Ecological and genetic determinants of plasmid distribution in Escherichia coli.

Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, little is known of the determinants of plasmid distribution in bacterial populations. Here the factors affecting the diversity and distribution of the large plasmids of Escherichia coli were explored in cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, the population genetic structure of bacterial hosts was chararacterized. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy.FM was supported by a joint Royal Holloway and Animal Health and Veterinary Laboratories Agency studentship, BR by a NERC Advanced Research fellowship

z ∼ 2–9 Galaxies Magnified by the Hubble Frontier Field Clusters. II. Luminosity Functions and Constraints on a Faint-end Turnover

We present new determinations of the rest-UV luminosity functions (LFs) at z = 2–9 to extremely low luminosities (>−14 mag) from a sample of >2500 lensed galaxies found behind the Hubble Frontier Fields (HFF) clusters. For the first time, we present faint-end slope results from lensed samples that are fully consistent with blank-field results over the redshift range z = 2–9, while reaching to much lower luminosities than possible from the blank-field studies. Combining the deep lensed sample with the large blank-field samples allows us to set tight constraints on the faint-end slope α of the z = 2–9 UV LFs and its evolution. We find a smooth flattening in α from −2.28 ± 0.10 (z = 9) to −1.53 ± 0.03 (z = 2) with cosmic time (dα/dz = −0.11 ± 0.01), fully consistent with dark matter halo buildup. We utilize these new results to present new measurements of the evolution in the UV luminosity density ρ UV brighter than −13 mag from z ∼ 9 to z ∼ 2. Accounting for the star formation rate (SFR) densities to faint luminosities implied by our LF results, we find that unobscured star formation dominates the SFR density at z ≳ 4, with obscured star formation dominant thereafter. Having shown we can quantify the faint-end slope α of the LF accurately with our lensed HFF samples, we also quantify the apparent curvature in the shape of the UV LF through a curvature parameter δ. The constraints on the curvature δ strongly rule out the presence of a turn-over brighter than −13.1 mag at z ∼ 3, −14.3 mag at z ∼ 6, and −15.5 mag at all other redshifts between z ∼ 9 and z ∼ 2

Blockade of Immunosuppressive Cytokines Restores NK Cell Antiviral Function in Chronic Hepatitis B Virus Infection

NK cells are enriched in the liver, constituting around a third of intrahepatic lymphocytes. We have previously demonstrated that they upregulate the death ligand TRAIL in patients with chronic hepatitis B virus infection (CHB), allowing them to kill hepatocytes bearing TRAIL receptors. In this study we investigated whether, in addition to their pathogenic role, NK cells have antiviral potential in CHB. We characterised NK cell subsets and effector function in 64 patients with CHB compared to 31 healthy controls. We found that, in contrast to their upregulated TRAIL expression and maintenance of cytolytic function, NK cells had a markedly impaired capacity to produce IFN-gamma in CHB. This functional dichotomy of NK cells could be recapitulated in vitro by exposure to the immunosuppressive cytokine IL-10, which was induced in patients with active CHB. IL-10 selectively suppressed NK cell IFN-gamma production without altering cytotoxicity or death ligand expression. Potent antiviral therapy reduced TRAIL-expressing CD56 bright NK cells, consistent with the reduction in liver inflammation it induced; however, it was not able to normalise IL-10 levels or the capacity of NK cells to produce the antiviral cytokine IFN-gamma. Blockade of IL-10 +/- TGF-beta restored the capacity of NK cells from both the periphery and liver of patients with CHB to produce IFN-gamma, thereby enhancing their non-cytolytic antiviral capacity. In conclusion, NK cells may be driven to a state of partial functional tolerance by the immunosuppressive cytokine environment in CHB. Their defective capacity to produce the antiviral cytokine IFN-gamma persists in patients on antiviral therapy but can be corrected in vitro by IL-10+/- TGF-beta blockade

Mean Hα+[N ii]+[S ii] EW inferred for star-forming galaxies at z ∼ 5.1–5.4 using high-quality Spitzer /IRAC photometry

Recent Spitzer/InfraRed Array Camera (IRAC) photometric observations have revealed that rest-frame optical emission lines contribute significantly to the broad-band fluxes of high-redshift galaxies. Specifically, in the narrow redshift range z ∼ 5.1–5.4 the [3.6]–[4.5] colour is expected to be very red, due to contamination of the 4.5 μm band by the dominant Hα line, while the 3.6 μm filter is free of nebular emission lines. We take advantage of new reductions of deep Spitzer/IRAC imaging over the Great Observatories Origins Deep Survey-North+South fields (Labbé et al. 2015) to obtain a clean measurement of the mean Hα equivalent width (EW) from the [3.6]–[4.5] colour in the redshift range z = 5.1–5.4. The selected sources either have measured spectroscopic redshifts (13 sources) or lie very confidently in the redshift range z = 5.1–5.4 based on the photometric redshift likelihood intervals (11 sources). Our zphot = 5.1–5.4 sample and zspec = 5.10–5.40 spectroscopic sample have a mean [3.6]–[4.5] colour of 0.31 ± 0.05 and 0.35 ± 0.07 mag, implying a rest-frame EW (Hα+[N II]+[S II]) of 665 ± 53 and 707 ± 74 Å, respectively, for sources in these samples. These values are consistent albeit slightly higher than derived by Stark et al. at z ∼ 4, suggesting an evolution to higher values of the Hα+[N II]+[S II] EW at z > 2. Using the 3.6 μm band, which is free of emission line contamination, we perform robust spectral energy distribution fitting and find a median specific star formation rate of sSFR = 17+2−517−5+2 Gyr−1, 7+1−2×7−2+1× higher than at z ∼ 2. We find no strong correlation (<2σ) between the Hα+[N II]+[S II] EW and the stellar mass of sources. Before the advent of JWST, improvements in these results will come through an expansion of current spectroscopic samples and deeper Spitzer/IRAC measurements

Phenomenology and Cosmology of an Electroweak Pseudo-Dilaton and Electroweak Baryons

In many strongly-interacting models of electroweak symmetry breaking the lowest-lying observable particle is a pseudo-Goldstone boson of approximate scale symmetry, the pseudo-dilaton. Its interactions with Standard Model particles can be described using a low-energy effective nonlinear chiral Lagrangian supplemented by terms that restore approximate scale symmetry, yielding couplings of the pseudo-dilaton that differ from those of a Standard Model Higgs boson by fixed factors. We review the experimental constraints on such a pseudo-dilaton in light of new data from the LHC and elsewhere. The effective nonlinear chiral Lagrangian has Skyrmion solutions that may be identified with the `electroweak baryons' of the underlying strongly-interacting theory, whose nature may be revealed by the properties of the Skyrmions. We discuss the finite-temperature electroweak phase transition in the low-energy effective theory, finding that the possibility of a first-order electroweak phase transition is resurrected. We discuss the evolution of the Universe during this transition and derive an order-of-magnitude lower limit on the abundance of electroweak baryons in the absence of a cosmological asymmetry, which suggests that such an asymmetry would be necessary if the electroweak baryons are to provide the cosmological density of dark matter. We revisit estimates of the corresponding spin-independent dark matter scattering cross section, with a view to direct detection experiments.Comment: 34 pages, 4 figures, additional references adde

Mass extinctions and supernova explosions

A nearby supernova (SN) explosion could have negatively influenced life on Earth, maybe even been responsible for mass extinctions. Mass extinction poses a significant extinction of numerous species on Earth, as recorded in the paleontologic, paleoclimatic, and geological record of our planet. Depending on the distance between the Sun and the SN, different types of threats have to be considered, such as ozone depletion on Earth, causing increased exposure to the Sun's ultraviolet radiation, or the direct exposure of lethal x-rays. Another indirect effect is cloud formation, induced by cosmic rays in the atmosphere which result in a drop in the Earth's temperature, causing major glaciations of the Earth. The discovery of highly intensive gamma ray bursts (GRBs), which could be connected to SNe, initiated further discussions on possible life-threatening events in Earth's history. The probability that GRBs hit the Earth is very low. Nevertheless, a past interaction of Earth with GRBs and/or SNe cannot be excluded and might even have been responsible for past extinction events.Comment: Chapter for forthcoming book: Handbook of Supernovae, P. Murdin and A. Alsabeti (eds.), Springer International Publishing (in press

Medium-term seed storage of 50 genera of forage legumes and evidence-based genebank monitoring intervals

Genebanks maintaining seeds for long-term genetic resources conservation monitor seed lots to detect early loss in viability. Monitoring is costly and depletes valuable seed. Three decades of genebank seed germination test results of diverse forage species from 50 legume genera in the International Livestock Research Institute’s medium-term store (circa 8° C with 5 % moisture content) were analysed to determine whether advice on seed monitoring intervals could be derived. Cumulative normal distributions were fitted by probit analysis for each seed lot and compared within each genus. Six patterns of within-genus variation were identified: no detectable trend in germination test results during storage (4 genera); detectable trends, but variable (positive to negative) amongst lots (5); consistent slope of loss in viability amongst lots (17); consistent slope of increase in ability to germinate amongst lots (21); common loss in viability amongst lots (2); common increase in ability to germinate amongst lots (1). Seed lot monitoring intervals for the medium-term store were derived for each of 19 genera with consistent loss in viability across seed lots: three genera provided comparatively rapid deterioration, five met the general expectations for a medium-term store (2-10 years’ maintenance of high viability), whilst 11 provided much better survival. Moreover, 26 further genera provided no evidence as yet of seed deterioration; of these, 22 improved in ability to germinate during storage indicating confounding of hardseededness with viability in germination tests