A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications

SummaryBromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions

Microstructural and mechanical characterisation of Fe-14Cr-0.22Hf alloy fabricated by spark plasma sintering

Fe-14Cr pre-alloyed powder and pure Hf powder were mechanically alloyed to produce powder with nominal composition Fe-14Cr-0.22Hf (wt. %) that was consolidated by the spark plasma sintering (SPS) technique in order to investigate the ability of Hf to produce a nanometric dispersion of oxide particles in a ferritic matrix. Comprehensive microstructural and mechanical characterisation of the as-milled powder and the consolidated material was performed using electron microscopy, X-ray diffraction, atom probe tomography and indentation techniques. It was shown that Hf additions can effectively produce, by internal oxidation, a fine scale dispersion of Hf-O nanoparticles in the consolidated material. A uniform grain structure was produced in the alloy. Although the nanoparticle dispersion was not homogeneous at the finest scale, the resulting dispersion strengthening contributed significantly to the hardness. According to these results, internal oxidation of reactive elements rather than direct addition of oxides may offer additional opportunities in the design and development of oxide dispersion strengthened steels

Evaluation of hazardous airborne carbonyls in five urban roadside dwellings: A comprehensive indoor air assessment in Sri Lanka

Indoor hazardous airborne carbonyls were quantified in five natural-ventilated roadside dwellings in Colombo, Sri Lanka. The total concentrations of all targeted carbonyls ranged from 13.6 to 18.6 mu g/m(3). Formaldehyde (C1) was the most abundant carbonyl, followed by acetaldehyde (C2) and acetone (C3K). The concentrations of C1 and C2 ranged from 3.3 to 8.5 mu g/m(3) and 2.3 to 4.4 mu g/m(3), respectively, which accounted for 23 to 42% and 18 to 26% respectively, to the total quantified carbonyls. The highest carbonyls levels were obtained in the dwelling located in an urban district with a mixture of industrial, commercial and residential areas. Much lower concentrations of carbonyls were measured in a light local traffic value was counted. Moderate correlations between individual combustion markers from vehicular emissions suggest the strong impacts from traffics to the indoor airs. The concentrations of C1 and C2 were compared with international indoor guidelines established by different authorities. A health assessment was conducted by estimation of inhalation cancer risk, implementing the inhalation unit risk values provided by Integrated Risk Information System (IRIS), associated with C1 and C2, which were 6.2 x 10(-5) and 7.7 x 10(-6), respectively. Even though the risks did not reach the action level (1 x 10(-4)), their health impact should not be overlooked. This kick-off indoor monitoring study provides valuable scientific data to the environmental science community since only limit data is available in Sri Lanka

Formalising the Continuous/Discrete Modeling Step

Formally capturing the transition from a continuous model to a discrete model is investigated using model based refinement techniques. A very simple model for stopping (eg. of a train) is developed in both the continuous and discrete domains. The difference between the two is quantified using generic results from ODE theory, and these estimates can be compared with the exact solutions. Such results do not fit well into a conventional model based refinement framework; however they can be accommodated into a model based retrenchment. The retrenchment is described, and the way it can interface to refinement development on both the continuous and discrete sides is outlined. The approach is compared to what can be achieved using hybrid systems techniques.Comment: In Proceedings Refine 2011, arXiv:1106.348

Assessment of the In Vivo Toxicity of Gold Nanoparticles

The environmental impact of nanoparticles is evident; however, their toxicity due to their nanosize is rarely discussed. Gold nanoparticles (GNPs) may serve as a promising model to address the size-dependent biological response to nanoparticles because they show good biocompatibility and their size can be controlled with great precision during their chemical synthesis. Naked GNPs ranging from 3 to 100 nm were injected intraperitoneally into BALB/C mice at a dose of 8 mg/kg/week. GNPs of 3, 5, 50, and 100 nm did not show harmful effects; however, GNPs ranging from 8 to 37 nm induced severe sickness in mice. Mice injected with GNPs in this range showed fatigue, loss of appetite, change of fur color, and weight loss. Starting from day 14, mice in this group exhibited a camel-like back and crooked spine. The majority of mice in these groups died within 21 days. Injection of 5 and 3 nm GNPs, however, did not induce sickness or lethality in mice. Pathological examination of the major organs of the mice in the diseased groups indicated an increase of Kupffer cells in the liver, loss of structural integrity in the lungs, and diffusion of white pulp in the spleen. The pathological abnormality was associated with the presence of gold particles at the diseased sites, which were verified by ex vivo Coherent anti-Stoke Raman scattering microscopy. Modifying the surface of the GNPs by incorporating immunogenic peptides ameliorated their toxicity. This reduction in the toxicity is associated with an increase in the ability to induce antibody response. The toxicity of GNPs may be a fundamental determinant of the environmental toxicity of nanoparticles

Disturbance distance: quantifying forests' vulnerability to disturbance under current and future conditions

Disturbances, both natural and anthropogenic, are critical determinants of forest structure, function, and distribution. The vulnerability of forests to potential changes in disturbance rates remains largely unknown. Here, we developed a framework for quantifying and mapping the vulnerability of forests to changes in disturbance rates. By comparing recent estimates of observed forest disturbance rates over a sample of contiguous US forests to modeled rates of disturbance resulting in forest loss, a novel index of vulnerability, Disturbance Distance, was produced. Sample results indicate that 20% of current US forestland could be lost if disturbance rates were to double, with southwestern forests showing highest vulnerability. Under a future climate scenario, the majority of US forests showed capabilities of withstanding higher rates of disturbance then under the current climate scenario, which may buffer some impacts of intensified forest disturbanceinfo:eu-repo/semantics/publishedVersio

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Galaxy and Mass Assembly (GAMA): merging galaxies and their properties

We derive the close pair fractions and volume merger rates for galaxies in the Galaxy and Mass Assembly (GAMA) survey with −23 < Mr < −17 (ΩM = 0.27, ΩΛ = 0.73, H0 = 100 km s−1 Mpc−1) at 0.01 < z < 0.22 (look-back time of <2 Gyr). The merger fraction is approximately 1.5 per cent Gyr−1 at all luminosities (assuming 50 per cent of pairs merge) and the volume merger rate is ≈3.5 × 10−4 Mpc−3 Gyr−1. We examine how the merger rate varies by luminosity and morphology. Dry mergers (between red/spheroidal galaxies) are found to be uncommon and to decrease with decreasing luminosity. Fainter mergers are wet, between blue/discy galaxies. Damp mergers (one of each type) follow the average of dry and wet mergers. In the brighter luminosity bin (−23 < Mr < −20), the merger rate evolution is flat, irrespective of colour or morphology, out to z ∼ 0.2. The makeup of the merging population does not appear to change over this redshift range. Galaxy growth by major mergers appears comparatively unimportant and dry mergers are unlikely to be significant in the buildup of the red sequence over the past 2 Gyr. We compare the colour, morphology, environmental density and degree of activity (BPT class, Baldwin, Phillips & Terlevich) of galaxies in pairs to those of more isolated objects in the same volume. Galaxies in close pairs tend to be both redder and slightly more spheroid dominated than the comparison sample. We suggest that this may be due to ‘harassment’ in multiple previous passes prior to the current close interaction. Galaxy pairs do not appear to prefer significantly denser environments. There is no evidence of an enhancement in the AGN fraction in pairs, compared to other galaxies in the same volume