Evaluation of diffusive gradients in thin-films using a Diphonix® resin for monitoring dissolved uranium in natural waters

Commercially available Diphonix® resin (TrisKem International) was evaluated as a receiving phase for use with the diffusive gradients in thin-films (DGT) passive sampler for measuring uranium. This resin has a high partition coefficient for actinides and is used in the nuclear industry. Other resins used as receiving phases with DGT for measuring uranium have been prone to saturation and significant chemical interferences. The performance of the device was evaluated in the laboratory and in field trials. In laboratory experiments uptake of uranium (all 100% efficiency) by the resin was unaffected by varying pH (4–9), ionic strength (0.01–1.00 M, as NaNO3) and varying aqueous concentrations of Ca2+ (100–500 mg L−1) and HCO3− (100–500 mg L−1). Due to the high partition coefficient of Diphonex®, several elution techniques for uranium were evaluated. The optimal eluent mixture was 1 M NaOH/1 M H2O2, eluting 90% of the uranium from the resin. Uptake of uranium was linear (R2 = 0.99) over time (5 days) in laboratory experiments using artificial freshwater showing no saturation effects of the resin. In field deployments (River Lambourn, UK) the devices quantitatively accumulated uranium for up to 7 days. In both studies uptake of uranium matched that theoretically predicted for the DGT. Similar experiments in seawater did not follow the DGT theoretical uptake and the Diphonix® appeared to be capacity limited and also affected by matrix interferences. Isotopes of uranium (U235/U238) were measured in both environments with a precision and accuracy of 1.6–2.2% and 1.2–1.4%, respectively. This initial study shows the potential of using Diphonix®-DGT for monitoring of uranium in the aquatic environment

Thermalkalibacillus uzonensis gen. nov. sp. nov, a novel aerobic alkali-tolerant thermophilic bacterium isolated from a hot spring in Uzon Caldera, Kamchatka

A novel thermophilic, alkali-tolerant, and CO-tolerant strain JW/WZ-YB58T was isolated from green mat samples obtained from the Zarvarzin II hot spring in the Uzon Caldera, Kamchatka (Far East Russia). Cells were Gram-type and Gram stain-positive, strictly aerobic, 0.7-0.8 μm in width and 5.5-12 μm in length and produced terminal spherical spores of 1.2-1.6 μm in diameter with the mother cell swelling around 2 μm in diameter (drumstick-type morphology). Cells grew optimally at pH25°C 8.2-8.4 and temperature 50-52°C and tolerated maximally 6% (w/v) NaCl. They were strict heterotrophs and could not use either CO or CO2 (both with or without H2) as sole carbon source, but tolerated up to 90% (v/v) CO in the headspace. The isolate grew on various complex substrates such as yeast extract, on carbohydrates, and organic acids, which included starch, d-galactose, d-mannose, glutamate, fumarate and acetate. Catalase reaction was negative. The membrane polar lipids were dominated by branched saturated fatty acids, which included iso-15:0 (24.5%), anteiso-15:0 (18.3%), iso-16:0 (9.9%), iso-17:0 (17.5%) and anteiso-17:0 (9.7%) as major constituents. The DNA G+C content of the strain is 45 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain JW/WZ-YB58T is distantly (\u3c93% similarity) related to members of Bacillaceae. On the basis of 16S rRNA gene sequence, physiological and phenotypic characteristics, the isolate JW/WZ-YB58T (ATCC BAA-1258; DSM 17740) is proposed to be the type strain for the type species of the new taxa within the family Bacillaceae, Thermalkalibacillus uzoniensis gen. nov. sp. nov. The Genbank accession number for the 16S rRNA gene sequence is DQ221694. © Springer-Verlag 2006

Clapper rails as indicators of mercury and PCB bioavailability in a Georgia saltmarsh system

Clapper rails (Rallus longirostris) were used as an indicator species of estuarine marsh habitat quality because of their strong site fidelity and predictable diet consisting of mostly benthic organisms. Mercury (Hg) and the polychlorinated biphenyl (PCB) Aroclor 1268 concentrations were determined for sediments, crabs, as well as clapper rail adults and chicks collected from salt marshes associated with the LCP Superfund site in Brunswick, Georgia. Home ranges were established for adult rails, and sediment and crab samples were taken from each individual’s range. The study was designed to minimize the spatial variability associated with trophic transfer studies by choosing an endpoint species with a potentially small home range and specifically sampling its foraging range. The mean home range for clapper rails was 1.2 ha with a median of 0.28 ha. Concentrations of Hg and Aroclor 1268 were shown to increase with each trophic level. Transfer factors between media followed the same pattern for both contaminants with the highest between fiddler crabs and clapper rail liver. Hg and PCB transfer factors were similar between sediment to fiddler crab and fiddler crab to muscle, however the PCB transfer factor from fiddler crabs to liver was over twice as large as for Hg. PCB congener profiles did not significantly differ between media types

Clapper rails as indicators of mercury and PCB bioavailability in a Georgia saltmarsh system

Clapper rails (Rallus longirostris) were used as an indicator species of estuarine marsh habitat quality because of their strong site fidelity and predictable diet consisting of mostly benthic organisms. Mercury (Hg) and the polychlorinated biphenyl (PCB) Aroclor 1268 concentrations were determined for sediments, crabs, as well as clapper rail adults and chicks collected from salt marshes associated with the LCP Superfund site in Brunswick, Georgia. Home ranges were established for adult rails, and sediment and crab samples were taken from each individual’s range. The study was designed to minimize the spatial variability associated with trophic transfer studies by choosing an endpoint species with a potentially small home range and specifically sampling its foraging range. The mean home range for clapper rails was 1.2 ha with a median of 0.28 ha. Concentrations of Hg and Aroclor 1268 were shown to increase with each trophic level. Transfer factors between media followed the same pattern for both contaminants with the highest between fiddler crabs and clapper rail liver. Hg and PCB transfer factors were similar between sediment to fiddler crab and fiddler crab to muscle, however the PCB transfer factor from fiddler crabs to liver was over twice as large as for Hg. PCB congener profiles did not significantly differ between media types

The Clapper Rail as an Indicator Species of Estuarine Marsh Health

Clapper Rails (Rallus longirostris) can potentially serve as an indicator species of estuarinemarsh health because of their strong site fi delity and predictable diet consisting predominantly of benthic organisms. These feeding habits increase the likelihood of individuals accumulating signifi - cant amounts of contaminants associated with coastal sediments. Moreover, since Clapper Rails are threatened in most of their western range, additional study of the effects of potential toxins on these birds is essential to conservation programs for this species. Here we present techniques (DNA strand breakage, eggshell structure, and human-consumption risk) that can be used to quantify detrimental effects to Clapper Rails exposed to multiple contaminants in disturbed ecosystems as well as humans who may eat them. Adult birds collected near a site contaminated with polychlorinated biphenyls (PCBs) and metals in Brunswick, Georgia had a high degree of strand breakage, while those collected from a nearby reference area had no strand breakage. Although, results showed that eggshell integrity was compromised in eggs from the contaminated sites, these results were more diffuse, reemphasizing that multiple endpoints should be used in ecological assessments. This study also shows that techniques such as eggshell integrity on hatched eggs and DNA strand breakage in adults can be used as non-lethal mechanisms to monitor the population health of more threatened populations such as those in the western US. We also present results from human-based risk assessment for PCBs as a third toxicological endpoint, since these species are hunted and consumed by the public in the southeastern US. Using standard human-risk thresholds, we show a potential risk to hunters who consume Clapper Rails shot near the contaminated site from PCBs because of the additional lifetime cancer risk associated with that consumption

The Clapper Rail as an Indicator Species of Estuarine Marsh Health

Clapper Rails (Rallus longirostris) can potentially serve as an indicator species of estuarinemarsh health because of their strong site fi delity and predictable diet consisting predominantly of benthic organisms. These feeding habits increase the likelihood of individuals accumulating signifi - cant amounts of contaminants associated with coastal sediments. Moreover, since Clapper Rails are threatened in most of their western range, additional study of the effects of potential toxins on these birds is essential to conservation programs for this species. Here we present techniques (DNA strand breakage, eggshell structure, and human-consumption risk) that can be used to quantify detrimental effects to Clapper Rails exposed to multiple contaminants in disturbed ecosystems as well as humans who may eat them. Adult birds collected near a site contaminated with polychlorinated biphenyls (PCBs) and metals in Brunswick, Georgia had a high degree of strand breakage, while those collected from a nearby reference area had no strand breakage. Although, results showed that eggshell integrity was compromised in eggs from the contaminated sites, these results were more diffuse, reemphasizing that multiple endpoints should be used in ecological assessments. This study also shows that techniques such as eggshell integrity on hatched eggs and DNA strand breakage in adults can be used as non-lethal mechanisms to monitor the population health of more threatened populations such as those in the western US. We also present results from human-based risk assessment for PCBs as a third toxicological endpoint, since these species are hunted and consumed by the public in the southeastern US. Using standard human-risk thresholds, we show a potential risk to hunters who consume Clapper Rails shot near the contaminated site from PCBs because of the additional lifetime cancer risk associated with that consumption

Primary Sources of Polycyclic Aromatic Hydrocarbons to Streambed Sediment in Great Lakes Tributaries Using Multiple Lines of Evidence

Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread and potentially toxic contaminants in Great Lakes (USA/Canada) tributaries. The sources of PAHs are numerous and diverse, and identifying the primary source(s) can be difficult. The present study used multiple lines of evidence to determine the likely sources of PAHs to surficial streambed sediments at 71 locations across 26 Great Lakes Basin watersheds. Profile correlations, principal component analysis, positive matrix factorization source-receptor modeling, and mass fractions analysis were used to identify potential PAH sources, and land-use analysis was used to relate streambed sediment PAH concentrations to different land uses. Based on the common conclusion of these analyses, coal-tar-sealed pavement was the most likely source of PAHs to the majority of the locations sampled. The potential PAH-related toxicity of streambed sediments to aquatic organisms was assessed by comparison of concentrations with sediment quality guidelines. The sum concentration of 16 US Environmental Protection Agency priority pollutant PAHs was 7.4-196 000 mu g/kg, and the median was 2600 mu g/kg. The threshold effect concentration was exceeded at 62% of sampling locations, and the probable effect concentration or the equilibrium partitioning sediment benchmark was exceeded at 41% of sampling locations. These results have important implications for watershed managers tasked with protecting and remediating aquatic habitats in the Great Lakes Basin.Environ Toxicol Chem2020;00:1-17. (c) 2020 The Authors.Environmental Toxicology and Chemistrypublished by Wiley Periodicals LLC on behalf of SETAC.Peer reviewe

An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas fluorescens </it>is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metabolites with potential as natural products. <it>P. fluorescens </it>isolate WH6 produces Germination-Arrest Factor (GAF), a predicted small peptide or amino acid analog with herbicidal activity that specifically inhibits germination of seeds of graminaceous species.</p> <p>Results</p> <p>We used a hybrid next-generation sequencing approach to develop a high-quality draft genome sequence for <it>P. fluorescens </it>WH6. We employed automated, manual, and experimental methods to further improve the draft genome sequence. From this assembly of 6.27 megabases, we predicted 5876 genes, of which 3115 were core to <it>P. fluorescens </it>and 1567 were unique to WH6. Comparative genomic studies of WH6 revealed high similarity in synteny and orthology of genes with <it>P. fluorescens </it>SBW25. A phylogenomic study also placed WH6 in the same lineage as SBW25. In a previous non-saturating mutagenesis screen we identified two genes necessary for GAF activity in WH6. Mapping of their flanking sequences revealed genes that encode a candidate anti-sigma factor and an aminotransferase. Finally, we discovered several candidate virulence and host-association mechanisms, one of which appears to be a complete type III secretion system.</p> <p>Conclusions</p> <p>The improved high-quality draft genome sequence of WH6 contributes towards resolving the <it>P. fluorescens </it>species, providing additional impetus for establishing two separate lineages in <it>P. fluorescens</it>. Despite the high levels of orthology and synteny to SBW25, WH6 still had a substantial number of unique genes and represents another source for the discovery of genes with implications in affecting plant growth and health. Two genes are demonstrably necessary for GAF and further characterization of their proteins is important for developing natural products as control measure against grassy weeds. Finally, WH6 is the first isolate of <it>P. fluorescens </it>reported to encode a complete T3SS. This gives us the opportunity to explore the role of what has traditionally been thought of as a virulence mechanism for non-pathogenic interactions with plants.</p

Granular flow down a rough inclined plane: transition between thin and thick piles

The rheology of granular particles in an inclined plane geometry is studied using molecular dynamics simulations. The flow--no-flow boundary is determined for piles of varying heights over a range of inclination angles $\theta$. Three angles determine the phase diagram: $\theta_{r}$, the angle of repose, is the angle at which a flowing system comes to rest; $\theta_{m}$, the maximum angle of stability, is the inclination required to induce flow in a static system; and $\theta_{max}$ is the maximum angle for which stable, steady state flow is observed. In the stable flow region $\theta_{r}<\theta<\theta_{max}$, three flow regimes can be distinguished that depend on how close $\theta$ is to $\theta_{r}$: i) $\theta>>\theta_{r}$: Bagnold rheology, characterized by a mean particle velocity $v_{x}$ in the direction of flow that scales as $v_{x}\propto h^{3/2}$, for a pile of height $h$, ii) $\theta\gtrsim\theta_{r}$: the slow flow regime, characterized by a linear velocity profile with depth, and iii) $\theta\approx\theta_{r}$: avalanche flow characterized by a slow underlying creep motion combined with occasional free surface events and large energy fluctuations. We also probe the physics of the initiation and cessation of flow. The results are compared to several recent experimental studies on chute flows and suggest that differences between measured velocity profiles in these experiments may simply be a consequence of how far the system is from jamming.Comment: 19 pages, 14 figs, submitted to Physics of Fluid

The discovery of potent, selective, and reversible inhibitors of the house dust mite peptidase allergen Der p 1: an innovative approach to the treatment of allergic asthma.

Blocking the bioactivity of allergens is conceptually attractive as a small-molecule therapy for allergic diseases but has not been attempted previously. Group 1 allergens of house dust mites (HDM) are meaningful targets in this quest because they are globally prevalent and clinically important triggers of allergic asthma. Group 1 HDM allergens are cysteine peptidases whose proteolytic activity triggers essential steps in the allergy cascade. Using the HDM allergen Der p 1 as an archetype for structure-based drug discovery, we have identified a series of novel, reversible inhibitors. Potency and selectivity were manipulated by optimizing drug interactions with enzyme binding pockets, while variation of terminal groups conferred the physicochemical and pharmacokinetic attributes required for inhaled delivery. Studies in animals challenged with the gamut of HDM allergens showed an attenuation of allergic responses by targeting just a single component, namely, Der p 1. Our findings suggest that these inhibitors may be used as novel therapies for allergic asthma