ALBERT

Description: : Multi-Image Genome (MIG) viewer is a web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. This methodology has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects. Availability: MIG is available at https://mig.molbiol.ox.ac.uk/mig/ Contact: simon.mcgowan@imm.ox.ac.uk

Description: Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specificity allowing cleavage of degenerate ‘star’ sites. Additionally, uncharacterized restriction endonucleases and engineered variants present novel activities. Traditionally, restriction endonuclease activity is assayed on simple substrates such as plasmids and synthesized oligonucleotides. We present and use high-throughput Illumina sequencing-based strategies to assay the sequence specificity and flanking sequence preference of restriction endonucleases. The techniques use fragmented DNA from sequenced genomes to quantify restriction endonuclease cleavage on a complex genomic DNA substrate in a single reaction. By mapping millions of restriction site–flanking reads back to the Escherichia coli and Drosophila melanogaster genomes we were able to quantitatively characterize the cognate and star site activity of EcoRI and MfeI and demonstrate genome-wide decreases in star activity with engineered high-fidelity variants EcoRI-HF and MfeI-HF, as well as quantify the influence on MfeI cleavage conferred by flanking nucleotides. The methods presented are readily applicable to all type II restriction endonucleases that cleave both strands of double-stranded DNA.

Description: We present a new submm/mm galaxy counterpart identification technique which builds on the use of Spitzer Infrared Array Camera (IRAC) colours as discriminators between likely counterparts and the general IRAC galaxy population. Using 102 radio- and Submillimeter Array-confirmed counterparts to AzTEC sources across three fields [Great Observatories Origins Deep Survey-North, -South and Cosmic Evolution Survey (COSMOS)], we develop a non-parametric IRAC colour–colour characteristic density distribution, which, when combined with positional uncertainty information via likelihood ratios, allows us to rank all potential IRAC counterparts around submillimetre galaxies (SMGs) and calculate the significance of each ranking via the reliability factor. We report all robust and tentative radio counterparts to SMGs, the first such list available for AzTEC/COSMOS, as well as the highest ranked IRAC counterparts for all AzTEC SMGs in these fields as determined by our technique. We demonstrate that the technique is free of radio bias and thus applicable regardless of radio detections. For observations made with a moderate beam size (~18 arcsec), this technique identifies ~85 per cent of SMG counterparts. For much larger beam sizes (30 arcsec), we report identification rates of 33–49 per cent. Using simulations, we demonstrate that this technique is an improvement over using positional information alone for observations with facilities such as AzTEC on the Large Millimeter Telescope and Submillimeter Common User Bolometer Array 2 on the James Clerk Maxwell Telescope.

Description: We present a large-scale study of the X-ray properties and near-IR-to-radio spectral energy distributions (SEDs) of submillimetre galaxies (SMGs) detected at 1.1 mm with the AzTEC instrument across a ~1.2 square degree area of the sky. Combining deep 2–4 Ms Chandra data with Spitzer IRAC/MIPS and Very Large Array data within the Great Observatories Origins Deep Survey North (GOODS-N), GOODS-S and COSMOS fields, we find evidence for active galactic nucleus (AGN) activity in ~14 per cent of 271 AzTEC SMGs, ~28 per cent considering only the two GOODS fields. Through X-ray spectral modelling and multiwavelength SED fitting using Monte Carlo Markov chain techniques to Siebenmorgen et al. (AGN) and Efstathiou, Rowan-Robinson & Siebenmorgen (starburst) templates, we find that while star formation dominates the IR emission, with star formation rates (SFRs) ~100–1000 M yr –1 , the X-ray emission for most sources is almost exclusively from obscured AGNs, with column densities in excess of 10 23 cm –2 . Only for ~6 per cent of our sources do we find an X-ray-derived SFR consistent with NIR-to-radio SED derived SFRs. Inclusion of the X-ray luminosities as a prior to the NIR-to-radio SED effectively sets the AGN luminosity and SFR, preventing significant contribution from the AGN template. Our SED modelling further shows that the AGN and starburst templates typically lack the required 1.1 mm emission necessary to match observations, arguing for an extended, cool dust component. The cross-correlation function between the full samples of X-ray sources and SMGs in these fields does not indicate a strong correlation between the two populations at large scales, suggesting that SMGs and AGNs do not necessarily trace the same underlying large-scale structure. Combined with the remaining X-ray-dim SMGs, this suggests that sub-mm-bright sources may evolve along multiple tracks, with X-ray-detected SMGs representing transitionary objects between periods of high star formation and AGN activity, while X-ray-faint SMGs represent a brief starburst phase of more normal galaxies.

Description: The ability of an organism to detect threats is fundamental to mounting a successful defense and this is particularly important when resisting parasites. Early detection of parasites allows for initiation of defense mechanisms, which are vital in mitigating the cost of infection and are likely to be especially important in social species, particularly those whose life history makes parasite pressure more significant. However, understanding the relative strength of behavioral responses in different species and situations is still limited. Here, we test the response of individual ants to fungal parasites in 3 different contexts, for 4 ant species with differing life histories. We found that ants from all 4 species were able to detect fungi on their food, environment, and nest mates and initiate avoidance or upregulate grooming behaviors accordingly to minimize the threat to themselves and the colony. Individuals avoided fungal-contaminated surfaces and increased grooming levels in response to fungal-contaminated nest mates. Ants from all species responded qualitatively in a similar way although the species differed quantitatively in some respects that may relate to life-history differences. The results show that ants of multiple species are capable of recognizing fungal threats in various contexts. The recognition of parasite threats may play an important role in enabling ant colonies to deal with the ever-present threat from disease.

Description: We present Southern African Large Telescope follow-up observations of seven massive clusters detected by the Atacama Cosmology Telescope (ACT) on the celestial equator using the Sunyaev–Zel'dovich (SZ) effect. We conducted multi-object spectroscopic observations with the Robert Stobie Spectrograph in order to measure galaxy redshifts in each cluster field, determine the cluster line-of-sight velocity dispersions, and infer the cluster dynamical masses. We find that the clusters, which span the redshift range 0.3 〈  z  〈 0.55, range in mass from (5–20) 10 14  M ( M 200 c ). Their masses, given their SZ signals, are similar to those of Southern hemisphere ACT clusters previously observed using Gemini and the VLT. We note that the brightest cluster galaxy in one of the systems studied, ACT-CL J0320.4+0032 at z  = 0.38, hosts a type II quasar. Only a handful of such systems are currently known, and therefore ACT-CL J0320.4+0032 may be a rare example of a very massive halo in which quasar-mode feedback is actively taking place.

Description: Using a radio-quiet subsample of the Sloan Digital Sky Survey spectroscopic quasar catalogue, spanning redshifts 0.5–3.5, we derive the mean millimetre and far-infrared quasar spectral energy distributions (SEDs) via a stacking analysis of Atacama Cosmology Telescope and Herschel -Spectral and Photometric Imaging REceiver data. We constrain the form of the far-infrared emission and find 3–4 evidence for the thermal Sunyaev–Zel'dovich (SZ) effect, characteristic of a hot ionized gas component with thermal energy (6.2 ± 1.7) x 10 60  erg. This amount of thermal energy is greater than expected assuming only hot gas in virial equilibrium with the dark matter haloes of (1–5) x 10 12 h –1 M that these systems are expected to occupy, though the highest quasar mass estimates found in the literature could explain a large fraction of this energy. Our measurements are consistent with quasars depositing up to $(14.5 \pm 3.3)\tau _8^{-1}$  per cent of their radiative energy into their circumgalactic environment if their typical period of quasar activity is 8 x 10 8 yr. For high quasar host masses, ~10 13 h –1 M , this percentage will be reduced. Furthermore, the uncertainty on this percentage is only statistical and additional systematic uncertainties enter at the 40 per cent level. The SEDs are dust dominated in all bands and we consider various models for dust emission. While sufficiently complex dust models can obviate the SZ effect, the SZ interpretation remains favoured at the 3–4 level for most models.

Description: We combine Spitzer and Herschel data of the star-forming region N11 in the Large Magellanic Cloud (LMC) to produce detailed maps of the dust properties in the complex and study their variations with the interstellar-medium conditions. We also compare Atacama Pathfinder EXperiment/Large APEX Bolometer Camera (APEX/LABOCA) 870 μm observations with our model predictions in order to decompose the 870 μm emission into dust and non-dust [free–free emission and CO(3–2) line] contributions. We find that in N11, the 870 μm can be fully accounted for by these three components. The dust surface density map of N11 is combined with H  i and CO observations to study local variations in the gas-to-dust mass ratios. Our analysis leads to values lower than those expected from the LMC low-metallicity as well as to a decrease of the gas-to-dust mass ratio with the dust surface density. We explore potential hypotheses that could explain the low ‘observed’ gas-to-dust mass ratios (variations in the X CO factor, presence of CO-dark gas or of optically thick H  i or variations in the dust abundance in the dense regions). We finally decompose the local spectral energy distributions (SEDs) using a principal component analysis (i.e. with no a priori assumption on the dust composition in the complex). Our results lead to a promising decomposition of the local SEDs in various dust components (hot, warm, cold) coherent with that expected for the region. Further analysis on a larger sample of galaxies will follow in order to understand how unique this decomposition is or how it evolves from one environment to another.

Description: Journal of Hydrometeorology, Volume 20, Issue 3, Page 447-466, March 2019. 〈br/〉

Description: Merging galaxy clusters with radio relics provide rare insights to the merger dynamics as the relics are created by the violent merger process. We demonstrate one of the first uses of the properties of the radio relic to reduce the uncertainties of the dynamical variables and determine the three-dimensional (3D) configuration of a cluster merger, ACT-CL J0102-4915, nicknamed El Gordo. From the double radio relic observation and the X-ray observation of a comet-like gas morphology induced by motion of the cool core, it is widely believed that El Gordo is observed shortly after the first core passage of the subclusters. We employ a Monte Carlo simulation to investigate the 3D configuration and dynamics of El Gordo. Using the polarization fraction of the radio relic, we constrain the estimate of the angle between the plane of the sky and the merger axis to be $\alpha = 21\mathrm{^{\circ }}\pm ^9_{11}$ . We find the relative 3D merger speed of El Gordo to be $2400\pm ^{400}_{200}\,\mathrm{km\,s}^{-1}$ at pericentre. The two possible estimates of the time since pericentre (TSP) are $0.46\pm ^{0.09}_{0.16}$ and $0.91\pm ^{0.22}_{0.39}$ Gyr for the outgoing and returning scenario, respectively. We put our estimates of the TSP into context by showing that if the time-averaged shock velocity is approximately equal to or smaller than the pericentre velocity of the corresponding subcluster in the centre-of-mass frame, the two subclusters are more likely to be moving towards, rather than away, from each other, post apocentre. We compare and contrast the merger scenario of El Gordo with that of the Bullet Cluster, and show that this late-stage merging scenario explains why the south-east (SE) dark matter lensing peak of El Gordo is closer to the merger centre than the SE cool core.