Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.

Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC) are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.

Linking selective chemical extraction of iron oxyhydroxides to arsenic bioaccessibility in soil.

The relationship between As bioaccessibility using the physiologically based extraction test (PBET) and As extracted by hydroxylamine hydrochloride (HH), targeting the dissolution of amorphous Fe oxyhydroxides, is established in soils from the British Geological Survey Geochemical Baseline Survey of SW England, UK, to represent low As background and high As mineralised/mined soils. The HH-extracted As was of the same order of magnitude as the As extracted in the bioaccessibility test and proved to be a better estimate of bioaccessible As than total As (bioaccessible As - total As: r = 0.955; bioaccessible As - HH-extracted As: r = 0.974; p-values = 0.000). These results provide a means of estimating soil As bioaccessibility on the basis of the HH extraction. Further selective extraction data, using hydrochloride acid that seeks to dissolve both amorphous and crystalline Fe oxyhydroxides, indicates a decrease in the As bioaccessible fraction with the increase of the soil Fe oxyhydroxide crystallinity.

Methodology for the determination of normal background concentrations of contaminants in English soil.

The revised Environmental Protection Act Part 2A contaminated land Statutory Guidance (England and Wales) makes reference to 'normal' levels of contaminants in soil. The British Geological Survey has been commissioned by the United Kingdom Department for Environment, Food and Rural Affairs (Defra) to estimate contaminant levels in soil and to define what is meant by 'normal' for English soil. The Guidance states that 'normal' levels of contaminants are typical and widespread and arise from a combination of both natural and diffuse pollution contributions. Available systematically collected soil data sets for England are explored for inorganic contaminants (As, Cd, Cu, Hg, Ni and Pb) and benzo[a]pyrene (BaP). Spatial variability of contaminants is studied in the context of the underlying parent material, metalliferous mineralisation and associated mining activities, and the built (urban) environment, the latter being indicative of human activities such as industry and transportation. The most significant areas of elevated contaminant concentrations are identified as contaminant domains. Therefore, rather than estimating a single national contaminant range of concentrations, we assign an upper threshold value to contaminant domains. Our representation of this threshold is a Normal Background Concentration (NBC) defined as the upper 95% confidence limit of the 95th percentile for the soil results associated with a particular domain. Concentrations of a contaminant are considered to be typical and widespread for the identified contaminant domain up to (and including) the calculated NBC. A robust statistical methodology for determining NBCs is presented using inspection of data distribution plots and skewness testing, followed by an appropriate data transformation in order to reduce the effects of point source contamination.

Effect of weathering product assemblages on Pb bioaccessibility in mine waste: implications for risk management.

General assessments of orebody types and associated mine wastes with regard to their environmental signature and human health hazards are needed to help in managing present and historical mine waste facilities. Bioaccessibility tests and mineralogical analysis were carried out on mine waste from a systematic sampling of mine sites from the Central Wales orefield, UK. The bioaccessible Pb widely ranged from 270 to 20,300 mg/kg (mean 7,250 mg/kg, median 4,890 mg/kg), and the bioaccessible fraction from 4.53 to >100% (mean 33.2%, median 32.2%), with significant (p=0.001) differences among the mine sites. This implies sensitivity of bioaccessibility to site-specific conditions and suggests caution in the use of models to assess human health impacts generalised on the basis of the mineral deposit type. Mineralogical similarities of the oxidation products of primary galena provided a better control over the observed Pb bioaccessibility range. The higher Pb bioaccessibility (%) was related to samples containing cerussite, irrespective of the presence of other Pb minerals in the mineral assemblage; lower Pb bioaccessibility resulted where anglesite was the main Pb mineral phase and cerussite was absent. A solubility diagram for the various Pb minerals in the waste was derived using PHREEQC model, and the experimental Pb concentrations, measured in the simulated gastric solution, were compared with the equilibrium modelling results. For samples containing cerussite, the model well predicted the soluble Pb concentrations measured in the gastric solution, indicative of the carbonate mineral phase control on the Pb in solution for these samples and little kinetic control on the dissolution of cerussite. On the contrary, most mine waste samples containing dominant anglesite and or plumbojarosite (no cerussite) had lower solution Pb values, falling at or below the anglesite and plumbojarosite solubility equilibrium concentrations, implying kinetic or textural factors hindering the dissolution.

Nucleolar protein trafficking in response to HIV-1 Tat: rewiring the nucleolus.

The trans-activator Tat protein is a viral regulatory protein essential for HIV-1 replication. Tat trafficks to the nucleoplasm and the nucleolus. The nucleolus, a highly dynamic and structured membrane-less sub-nuclear compartment, is the site of rRNA and ribosome biogenesis and is involved in numerous cellular functions including transcriptional regulation, cell cycle control and viral infection. Importantly, transient nucleolar trafficking of both Tat and HIV-1 viral transcripts are critical in HIV-1 replication, however, the role(s) of the nucleolus in HIV-1 replication remains unclear. To better understand how the interaction of Tat with the nucleolar machinery contributes to HIV-1 pathogenesis, we investigated the quantitative changes in the composition of the nucleolar proteome of Jurkat T-cells stably expressing HIV-1 Tat fused to a TAP tag. Using an organellar proteomic approach based on mass spectrometry, coupled with Stable Isotope Labelling in Cell culture (SILAC), we quantified 520 proteins, including 49 proteins showing significant changes in abundance in Jurkat T-cell nucleolus upon Tat expression. Numerous proteins exhibiting a fold change were well characterised Tat interactors and/or known to be critical for HIV-1 replication. This suggests that the spatial control and subcellular compartimentaliation of these cellular cofactors by Tat provide an additional layer of control for regulating cellular machinery involved in HIV-1 pathogenesis. Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. We present here the first differential profiling of the nucleolar proteome of T-cells expressing HIV-1 Tat. We discuss how these proteins collectively participate in interconnected networks converging to adapt the nucleolus dynamic activities, which favor host biosynthetic activities and may contribute to create a cellular environment supporting robust HIV-1 production.

Limited effect on NS3-NS4A protein cleavage after alanine substitutions within the immunodominant HLA-A2-restricted epitope of the hepatitis C virus genotype 3a non-structural 3/4A protease.

It has been well established that immunological escape mutations within the hepatitis C virus genotype (gt) 1a non-structural (NS) 3/4A protease are partly prevented by a reduction in viral protease fitness. Surprisingly little is known about whether similar mutations affect proteases from other genotypes. In the present study, we assessed both the HLA-A2-restricted CTL response and gt3a NS3/4A protease fitness. Similar to gt1, the 1073-1081 epitope was immunodominant within the gt3a-specific HLA-A2-restricted CTL response, despite sequence similarity of only 56 % between the gt1a and gt3a genes. However, unlike the gt1a NS3/4A protease, all residues within the gt3a 1073-1081 epitope could be replaced sequentially by alanine while retaining protease activity, at least in part.

Impact of gut passage and mucus secretion by the earthworm Lumbricus terrestris on mobility and speciation of arsenic in contaminated soil.

Earthworms inhabiting arsenic contaminated soils may accelerate the leaching of As into surface and ground waters. We carried out three experiments to determine the impact of passage of As contaminated soil (1150 mg As kg(-1)) through the gut of the earthworm Lumbricus terrestris on the mobility and speciation of As and the effects of earthworm mucus on As mobility. The concentration of water soluble As in soil increased (from 1.6 to 18 mg kg(-1)) after passage through the earthworm gut. Casts that were aged for 56 days still contained more than nine times greater water soluble As than bulk earthworm inhabited soil. Changes were due to increases in As(V) mobility, with no change in As(III). Dilute mucus extracts reduced As mobility through the formation of As-amino acid-iron oxide ternary complexes. More concentrated mucus extracts increased As mobility. These changes, together with those due to the passage through the gut, were due to increases in pH, phosphate and soluble organic carbon. The mobilisation of As from contaminated soils in the environment by cast production and mucus secretion may allow for accelerated leaching or uptake into biota which is underestimated when bulk soil samples are analysed and the influence of soil biota ignored.

Metabolomic profile of hepatitis C virus-infected hepatocytes.

Hepatitis C virus (HCV) is capable of disrupting different facets of lipid metabolism and lipids have been shown to play a crucial role in the viral life cycle. The aim of this study was to examine the effect HCV infection has on the hepatocyte metabolome. Huh-7.5 cells were infected using virus produced by the HCV J6/JFH1 cell culture system and cells were harvested 24, 48, and 72-hours following infection. Metabolic profiling was performed using a non-targeted multiple platform methodology combining ultrahigh performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS(2)) and gas chromatography/mass spectrometry (GC/MS). There was a significant increase in a number of metabolites involved in nucleotide synthesis and RNA replication during early HCV infection. NAD levels were also significantly increased along with several amino acids. A number of lipid metabolic pathways were disrupted by HCV infection, resulting in an increase in cholesterol and sphingolipid levels, altered phospholipid metabolism and a possible disruption in mitochondrial fatty acid transport. Fluctuations in 5'-methylthioadenosine levels were also noted, along with alterations in the glutathione synthesis pathway. These results highlight a number of previously unreported metabolic interactions and give a more in depth insight into the effect HCV has on host cell biochemical processes.

Impact of earthworms on trace element solubility in contaminated mine soils amended with green waste compost.

The common practice of remediating metal contaminated mine soils with compost can reduce metal mobility and promote revegetation, but the effect of introduced or colonising earthworms on metal solubility is largely unknown. We amended soils from an As/Cu (1150 mg As kg(-1) and 362 mg Cu kg(-1)) and Pb/Zn mine (4550 mg Pb kg(-1) and 908 mg Zn kg(-1)) with 0, 5, 10, 15 and 20% compost and then introduced Lumbricus terrestris. Porewater was sampled and soil extracted with water to determine trace element solubility, pH and soluble organic carbon. Compost reduced Cu, Pb and Zn, but increased As solubility. Earthworms decreased water soluble Cu and As but increased Pb and Zn in porewater. The effect of the earthworms decreased with increasing compost amendment. The impact of the compost and the earthworms on metal solubility is explained by their effect on pH and soluble organic carbon and the environmental chemistry of each element.

Impacts of epigeic, anecic and endogeic earthworms on metal and metalloid mobility and availability.

The introduction of earthworms into soils contaminated with metals and metalloids has been suggested to aid restoration practices. Eisenia veneta (epigeic), Lumbricus terrestris (anecic) and Allolobophora chlorotica (endogeic) earthworms were cultivated in columns containing 900 g soil with 1130, 345, 113 and 131 mg kg(-1) of As, Cu, Pb and Zn, respectively, for up to 112 days, in parallel with earthworm-free columns. Leachate was produced by pouring water on the soil surface to saturate the soil and generate downflow. Ryegrass was grown on the top of columns to assess metal uptake into biota. Different ecological groups affected metals in the same way by increasing concentrations and free ion activities in leachate, but anecic L. terrestris had the greatest effect by increasing leachate concentrations of As by 267%, Cu by 393%, Pb by 190%, and Zn by 429% compared to earthworm-free columns. Ryegrass grown in earthworm-bearing soil accumulated more metal and the soil microbial community exhibited greater stress. Results are consistent with earthworm enhanced degradation of organic matter leading to release of organically bound elements. The degradation of organic matter also releases organic acids which decrease the soil pH. The earthworms do not appear to carry out a unique process, but increase the rate of a process that is already occurring. The impact of earthworms on metal mobility and availability should therefore be considered when inoculating earthworms into contaminated soils as new pathways to receptors may be created or the flow of metals and metalloids to receptors may be elevated.

Impact of the earthworm Lumbricus terrestris (L.) on As, Cu, Pb and Zn mobility and speciation in contaminated soils.

To assess the risks that contaminated soils pose to the environment properly a greater understanding of how soil biota influence the mobility of metal(loid)s in soils is required. Lumbricus terrestris L. were incubated in three soils contaminated with As, Cu, Pb and Zn. The concentration and speciation of metal(loid)s in pore waters and the mobility and partitioning in casts were compared with earthworm-free soil. Generally the concentrations of water extractable metal(loid)s in earthworm casts were greater than in earthworm-free soil. The impact of the earthworms on concentration and speciation in pore waters was soil and metal specific and could be explained either by earthworm induced changes in soil pH or soluble organic carbon. The mobilisation of metal(loid)s in the environment by earthworm activity may allow for leaching or uptake into biota.

Phenotypic characterization of lymphocytes in HCV/HIV co-infected patients.

While hepatitis C virus (HCV)-specific immune responses are attenuated in HCV/HIV co-infected patients compared to those infected with HCV alone, the reasons for this remain unclear. In this study, the proportions of regulatory, naïve, and memory T cells, along with chemokine receptor expression, were measured in co-infected and mono-infected patients to determine if there is an alteration in the phenotypic profile of lymphocytes in these patients. HCV/HIV co-infected patients had increased proportions of CD4(+) naïve cells and decreased proportions of CD4(+) effector cells when compared to HCV mono-infected patients. The proportions of CD4(+) Tregs and CD4(+) CXCR3(+) T cells were also significantly lower in co-infected patients. A decrease in CD4(+) Tregs and subsequent loss of immunosuppressive function may contribute to the accelerated progression to liver disease in co-infected individuals. Dysregulation of immune responses following reduction in the proportions of CD4(+) CXCR3(+) Th-1 cells may contribute to the reduced functional capacity of HCV-specific immune responses in co-infected patients. The findings of this study provide new information on the T-cell immunophenotype in HCV/HIV co-infected patients when compared to those infected with HCV alone, and may provide insight into why cell-mediated immune responses are diminished during HCV infection.

Cellular and molecular interactions in coinfection with hepatitis C virus and human immunodeficiency virus.

Coinfection with hepatitis C virus (HCV) and human immunodeficiency virus (HIV) is associated with increased HCV replication and a more rapid progression to severe liver disease, including the development of cirrhosis and hepatocellular carcinoma. In this review, we discuss the current understanding of the pathogenesis of HCV/HIV coinfection and the cellular and molecular mechanisms associated with the accelerated course of liver disease. The strength and breadth of HCV-specific T-cell responses are reduced in HCV/HIV-coinfected patients compared with those infected with HCV alone, suggesting that the immunosuppression induced by HIV compromises immune responses to HCV. HCV is not directly cytopathic, but many of the pathological changes observed in the liver of infected patients are a direct result of the intrahepatic antiviral immune responses. Apoptosis also has a role in HCV-mediated liver damage through the induction of apoptotic pathways involving the host immune response and HCV viral proteins. This review summarises the evidence correlating the role of cell-mediated immune responses and apoptosis with liver disease progression in HCV/HIV-coinfected patients.

Elevated serum levels of interferon- gamma -inducible protein-10 in patients coinfected with hepatitis C virus and HIV.

Coinfection with hepatitis C virus (HCV) and human immunodeficiency virus (HIV) is associated with an accelerated course of HCV infection and a faster progression to severe liver disease. We have investigated whether the development of liver disease in coinfected patients is associated with specific chemokine and cytokine production. Four cohorts--HCV/HIV-coinfected patients, HCV-monoinfected patients, HIV-monoinfected patients, and healthy control subjects--were studied. Serum levels of the 10-kDa interferon- gamma -inducible protein (IP-10) were higher in all 3 groups of infected patients than in control subjects (P<.0001). HCV/HIV-coinfected patients had significantly higher IP-10 levels than monoinfected patients. In HCV-monoinfected patients, liver fibrosis scores and liver enzyme levels were positively correlated with IP-10 levels. Elevated IP-10 levels are associated with and may contribute to liver damage in both HCV-monoinfected and HCV/HIV-coinfected patients.

Bioaccessibility of arsenic in mine waste-contaminated soils: a case study from an abandoned arsenic mine in SW England (UK).

This study characterises the total As concentrations and As bioaccessibility in 109 soils from Devon Great Consols Mine, an abandoned Cu-As mine in Devon, SW England, UK and discusses the soil and mineralogical factors that influence the bioaccessibility of this element. These data provide the basis for developing more accurate exposure estimates for use in human health risk assessments. The median value of the percent bioaccesible As of 15% for these As rich soils contaminated by mining activities indicated that relatively little of the total As is present in a bioaccessible form. Spatial variability of As bioaccesibility in the soils was also recognised throughout the mine site as a function of mineralogy. Multivariate statistical analysis identified a sulphide component responsible for the reduced As bioaccessibility of one cluster of soils. In the larger cluster of acidic mine soils covered by woodland As is mainly hosted in Fe oxyhydroxides whose partial dissolution is responsible for the bioaccessible As fraction. It was highlighted that the degree of Fe oxyhydroxide crystallinity might represent an important factor influencing arsenic bioaccessibility. Mine soils from Devon Great Consols Mine showed overall higher As bioaccessibility (15%) than other mineralised soils not affected by mining activities and background soils within the Tamar Catchment whose percent bioaccessible As median values were 9%.

An oral (gavage) control embryo-fetal development study in the Wistar Hannover rat.

Many of the studies conducted to examine the developmental and reproductive toxicity potential of candidate pharmaceuticals use the Sprague-Dawley rat as the animal model. This is due in part to the large database for this outbred rat available for comparison of litter data, and the low incidence of fetal malformations and variations. The following study was conducted to generate information on potential embryo-fetal developmental defects and litter data in another outbred stock of rat, the Wistar Hannover. One hundred fifty pregnant female Wistar Hannover rats (Tac:Glx:WIfBR) were dosed orally once per day with distilled water from Gestation Days (GD) 6 through 17 covering the time from implantation to closure of the hard palate (GD0 = day of insemination). Caesarean sections were performed on Day 20 of gestation. All fetuses were examined for external, visceral and skeletal malformations and variations. Macroscopic and histomorphologic examinations were also completed for the F0 females at termination. The percent pregnant (88%) and litter size (average 10.6) were found to be lower than that commonly reported for the Sprague-Dawley rat (Crl:CD (SD)BR; 95.4% and 14.6, respectively). Pre-implantation loss (14.1%), post-implantation loss (7.4%) and percent resorptions (7.2%) occurred at a higher incidence than typically seen in the Sprague-Dawley rat (5.9, 5.6 and 5.1%, respectively). The average fetal body weights for both the female and male rats were lower than those typically seen in the Sprague-Dawley rat. External, visceral and skeletal examination of the F1 fetuses revealed numerous malformations and variations which also occurred at higher incidences than those reported for the Sprague-Dawley rat. Routine macroscopic and histomorphologic examination showed there were no changes that would be interpreted to have impaired mating performance, fertility or gestation. Thus, this study provides information on the reproductive effects and the background incidence of embryo-fetal development defects that could be used for comparison to those identified when using this outbred rat for developmental and reproductive toxicity studies, as well as for comparison to the more commonly used rat stock, the Sprague-Dawley rat. For the parameters evaluated, the Wistar Hannover rat had greater variability and an increased incidence of spontaneous malformations as compared to the Crl:CD (SD)BR Sprague-Dawley rat. These findings should be considered if this stock of rat is selected in the conduct of developmental and reproductive toxicity studies.