FlyAtlas: database of gene expression in the tissues of drosophila melanogaster

The FlyAtlas resource contains data on the expression of the genes of Drosophila melanogaster in different tissues (currently 25—17 adult and 8 larval) obtained by hybridization of messenger RNA to Affymetrix Drosophila Genome 2 microarrays. The microarray probe sets cover 13 250 Drosophila genes, detecting 12 533 in an unambiguous manner. The data underlying the original web application (http://flyatlas.org) have been restructured into a relational database and a Java servlet written to provide a new web interface, FlyAtlas 2 (http://flyatlas.gla.ac.uk/), which allows several additional queries. Users can retrieve data for individual genes or for groups of genes belonging to the same or related ontological categories. Assistance in selecting valid search terms is provided by an Ajax ‘autosuggest’ facility that polls the database as the user types. Searches can also focus on particular tissues, and data can be retrieved for the most highly expressed genes, for genes of a particular category with above-average expression or for genes with the greatest difference in expression between the larval and adult stages. A novel facility allows the database to be queried with a specific gene to find other genes with a similar pattern of expression across the different tissues

Adsorbate-induced surface stress, surface strain and surface reconstruction : S on Cu(100) and Ni(100)

Density functional theory (DFT) calculations have been applied to investigate the known difference in behaviour of S adsorption on Cu(100) and Ni(100). Both surfaces form a 0.25 ML (2 × 2) adsorption phase, but while at higher coverage a 0.5 ML c(2 × 2) phase forms on Ni(100), on Cu(100) only a reconstructed 0.47 ML (√17 × √17)R14° structure occurs. Calculations of the energy, structure, and surface stress of (2 × 2) and c(2 × 2) phases on both substrates show there is an energy advantage on both surfaces to form the higher coverage phase, but that both surfaces show local surface strain around the S atoms in the (2 × 2) phase, a phenomenon previously investigated only on Cu(100). More than forty different structural models of the Cu(100)(√17 × √17)R14°-S phase have been investigated. The pseudo-(100)c(2 × 2) structure previously proposed, containing 16 Cu adatoms per unit mesh in the reconstructed layer, is found to be less energetically favourable than many other possible structures, even after taking account of local structural relaxations. Significantly more favourable is a structure with 12 Cu adatoms per (√17 × √17)R14° unit mesh, previously proposed on the basis of scanning tunnelling microscopy (STM), and found to yield simulated STM images in good agreement with experiment. This model has all S atoms in local 4-fold coordinated hollows relative to the Cu atoms below, half being located above Cu adatoms with the remainder lying above the underlying outermost substrate layer. However, an alternative model with only 4 Cu adatoms and with half the S atoms at 3-fold coordinated sites on the periphery of the Cu adatom cluster, has an even lower energy and gives simulated STM images in excellent agreement with experiment

MEIS investigations of surface structure

The early work of the FOM-AMOLF group in Amsterdam clearly demonstrated the potential of medium energy ion scattering (MEIS), typically using 100 keV H+ incident ions, to investigate the structure of surfaces, but most current applications of the method are focussed on near-surface compositional studies of non-crystalline films. However, the key strengths of the MEIS technique, notably the use of blocking curves in double-alignment experiments and absolute yield measurements, are extremely effective in providing detailed near-surface structural information for a wide range of crystalline materials. This potential and the underlying methodology, is illustrated through examples of applications to the study of layer-dependent composition and structure in alloy surfaces, in studies of the surface crystallography of an oxide surface (rutile TiO2(1 1 0)) and in investigations of complex adsorbate-induced reconstruction of metal surfaces, including the pseudo-(1 0 0) reconstruction of Cu(1 1 1) induced by adsorption of atomic N and molecular methylthiolate (CH3S–). In addition to the use of calibrated blocking curves, the use of the detailed spectral shape of the surface peak in the scattered ion energy spectra, as a means of providing single-atomic layer resolution of the surface structure, is also discussed

Density functional theory calculations of adsorption-induced surface stress changes

Density functional theory calculations of adsorbate-induced surface stress changes have been performed for a number of adsorbate and overlayer systems for which experimental data exists, namely: oxygen and sulphur adsorption on Ni(1 0 0); oxygen adsorption on W(1 1 0); pseudomorphic growth of Ni on Cu(1 0 0) and of Fe on W(1 1 0); oxygen adsorption on a 5 ML pseudomorphic film of Ni(1 0 0) grown on Cu(1 0 0). The theoretical calculations reproduce all the qualitative features of the experimental data, but there are some significant quantitative differences, most notably for the two atomic adsorbates on the bulk Ni(1 0 0) surface, for which the theoretical stress changes are substantially smaller than the experimental ones, a situation not obviously attributable to experimental error. For the W(1 1 0)/Fe system there is also a marked difference between experiment and theory in the coverage at which key surface stress changes occur

First Results from the DRIFT-IIa Dark Matter Detector

Data from the DRIFT-IIa directional dark matter experiment are presented, collected during a near continuous 6 month running period. A detailed calibration analysis comparing data from gamma-ray, x-ray and neutron sources to a GEANT4 Monte Carlo simulations reveals an efficiency for detection of neutron induced recoils of 94+/-2(stat.)+/-5(sys.)%. Software-based cuts, designed to remove non-nuclear recoil events, are shown to reject 60Co gamma-rays with a rejection factor of better than 8x10-6 for all energies above threshold. An unexpected event population has been discovered and is shown here to be due to the alpha-decay of 222Rn daughter nuclei that have attached to the central cathode. A limit on the flux of neutrons in the Boulby Underground Laboratory is derived from analysis of unshielded and shielded data.Comment: 43 pages, 14 figures, submitted to Astroparticle Physic

The telomerase reverse transcriptase is limiting and necessary for telomerase function in vivo

Mammalian telomerase is essential for the maintenance of telomere length [1–5]. Its catalytic core comprises a reverse transcriptase component (TERT) and an RNA component. While the biochemical role of mammalian TERT is well established [6–11], it is unknown whether it is sufficient for telomere-length maintenance, chromosome stability or other cellular processes. Cells from mice in which the mTert gene had been disrupted showed progressive loss of telomere DNA, a phenotype similar to cells in which the gene encoding the telomerase RNA component (mTR) has been disrupted [1,12]. On prolonged growth, mTert-deficient embryonic stem (ES) cells exhibited genomic instability, aneuploidy and telomeric fusions. ES cells heterozygous for the mTert disruption also showed telomere attrition, a phenotype that differs from heterozygous mTR cells [12]. Thus, telomere maintenance in mammals is carried out by a single, limiting TERT

CASSETTE—clindamycin adjunctive therapy for severe Staphylococcus aureus treatment evaluation: Study protocol for a randomised controlled trial

Background Exotoxins are important virulence factors in Staphylococcus aureus. Clindamycin, a protein synthesis inhibitor antibiotic, is thought to limit exotoxin production and improve outcomes in severe S. aureus infections. However, randomised prospective data to support this are lacking. Methods An open-label, multicentre, randomised controlled trial (RCT) will compare outcome differences in severe S. aureus infection between standard treatment (flucloxacillin/cefazolin in methicillin-susceptible S. aureus; and vancomycin/daptomycin in methicillin-resistant S. aureus) and standard treatment plus an additional clindamycin given for 7 days. We will include a minimum of 60 participants (both adult and children) in the pilot study. Participants will be enrolled within 72 h of an index culture. Severe infections will include septic shock, necrotising pneumonia, or multifocal and non-contiguous skin and soft tissue/osteoarticular infections. Individuals who are immunosuppressed, moribund, with current severe diarrhoea or Clostridiodes difficile infection, pregnant, and those with anaphylaxis to β-lactams or lincosamides will be excluded. The primary outcomes measure is the number of days alive and free (1 or 0) of systemic inflammatory response syndrome (SIRS) within the first 14 days post randomisation. The secondary outcomes measure will include all-cause mortality at 14, 42, and 90 days, time to resolution of SIRS, proportion with microbiological treatment failure, and rate of change of C-reactive protein over time. Impacts of inducible clindamycin resistance, strain types, methicillin susceptibility, and presence of various exotoxins will also be analysed. Discussion This study will assess the effect of adjunctive clindamycin on patient-centred outcomes in severe, toxin-mediated S. aureus infections. The pilot study will provide feasibility for a much larger RCT. Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12617001416381p. Registered on 6 October 2017

The local adsorption geometry of benzenethiolate on Cu(1 0 0)

The local adsorption geometry of benzenethiolate in the ordered c(2 × 6) phase on Cu(1 0 0) has been investigated by a combination of S K-edge near-edge X-ray absorption fine structure (NEXAFS), normal incidence X-ray standing waves (NIXSW) and S 1s scanned-energy mode photoelectron diffraction (PhD). NEXAFS and PhD show that the molecular plane is tilted from the surface normal by 20 ± 15°, while NIXSW clearly identifies the S head-group as occupying the four-fold coordinated hollow sites. PhD shows the S atoms lies 1.34 ± 0.04 Å above the outermost Cu atomic layer, leading to a Cu–S bondlength of 2.25 ± 0.02 Å. The combination of the PhD and NIXSW results shows the Cu surface layer has an outward relaxation of 0.15 ± 0.06 Å. Possible origins for this large adsorbate-induced relaxation are discussed

Track Reconstruction and Performance of DRIFT Directional Dark Matter Detectors using Alpha Particles

First results are presented from an analysis of data from the DRIFT-IIa and DRIFT-IIb directional dark matter detectors at Boulby Mine in which alpha particle tracks were reconstructed and used to characterise detector performance--an important step towards optimising directional technology. The drift velocity in DRIFT-IIa was [59.3 +/- 0.2 (stat) +/- 7.5 (sys)] m/s based on an analysis of naturally-occurring alpha-emitting background. The drift velocity in DRIFT-IIb was [57 +/- 1 (stat) +/- 3 (sys)] m/s determined by the analysis of alpha particle tracks from a Po-210 source. 3D range reconstruction and energy spectra were used to identify alpha particles from the decay of Rn-222, Po-218, Rn-220 and Po-216. This study found that (22 +/- 2)% of Po-218 progeny (from Rn-222 decay) are produced with no net charge in 40 Torr CS2. For Po-216 progeny (from Rn-220 decay) the uncharged fraction is (100 +0 -35)%.Comment: 27 pages, 12 figures, 5 tables. Submitted to Nuclear Instruments and Methods in Physics Research, Section A. Subj-class: Instrumentation and Detector