Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. ...This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.
Abstract
We present a deep, low-frequency radio continuum study of the nearby Fanaroff–Riley class I (FR I) radio galaxy 3C 31 using a combination of LOw Frequency ARray (LOFAR; 30–85 and ...115–178 MHz), Very Large Array (VLA; 290–420 MHz), Westerbork Synthesis Radio Telescope (WSRT; 609 MHz) and Giant Metre Radio Telescope (GMRT; 615 MHz) observations. Our new LOFAR 145-MHz map shows that 3C 31 has a largest physical size of 1.1 Mpc in projection, which means 3C 31 now falls in the class of giant radio galaxies. We model the radio continuum intensities with advective cosmic ray transport, evolving the cosmic ray electron population and magnetic field strength in the tails as functions of distance to the nucleus. We find that if there is no in situ particle acceleration in the tails, then decelerating flows are required that depend on radius r as v∝rβ (β ≈ −1). This then compensates for the strong adiabatic losses due to the lateral expansion of the tails. We are able to find self-consistent solutions in agreement with the entrainment model of Croston & Hardcastle, where the magnetic field provides ≈1/3 of the pressure needed for equilibrium with the surrounding intracluster medium. We obtain an advective time-scale of ≈190 Myr, which, if equated to the source age, would require an average expansion Mach number ${\cal M} \approx 5$ over the source lifetime. Dynamical arguments suggest that instead either the outer tail material does not represent the oldest jet plasma or else the particle ages are underestimated due to the effects of particle acceleration on large scales.
Maternal recognition of pregnancy (MRP) in the mare is an unknown process. In a non-pregnant mare on day 14 post-ovulation (PO), prostaglandin F2α (PGF) is secreted by the endometrium causing ...regression of the corpus luteum. Prior to day 14, MRP must occur in order to attenuate secretion of PGF. The embryo is mobile throughout the uterus due to uterine contractions from day of entry to day 14. It is unknown what signaling is occurring. Literature stated that infusing oil or placing a glass marble into the equine uterus prolongs luteal lifespan and that in non-pregnant mares, serum exosomes contain miRNA that are targeting the focal adhesion (FA) pathway. The hypothesis of this study is embryo contact with endometrium causes a change in abundance of focal adhesion molecules (FA) in the endometrium leading to decrease in PGF secretion. Mares (n = 3/day) were utilized in a cross-over design with each mare serving as a pregnant and non-pregnant (non-mated) control on days 9 and 11 PO. Mares were randomly assigned to collection day and endometrial samples and embryos were collected on the specified day. Biopsy samples were divided into five pieces, four for culture for 24 hours and one immediately snap frozen. Endometrial biopsies for culture were placed in an incubator with one of four treatments: 1 an embryo in contact on the luminal side of the endometrium, 2 beads in contact on the luminal side of the endometrium, 3 peanut oil in contact on the luminal side of the endometrium or 4 the endometrium by itself. Biopsies and culture medium were frozen for further analysis. RNA and protein were isolated from biopsies for PCR and Western blot analysis for FA. PGF assays were performed on culture medium to determine concentration of PGF. Statistics were performed using SAS (P ≤ 0.05 indicated significance). The presence of beads on day 9 impacted samples from pregnant mares more than non-pregnant mares and had very little impact on day 11. Presence of oil decreased FA in samples from pregnant mares on day 9. On day 11, oil decreased FA abundance in samples from non-pregnant mares. Embryo contact caused multiple changes in RNA and protein abundance in endometrium from both pregnant and non-pregnant mares. The PGF secretion after 24 hours with each treatment was also determined. On day 9, there was no change in PGF secretion compared to any treatments. On day 11, presence of peanut oil increased PGF secretion in samples from non-pregnant mares. In samples from non-pregnant mares, presence of an embryo decreased PGF secretion compared to control samples from non-pregnant mares. Results revealed that while beads and peanut oil may impact abundance of FA RNA and protein in endometrial samples, it does not appear to impact PGF secretion. Conversely, embryo contact for 24 hours with endometrium from a non-pregnant mare causes a decrease in PGF secretion. These results suggest that it is not just contact of any substance/object causing attenuation of PGF secretion, but the embryo itself is necessary to decrease PGF secretion.
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ABSTRACT
We investigate the relationship between the environment and the galaxy main sequence (the relationship between stellar mass and star formation rate), as well as the relationship between the ...environment and radio luminosity ($P_{\rm 1.4\, GHz}$), to shed new light on the effects of the environment on galaxies. We use the VLA-COSMOS 3-GHz catalogue, which consists of star-forming galaxies and quiescent galaxies (active galactic nuclei) in three different environments (field, filament, cluster) and for three different galaxy types (satellite, central, isolated). We perform for the first time a comparative analysis of the distribution of star-forming galaxies with respect to the main-sequence consensus region from the literature, taking into account galaxy environment and using radio observations at 0.1 ≤ z ≤ 1.2. Our results corroborate that the star formation rate is declining with cosmic time, which is consistent with the literature. We find that the slope of the main sequence for different z and M* bins is shallower than the main-sequence consensus, with a gradual evolution towards higher redshift bins, irrespective of environment. We see no trends for star formation rate in either environment or galaxy type, given the large errors. In addition, we note that the environment does not seem to be the cause of the flattening of the main sequence at high stellar masses for our sample.
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline ...genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys' unique biology and evolutionary/comparative perspective.
Context.
Repeating fast radio bursts (FRBs) present excellent opportunities to identify FRB progenitors and host environments as well as to decipher the underlying emission mechanism. Detailed ...studies of repeating FRBs might also hold clues as to the origin of FRBs as a population.
Aims.
We aim to detect bursts from the first two repeating FRBs, FRB 121102 (R1) and FRB 180814.J0422+73 (R2), and to characterise their repeat statistics. We also want to significantly improve the sky localisation of R2 and identify its host galaxy.
Methods.
We used the Westerbork Synthesis Radio Telescope to conduct extensive follow-up of these two repeating FRBs. The new phased-array feed system, Apertif, allows one to cover the entire sky position uncertainty of R2 with fine spatial resolution in a single pointing. The data were searched for bursts around the known dispersion measures of the two sources. We characterise the energy distribution and the clustering of detected R1 bursts.
Results.
We detected 30 bursts from R1. The non-Poissonian nature is clearly evident from the burst arrival times, which is consistent with earlier claims. Our measurements indicate a dispersion measure (DM) of 563.5(2) pc cm
−3
, suggesting a significant increase in DM over the past few years. Assuming a constant position angle across the burst, we place an upper limit of 8% on the linear polarisation fraction for the brightest burst in our sample. We did not detect any bursts from R2.
Conclusions.
A single power-law might not fit the R1 burst energy distribution across the full energy range or widely separated detections. Our observations provide improved constraints on the clustering of R1 bursts. Our stringent upper limits on the linear polarisation fraction imply a significant depolarisation, either intrinsic to the emission mechanism or caused by the intervening medium at 1400 MHz, which is not observed at higher frequencies. The non-detection of any bursts from R2, despite nearly 300 h of observations, implies either a highly clustered nature of the bursts, a steep spectral index, or a combination of the two assuming that the source is still active. Another possibility is that R2 has turned off completely, either permanently or for an extended period of time.
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Super massive black holes at the centres of galaxies can cycle through periods of activity and quiescence. Characterising the duty cycle of active galactic nuclei (AGN) is crucial for understanding ...the impact of the energy they release on the host galaxy. For radio AGN, this can be done by identifying dying (remnant) and restarted radio galaxies from their radio spectral properties. Using the combination of the images at 1400 MHz produced by Apertif, the new phased-array feed receiver installed on the Westerbork Synthesis Radio Telescope, and images at 150 MHz provided by LOFAR, we have derived resolved spectral index images (at a resolution of ~15 arcsec) for all the sources within an approximately 6 deg
2
area of the Lockman Hole region. In this way, we were able to select 15 extended radio sources with emission (partly or entirely) characterised by extremely steep spectral indices (steeper than 1.2). These objects represent cases of radio sources in the remnant or the restarted phases of their life cycle. Our findings confirm that these objects are not as rare as previously thought, suggesting a relatively fast cycle. They also show a variety of properties that can be relevant for modelling the evolution of radio galaxies. For example, the restarted activity can occur while the remnant structure from a previous phase of activity is still visible. This provides constraints on the duration of the “off” (dying) phase. In extended remnants with ultra-steep spectra at low frequencies, the activity likely stopped a few hundred megayears ago, and they correspond to the older tail of the age distribution of radio galaxies, in agreement with the results of simulations of radio source evolution. We find remnant radio sources with a variety of structures (from double-lobed to amorphous), possibly suggesting different types of progenitors. The present work sets the stage for exploiting the powerful tool of low-frequency spectral index studies of extended sources by taking advantage of the large areas common to the LOFAR and the Apertif surveys.
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Context.
Detection of the electromagnetic emission from coalescing binary neutron stars (BNS) is important for understanding the merger and afterglow.
Aims.
We present a search for a radio ...counterpart to the gravitational-wave (GW) source GW190425, a BNS merger, using Apertif on the Westerbork Synthesis Radio Telescope (WSRT).
Methods.
We observed a field of high probability in the associated localisation region for three epochs at Δ
T
= 68, 90, 109 d post merger. We identified all sources that exhibit flux variations consistent with the expected afterglow emission of GW190425. We also looked for possible transients. These are sources that are only present in one epoch. In addition, we quantified our ability to search for radio afterglows in the fourth and future observing runs of the GW detector network using Monte Carlo simulations.
Results.
We found 25 afterglow candidates based on their variability. None of these could be associated with a possible host galaxy at the luminosity distance of GW190425. We also found 55 transient afterglow candidates that were only detected in one epoch. All of these candidates turned out to be image artefacts. In the fourth observing run, we predict that up to three afterglows will be detectable by Apertif.
Conclusions.
While we did not find a source related to the afterglow emission of GW190425, the search validates our methods for future searches of radio afterglows.
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ABSTRACT
We report the detection of a bright fast radio burst, FRB 191108, with Apertif on the Westerbork Synthesis Radio Telescope. The interferometer allows us to localize the FRB to a narrow 5 ...arcsec × 7 arcmin ellipse by employing both multibeam information within the Apertif phased-array feed beam pattern, and across different tied-array beams. The resulting sightline passes close to Local Group galaxy M33, with an impact parameter of only 18 kpc with respect to the core. It also traverses the much larger circumgalactic medium (CGM) of M31, the Andromeda Galaxy. We find that the shared plasma of the Local Group galaxies could contribute ∼10 per cent of its dispersion measure of 588 pc cm−3. FRB 191108 has a Faraday rotation measure (RM) of +474 $\pm \, 3$ rad m−2, which is too large to be explained by either the Milky Way or the intergalactic medium. Based on the more moderate RMs of other extragalactic sources that traverse the halo of M33, we conclude that the dense magnetized plasma resides in the host galaxy. The FRB exhibits frequency structure on two scales, one that is consistent with quenched Galactic scintillation and broader spectral structure with Δν ≈ 40 MHz. If the latter is due to scattering in the shared M33/M31 CGM, our results constrain the Local Group plasma environment. We found no accompanying persistent radio sources in the Apertif imaging survey data.
H I content in Coma cluster substructure Healy, J.; Blyth, S.-L.; Verheijen, M. A. W. ...
Astronomy and astrophysics (Berlin),
06/2021, Volume:
650
Journal Article
Peer reviewed
Open access
Context.
Galaxy clusters are some of largest structures in the universe. These very dense environments tend to be home to higher numbers of evolved galaxies than found in lower-density environments. ...It is well known that dense environments can influence the evolution of galaxies through the removal of the neutral gas (H
I
) reservoirs that fuel star formation. It is unclear which environment has a stronger effect: the local environment (i.e., the substructure within the cluster), or the cluster itself.
Aims.
Using the new H
I
data from the Westerbork Coma Survey, we explore the average H
I
content of galaxies across the cluster comparing galaxies that reside in substructure to those that do not.
Methods.
We applied the Dressler–Shectman test to our newly compiled redshift catalogue of the Coma cluster to search for substructure. With so few of the Coma galaxies directly detected in H
I
, we used the H
I
stacking technique to probe the average H
I
content below what can be directly detected.
Results.
Using the Dressler–Shectman test, we find 15 substructures within the footprint of the Westerbork Coma Survey. We compare the average H
I
content for galaxies within substructure to those not in substructure. Using the H
I
stacking technique, we find that those Coma galaxies not detected in H
I
are more than 10–50 times more H
I
deficient than expected, which supports the scenario of an extremely efficient and rapid quenching mechanism. By studying the galaxies that are not directly detected in H
I
, we also find Coma to be more H
I
deficient than previously thought.
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