Analysis of the effect of copper on the virulence of a pathogenic Edwardsiella tarda strain

Aim: To investigate the effect of copper on the virulence of Edwardsiella tarda. Methods and Results: The pathogenic Edw. tarda strain TX5 was cultured under copper-stressed conditions and examined for any potential alteration in capacities that are associated with pathogenicity. The results showed that compared to untreated TX5, Cu-treated TX5 exhibits reduced planktonic and biofilm growth, an impaired ability to adhere to host mucus, modulation of host immune response, and dissemination in host blood and liver. Consistent with these observations, the overall bacterial virulence of Cu-treated TX5 is significantly attenuated. SDS-PAGE analyses of whole cell protein production showed that Cu-treated TX5 differs from the untreated TX5 in its production of at least one protein. Quantitative real time reverse transcriptase PCR analyses showed that copper treatment decreased the expression of virulence-associated genes encoding components of the type III and type VI secretion systems, the Eth haemolysin system, and the LuxS/AI-2 quorum-sensing system. Conclusions: Prolonged exposure to copper has multiple effects on TX5 and results in significant attenuation of bacterial virulence. Significance and Impact of the Study: The results of this study demonstrate that copper treatment has a broad and profound effect on the virulence-associated capacities of TX5, which is exerted at least in part at the transcription level. These findings provide new insights to the antimicrobial mechanism of copper.

Molecular analysis of the copper-responsive CopRSCD of a pathogenic Pseudomonas fluorescens strain

CopRS/CopABCD is one of the known systems that control copper homeostasis in bacteria. Although CopRS/CopABCD homologues are found to exist in Pseudomonas fluorescens, the potential role of this system in P. fluorescens has not been investigated. In this study a genetic cluster, consisting of copR, S, C, and D but lacking copAB, was identified in a pathogenic P. fluorescens strain (TSS) isolated from diseased fish. The copRSCD cluster was demonstrated to be required for full copper resistance and regulated at the transcription level by Cu. Expression of copCD is regulated directly by the two-component response regulator CopR, which also regulates its own expression. Interruption of the regulated expression of copR affected bacterial growth, biofilm formation, and tissue dissemination and survival. A mutant CopR, which lacks the N-terminal signal receiver domain and is constitutively active, was found to have an attenuating effect on bacterial virulence when expressed in TSS. To our knowledge, this is the first report that suggests a link between CopR and bacterial pathogenicity in P. fluorescens.

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

The contribution of trace elements from seawater to chimneys: a case study of the native sulfur chimneys in the sea area off Kueishantao, northeast of Taiwan Island

Hydrothermal fluid containing abundant matter erupts from seafloor, meets ambient cold seawater and forms chimneys. So the main matter origins of chimneys are seawater and matter which are taken by hydrothermal fluid from deep reservoir. However, because of seawater's little contribution to the forming of chimneys, it is usually covered by the abundant matter which is taken by hydrothermal fluid. Therefore, chimneys formed in ordinary deep seawater hydrothermal activity, containing complex elements, cannot be used to study the seawater's contribution to their formation. While the native sulfur chimneys, formed by hydrothermal activity near the sea area off Kueishantao, are single sulfur composition (over 99%), and within chimneys distinct layers are seen. Different layers were sampled for trace element determination, with Inductively Coupled Plasma Mass Spectrometry (ICP-MS). By analyzing the data, we consider C-layer (secondary inner-layer) as the framework layer of the chimney which formed early (Fig. 4), and its trace elements derive from hydrothermal fluid. While the trace elements within A, B, D layers have undergone later alteration. A, B layers are affected by seawater and D layer by hydrothermal fluid. The increase of trace elements of A and B layers was calculated using C layer as background. Based on the known typical volume of chimneys of the near sea area off Kueishantao, we calculated the volume of seawater that contributed trace element to chimneys formation to be about 6.37 x 10(4) L. This simple quantified estimate may help us better understand the seafloor hydrothermal activity and chimneys.

Simultaneous determination of four phases of copper in geological samples

According to the specific property of respective phases in copper ore, optimal extracting condition for, tour phases of copper with five infusion was examined. After a series of experiments, for example, different weight Of sample, artificial mixed single phases sample and repeated experiment, the extracting ratio constants foil all phases in different infusions were obtained. The mathematical model which is on the basis of the stable extracting constant is established. Based on the purpose-control genetic algorithms, we only need to determine the total copper in the sample in different infusions under the selected condition, then the value of respective phase could be calculated. The-relative standard deviation are (%) free oxidized copper phase:1.5, conjunction oxidized copper phase: 17.6,, secondary copper sulfide phase: 1.9, primary copper sulfide phase : 2.7,total copper: 0.8.

Origin of a native sulfur chimney in the Kueishantao hydrothermal field, offshore northeast Taiwan

Analyses of rare earth and trace element concentrations of native sulfur samples from the Kueishantao hydrothermal field were performed at the Seafloor Hydrothermal Activity Laboratory of the Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences. Using an Elan DRC II ICP-MS, and combining the sulfur isotopic compositions of native sulfur samples, we studied the sources and formation of a native sulfur chimney. The results show, when comparing them with native sulfur from crater lakes and other volcanic areas, that the native sulfur content of this chimney is very high (99.96%), the rare earth element (REE) and trace element constituents of the chimney are very low (Sigma REE < 21x10(-9)), and the chondrite-normalized REE patterns of the native sulfur samples are similar to those of the Kueishantao andesite, implying that the interaction of subseafloor fluid-andesite at the Kueishantao hydrothermal field was of short duration. The sulfur isotopic compositions of the native sulfur samples reveal that the sulfur of the chimney, from H2S and SO2, originated by magmatic degassing and that the REEs and trace elements are mostly from the Kueishantao andesite and partly from seawater. Combining these results with an analysis of the thermodynamics, it is clear that from the relatively low temperature (< 116 degrees C), the oxygenated and acidic environment is favorable for formation of this native sulfur chimney in the Kueishantao hydrothermal field.

Distribution and mobility of metals in agricultural soils near a copper smelter in South China

The distribution and mobility of heavy metals in the paddy soils surrounding a copper smelting plant in south China was investigated. We assessed the degree of metal contamination using an index of geoaccumulation. The metals were divided into two groups: (1) Cu, Zn, Pb and Cd, whose concentrations were heavily affected by anthropogenic inputs, and (2) Ni, Co and Cr, which were mainly of geochemical origin. Concentrations of Cu, Cd, Zn, and Pb in the polluted soils were higher than the Chinese soil quality criteria. The chemical partitioning patterns of Pb, Zn and Cu indicated that Pb was largely associated with the residual and NH2OH HCl extractable fractions. In contrast, Cd was predominantly associated with the MgCl2 extractable fraction. A large proportion of Cu was bound to the acidic H2O2 extractable fractions, while Zn was predominantly found in the residual phase. The fraction of mobile species, which potentially is the most harmful to the environment, was found to be elevated compared to unpolluted soils in which heavy metals are more strongly bound to the matrix. The mobility of the metals was studied by water extraction using a modification of Tessier's procedure, and the order of mobility was Zn > Cd > Cu > Ce > Pb.

Cloning, characterization, and expression analysis of extracellular copper/zinc superoxide dismutase gene from bay scallop Argopecten irradians

Extracellular superoxide dismutase (ECSOD) is a major extracellular antioxidant enzyme that protects organs from damage by reactive oxygen species (ROS). We cloned a novel ECSOD from the bay scallop Argopecten irradians (AiECSOD) by 3' and 5' RACE. The full-length cDNA of AiECSOD was 893 bp with a 657 bp open reading frame encoding 218 amino acids. The deduced amino acid sequence contained a putative signal peptide of 20 amino acids, and sequence comparison showed that AiECSOD had low degree of homology to ECSODs of other organisms. The genomic length of the AiECSOD gene was about 5276 bp containing five exons and six introns. The promoter region contained many putative transcription factor binding sites such as c-Myb, Oct-1, Sp1, Kruppel-like, c-ETS, NF kappa B, GATA-1, AP-1, and Ubx binding sites. Furthermore, tissue-specific expressions of AiECSOD and temporal expressions of AiECSOD in haemocytes of bay scallops challenged with bacteria Vibrio anguillarum were quantified using qRT-PCR. High levels of expression were detected in haemocytes, but not in gonad and mantle. The expression of AiECSOD reached the highest level at 12 h post-injection with V. anguillarum and then returned to normal between 24 h and 48 h post-injection. These results indicated that AiECSOD was an inducible protein and that it may play an important role in the immune responses against V anguillarum. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved.

Intracellular copper/zinc superoxide dismutase from bay scallop Argopecten irradians: Its gene structure, mRNA expression and recombinant protein

Superoxide dismutases are an ubiquitous family of enzymes that function to efficiently catalyze the dismutation of superoxide anions. Two unique and highly compartmentalized bay scallop Argopecten irradians superoxide dismutases: MnSOD and ecCuZnSOD, have been molecularly characterized in our previous study. To complete characterize the SOD family in A. irradians, a novel intracellular copper/zinc SOD from the A. irradians (Ai-icCuZnSOD) was obtained and characterized. The full-length cDNA of Ai-icCuZnSOD was 1047 bp with a 459 bp open reading frame encoding 152 amino acids. The genomic length of the Ai-icCuZnSOD gene was about 4279 bp containing 4 exons and 3 introns. The promoter region containing many putative transcription factor binding sites were analyzed. Furthermore, quantitative reverse transcriptase real-time PCR (qRT-PCR) analysis indicated that the highest expression of the Ai-icCuZnSOD was detected in gill and the expression profiles in hemocytes of bay scallops challenged with bacteria Vibrio anguillarum and lipopolysaccharide (LPS) were different. The result presented an increased expression after injection with LPS whereas no significant changes were observed after V. anguillarum injection. A fusion protein containing Ai-icCuZnSOD was produced in vitro. The rAi-icCuZnSOD is a stable enzyme, retaining more than 80% of its activity between 10 and 60 degrees C and keeping above 88% of its activity at pH values between 5.8 and 9. Ai-icCuZnSOD is more stable under alkaline than acidic conditions. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

Biosorption of copper(II) from aqueous solutions by green alga Cladophora fascicularis

Biosorption is an effective means of removal of heavy metals from wastewater. In this work the biosorption behavior of Cladophora fascicularis was investigated as a function of pH, amount of biosorbent, initial Cu2+ concentration, temperature, and co-existing ions. Adsorption equilibria were well described by Langmuir isotherm models. The enthalpy change for the biosorption process was found to be 6.86 kJ mol(-1) by use of the Langmuir constant b. The biosorption process was found to be rapid in the first 30 min. The presence of co-existing cations such as Na+, K+, Mg2+, and Ca2+ and anions such as chloride, nitrate, sulfate, and acetate did not significantly affect uptake of Cu2+ whereas EDTA substantially affected adsorption of the metal. When experiments were performed with different desorbents the results indicated that EDTA was an efficient desorbent for the recovery of Cu2+ from biomass. IR spectral analysis suggested amido or hydroxy, C=O, and C-O could combine strongly with Cu2+.

Biosorption of copper (II) and lead (II) from aqueous solutions by nonliving green algae Cladophora fascicularis: Equilibrium, kinetics and environmental effects

Biosorption of Cu2+ and Pb2+ by Cladophora fascicularis was investigated as a function of initial pH, initial heavy metal concentrations, temperature and other co-existing ions. Adsorption equilibriums were well described by Langmuir and Freundlich isotherm models. The maximum adsorption capacities were 1.61 mmol/ g for Cu2+ and 0.96 mmol/ g for Pb2+ at 298K and pH 5.0. The adsorption processes were endothermic and biosorption heats calculated by the Langmuir constant b were 39.0 and 29.6 kJ/ mol for Cu2+ and Pb2+, respectively. The biosorption kinetics followed the pseudo- second order model. No significant effect on the uptake of Cu2+ and Pb2+ by co-existing cations and anions was observed, except EDTA. Desorption experiments indicated that Na(2)EDTA was an efficient desorbent for the recovery of Cu2+ and Pb2+ from biomass. The results showed that Cladophora fascicularis was an effective and economical biosorbent material for the removal and recovery of heavy metal ions from wastewater.

Preparation of Dendritic Copper Nanostructures and Their Characterization for Electroreduction

Dendritic copper nanostructures of different morphologies were synthesized by a surfactant-free electrochemical method. Single crystal nature of the nanostructures was revealed from their X-ray diffraction and electron diffraction patterns. Mechanism of dendrite formation was discussed from thermodynamic aspects using the concept of supersaturation. Supersaturation of the copper metal reduced on the surface of the electrode was the crucial factor for the generation of different morphologies. Effects of applied potential, temperature, and the solution concentration on the supersaturation were studied. The NO3- and H2O2 electroreduction ability of the dendritic materials was tested. Use of copper dendrite-modified electrode as NO3- sensor was demonstrated.

Copper complexation by fulvic acid affects copper toxicity to the larvae of the polychaete Hydroides elegans

Copper toxicity is influenced by a variety of environmental factors including dissolved organic matter (DOM). We examined the complexation of copper by fulvic acid (FA), one of the major components of DOM, by measuring the decline in labile copper by anodic stripping voltammetrically (ASV). The data were described using a one-site ligand binding model, with a ligand concentration of 0.19 mu mol site mg(-1) C, and a logK' of 6.2. The model was used to predict labile copper concentration in a bioassay designed to quantify the extent to which Cu-FA complexation affected copper toxicity to the larvae of marine polychaete Hydroides elegans. The toxicity data, when expressed as labile copper concentration causing abnormal development, were independent of FA concentration and could be modeled as a logistic function, with a 48-h EC50 of 58.9 mu g 1(-1). However, when the data were expressed as a function of total copper concentration, the toxicity was dependent on FA concentration, with a 48-h EC50 ranging from 55.6 mu g 1(-1) in the no-FA control to 137.4 mu g 1(-1) in the 20 mg 1(-1) FA treatment. Thus, FA was protective against copper toxicity to the larvae, and such an effect was caused by the reduction in labile copper due to Cu-FA complexation. Our results demonstrate the potential of ASV as a useful tool for predicting metal toxicity to the larvae in coastal environment where DOM plays an important role in complexing metal ions. (c) 2007 Elsevier Ltd. All rights reserved.