L-1 solution labile Cu concentration decreased with increasing EDTA concentration. These trends are attributed to complexation of free Cu ions with EDTA molecules, and the non-bioavailable nature of the resultant Cu-EDTA complex. (C) 2007 Elsevier Ltd. All rights reserved.

Biosensor-based diagnostics of contaminated groundwater: assessment and remediation strategy

Shallow groundwater beneath a former airfield site in southern England has been heavily contaminated with a wide range of chlorinated solvents. The feasibility of using bacterial biosensors to complement chemical analysis and enable cost-effective, and focussed sampling has been assessed as part of a site evaluation programme. Five different biosensors, three metabolic (Vibrio fischeri, Pseudomonas fluorescens 10568 and Escherichia coli HB101) and two catabolic (Pseudomonas putida TVA8 and E. coli DH5alpha), were employed to identify areas where the availability and toxicity of pollutants is of most immediate environmental concern. The biosensors used showed different sensitivities to each other and to the groundwater samples tested. There was generally a good agreement with chemical analyses. The potential efficacy of remediation strategies was explored by coupling sample manipulation to biosensor tests. Manipulation involved sparging and charcoal treatment procedures to simulate remediative engineering solutions. Sparging was sufficient at most locations. (C) 2004 Elsevier Ltd. All rights reserved.

Measuring and modelling mixture toxicity of imidacloprid and thiacloprid on Caenorhabditis elegans and Eisenia fetida

While the standard models of concentration addition and independent action predict overall toxicity of multicomponent mixtures reasonably, interactions may limit the predictive capability when a few compounds dominate a mixture. This study was conducted to test if statistically significant systematic deviations from concentration addition (i.e. synergism/antagonism, dose ratio- or dose level-dependency) occur when two taxonomically unrelated species, the earthworm Eisenia fetida and the nematode Caenorhabditis elegans were exposed to a full range of mixtures of the similar acting neonicotinoid pesticides imidacloprid and thiacloprid. The effect of the mixtures on C. elegans was described significantly better (p<0.01) by a dose level-dependent deviation from the concentration addition model than by the reference model alone, while the reference model description of the effects on E. fetida could not be significantly improved. These results highlight that deviations from concentration addition are possible even with similar acting compounds, but that the nature of such deviations are species dependent. For improving ecological risk assessment of simple mixtures, this implies that the concentration addition model may need to be used in a probabilistic context, rather than in its traditional deterministic manner. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.

Survival, Pb-uptake and behaviour of three species of earthworm in Pb treated soils determined using an OECD-style toxicity test and a soil avoidance test

Mature (clitellate) Eisenia andrei Bouche (ultra epigeic), Lumbricus rubellus Hoffmeister (epigeic), and Aporrectodea caliginosa (Savigny) (endogeic) earthworms were placed in soils treated with Pb(NO3)(2) to have concentrations in the range 1000 to 10 000 mg Pb kg(-1). After 28 days LC50(-95%confidence limit) (+95%confidence limit) values were E. andrei 5824(-361)(+898) mg Pb kg(-1), L. rubellus 2867(-193)(+145) mg Pb kg(-1) and A. caliginosa 2747(-304)(+239) mg Pb kg(-1) and EC50s for weight change were E. andrei 2841(-68)(+150) Pb kg(-1), L. rubellus 1303(-201)(+204) mg Pb kg(-1) and A. caliginosa 1208(-206)(+212) Mg Pb kg(-1). At any given soil Pb concentration, Pb tissue concentrations after 28 days were the same for all three earthworm species. In a soil avoidance test there was no difference between the behaviour of the different species. The lower sensitivity to Pb exhibited by E. andrei is most likely due to physiological adaptations associated with the modes of life of the earthworms, and could have serious implications for the use of this earthworm as the species of choice in standard toxicological testing. (c) 2005 Elsevier Ltd. All rights reserved.

Inherited resistance to arsenate toxicity in two populations of Lumbricus rubellus

No unequivocal evidence exists of genetically inherited resistance to metals/metalloids in field populations of earthworms. We studied cocoon production in adult Lumbricus rubellus Hoffmeister collected from an abandoned arsenic and copper mine (Devon Great Consols, Devon, UK), and abandoned tungsten mine (Carrock Fell, Cumbria, UK) and an uncontaminated cultured population. The earthworms were kept in uncontaminated soil for nine weeks. From a total of 42 L. rubellus from each site, Devon Great Consols adults produced 301 cocoons, of which 42 were viable; Carrock Fell 60 cocoons, of which 11 were viable; and the reference population 101 cocoons, of which 62 were viable. The hatchlings were collected and stored at 4degreesC at weekly intervals. After 12 weeks, all hatchlings were transferred to clean soil and maintained at 15degreesC for 20 weeks until they showed evidence of a clitellum. In toxicity trials, F1 generation L. rubellus were exposed to 2,000 mg As/kg as sodium arsenate or 300 mg Cu/kg as copper chloride for 28 d. The F1 generation L. rubellus from Devon Great Consols mine demonstrated resistance to arsenate but not copper. All L. rubellus from Devon Great Consols kept in soil treated with sodium arsenate remained in good condition over the 28-d period but lost condition rapidly and suffered high mortality in soil treated with copper chloride. The control population suffered high mortality in soil treated with sodium arsenate and copper chloride. Previous work has shown that field-collected adults demonstrate resistance to both arsenate and Cu toxicity under these conditions. Thus, while arsenate resistance may be demonstrated in F1 generation L. rubellus from one of the contaminated sites, Cu resistance is not. The F1 adults and F2 cocoons did not have significantly higher levels of As than the control population, with no residual As tissue burden, suggesting that resistance to As in these populations may be inherited.

MEASUREMENT AND MODELING OF THE TOXICITY OF BINARY MIXTURES IN THE NEMATODE CAENORHABDITIS ELEGANS-A TEST OF INDEPENDENT ACTION

Ecological risk assessments must increasingly consider the effects of chemical mixtures on the environment as anthropogenic pollution continues to grow in complexity. Yet testing every possible mixture combination is impractical and unfeasible; thus, there is an urgent need for models that can accurately predict mixture toxicity from single-compound data. Currently, two models are frequently used to predict mixture toxicity from single-compound data: Concentration addition and independent action (IA). The accuracy of the predictions generated by these models is currently debated and needs to be resolved before their use in risk assessments can be fully justified. The present study addresses this issue by determining whether the IA model adequately described the toxicity of binary mixtures of five pesticides and other environmental contaminants (cadmium, chlorpyrifos, diuron, nickel, and prochloraz) each with dissimilar modes of action on the reproduction of the nematode Caenorhabditis elegans. In three out of 10 cases, the IA model failed to describe mixture toxicity adequately with significant or antagonism being observed. In a further three cases, there was an indication of synergy, antagonism, and effect-level-dependent deviations, respectively, but these were not statistically significant. The extent of the significant deviations that were found varied, but all were such that the predicted percentage effect seen on reproductive output would have been wrong by 18 to 35% (i.e., the effect concentration expected to cause a 50% effect led to an 85% effect). The presence of such a high number and variety of deviations has important implications for the use of existing mixture toxicity models for risk assessments, especially where all or part of the deviation is synergistic.

The fate and toxicity of the flavonoids naringenin and formononetin in soil

The flavonoid class of plant secondary metabolites play a multifunctional role in below-ground plant-microbe interactions with their best known function as signals in the nitrogen fixing legume-rhizobia symbiosis. Flavonoids enter rhizosphere soil as a result of root exudation and senescence but little is known about their subsequent fate or impacts on microbial activity. Therefore, the present study examined the sorptive behaviour, biodegradation and impact on dehydrogenase activity (as determined by iodonitrotetrazolium chloride reduction) of the flavonoids naringenin and formononetin in soil. Organic carbon normalised partition coefficients, log K-oc, of 3.12 (formononetin) and 3.19 (naringenin) were estimated from sorption isotherms and, after comparison with literature log K-oc values for compounds whose soil behaviour is better characterised, the test flavonoids were deemed to be moderately sorbed. Naringenin (spiked at 50 mu g g(-1)) was biodegraded without a detectable lag phase with concentrations reduced to 0.13 +/- 0.01 mu g g(-1) at the end of the 96 h time course. Biodegradation of formononetin proceeded after a lag phase of similar to 24 with concentrations reduced to 4.5 +/- 1% of the sterile control after 72 h. Most probable number (MPN) analysis revealed that prior to the addition of flavonoids, the soil contained 5.4 x 10(6) MPNg(-1) (naringenin) and 7.9 x 10(5) MPNg(-1) (formononetin) catabolic microbes. Formononetin concentration had no significant (p > 0.05) effect on soil dehydrogenase activity, whereas naringenin concentration had an overall but non-systematic impact (p = 0.045). These results are discussed with reference to likely total and bioavailable concentrations of flavonoids experienced by microbes in the rhizosphere. (c) 2007 Elsevier Ltd. All rights reserved.

Effect of acyl chain length on transfection efficiency and toxicity of polyethylenimine

Polyethylenimine (PEI) is an efficient nonviral gene delivery vector because of its high buffering capacity and DNA condensation ability. In our study, the amino groups on the polymeric backbone were acylated using acetic or propionic anhydride to alter the protonation behaviour and the hydrophilic/hydrophobic balance of the polymer. The concentration of acylated primary amines was determined using trinitrobenzene sulphonic acid assay. Results showed that our modified polymers had lower buffering capacities in solutions compared to PEI. The polymers were complexed with plasmid encoding enhanced green fluorescent protein at three different ratios (1:1, 1:2 and 1:10 w/w DNA to polymer) to form polyplexes and their toxicities and transfection efficiencies were evaluated in HEK 293 cells. Acylation reduced the number of primary amines on the polymer and the surface charge, improving haemocompatibility and reducing cytotoxicity. The reduction in the concentration of amino groups helped to optimise DNA compaction and facilitated polyplex dissociation in the cell, which increased transfection efficiency of the modified polymers compared to the parent polymer. Polymers with buffering capacities greater than 50% and less than 80% relative to PEI, showed higher transfection efficiencies than PEI. The propionic anhydride modified polymers had appropriate interactions with DNA which provided both DNA compaction and polyplex dissociation. These systems interacted better with the cell membrane because of their slightly higher lipophilicity and formed polyplexes which were less cytotoxic than polyplexes of acetic anhydride modified polymers. Among the vectors tested, 1:0.3 mol/mol PEI:propionic anhydride in a 1:2 w/w DNA:polymer composition provided the best transfection system with improved transfection efficiency and reduced cytotoxicity.

A capture–recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 × 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture–recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture–recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.