ALBERT

Description: Although we are nearing a consensus that most ultraluminous X-ray sources (ULXs) below 10 41 erg s –1 represent stellar mass black holes accreting in a super-Eddington ‘ultraluminous’ accretion state, little is yet established of the physics of this extreme accretion mode. Here, we use a combined X-ray spectral and timing analysis of an XMM–Newton sample of ULXs to investigate this new accretion regime. We start by suggesting an empirical classification scheme that separates ULXs into three classes based on the spectral morphologies observed by Gladstone et al.: a singly peaked broadened disc class, and two-component hard ultraluminous and soft ultraluminous regimes, with the spectra of the latter two classes dominated by the harder and softer component, respectively. We find that at the lowest luminosities ( L X  〈 3 10 39 erg s –1 ) the ULX population is dominated by sources with broadened disc spectra, whilst ULXs with two-component spectra are seen almost exclusively at higher luminosities, suggestive of a distinction between ~Eddington and super-Eddington accretion modes. We find high levels of fractional variability are limited to ULXs with soft ultraluminous spectra, and a couple of the broadened disc sources. Furthermore, the variability in these sources is strongest at high energies, suggesting it originates in the harder of the two spectral components. We argue that these properties are consistent with current models of super-Eddington emission, where a massive radiatively driven wind forms a funnel-like geometry around the central regions of the accretion flow. As the wind provides the soft spectral component this suggests that inclination is the key determinant in the observed two-component X-ray spectra, which is very strongly supported by the variability results if this originates due to clumpy material at the edge of the wind intermittently obscuring our line-of-sight to the spectrally hard central regions of the ULX. The pattern of spectral variability with luminosity in two ULXs that straddle the hard/soft ultraluminous regime boundary is consistent with the wind increasing at higher accretion rates, and thus narrowing the opening angle of the funnel. Hence, this work suggests that most ULXs can be explained as stellar mass black holes accreting at and above the Eddington limit, with their observed characteristics dominated by two variables: accretion rate and inclination.

Description: Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N 6 -adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N 6 -adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY m6 A G-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC m6 A CC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC m6 A GC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY m6 A G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC m6 A GG-3' sites, to 100% at 5'-ACGT m6 A GG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.

Description: The known members of the class of hyperluminous X-ray sources (HLXs) are few in number, yet they are of great interest as they are regarded as the likeliest intermediate-mass black hole (IMBH) candidates amongst the wider population of ultraluminous X-ray sources (ULXs). Here we report optical photometry and spectroscopy of an HLX candidate associated with the galaxy IC 4320, that reveal it is a background AGN. We discuss the implications of the exclusion of this object from the small number of well-studied HLXs, that appears to accentuate the difference in characteristics between the good IMBH candidate ESO 243-49 HLX-1 and the small handful of other HLXs.

Description: Motivation: Second-generation sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem. In this article, we describe a new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error. Our method transforms large numbers of paired-end reads into a much smaller number of longer ‘super-reads’. The use of super-reads allows us to assemble combinations of Illumina reads of differing lengths together with longer reads from 454 and Sanger sequencing technologies, making it one of the few assemblers capable of handling such mixtures. We call our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced ‘mazurka’). Results: We evaluate the performance of MaSuRCA against two of the most widely used assemblers for Illumina data, Allpaths-LG and SOAPdenovo2, on two datasets from organisms for which high-quality assemblies are available: the bacterium Rhodobacter sphaeroides and chromosome 16 of the mouse genome. We show that MaSuRCA performs on par or better than Allpaths-LG and significantly better than SOAPdenovo on these data, when evaluated against the finished sequence. We then show that MaSuRCA can significantly improve its assemblies when the original data are augmented with long reads. Availability: MaSuRCA is available as open-source code at ftp://ftp.genome.umd.edu/pub/MaSuRCA/ . Previous (pre-publication) releases have been publicly available for over a year. Contact: alekseyz@ipst.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Sedimentary magnetizations are fundamental to palaeomagnetism, but the mechanisms that control remanence acquisition remain poorly constrained. Observed sedimentary natural remanent magnetizations are often orders of magnitude smaller than the saturation remanent magnetization of the same sediment, which indicates inefficient remanence acquisition. We present a statistical model, based on the von Mises–Fisher distribution, in which magnetic particle reorientations towards an ambient field are considered, without representing the physics of the magnetization acquisition process. The results provide insights into the nature of sedimentary magnetizations. Specifically, an assemblage of randomly oriented magnetic particles can acquire a high-fidelity palaeomagnetic signal with only small rotations (in some cases 〈1°) of particles towards the ambient field direction. This demonstrates that the action of a geomagnetic torque on individual magnetic mineral particle orientation may be minor, and that a weak directional bias on an assemblage of particles could be responsible for the typically observed inefficiency of sedimentary remanence acquisition. Additionally, we demonstrate that weak fields produce sedimentary magnetizations with larger directional uncertainties. For natural sediments, however, these uncertainties appear to be small enough to allow reliable recording of directional geomagnetic field behaviour during periods with weak fields, such as palaeomagnetic reversals and excursions.

Description: A sub-set of the brightest ultraluminous X-ray sources (ULXs), with X-ray luminosities well above 10 40  erg s –1 , typically have energy spectra which can be well described as hard power laws, and short-term variability in excess of ~10 per cent. This combination of properties suggests that these ULXs may be some of the best candidates to host intermediate-mass black holes (IMBHs), which would be accreting at sub-Eddington rates in the hard state seen in Galactic X-ray binaries. In this work, we present a temporal and spectral analysis of all of the available XMM–Newton data from one such ULX, the previously poorly studied 2XMM J143242.1–440939, located in NGC 5643. We report that its high-quality EPIC spectra can be better described by a broad, thermal component, such as an advection-dominated disc or an optically thick Comptonizing corona. In addition, we find a hint of a marginal change in the short-term variability which does not appear to be clearly related to the source unabsorbed luminosity. We discuss the implications of these results, excluding the possibility that the source may be host an IMBH in a low state, and favouring an interpretation in terms of super-Eddington accretion on to a black hole of stellar origin. The properties of NGC 5643 ULX1 allow us to associate this source to the population of the hard/ultraluminous ULX class.

Description: Chromatin remodelers are essential for establishing and maintaining the placement of nucleosomes along genomic DNA. Yet how chromatin remodelers recognize and respond to distinct chromatin environments surrounding nucleosomes is poorly understood. Here, we use Lac repressor as a tool to probe how a DNA-bound factor influences action of the Chd1 remodeler. We show that Chd1 preferentially shifts nucleosomes away from Lac repressor, demonstrating that a DNA-bound factor defines a barrier for nucleosome positioning. Rather than an absolute block in sliding, the barrier effect was achieved by altered rates of nucleosome sliding that biased redistribution of nucleosomes away from the bound Lac repressor site. Remarkably, in addition to slower sliding toward the LacO site, the presence of Lac repressor also stimulated sliding in the opposite direction. These experiments therefore demonstrate that Chd1 responds to the presence of a bound protein on both entry and exit sides of the nucleosome. This sensitivity to both sides of the nucleosome allows for a faster and sharper response than would be possible by responding to only the entry side, and we speculate that dual entry/exit sensitivity is also important for regularly spaced nucleosome arrays generated by Chd1 and the related ISWI remodelers.

Description: We present a multimission X-ray analysis of a bright (peak observed 0.3–10 keV luminosity of ~6  x 10 40 erg s –1 ), but relatively highly absorbed ultraluminous X-ray source (ULX) in the edge-on spiral galaxy NGC 5907. The ULX is spectrally hard in X-rays ( ~ 1.2–1.7, when fitted with an absorbed power law), and has a previously reported hard spectral break consistent with it being in the ultraluminous accretion state. It is also relatively highly absorbed for a ULX, with a column of ~0.4–0.9  x 10 22 atom cm –2 in addition to the line-of-sight column in our Galaxy. Although its X-ray spectra are well represented by accretion disc models, its variability characteristics argue against this interpretation. The ULX spectra instead appear dominated by a cool, optically thick Comptonizing corona. We discuss how the measured 9 per cent rms variability and a hardening of the spectrum as its flux diminishes might be reconciled with the effects of a very massive, radiatively driven wind and subtle changes in the corona, respectively. We speculate that the cool disc-like spectral component thought to be produced by the wind in other ULXs may be missing from the observed spectrum due to a combination of a low temperature (~0.1 keV), and the high column to the ULX. We find no evidence, other than its extreme X-ray luminosity, for the presence of an intermediate mass black hole (MsBHs, ~ 10 2 –10 4 M ) in this object. Rather, the observations can be consistently explained by a massive ( 20 M ) stellar remnant black hole in a super-Eddington accretion state.

Description: Teniswood, C. M. H., Roberts, D., Howard, W. R., and Bradby, J. E. 2013. A quantitative assessment of the mechanical strength of the polar pteropod Limacina helicina antarctica s hell. – ICES Journal of Marine Science, 70: . This work directly measures the mechanical properties of pteropod shells collected from the Southern Ocean on the 2007 midsummer Subantarctic Zone Sensitivity to Environmental Change (SAZ-Sense) voyage. Shells from the common Southern Ocean pteropod Limacina helicina antarctica were subjected to mechanical analyses in combination with detailed morphological studies. Average hardness and modulus of 2.30 ± 0.07 GPa and 45.27 ± 0.91 GPa, respectively were calculated from several hundred nanoindentation measurements taken from multiple positions across twelve shells of the same species collected under identical conditions. Quantitative data such as these are critical to establish a reference point for future comparative studies and to both understand and evaluate the implications of further ocean acidification on the structural integrity of these common polar calcifiers, particularly in light of their role in the Southern Ocean carbon cycle and food web.

Description: We consider the existence of bibundles, in other words locally trivial principal G spaces with commuting left and right G actions. We show that their existence is closely related to the structure of the group Out( G ) of outer automorphisms of G . We also develop a classifying theory for bibundles. The theory is developed in full generality for ( H , G ) bibundles for a crossed module ( H , G ) and we show with examples the close links with loop group bundles.