765 research outputs found

    CHARMM-DYES : Parameterization of fluorescent dyes for use with the CHARMM force field

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    We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments to resolve the dynamics of proteins and nucleic acids at the nanoscale. However, little is known about the accuracy of the theoretical approximations used in determining the dynamics from the spectroscopic data. Molecular dynamics simulations can provide valuable insights into these dynamics at an atomistic level, but this requires accurate parameters for the dyes. The complex structure of the dyes and the importance of this in determining their spectroscopic properties mean that parameters generated by analogy to existing parameters do not give meaningful results. Through validation relative to quantum chemical calculation and experiments, the new parameters are shown to significantly outperform those that can be generated automatically, giving better agreement in both the charge distributions and structural properties. These improvements, in particular with regard to orientation of the dipole moments on the dyes, are vital for accurate simulation of FRET processes

    Organic Pollutants, Heavy Metals and Toxicity in Oil Spill impacted Salt Marsh Sediment Cores, Staten Island, New York City, USA

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    Sediment cores from Staten Island's salt marsh contain multiple historical oil spill events that impact ecological health. Microtox solid phase bioassay indicated moderate to high toxicity. Multiple spikes of TPH (6524 to 9586 mg/kg) and Σ16 PAH (15.5 to 18.9 mg/kg) were co-incident with known oil spills. A high TPH background of 400–700 mg/kg was attributed to diffuse sources. Depth-profiled metals Cu (1243 mg/kg), Zn (1814 mg/kg), Pb (1140 mg/kg), Ni (109 mg/kg), Hg (7 mg/kg), Cd 15 (mg/kg) exceeded sediment quality guidelines confirming adverse biological effects. Changes in Pb206/207 suggested three metal contaminant sources and diatom assemblages responded to two contamination events. Organic and metal contamination in Saw Mill Creek Marsh may harm sensitive biota, we recommend caution in the management of the 20–50 cm sediment interval because disturbance could lead to remobilisation of pre-existing legacy contamination into the waterway

    Relative sea-level change in Newfoundland, Canada during the past ∼3000 years

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    Several processes contributing to coastal relative sea-level (RSL) change in the North Atlantic Ocean are observed and/or predicted to have distinctive spatial expressions that vary by latitude. To expand the latitudinal range of RSL records spanning the past ∼3000 years and the likelihood of recognizing the characteristic fingerprints of these processes, we reconstructed RSL at two sites (Big River and Placentia) in Newfoundland from salt-marsh sediment. Bayesian transfer functions established the height of former sea level from preserved assemblages of foraminifera and testate amoebae. Age-depth models constrained by radiocarbon dates and chronohorizons estimated the timing of sediment deposition. During the past ∼3000 years, RSL rose by ∼3.0 m at Big River and by ∼1.5 m at Placentia. A locally calibrated geotechnical model showed that post-depositional lowering through sediment compaction was minimal. To isolate and quantify contributions to RSL from global, regional linear, regional non-linear, and local-scale processes, we decomposed the new reconstructions (and those in an expanded, global database) using a spatio-temporal statistical model. The global component confirms that 20th century sea-level rise occurred at the fastest, century-scale rate in over 3000 years (P > 0.999). Distinguishing the contributions from local and regional non-linear processes is made challenging by a sparse network of reconstructions. However, only a small contribution from local-scale processes is necessary to reconcile RSL reconstructions and modeled RSL trends. We identified three latitudinally-organized groups of sites that share coherent regional non-linear trends and indicate that dynamic redistribution of ocean mass by currents and/or winds was likely an important driver of sea-level change in the North Atlantic Ocean during the past ∼3000 years

    Entangled quantum heat engines based on two two-spin systems with Dzyaloshinski-Moriya anisotropic antisymmetric interaction

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    We construct an entangled quantum heat engine (EQHE) based on two two-spin systems with Dzyaloshinski-Moriya (DM) anisotropic antisymmetric interaction. By applying the explanations of heat transferred and work performed at the quantum level in Kieu's work [PRL, 93, 140403 (2004)], the basic thermodynamic quantities, i.e., heat transferred, net work done in a cycle and efficiency of EQHE are investigated in terms of DM interaction and concurrence. The validity of the second law of thermodynamics is confirmed in the entangled system. It is found that there is a same efficiency for both antiferromagnetic and ferromagnetic cases, and the efficiency can be controlled in two manners: 1. only by spin-spin interaction J and DM interaction D; 2. only by the temperature T and concurrence C. In order to obtain a positive net work, we need not entangle all qubits in two two-spin systems and we only require the entanglement between qubits in a two-spin system not be zero. As the ratio of entanglement between qubits in two two-spin systems increases, the efficiency will approach infinitely the classical Carnot one. An interesting phenomenon is an abrupt transition of the efficiency when the entanglements between qubits in two two-spin systems are equal

    Toxic effect of herbicides used for water hyacinth control on two insects released for its biological control in South Africa

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    The integrated control of water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach (Pontederiaceae) has become necessary in South Africa, as biological control alone is perceived to be too slow in controlling the weed. In total, seven insect biological control agents have been released on water hyacinth in South Africa. At the same time, herbicides are applied by the water authorities in areas where the weed continues to be troublesome. This study investigated the assumption that the two control methods are compatible by testing the direct toxicity of a range of herbicide formulations and surfactants on two of the biological control agents released against water hyacinth, the weevil, Neochetina eichhorniae Warner (Coleoptera: Curculionidae) and the water hyacinth mirid,Eccritotarsus catarinensis (Carvalho) (Hemiptera: Miridae). A number of the formulations used resulted in significant mortality of the mirid and the weevil. Products containing 2,4-D amine and diquat as active ingredients caused higher mortality of both agents (up to 80% for the mirid) than formulations containing glyphosate. Furthermore, when surfactants were added to enhance herbicide efficiency, it resulted in increased toxicity to the insects. We recommend that glyphosate formulations should be used in integrated control programmes, and that surfactants be avoided in order to reduce the toxic nature of spray formulations to the insect biological control agents released against water hyacinth

    Safeguarding pollinators and their values to human well-being

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    Wild and managed pollinators provide a wide range of benefits to society in terms of contributions to food security, farmer and beekeeper livelihoods, social and cultural values, as well as the maintenance of wider biodiversity and ecosystem stability. Pollinators face numerous threats, including changes in land-use and management intensity, climate change, pesticides and genetically modified crops, pollinator management and pathogens, and invasive alien species. There are well-documented declines in some wild and managed pollinators in several regions of the world. However, many effective policy and management responses can be implemented to safeguard pollinators and sustain pollination services.Environmental Biolog

    Measurement of ammonia emissions from temperate and sub-polar seabird colonies

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    The chemical breakdown of marine derived reactive nitrogen transported to the land as seabird guano represents a significant source of ammonia (NH3) in areas far from other NH3 sources. Measurements made at tropical and temperate seabird colonies indicate substantial NH3 emissions, with emission rates larger than many anthropogenic point sources. However, several studies indicate that thermodynamic processes limit the amount of NH3 emitted from guano, suggesting that the percentage of guano volatilizing as NH3 may be considerably lower in colder climates. This study undertook high resolution temporal ammonia measurements in the field and coupled results with modelling to estimate NH3 emissions at a temperate puffin colony and two sub-polar penguin colonies (Signy Island, South Orkney Islands and Bird Island, South Georgia) during the breeding season. These emission rates are then compared with NH3 volatilization rates from other climates. Ammonia emissions were calculated using a Lagrangian atmospheric dispersion model, resulting in mean emissions of 5 μg m-2 s-1 at the Isle of May, 12 μg m-2 s-1 at Signy Island and 9 μg m-2 s-1 at Bird Island. The estimated percentage of total guano nitrogen volatilized was 5% on the Isle of May, 3% on Signy and 2% on Bird Island. These values are much smaller than the percentage of guano nitrogen volatilized in tropical contexts (31-65%). The study confirmed temperature, wind speed and water availability have a significant influence on the magnitude of NH3 emissions, which has implications for reactive nitrogen in both modern remote regions and pre-industrial atmospheric composition and ecosystem interactions
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