Duplex stability of DNA.DNA and DNA.RNA duplexes containing 3 '-S-phosphorothiolate linkages

3′-S-Phosphorothiolate (3′-SP) linkages have been incorporated into the DNA strand of both a DNA·RNA duplex and a DNA·DNA duplex. Thermal melting (Tm) studies established that this modification significantly stabilises the DNA·RNA duplex with an average increase in Tm of about 1.4 °C per modification. For two or three modifications, the increase in Tm was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on Tm. In contrast to the DNA·RNA duplex, the 3′-S-phosphorothiolate linkage destabilised the DNA·DNA duplex, irrespective of the arrangement of the 3′-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA·DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.

The nature of Arctic polar vortices in chemistry-climate models

The structure of the Arctic stratospheric polar vortex in three chemistry–climate models (CCMs) taken from the CCMVal-2 intercomparison is examined using zonal mean and geometric-based methods. The geometric methods are employed by taking 2D moments of potential vorticity fields that are representative of the polar vortices in each of the models. This allows the vortex area, centroid location and ellipticity to be determined, as well as a measure of vortex filamentation. The first part of the study uses these diagnostics to examine how well the mean state, variability and extreme variability of the polar vortices are represented in CCMs compared to ERA-40 reanalysis data, and in particular for the UMUKCA-METO, NIWA-SOCOL and CCSR/NIES models. The second part of the study assesses how the vortices are predicted to change in terms of the frequency of sudden stratospheric warmings and their general structure over the period 1960–2100. In general, it is found that the vortices are climatologically too far poleward in the CCMs and produce too few large-scale filamentation events. Only a small increase is observed in the frequency of sudden stratospheric warming events from the mean of the CCMVal-2 models, but the distribution of extreme variability throughout the winter period is shown to change towards the end of the twentyfirst century.

Genome scale reconstruction of a Salmonella metabolic model comparison of similarity and differences with a commensal Escherichia coli strain

Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.

A global view of the extratropical tropopause transition layer from Atmospheric Chemistry Experiment Fourier Transform Spectrometer O3, H2O, and CO

The global behavior of the extratropical tropopause transition layer (ExTL) is investigated using O3, H2O, and CO measurements from the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) on Canada’s SCISAT-1 satellite obtained between February 2004 and May 2007. The ExTL depth is derived using H2O-O3 and CO-O3 correlations. The ExTL top derived from H2O-O3 shows an increase from roughly 1–1.5 km above the thermal tropopause in the subtropics to 3–4 km (2.5–3.5 km) in the north (south) polar region, implying somewhat weaker tropospherestratosphere- transport in the Southern Hemisphere. The ExTL bottom extends ~1 km below the thermal tropopause, indicating a persistent stratospheric influence on the troposphere at all latitudes. The ExTL top derived from the CO-O3 correlation is lower, at 2 km or ~345 K (1.5 km or ~335 K) in the Northern (Southern) Hemisphere. Its annual mean coincides with the relative temperature maximum just above the thermal tropopause. The vertical CO gradient maximizes at the thermal tropopause, indicating a local minimum in mixing within the tropopause region. The seasonal changes in and the scales of the vertical H2O gradients show a similar pattern as the static stability structure of the tropopause inversion layer (TIL), which provides observational support for the hypothesis that H2O plays a radiative role in forcing and maintaining the structure of the TIL.

The importance of attractive three-point interaction in enantioselective surface chemistry: stereospecific adsorption of serine on the intrinsically chiral Cu{531} surface

Both enantiomers of serine adsorb on the intrinsically chiral Cu{531} surface in two different adsorption geometries, depending on the coverage. At saturation, substrate bonds are formed through the two oxygen atoms of the carboxylate group and the amino group (μ3 coordination), whereas at lower coverage, an additional bond is formed through the deprotonated β−OH group (μ4 coordination). The latter adsorption geometry involves substrate bonds through three side groups of the chiral center, respectively, which leads to significantly larger enantiomeric differences in adsorption geometries and energies compared to the μ3 coordination, which involves only two side groups. This relatively simple model system demonstrates, in direct comparison, that attractive interactions of three side groups with the substrate are much more effective in inducing strong enantiomeric differences in heterogeneous chiral catalyst systems than hydrogen bonds or repulsive interactions.

Surface chemistry of glycine on Pt{111} in different aqueous environments

Adsorption of glycine on Ptf111g under UHV conditions and in different aqueous environments was studied by XPS (UHV and ambient pressure) and NEXAFS. Under UHV conditions, glycine adsorbs in its neutral molecular state up to about 0.15 ML. Further deposition leads to the formation of an additional zwitterionic species, which is in direct contact with the substrate surface, followed by the growth of multilayers, which also consist of zwitterions. The neutral surface species is most stable and decomposes at 360 K through a multi-step process which includes the formation of methylamine and carbon monoxide. When glycine and water are co-adsorbed in UHV at low temperatures (< 170 K) inter-layer diffusion is inhibited and the surface composition depends on the adsorption sequence. Water adsorbed on top of a glycine layer does not lead to significant changes in its chemical state. When glycine is adsorbed on top of a pre-adsorbed chemisorbed water layer or thick ice layer, however, it is found in its zwitterionic state, even at low coverage. No difference is seen in the chemical state of glycine when the layers are exposed to ambient water vapor pressure up to 0.2 Torr at temperatures above 300 K. Also the decomposition temperature stays the same, 360 K, irrespective of the water vapor pressure. Only the reaction path of the decomposition products is affected by ambient water vapor.

Synthesis, structure and electrochemical properties of some thiosemicarbazone complexes of ruthenium

Reaction of salicylaldehyde thiosemicarbazone (L-1), 2-hydroxyacetophenone thiosemicarbazone (L-2) and 2-hydroxynapthaldehyde thiosemicarbazone (L-3) with [Ru(dmso)(4)Cl-2] affords a family of three dimeric complexes (1), (2) and (3) respectively. Crystal structure of the complex (3) has been determined. In these complexes, each monomeric unit consists of one ruthenium center and two thiosemicarbazone ligands, one of which is coordinated to ruthenium as O,N,S-donor and the other as N,S-donor forming a five-membered chelate ring. Two such monomeric units remain bridged by the sulfur atoms of the O,N,S-coordinated thiosemicarbazones. Due to this sulfur bridging, the two ruthenium centers become so close to each other, that a ruthenium-ruthenium single bond is also formed. All the complexes are diamagnetic in the solid state and in dimethylsulfoxide solution show intense absorptions in the visible and ultraviolet region. Origin of these spectral transitions has been established from DFT calculations. Cyclic voltammetry on the complexes shows two irreversible ligand oxidations on the positive side of SCE and two irreversible ligand reductions on the negative side.

The interplay of secondary Hg⋯S, Hg⋯N and Hg⋯π bonding interactions in supramolecular structures of phenylmercury(ii) dithiocarbamates

Three new phenylmercury(II) and one mercury(II) dithiocarbamate complexes viz. PhHg S2CN(PyCH2) Bz (1), PhHg S2CN(PyCH2)CH3 (2), PhHg S2CN(Bz)CH3 (3), and [Hg (NCS2(PyCH2)Bz)(2)] (4) (Py = pyridine; Bz = benzyl) have been synthesized and characterized by elemental analyses, IR, electronic absorption, H-1 and C-13 NMR spectroscopy. The crystal structures of 1, 2 and 3 showed a linear S-Hg-C core at the centre of the molecule, in which the metal atom is bound to the sulfur atom of the dithiocarbamate ligand and a carbon atom of the aromatic ring. In contrast the crystal structure of 4 showed a linear S-Hg-S core at the Hg(II) centre of the molecule. Weak intermolecular Hg center dot center dot center dot N (Py) interactions link molecules into a linear chain in the case of 1, whereas chains of dimers are formed in 2 through intermolecular Hg center dot center dot center dot N (Py) and Hg center dot center dot center dot S interactions. 3 forms a conventional face-to-edge dimeric structure through intermolecular Hg center dot center dot center dot S secondary bonding and 4 forms a linear chain of dimers through face-to-face Hg center dot center dot center dot S secondary bonding. In order to elucidate the nature of these secondary bonding interactions and the electronic absorption spectra of the complexes, ab initio quantum chemical calculations at the MP2 level and density functional theory calculations were carried out for 1-3. Complexes 1 and 2 exhibited photoluminescent properties in the solid state as well as in the solution phase. Studies indicate that Hg center dot center dot center dot S interactions decrease and Hg center dot center dot center dot N interactions increase the chances of photoluminescence in the solid phase

Review of the formulation of present‐generation stratospheric chemistry‐climate models and associated external forcings

The goal of the Chemistry‐Climate Model Validation (CCMVal) activity is to improve understanding of chemistry‐climate models (CCMs) through process‐oriented evaluation and to provide reliable projections of stratospheric ozone and its impact on climate. An appreciation of the details of model formulations is essential for understanding how models respond to the changing external forcings of greenhouse gases and ozonedepleting substances, and hence for understanding the ozone and climate forecasts produced by the models participating in this activity. Here we introduce and review the models used for the second round (CCMVal‐2) of this intercomparison, regarding the implementation of chemical, transport, radiative, and dynamical processes in these models. In particular, we review the advantages and problems associated with approaches used to model processes of relevance to stratospheric dynamics and chemistry. Furthermore, we state the definitions of the reference simulations performed, and describe the forcing data used in these simulations. We identify some developments in chemistry‐climate modeling that make models more physically based or more comprehensive, including the introduction of an interactive ocean, online photolysis, troposphere‐stratosphere chemistry, and non‐orographic gravity‐wave deposition as linked to tropospheric convection. The relatively new developments indicate that stratospheric CCM modeling is becoming more consistent with our physically based understanding of the atmosphere.

Stratosphere‐troposphere coupling and annular mode variability in chemistry‐climate models

The internal variability and coupling between the stratosphere and troposphere in CCMVal‐2 chemistry‐climate models are evaluated through analysis of the annular mode patterns of variability. Computation of the annular modes in long data sets with secular trends requires refinement of the standard definition of the annular mode, and a more robust procedure that allows for slowly varying trends is established and verified. The spatial and temporal structure of the models’ annular modes is then compared with that of reanalyses. As a whole, the models capture the key features of observed intraseasonal variability, including the sharp vertical gradients in structure between stratosphere and troposphere, the asymmetries in the seasonal cycle between the Northern and Southern hemispheres, and the coupling between the polar stratospheric vortices and tropospheric midlatitude jets. It is also found that the annular mode variability changes little in time throughout simulations of the 21st century. There are, however, both common biases and significant differences in performance in the models. In the troposphere, the annular mode in models is generally too persistent, particularly in the Southern Hemisphere summer, a bias similar to that found in CMIP3 coupled climate models. In the stratosphere, the periods of peak variance and coupling with the troposphere are delayed by about a month in both hemispheres. The relationship between increased variability of the stratosphere and increased persistence in the troposphere suggests that some tropospheric biases may be related to stratospheric biases and that a well‐simulated stratosphere can improve simulation of tropospheric intraseasonal variability.

Chemistry‐climate model simulations of spring Antarctic ozone

Coupled chemistry‐climate model simulations covering the recent past and continuing throughout the 21st century have been completed with a range of different models. Common forcings are used for the halogen amounts and greenhouse gas concentrations, as expected under the Montreal Protocol (with amendments) and Intergovernmental Panel on Climate Change A1b Scenario. The simulations of the Antarctic ozone hole are compared using commonly used diagnostics: the minimum ozone, the maximum area of ozone below 220 DU, and the ozone mass deficit below 220 DU. Despite the fact that the processes responsible for ozone depletion are reasonably well understood, a wide range of results is obtained. Comparisons with observations indicate that one of the reasons for the model underprediction in ozone hole area is the tendency for models to underpredict, by up to 35%, the area of low temperatures responsible for polar stratospheric cloud formation. Models also typically have species gradients that are too weak at the edge of the polar vortex, suggesting that there is too much mixing of air across the vortex edge. Other models show a high bias in total column ozone which restricts the size of the ozone hole (defined by a 220 DU threshold). The results of those models which agree best with observations are examined in more detail. For several models the ozone hole does not disappear this century but a small ozone hole of up to three million square kilometers continues to occur in most springs even after 2070.

Transient climate change simulations with a coupled atmosphere–ocean GCM including the tropospheric sulfur cycle

The time-dependent climate response to changing concentrations of greenhouse gases and sulfate aerosols is studied using a coupled general circulation model of the atmosphere and the ocean (ECHAM4/OPYC3). The concentrations of the well-mixed greenhouse gases like CO2, CH4, N2O, and CFCs are prescribed for the past (1860–1990) and projected into the future according to International Panel on Climate Change (IPCC) scenario IS92a. In addition, the space–time distribution of tropospheric ozone is prescribed, and the tropospheric sulfur cycle is calculated within the coupled model using sulfur emissions of the past and projected into the future (IS92a). The radiative impact of the aerosols is considered via both the direct and the indirect (i.e., through cloud albedo) effect. It is shown that the simulated trend in sulfate deposition since the end of the last century is broadly consistent with ice core measurements, and the calculated radiative forcings from preindustrial to present time are within the uncertainty range estimated by IPCC. Three climate perturbation experiments are performed, applying different forcing mechanisms, and the results are compared with those obtained from a 300-yr unforced control experiment. As in previous experiments, the climate response is similar, but weaker, if aerosol effects are included in addition to greenhouse gases. One notable difference to previous experiments is that the strength of the Indian summer monsoon is not fundamentally affected by the inclusion of aerosol effects. Although the monsoon is damped compared to a greenhouse gas only experiment, it is still more vigorous than in the control experiment. This different behavior, compared to previous studies, is the result of the different land–sea distribution of aerosol forcing. Somewhat unexpected, the intensity of the global hydrological cycle becomes weaker in a warmer climate if both direct and indirect aerosol effects are included in addition to the greenhouse gases. This can be related to anomalous net radiative cooling of the earth’s surface through aerosols, which is balanced by reduced turbulent transfer of both sensible and latent heat from the surface to the atmosphere.

O_3-N_2O correlations from the Atmospheric Chemistry Experiment: revisiting a diagnostic of transport and chemistry in the stratosphere

Our knowledge of stratospheric O3-N2O correlations is extended, and their potential for model-measurement comparison assessed, using data from the Atmospheric Chemistry Experiment (ACE) satellite and the Canadian Middle Atmosphere Model (CMAM). ACE provides the first comprehensive data set for the investigation of interhemispheric, interseasonal, and height-resolved differences of the O_3-N_2O correlation structure. By subsampling the CMAM data, the representativeness of the ACE data is evaluated. In the middle stratosphere, where the correlations are not compact and therefore mainly reflect the data sampling, joint probability density functions provide a detailed picture of key aspects of transport and mixing, but also trace polar ozone loss. CMAM captures these important features, but exhibits a displacement of the tropical pipe into the Southern Hemisphere (SH). Below about 21 km, the ACE data generally confirm the compactness of the correlations, although chemical ozone loss tends to destroy the compactness during late winter/spring, especially in the SH. This allows a quantitative comparison of the correlation slopes in the lower and lowermost stratosphere (LMS), which exhibit distinct seasonal cycles that reveal the different balances between diabatic descent and horizontal mixing in these two regions in the Northern Hemisphere (NH), reconciling differences found in aircraft measurements, and the strong role of chemical ozone loss in the SH. The seasonal cycles are qualitatively well reproduced by CMAM, although their amplitude is too weak in the NH LMS. The correlation slopes allow a "chemical" definition of the LMS, which is found to vary substantially in vertical extent with season.

Maximising umami taste in meat using natural ingredients: effects on chemistry, sensory perception and hedonic liking in young and old consumers

BACKGROUND: Umami taste in foods is elicited predominantly by the presence of glutamic acid and 5’-ribonucleotides, which act synergistically. This study aimed to use natural ingredients to maximise umami taste of a meat formulation and determine effects on liking of older consumers. METHODS: Cooked meat products with added natural ingredients (yeast extract, mycoscent, shiitake extract, tomato puree, soy sauce and soy bean paste) or monosodium glutamate (MSG) were prepared and compared to a control sample analytically (umami compounds), sensorially (sensory profile) and hedonically (liking by younger and older volunteers). Taste detection thresholds of sodium chloride and MSG of volunteers were collected. RESULTS: Four of the seven cooked meat products developed had a significantly higher content of umami-contributing compounds compared to the control. All products, except those containing MSG or tomato puree, were scored (by trained sensory panel) perceptually significantly higher in umami and / or salty taste compared to the control. Consumer tests showed a correlation of liking by the older cohort with perceived saltiness (ρ=0.76). CONCLUSION: The addition of natural umami-containing ingredients during the cooking of meat can provide enhanced umami and salty taste characteristics, this can lead to increased liking by some consumers, particularly those with raised taste detection thresholds.