Computational simulation of mechanism and isotope effects on acetal heterolysis as a model for glycoside hydrolysis.

DFT calculations for the equilibrium isotope effect for deuterium substitution at the anomeric centre Cα in 2-(p-nitrophenoxy)tetrahydropyran with continuum solvation show significant variation in the range of relative permittivity 2 ≤ ε ≤ 10. One-dimensional scans of potential energy (with implicit solvation by water) or of free energy (from QM/MM potentials of mean force with explicit aqueous solvation with a hybrid AM1/OPLS method) for heterolysis of the bond between Cα and the nucleofuge do not show a transition state. A two-dimensional free-energy surface that considers also the distance between Cα and a nucleophilic water indicates a pre-association DN*ANint‡ mechanism with a transition state involving nucleophilic attack upon an ion-pair intermediate, and this is supported by good agreement between the mean values of the calculated and experimental α-D KIEs. However, the magnitudes of the standard deviations about the mean values for the making and breaking C–O bonds suggest that the transition state is rather plastic, with Cα–Onu ≈ 2 ± 0.4 Å and Cα–Olg ≈ 3 ± 0.5 Å. Not only is nucleophilic solvent assistance necessary, but there is also evidence for electrophilic assistance through specific hydrogen bonding to the nucleofuge

Dark matter annihilation and decay in dwarf spheroidal galaxies: The classical and ultrafaint dSphs

Dwarf spheroidal (dSph) galaxies are prime targets for present and future gamma-ray telescopes hunting for indirect signals of particle dark matter. The interpretation of the data requires careful assessment of their dark matter content in order to derive robust constraints on candidate relic particles. Here, we use an optimised spherical Jeans analysis to reconstruct the `astrophysical factor' for both annihilating and decaying dark matter in 21 known dSphs. Improvements with respect to previous works are: (i) the use of more flexible luminosity and anisotropy profiles to minimise biases, (ii) the use of weak priors tailored on extensive sets of contamination-free mock data to improve the confidence intervals, (iii) systematic cross-checks of binned and unbinned analyses on mock and real data, and (iv) the use of mock data including stellar contamination to test the impact on reconstructed signals. Our analysis provides updated values for the dark matter content of 8 `classical' and 13 `ultrafaint' dSphs, with the quoted uncertainties directly linked to the sample size; the more flexible parametrisation we use results in changes compared to previous calculations. This translates into our ranking of potentially-brightest and most robust targets---viz., Ursa Minor, Draco, Sculptor---, and of the more promising, but uncertain targets---viz., Ursa Major 2, Coma---for annihilating dark matter. Our analysis of Segue 1 is extremely sensitive to whether we include or exclude a few marginal member stars, making this target one of the most uncertain. Our analysis illustrates challenges that will need to be addressed when inferring the dark matter content of new `ultrafaint' satellites that are beginning to be discovered in southern sky surveys.Comment: 19 pages, 14 figures, submitted to MNRAS. Supplementary material available on reques

Large-scale survey of seasonal drinking water quality in Malawi using in situ tryptophan-like fluorescence and conventional water quality indicators

Faecally-contaminated drinking water is a risk to human health, with the greatest risks to those living in developing countries. UN Sustainable Development Goal 6 aims to address this issue. Tryptophan-like fluorescence (TLF) shows potential as a rapid method for detecting microbial contamination in drinking water, which could reduce the spread of waterborne diseases. This study is the first to investigate the effectiveness of TLF for a large-scale survey using a randomised, spot-sampling approach. The large-scale survey took place in Malawi, sub-Saharan Africa, in the dry season (n = 183). A subset of sources were revisited at the end of the following wet season (n = 41). The effectiveness of TLF was assessed by comparing TLF results to thermotolerant coliforms (TTC), humic-like fluorescence (HLF), inorganic hydrochemical data and sanitary risk scores. The most prominent differences in microbial water quality were observed between source types, with little variation between districts and seasons. TLF, TTCs, turbidity and sanitary risk scores were all elevated at alternative sources (shallow wells and tap stands) compared to hand-pumped boreholes. In the dry season, 18% of hand-pumped boreholes showed TTC contamination, which increase to 21% in the wet season. Groundwater recharge processes are likely responsible for seasonal variability of inorganic hydrochemistry at hand-pumped boreholes. TLF was able to distinguish no and low WHO risk classes (TTC 0–9 cfu/100 mL) from medium, high and very high risk classes (TTC 10 – >1000 cfu/100 mL). TLF failed to distinguish between no and low risk classes, which limits the use of TLF for assessing water quality to drinking water standards. This dataset indicates that HLF may raise baseline TLF for samples with low TLF values, increasing false positives. Therefore, TLF is better suited as a rapid high-level water quality screening tool to assess moderate and high levels of faecal contamination

Tryptophan-like fluorescence as a high-level screening tool for detecting microbial contamination in drinking water

Regular monitoring of drinking water quality is vital to identify contamination of potable water supplies. Testing for microbial contamination is important to prevent transmission of waterborne disease, but establishing and maintaining a water quality monitoring programme requires sustained labour, consumables and resources. In low resource settings such as developing countries, this can prove difficult, but measuring microbial contamination is listed as a requirement of reaching the UN's Sustainable Development Goal 6 for water and sanitation. A nine-month water quality monitoring programme was conducted in rural Malawi to assess the suitability of tryptophan-like fluorescence (TLF), an emerging method for rapidly detecting microbial contamination, as a drinking water quality monitoring tool. TLF data was compared with thermotolerant coliforms (TTCs, E. coli) and inorganic hydrochemical parameters. A large (n = 235) temporal dataset was collected from five groundwater drinking water sources, with samples collected once or twice weekly depending on the season. The results show that TLF can indicate a broader contamination risk but is not as sensitive to short term variability when compared to other faecal indicators. This is likely due to a broad association of TLF with elevated DOC concentrations from a range of different sources. Elevated TLF may indicate preferential conditions for the persistence of TTCs and/or E. coli, but not necessarily a public health risk from microbial contamination. TLF is therefore a more precautionary risk indicator than microbial culturing techniques and could prove useful as a high-level screening tool for initial risk assessment. For widespread use of TLF to be successful, standardisation of TLF values associated with different levels of risk is required, however, this study highlights the difficulties of equating TLF thresholds to TTCs or E. coli data because of the influence of DOC/HLF on the TLF signal

Periodic "stick-slip" transition within a continuum model for entangled supramolecular polymers

We investigate shear flow instabilities using a recently-derived constitutive law, designed for describing the rheology of entangled telechelic polymers. The continuum model displays shear banding, often accompanied by a strong elastic recoil in the transient response, which appears as an "apparent'" wall slip. For certain parameters, the model also displays a novel "apparent" stick-slip behavior, giving rise to strong nonlinear oscillations in the stress response driven by a repeating cycle of elastic recoil followed by diffusive rehomogenization of the flow. We elucidate the detailed mechanism behind this oscillatory response, demonstrating that it arises from a competition between shear-induced breaking of sticky bonds, which leads to recoil and banding, and a diffusive rehomogenization of the flow. We discuss the relation between the apparent stick-slip in our continuum model with similar behavior in "true" wall slip

Kondo Insulator: p-wave Bose Condensate of Excitons

In the Anderson lattice model for a mixed-valent system, the $d-f$ hybridization can possess a $p$-wave symmetry. The strongly-correlated insulating phase in the mean-field approximation is shown to be a $p$-wave Bose condensate of excitons with a spontaneous lattice deformation. We study the equilibrium and linear response properties across the insulator-metal transition. Our theory supports the empirical correlation between the lattice deformation and the magnetic susceptibility and predicts measurable ultrasonic and high-frequency phonon behavior in mixed-valent semiconductors.Comment: 5 pages, 3 encapsulated PostScript figure

Tracing carbon and nitrogen microbial assimilation in suspended particles in freshwaters

The dynamic interactions between dissolved organic matter (DOM) and particulate organic matter (POM) are central in nutrient cycling in freshwater ecosystems. However, the molecular-level mechanisms of such interactions are still poorly defined. Here, we study spatial differences in the chemical (i.e., individual proteinaceous amino acids) and microbial (i.e., 16S rRNA) composition of suspended sediments in the River Chew, UK. We then applied a compound-specific stable isotope probing (SIP) approach to test the potential assimilation of 13C,15N-glutamate (Glu) and 15N-NO3− into proteinaceous biomass by particle-associated microbial communities over a 72-h period. Our results demonstrate that the composition of suspended particles is strongly influenced by the effluent of sewage treatment works. Fluxes and percentages of assimilation of both isotopically labelled substrates into individual proteinaceous amino acids showed contrasting dynamics in processing at each site linked to primary biosynthetic metabolic pathways. Preferential assimilation of the organic molecule glutamate and evidence of its direct assimilation into newly synthesised biomass was obtained. Our approach provides quantitative molecular information on the mechanisms by which low molecular weight DOM is mineralised in the water column compared to an inorganic substrate. This is paramount for better understanding the processing and fate of organic matter in aquatic ecosystems