Erratum to "Ecotoxicological impact of pharmaceuticals found in treated wastewaters: study of carbamazepine, clofibric acid, and diclofenac": [Ecotoxicol. Environ. Saf. 55 (2003) 359–370]

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Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

Introduction Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species. Methods We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol. Results The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates. Discussion Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices

Utilisation des communautés d’oligochètes pour l’évaluation de la qualité biologique et du fonctionnement des cours d’eau : un bilan à partir de données genevoises (Suisse)

Use of oligochaete communities for the assessment of the biological quality and the functioning of watercourses : a review of data from the Geneva area (Switzerland). – Oligochaetes are used in some cantons in Switzerland to assess the biological quality of watercourse and lake sediments. The oligochaete index of sediment bioindication (IOBS) allows to assess the quality of fine/sandy sediments of watercourses, while the Functional traits method (TRF) is dedicated to assess the quality of surficial coarse sediments and of the hyporheic zone. The TRF method also allows to know the dynamics of hydrological exchanges between surface water and groundwater. In the Geneva area, the IOBS index was applied in routine from 2008 to 2013 (92 samples) and the TRF method was tested in 2012 and 2013. The IOBS index proved to be a good bioindicator of chemical quality of the sediments. Metal toxicity thresholds in sediments were established and proposed. The implementation of the IOBS index in complement to the Swiss Biotic Index (IBCH) allowed to refine the ecological diagnostics. The TRF approach proved to be of great interest to simultaneously assess the biological quality of coarse habitats and of the vertical hydrological exchanges. The IOBS and TRF methods should be more integrated in the monitoring programs of watercourse quality. The current development of methods based on the identification of oligochaetes using genetic barcodes could allow to overcome the problems related to the morphological identification of species and a wider use of oligochaetes as bioindicators

Flux-noise spectra around the Kosterlitz-Thouless transition for two-dimensional superconductors

The flux-noise spectra around the Kosterlitz-Thouless transition are obtained from simulations of the two-dimensional resistively shunted junction model. In particular the dependence on the distance $d$ between the pick-up coil and the sample is investigated. The typical experimental situation corresponds to the large-$d$ limit and a simple relation valid in this limit between the complex impedance and the noise spectra is clarified. Features, which distinguish between the large- and small-$d$ limit, are identified and the possibility of observing these features in experiments is discussed.Comment: 12 pages including 8 figures, submitted to Phys. Rev.

Assessment of the effects of wastewater treatment plant effluents on receiving streams using oligochaete communities of the porous matrix

Human activities can disturb the natural dynamics of exchanges between surface water and groundwater in rivers. Such exchanges contribute to the self-purification of the environment and an excess of infiltration can lead to contamination of groundwater. In addition, the porous matrix (coarse surface sediments and hyporheic zone), through which water exchanges occur, is a sink for pollutants. For environmental monitoring programs, it is therefore essential to take into account both the dynamics of vertical hydrological exchanges and the biological quality of this matrix. The functional trait (FTR) method, which is based on the study of oligochaete communities in coarse surface sediments and the hyporheic zone, was proposed as a tool to simultaneously assess the dynamics of vertical hydrological exchanges and the effects of pollutants present in the porous matrix. Here, we applied this method during two different periods (in March and September 2016), upstream and downstream of locations affected by discharges from wastewater treatment plants (WWTP) located in Switzerland. The biological quality of surface sediments and the hyporheic zone was shown to be better upstream of the WWTP in both campaigns. In addition, results suggested that the capacity for self-purification was lower downstream of the WWTP, and that groundwater at these locations was vulnerable to pollution by surface water. The FTR method proved valuable as a field method for detecting the effects of point source contamination on receiving streams. In the near future, this community-based approach will benefit from advances in the use of DNA barcodes for oligochaete species identification

A note on quasinormal modes: A tale of two treatments

There is an apparent discrepancy in the literature with regard to the quasinormal mode frequencies of Schwarzschild-de Sitter black holes in the degenerate-horizon limit. On the one hand, a Poschl-Teller-inspired method predicts that the real part of the frequencies will depend strongly on the orbital angular momentum of the perturbation field whereas, on the other hand, the degenerate limit of a monodromy-based calculation suggests there should be no such dependence (at least, for the highly damped modes). In the current paper, we provide a possible resolution by critically re-assessing the limiting procedure used in the monodromy analysis.Comment: 11 pages, Revtex format; (v2) new addendum in response to reader comments, also references, footnote and acknowledgments adde

Gibbs' paradox and black-hole entropy

In statistical mechanics Gibbs' paradox is avoided if the particles of a gas are assumed to be indistinguishable. The resulting entropy then agrees with the empirically tested thermodynamic entropy up to a term proportional to the logarithm of the particle number. We discuss here how analogous situations arise in the statistical foundation of black-hole entropy. Depending on the underlying approach to quantum gravity, the fundamental objects to be counted have to be assumed indistinguishable or not in order to arrive at the Bekenstein--Hawking entropy. We also show that the logarithmic corrections to this entropy, including their signs, can be understood along the lines of standard statistical mechanics. We illustrate the general concepts within the area quantization model of Bekenstein and Mukhanov.Comment: Contribution to Mashhoon festschrift, 13 pages, 4 figure

More on N=1 Matrix Model Curve for Arbitrary N

Using both the matrix model prescription and the strong-coupling approach, we describe the intersections of n=0 and n=1 non-degenerated branches for quartic (polynomial of adjoint matter) tree-level superpotential in N=1 supersymmetric SO(N)/USp(2N) gauge theories with massless flavors. We also apply the method to the degenerated branch. The general matrix model curve on the two cases we obtain is valid for arbitrary N and extends the previous work from strong-coupling approach. For SO(N) gauge theory with equal massive flavors, we also obtain the matrix model curve on the degenerated branch for arbitrary N. Finally we discuss on the intersections of n=0 and n=1 non-degenerated branches for equal massive flavors.Comment: 36pp; to appear in JHE

Analytic calculation of quasi-normal modes

We discuss the analytic calculation of quasi-normal modes of various types of perturbations of black holes both in asymptotically flat and anti-de Sitter spaces. We obtain asymptotic expressions and also show how corrections can be calculated perturbatively. We pay special attention to low-frequency modes in anti-de Sitter space because they govern the hydrodynamic properties of a gauge theory fluid according to the AdS/CFT correspondence. The latter may have experimental consequencies for the quark-gluon plasma formed in heavy ion collisions.Comment: 33 pages, prepared for the proceedings of the 4th Aegean Summer School on Black Holes, Mytilene, Greece, September 200

The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography

Sporulation in Bacillus involves the induction of scores of genes in a temporally and spatially co-ordinated programme of cell development. Its initiation is under the control of an expanded two-component signal transduction system termed a phosphorelay. The master control element in the decision to sporulate is the response regulator, Spo0A, which comprises a receiver or phosphoacceptor domain and an effector or transcription activation domain. The receiver domain of Spo0A shares sequence similarity with numerous response regulators, and its structure has been determined in phosphorylated and unphosphorylated forms. However, the effector domain (C-Spo0A) has no detectable sequence similarity to any other protein, and this lack of structural information is an obstacle to understanding how DNA binding and transcription activation are controlled by phosphorylation in Spo0A. Here, we report the crystal structure of C-Spo0A from Bacillus stearothermophilus revealing a single alpha -helical domain comprising six alpha -helices in an unprecedented fold. The structure contains a helix-turn-helix as part of a three alpha -helical bundle reminiscent of the catabolite gene activator protein (CAP), suggesting a mechanism for DNA binding. The residues implicated in forming the sigma (A)-activating region clearly cluster in a flexible segment of the polypeptide on the opposite side of the structure from that predicted to interact with DNA. The structural results are discussed in the context of the rich array of existing mutational data