Relativistic iron K X-ray Reverberation in NGC 4151

Recent X-ray observations have enabled the study of reverberation delays in AGN for the first time. All the detections so far are in sources with a strong soft excess, and the measured delay is between the hard (1-3 keV) direct continuum and the soft excess (0.5-1 keV), interpreted as the reflection continuum smeared by relativistic effects. There is however an inherent ambiguity in identifying and studying the details of the lines in the soft excess. Here we report the first detection of reverberation in the iron K band in any AGN. Using XMM-Newton observations of NGC 4151, we find delays of order 2000 s on time-scales of 10e5 s between the 5-6 keV band and 2-3 and 7-8 keV bands, with a broad lag profile resembling a relativistically-broadened iron line. The peak of the lag spectra shifts to lower energies at higher frequencies, consistent with the red wing of the line being emitted at smaller radii, as expected from reflection off the inner accretion disk. This is a first detection of a broad iron line using timing studies.Comment: final version, corrected small typo

INTEGRAL observations of the Small Magellanic Cloud

The first INTEGRAL observations of the Small Magellanic Cloud (carried out in 2003) are reported in which two sources are clearly detected. The first source, SMC X-1, shows a hard X-ray eclipse and measurements of its pulse period indicate a continuation of the long-term spin-up now covering ~30 years. The second source is likely to be a high mass X-ray binary, and shows a potential periodicity of 6.8s in the IBIS lightcurve. An exact X-ray or optical counterpart cannot be designated, but a number of proposed counterparts are discussed. One of these possible counterparts shows a strong coherent optical modulation at ~2.7d, which, together with the measured hard X-ray pulse period, would lead to this INTEGRAL source being classified as the fourth known high mass Roche lobe overflow system.Comment: Accepted for publication in MNRA

Now you see it, now you don't - the circumstellar disk in the GRO J1008--57 system

Multiwavelength observations are reported here of the Be/X-ray binary pulsar system GRO J1008-57. Over ten years worth of data are gathered together to show that the periodic X-ray outbursts are dependant on both the binary motion and the size of the circumstellar disk. In the first instance an accurate orbital solution is determined from pulse periods, and in the second case the strength and shape of the Halpha emission line is shown to be a valuable indicator of disk size and its behaviour. Furthermore, the shape of the emission line permits a direct determination of the disk size which is in good agreement with theoretical estimates. A detailed study of the pulse period variations during outbursts determined the binary period to be 247.8, in good agreement with the period determined from the recurrence of the outbursts.Comment: Accepted for publication in MNRA

A high-throughput multiplexing and selection strategy to complete bacterial genomes

Background: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. Results: Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. Conclusions: The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.Peer reviewe

X-ray Fluctuation Power Spectral Densities of Seyfert 1 Galaxies

By combining complementary monitoring observations spanning long, medium and short time scales, we have constructed power spectral densities (PSDs) of six Seyfert~1 galaxies. These PSDs span $\gtrsim$4 orders of magnitude in temporal frequency, sampling variations on time scales ranging from tens of minutes to over a year. In at least four cases, the PSD shows a "break," a significant departure from a power law, typically on time scales of order a few days. This is similar to the behavior of Galactic X-ray binaries (XRBs), lower mass compact systems with breaks on time scales of seconds. NGC 3783 shows tentative evidence for a doubly-broken power law, a feature that until now has only been seen in the (much better-defined) PSDs of low-state XRBs. It is also interesting that (when one previously-observed object is added to make a small sample of seven), an apparently significant correlation is seen between the break time scale $T$ and the putative black hole mass $M_{\rm BH}$, while none is seen between break time scale and luminosity. The data are consistent with the linear relation T = M_{\rm BH}/10^{6.5} \Msun; extrapolation over 6--7 orders of magnitude is in reasonable agreement with XRBs. All of this strengthens the case for a physical similarity between Seyfert~1s and XRBs.Comment: 27 pages, 13 figures. Accepted for publication in ApJ. Typo correcte

Analysing the Suzaku Spectra of the Broad-Line Seyfert 1 Galaxy CBS 126

We analysed new simultaneous \emph{Suzaku} and \emph{Swift} data of the Broad Line Seyfert 1 (BLS1) galaxy CBS 126. A clear Fe emission line and a strong soft excess are present in the source spectra. We fit the spectra with a relativistic reflection model and find the model tends to fit the data with a high iron abundance possibly due to the large soft excess present. By checking the difference and the RMS spectra, we find there is likely an absorption edge at $\sim$ 0.89 keV, which might be caused by oxygen or neon. We also produced an analysis of the time-resolved spectra in order to examine the existence of the edge. Although high iron abundance is required more in the time-resolved spectra, a model of solar iron abundance together with an absorption edge gives a more physical explanation. Variation of the ionisation parameter is an alternative, plausible explanation for the excess seen in the difference spectra. It is difficult to know if there are warm absorbers in this source from the current data. To further investigate the presence of possible warm absorbers, higher signal-to-noise low-energy data are needed. The work presented here tentatively suggests that the spectra of a BLS1 can be explained by a relativistic reflection model similar to that often seen in their narrow-line cousins.Comment: 10 pages, 12 figures, accepted for publication in MNRA

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium. Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faecium. IMPORTANCE Enterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.Peer reviewe

4U 1344-60: a bright intermediate Seyfert galaxy at z=0.012 with a relativistic Fe Kalpha emission line

We present analysis of the optical and X-ray spectra of the low Galactic latitude bright (F(2-10) = 3.6 10^{-11} erg/cm2/s) source 4U 1344-60. On the basis of the optical data we propose to classify 4U 1344-60 as an intermediate type Seyfert galaxy and we measure a value of z=0.012+/-0.001 for its redshift. From the XMM-Newton observation we find that the overall X-ray spectral shape of 4U 1344-60 is complex and can be described by a power-law continuum (Gamma ~ 1.55) obscured by two neutral absorption components (Nh(f) ~ 10^{22} cm^{-2} and Nh(p) ~ 4 10^{22} cm^{-2}), the latter covering only the ~50% of the primary X-ray source. The X-ray data therefore lend support to our classification of 4U 1344-60. It exhibits a broad and skewed Fe Kalpha line at 6.4 keV, which suggests the existence of an accretion disk that is able to reprocess the primary continuum down to a few gravitational radii. Such a line represents one of the clearest examples of a relativistic line observed by XMM-Newton so far. Our analysis has also revealed the marginal presence of two narrow line-like emission features at ~4.9 and ~5.2 keV.Comment: Accepted for publication in Astronomy & Astrophysic

Unveiling the broad band X-ray continuum and iron line complex in Mkr 841

Mkr 841 is a bright Seyfert 1 galaxy known to harbor a strong soft excess and a variable K$\alpha$ iron line. It has been observed during 3 different periods by XMM for a total cumulated exposure time of $\sim$108 ks. We present in this paper a broad band spectral analysis of the complete EPIC-pn data sets. We were able to test two different models for the soft excess, a relativistically blurred photoionized reflection (\r model) and a relativistically smeared ionized absorption (\a model). The continuum is modeled by a simple cut-off power law and we also add a neutral reflection. These observations reveal the extreme and puzzling spectral and temporal behaviors of the soft excess and iron line. The 0.5-3 keV soft X-ray flux decreases by a factor 3 between 2001 and 2005 and the line shape appears to be a mixture of broad and narrow components. We succeed in describing this complex broad-band 0.5-10 keV spectral variability using either \r or \a to fit the soft excess. Both models give statistically equivalent results even including simultaneous BeppoSAX data up to 200 keV. Both models are consistent with the presence of remote reflection characterized by a constant narrow component in the data. However they differ in the presence of a broad line component present in \r but not needed in \a. This study also reveals the sporadic presence of relativistically redshifted narrow iron lines.Comment: Accepted in A&A. 17 pages and 21 figure