Highly efficient bi-allelic mutation rates using TALENs in Xenopus tropicalis

In the past decade, Xenopus tropicalis has emerged as a powerful new amphibian genetic model system, which offers all of the experimental advantages of its larger cousin, Xenopus laevis. Here we investigated the efficiency of transcription activator-like effector nucleases (TALENs) for generating targeted mutations in endogenous genes in X. tropicalis. For our analysis we targeted the tyrosinase (oculocutaneous albinism IA) (tyr) gene, which is required for the production of skin pigments, such as melanin. We injected mRNA encoding TALENs targeting the first exon of the tyr gene into two-cell-stage embryos. Surprisingly, we found that over 90% of the founder animals developed either partial or full albinism, suggesting that the TALENs induced bi-allelic mutations in the tyr gene at very high frequency in the F0 animals. Furthermore, mutations tyr gene were efficiently transmitted into the F1 progeny, as evidenced by the generation of albino offspring. These findings have far reaching implications in our quest to develop efficient reverse genetic approaches in this emerging amphibian model

Design of crystal-like aperiodic solids with selective disorder--phonon coupling

Functional materials design normally focuses on structurally-ordered systems because disorder is considered detrimental to many important physical properties. Here we challenge this paradigm by showing that particular types of strongly-correlated disorder can give rise to useful characteristics that are inaccessible to ordered states. A judicious combination of low-symmetry building unit and high-symmetry topological template leads to aperiodic "procrystalline" solids that harbour this type of topological disorder. We identify key classes of procrystalline states together with their characteristic diffraction behaviour, and establish a variety of mappings onto known and target materials. Crucially, the strongly-correlated disorder we consider is associated with specific sets of modulation periodicities distributed throughout the Brillouin zone. Lattice dynamical calculations reveal selective disorder-phonon coupling to lattice vibrations characterised by these same periodicities. The principal effect on the phonon spectrum is to bring about dispersion in energy rather than wave-vector, as in the poorly-understood "waterfall" effect observed in relaxor ferroelectrics. This property of procrystalline solids suggests a mechanism by which strongly-correlated topological disorder might allow new and useful functionalities, including independently-optimised thermal and electronic transport behaviour as required for high-performance thermoelectrics.Comment: 4 figure

Kinetics of Facultative Heterochromatin and Polycomb Group Protein Association with the Herpes Simplex Viral Genome during Establishment of Latent Infection

ABSTRACT The herpes simplex virus (HSV) genome is associated with heterochromatic histone modifications, including trimethylation of the lysine 27 residue of histone H3 (H3K27me3), during latent infection of neurons. Here we have examined the kinetics of general chromatin and H3K27me3 association with the viral genome during establishment of latent infection. Using both wild-type virus and a mutant virus that is unable to undergo replication in neurons, we found that histone H3 associates with viral gene promoters by 7 days postinfection (dpi). Levels of H3K27me3 were low at 7 dpi but increased dramatically by 14 dpi. Hence, general chromatin association and/or other factors may play a key role(s) in the initial silencing of lytic genes, and H3K27me3 may play a role in further suppression of the genome and/or the maintenance of latency. A component of Polycomb repressive complex 2 (PRC2), which mediates the addition of K27me3 to histone H3 (Suz12), was also recruited by 14 dpi. We have shown previously that the levels of H3K27me3 during latent infection are increased in the presence of the latency-associated transcript (LAT). However, the initial targeting of PRC2 was not found to be dependent on the LAT. We found that a component of the PRC1 complex (Bmi1), which binds to H3K27me3, was not enriched at promoters found previously to be enriched for H3K27me3. Our results are consistent with (i) chromatinization of viral DNA or other mechanisms causing the initial silencing of HSV lytic genes and (ii) facultative heterochromatin maintaining that silencing during latent infection of neurons

Harm minimisation for the management of self-harm: a mixed-methods analysis of electronic health records in secondary mental healthcare

BACKGROUND: Prevalence of self-harm in the UK was reported as 6.4% in 2014. Despite sparse evidence for effectiveness, guidelines recommend harm minimisation; a strategy in which people who self-harm are supported to do so safely. AIMS: To determine the prevalence, sociodemographic and clinical characteristics of those who self-harm and practise harm minimisation within a London mental health trust. METHOD: We included electronic health records for patients treated by South London and Maudsley NHS Trust. Using an iterative search strategy, we identified patients who practise harm minimisation, then classified the approaches using a content analysis. We compared the sociodemographic characteristics with that of a control group of patients who self-harm and do not use harm minimisation. RESULTS: In total 22 736 patients reported self-harm, of these 693 (3%) had records reporting the use of harm-minimisation techniques. We coded the approaches into categories: (a) ‘substitution’ (>50% of those using harm minimisation), such as using rubber bands or using ice; (b) ‘simulation’ (9%) such as using red pens; (c) ‘defer or avoid’ (7%) such as an alternative self-injury location; (d) ‘damage limitation’ (9%) such as using antiseptic techniques; the remainder were unclassifiable (24%). The majority of people using harm minimisation described it as helpful (>90%). Those practising harm minimisation were younger, female, of White ethnicity, had previous admissions and were less likely to have self-harmed with suicidal intent. CONCLUSIONS: A small minority of patients who self-harm report using harm minimisation, primarily substitution techniques, and the large majority find harm minimisation helpful. More research is required to determine the acceptability and effectiveness of harm-minimisation techniques and update national clinical guidelines

Co-combustion of refuse derived fuel with coal in a fluidised bed combustor

Power generation from biomass is an attractive technology which utilizes municipal solid waste-based refused derived fuel. In order to explain the behavior of biomass-fired fluidized bed incinerator, biomass sources from refuse derived fuel was co-fired with coal in a 0.15 m diameter and 2.3 m high fluidized bed combustor. The combustion efficiency and carbon monoxide emissions were studied and compared with those from pure coal combustion. This study proved that the blending effect had increased the carbon combustion efficiency up to 12% as compared to single MSW-based RDF. Carbon monoxide levels fluctuated between 200-1600 ppm were observed when coal is added. It is evident from this research that efficient co-firing of biomass with coal can be achieved with minimum modification of existing coal-fired boilers

Realistic atomistic structure of amorphous silicon from machine-learning-driven molecular dynamics

Amorphous silicon (a-Si) is a widely studied noncrystalline material, and yet the subtle details of its atomistic structure are still unclear. Here, we show that accurate structural models of a-Si can be obtained using a machine-learning-based interatomic potential. Our best a-Si network is obtained by simulated cooling from the melt at a rate of 1011 K/s (that is, on the 10 ns time scale), contains less than 2% defects, and agrees with experiments regarding excess energies, diffraction data, and 29Si NMR chemical shifts. We show that this level of quality is impossible to achieve with faster quench simulations. We then generate a 4096-atom system that correctly reproduces the magnitude of the first sharp diffraction peak (FSDP) in the structure factor, achieving the closest agreement with experiments to date. Our study demonstrates the broader impact of machine-learning potentials for elucidating structures and properties of technologically important amorphous materials

Co-combustion of agricultural residues with coal in a fluidised bed combustor

Power generation from biomass is an attractive technology that utilizes agricultural residual waste. In order to explain the behavior of biomass-fired fluidised bed incinerator, biomass sources from agricultural residues (rice husk and palm kernel) were co-fired with coal in a 0.15 m diameter and 2.3 m high fluidised bed combustor. The combustion efficiency and carbon monoxide emissions were studied and compared with those for pure coal combustion. Co-combustion of a mixture of biomass with coal in a fluidised bed combustor designed for coal combustion increased combustion efficiency up to 20% depending upon excess air levels. Observed carbon monoxide levels fluctuated between 200 and 900 ppm with the addition of coal. It is evident from this research that efficient co-firing of biomass with coal can be achieved with minimal modifications to existing coal-fired boilers

Goal-oriented a posteriori error estimation for the travel time functional in porous media flows

In this article we consider the a posteriori error estimation and adaptive mesh refinement for the numerical approximation of the travel time functional arising in porous media flows. The key application of this work is in the safety assessment of radioactive waste facilities; in this setting, the travel time functional measures the time taken for a non-sorbing radioactive solute, transported by groundwater, to travel from a potential site deep underground to the biosphere. To ensure the computability of the travel time functional, we employ a mixed formulation of Darcy's law and conservation of mass, together with Raviart-Thomas H(div) conforming finite elements. The proposed a posteriori error bound is derived based on a variant of the standard Dual-Weighted-Residual approximation, which takes into account the lack of smoothness of the underlying functional of interest. The proposed adaptive refinement strategy is tested on both a simple academic test case and a problem based on the geological units found at the Sellafield site in the UK