Quantitative analysis of the effect of derivatisation of [Ru(BPY) phen] with a quinoline moiety on the interaction with DNA

The bifunctional Ru(II) complex [Ru(BPY)2POQ-Nmet]2+ (1), in which the metallic unit is tethered by an aliphatic chain to an organic DNA binder, was designed in order to increase the affinity toward nucleic acids. The interaction of 1 with DNA was characterised from luminescence and absorption data and compared with the binding of its monofunctional metallic and organic analogues, [Ru(BPY)2(ac)phen]2+ (2) and Nmet-quinoline (3). The bifunctional complex has a binding affinity one order of magnitude higher than that of each of its separated moieties. Absorption changes induced upon addition of DNA at different pH indicate protonation of the organic sub-unit upon interaction with DNA under neutral conditions. The combination of the luminescence data under steady-state and time-resolved conditions shows that the attachment of the organic unit in 1 induces modifications of the association modes of the metallic unit, owing to the presence of the aliphatic chain which probably hinders the metallic moiety binding. The salt dependence of the binding constants was analysed in order to compare the thermodynamic parameters describing the association with DNA for each complex. This study demonstrates the interest of the derivatisation of a Ru(II) complex with an organic moiety (ia the bifunctional ligand POQ-Nmet) for the development of high affinity DNA probes or photoreactive agents.

Effect of different jump distributions on the dynamics of jump processes

The paper investigates stochastic processes forced by independent and identically distributed jumps occurring according to a Poisson process. The impact of different distributions of the jump amplitudes are analyzed for processes with linear drift. Exact expressions of the probability density functions are derived when jump amplitudes are distributed as exponential, gamma, and mixture of exponential distributions for both natural and reflecting boundary conditions. The mean level-crossing properties are studied in relation to the different jump amplitudes. As an example of application of the previous theoretical derivations, the role of different rainfall-depth distributions on an existing stochastic soil water balance model is analyzed. It is shown how the shape of distribution of daily rainfall depths plays a more relevant role on the soil moisture probability distribution as the rainfall frequency decreases, as predicted by future climatic scenarios. © 2010 The American Physical Society.

Effect of peak inert-mode temperature on elemental carbon measured using thermal-optical analysis

Thermal-optical analysis is a conventional method for classifying carbonaceous aerosols as organic carbon (OC) and elemental carbon (EC). This article examines the effects of three different temperature protocols on the measured EC. For analyses of parallel punches from the same ambient sample, the protocol with the highest peak helium-mode temperature (870°C) gives the smallest amount of EC, while the protocol with the lowest peak helium-mode temperature (550°C) gives the largest amount of EC. These differences are observed when either sample transmission or reflectance is used to define the OC/EC split. An important issue is the effect of the peak helium-mode temperature on the relative rate at which different types of carbon with different optical properties evolve from the filter. Analyses of solvent-extracted samples are used to demonstrate that high temperatures (870°C) lead to premature EC evolution in the helium-mode. For samples collected in Pittsburgh, this causes the measured EC to be biased low because the attenuation coefficient of pyrolyzed carbon is consistently higher than that of EC. While this problem can be avoided by lowering the peak helium-mode temperature, analyses of wood smoke dominated ambient samples and levoglucosan-spiked filters indicate that too low helium-mode peak temperatures (550°C) allow non-light absorbing carbon to slip into the oxidizing mode of the analysis. If this carbon evolves after the OC/EC split, it biases the EC measurements high. Given the complexity of ambient aerosols, there is unlikely to be a single peak helium-mode temperature at which both of these biases can be avoided. Copyright © American Association for Aerosol Research.

Four-decade responses of soil trace elements to an aggrading old-field forest: B, Mn, Zn, Cu, and Fe.

In the ancient and acidic Ultisol soils of the Southern Piedmont, USA, we studied changes in trace element biogeochemistry over four decades, a period during which formerly cultivated cotton fields were planted with pine seedlings that grew into mature forest stands. In 16 permanent plots, we estimated 40-year accumulations of trace elements in forest biomass and O horizons (between 1957 and 1997), and changes in bioavailable soil fractions indexed by extractions of 0.05 mol/L HCl and 0.2 mol/L acid ammonium oxalate (AAO). Element accumulations in 40-year tree biomass plus O horizons totaled 0.9, 2.9, 4.8, 49.6, and 501.3 kg/ha for Cu, B, Zn, Mn, and Fe, respectively. In response to this forest development, samples of the upper 0.6-m of mineral soil archived in 1962 and 1997 followed one of three patterns. (1) Extractable B and Mn were significantly depleted, by -4.1 and -57.7 kg/ha with AAO, depletions comparable to accumulations in biomass plus O horizons, 2.9 and 49.6 kg/ha, respectively. Tree uptake of B and Mn from mineral soil greatly outpaced resupplies from atmospheric deposition, mineral weathering, and deep-root uptake. (2) Extractable Zn and Cu changed little during forest growth, indicating that nutrient resupplies kept pace with accumulations by the aggrading forest. (3) Oxalate-extractable Fe increased substantially during forest growth, by 275.8 kg/ha, about 10-fold more than accumulations in tree biomass (28.7 kg/ha). The large increases in AAO-extractable Fe in surficial 0.35-m mineral soils were accompanied by substantial accretions of Fe in the forest's O horizon, by 473 kg/ha, amounts that dwarfed inputs via litterfall and canopy throughfall, indicating that forest Fe cycling is qualitatively different from that of other macro- and micronutrients. Bioturbation of surficial forest soil layers cannot account for these fractions and transformations of Fe, and we hypothesize that the secondary forest's large inputs of organic additions over four decades has fundamentally altered soil Fe oxides, potentially altering the bioavailability and retention of macro- and micronutrients, contaminants, and organic matter itself. The wide range of responses among the ecosystem's trace elements illustrates the great dynamics of the soil system over time scales of decades.

The Effect of Wood Burial and Submersion on Decomposition: Implications for Reducing Carbon Emissions

Gemstone Team Carbon Sinks

Effect of adding 0.3 wt% Ni into the Sn–0.7 wt%Cu solder: part I: wetting behavior on Cu and Ni substrates

Comparative wetting behavior of Sn-0.7Cu and Sn-0.7Cu-0.3Ni solders on Cu and Ni substrates were assessed through the wetting balance test. No-clean (NC), non-activated (R) and water soluble organic acid (WS) fluxes were used to assess the wetting behavior for three different solder bath temperatures of 255, 275 and 295 °C. Experimental results unveiled that adding of 0.3 wt% Ni into Sn-0.7Cu solder can improve the wetting on Cu substrate when NC and WS fluxes are used. However, such addition of Ni did not improve the wetting of Sn-0.7Cu solder for R-type flux. In the case of Ni substrate, addition of Ni helped to improve the wetting for all three types of fluxes as higher wetting forces were documented for Sn-0.7Cu-0.3Ni solder compared to the Sn-0.7Cu solder. Among the fluxes, worst performance was observed for R-type flux. Very large contact angles were recorded for both solders with this kind of flux. Experimental results also revealed that higher solder bath temperature played an important role to lower the contact angle, to increase the wetting force and to enhance the wetting. Computer modeling of wetting balance test also revealed that both the wetting force and meniscus height are inversely proportional to the contact angles. Besides, solder bath depth and radius do not affect significantly on the wetting behavior.

Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord

In the frame of the European Project on Ocean Acidification (EPOCA), the response of an Arctic pelagic community (<3 mm) to a gradient of seawater pCO(2) was investigated. For this purpose 9 large-scale in situ mesocosms were deployed in Kongsfjorden, Svalbard (78 degrees 56.2' N, 11 degrees 53.6' E), in 2010. The present study investigates effects on the communities of particle-attached (PA; >3 mu m) and free-living (FL; <3 mu m > 0.2 mu m) bacteria by Automated Ribosomal Intergenic Spacer Analysis (ARISA) in 6 of the mesocosms, ranging from 185 to 1050 mu atm initial pCO(2), and the surrounding fjord. ARISA was able to resolve, on average, 27 bacterial band classes per sample and allowed for a detailed investigation of the explicit richness and diversity. Both, the PA and the FL bacterioplankton community exhibited a strong temporal development, which was driven mainly by temperature and phytoplankton development. In response to the breakdown of a picophytoplankton bloom, numbers of ARISA band classes in the PA community were reduced at low and medium CO2 (similar to 185-685 mu atm) by about 25 %, while they were more or less stable at high CO2 (similar to 820-1050 mu atm). We hypothesise that enhanced viral lysis and enhanced availability of organic substrates at high CO2 resulted in a more diverse PA bacterial community in the post-bloom phase. Despite lower cell numbers and extracellular enzyme activities in the post-bloom phase, bacterial protein production was enhanced in high CO2 mesocosms, suggesting a positive effect of community richness on this function and on carbon cycling by bacteria.

The effect of pressure on leucine and thymidine incorporation by free-living bacteria and by bacteria attached to sinking oceanic particles

The effect of pressure on upper ocean free-living bacteria and bacteria attached to rapidly sinking particles was investigated through studying their ability to synthesize DNA and protein by measuring their rate of 3H-thymidine and 3H-leucine incorporation. Studies were carried out on samples from the NE Atlantic under the range of pressures (1–430 atm) encountered by sinking aggregates during their journey to the deep-sea bed. Thymidine and leucine incorporation rates per bacterium attached to sinking particles from 200 m were about six and ten times higher, respectively, than the free-living bacterial assemblage. The ratio of leucine incorporation rate per cell to thymidine incorporation rate per cell was significantly different between the larger attached (18.9:1) and smaller free-living (10.4:1) assemblages. The rates of leucine and thymidine incorporation decreased exponentially with increasing pressure for the free-living and linearly for attached bacteria, while there was no significant influence of pressure on cell numbers. At 100 atm leucine and thymidine incorporation rate per free-living bacterium was reduced to 73 and 20%, respectively, relative to that measured at 1 atm. Pressure of 100 atm reduced leucine and thymidine incorporation per attached bacterium to 94 and 70%, and at 200 atm these rates were reduced to 34 and 51%, respectively, relative to those measured at 1 atm. There was no significant uncoupling of thymidine and leucine incorporation for either the free-living or attached bacterial assemblages with increasing pressure, indicating that the processess of DNA and protein synthesis may be equally affected by increasing pressure. It is therefore unlikely that bacteria, originating from surface waters, attached to rapidly sinking particles play a role in particle remineralization below approximately 1000–2000 m. These results may help to explain the occurrence of relatively fresh aggregates on the deep-sea bed that still contain sufficient organic carbon to fuel the rapid growth of benthic micro-organisms; they also indicate that the effect of pressure on microbial processes may be important in oceanic biogeochemical cycles.

The effect of anisotropic elasticity on the yielding characteristics of overconsolidated natural clay

Quantitative application of elastoplastic theory to the yielding behaviour of natural soils has always been uncertain. Part of the reason is that the theory was developed for reconstituted materials with isotropic structure, in contrast to natural soils that are usually anisotropic. The approach considered in this study assumes that pre-yielding behaviour is governed by the theory of linear anisotropic elasticity and that yield loci in the mean effective stress ( p') – deviator stress (q) plane are aligned approximately along the coefficient of earth pressure (K0) line. The assumption of a rotated yield locus associated with anisotropic elastic behaviour within the state boundary surface indicates that the elastic wall within the state boundary surface is inclined. The form of the state boundary surface has been determined mathematically in terms of anisotropic elastic and Cam-Clay soil parameters. Stress path tests were conducted on samples of Belfast Upper Boulder Clay removed from a depth of 28 m below ground surface. Good agreement was found between predicted and measured yield loci. The study also examined the influence of subsequent isotropic compression on the yielding characteristics of the natural clay. The indications are that the anisotropy developed during deposition disappears when the sample is loaded to a stress level at least twice the stress generated during the original deposition process. The methods developed in the paper have also been applied to test results reported previously on Winnipeg clay, and good agreement was obtained.

Synthesis of Piano Stool Complexes Employing the Pentafluorophenyl Substituted Diphosphine (C6F5)2PCH2P(C6F5)2 and the Effect of Phosphine Modifiers on Hydrogen Transfer Catalysis.

Ruthenium, rhodium, and iridium piano stool complexes of the pentafluorophenyl-substituted diphosphine (C6F5)2PCH2P(C6F5)2 (2) have been prepared and structurally characterized by single-crystal X-ray diffraction. The Cp-P tethered complex [{(C5Me4CH2C6F4(C6F5)CH2P(C6F5)2}RhCl2] (9), in which only one phosphorus is coordinated to the rhodium, was prepared by thermolysis of a slurry of [Cp*RhCl(-Cl)]2 and 2 and was structurally characterized by single-crystal X-ray diffraction. The tethering occurs by intramolecular dehydrofluorinative coupling of the pentamethylcyclopentadienyl ligand and P,P-coordinated 2. The geometric changes that occur on tethering force dissociation of one of the phosphorus atoms. The effects of introducing phosphine ligands to the coordination sphere of piano stool hydrogen transfer catalysts have been studied. The complexes of fluorinated phosphine complexes are found to transfer hydrogen at rates that compare favorably with leading catalysts, particularly when the phosphine and cyclopentadienyl functionalities are tethered. The highly chelating Cp-PP complex [(C5Me4CH2-2-C5F3N-4-PPhCH2CH2PPh2)RhCl]BF4 (1) was found to outperform all other complexes tested. The mechanism of hydrogen transfer catalyzed by piano stool phosphine complexes is discussed with reference to the trends in activity observed.

Retrospective assessment of dryland soil stability in relation to grazing and climate change

Accelerated soil erosion is an aspect of dryland degradation that is affected by repeated intense drought events and land management activities such as commercial livestock grazing. A soil stability index (SSI) that detects the erosion status and susceptibility of a landscape at the pixel level, i.e., stable, erosional, or depositional pixels, was derived from the spectral properties of an archived time series (from 1972 to 1997) of Landsat satellite data of a commercial ranch in northeastern Utah. The SSI was retrospectively validated with contemporary field measures of soil organic matter and erosion status that was surveyed by US federal land management agencies. Catastrophe theory provided the conceptual framework for retrospective assessment of the impact of commercial grazing and soil water availability on the SSI. The overall SSI trend was from an eroding landscape in the early drier 1970s towards stable conditions in the wetter mid-1980s and late 1990s. The landscape catastrophically shifted towards an extreme eroding state that was coincident with the “The Great North American Drought of 1988”. Periods of landscape stability and trajectories toward stability were coincident with extremely wet El Niño events. Commercial grazing had less correlation with soil stability than drought conditions. However, the landscape became more susceptible to erosion events under multiple droughts and grazing. Land managers now have nearly a year warning of El Niño and La Niña events and can adjust their management decisions according to predicted landscape erosion conditions.

Determination of absolute configuration of conformationally flexible cis-dihydrodiol metabolites: Effect of diene substitution pattern on the circular dichroism spectra and optical rotations

Absolute configurations of a number of cis-dihydrodiols (cis-1,2-dihydroxy-3,5-cyclohexadienes), synthetically useful products of TDO-catalyzed dihydroxylations of 1,2- and 1,3-disubstituted benzene derivatives, have been determined by a comparison of calculated and experimental CD spectra and optical rotations and by methods involving X-ray crystallography, H-1 NMR spectra of diastereoisomeric derivatives, and by stereochemical correlations. The computations disclosed a significant effect of the substituents on conformational equilibria of cis-dihydrodiols and chiroptical properties of individual conformers. The assigned absolute configurations of cis-dihydrodiols have allowed the validity of a simple predictive model for TDO-catalyzed arene dihydroxylations to be extended.