Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus

Background: E.coli ST131 is a globally disseminated clone of multi-drug resistant E. coli responsible for that vast majority of global extra-intestinal E. coli infections. Recent global genomic epidemiological studies have highlighted the highly clonal nature of this group of bacteria, however there appears to be inconsistency in some phenotypes associated with the clone, in particular capsule types as determined by K-antigen testing both biochemically and by PCR. Results: We performed improved quality assemblies on ten ST131 genomes previously sequenced by our group and compared them to a new reference genome sequence JJ1886 to identify the capsule loci across the drug-resistant clone H30Rx. Our data shows considerable genetic diversity within the capsule locus of H30Rx clone strains which is mirrored by classical K antigen testing. The varying capsule locus types appear to be randomly distributed across the H30Rx phylogeny suggesting multiple recombination events at this locus, but that this capsule heterogeneity has little to no effect on virulence associated phenotypes in vitro. Conclusions: Our data provides a framework for determining the capsular genetics of E. coli ST131 and further beyond to ExPEC strains, and highlights how capsular mosaicism may be an important strategy in becoming a successful globally disseminated human pathogen

Multidisciplinary studies in environmental archaeology with particular reference to China: an introduction to the special issue

An important focus in research over the past decade is the relationship between climatic/environmental change and human cultural evolution during the Holocene. This decade saw an increasing number of natural scientists involved in this research, which led to debates and collaborations between natural scientists and archaeologists/anthropologists. This decade also witnessed an increase in multidisciplinary research across these subjects, which has improved significantly the understanding of the human-environment relationship. As part of this research drive, this Special Issue highlights the importance of multidisciplinary studies, mainly from China, on early rice agriculture, impacts of environmental change in Neolithic communities, and new approaches for environmental reconstruction. © The Author(s) 2012.published_or_final_versio

Accelerating universe from gravitational leakage into extra dimensions: confrontation with SNeIa

There is mounting observational evidence that the expansion of our universe is undergoing an acceleration. A dark energy component has usually been invoked as the most feasible mechanism for the acceleration. However, it is desirable to explore alternative possibilities motivated by particle physics before adopting such an untested entity. In this work, we focus our attention on an acceleration mechanism: one arising from gravitational leakage into extra dimensions. We confront this scenario with high-$z$ type Ia supernovae compiled by Tonry et al. (2003) and recent measurements of the X-ray gas mass fractions in clusters of galaxies published by Allen et al. (2002,2003). A combination of the two databases gives at a 99% confidence level that $\Omega_m=0.29^{+0.04}_{-0.02}$, $\Omega_{rc}=0.21^{+0.08}_{-0.08}$, and $\Omega_k=-0.36^{+0.31}_{-0.35}$, indicating a closed universe. We then constrain the model using the test of the turnaround redshift, $z_{q=0}$, at which the universe switches from deceleration to acceleration. We show that, in order to explain that acceleration happened earlier than $z_{q=0} = 0.6$ within the framework of gravitational leakage into extra dimensions, a low matter density, $\Omega_m < 0.27$, or a closed universe is necessary.Comment: 16 pages, 4 figures, accepted for publication in Ap

Escherichia coli of sequence type 3835 carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12

New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. blaNDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (blaCMY-42) and two extended-spectrum β-lactamase genes (blaCTX-M-15 and blaSHV-12). blaNDM-1 and blaSHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. blaCMY-42 was carried by a 64-kb IncI1 plasmid and blaCTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). blaCMY-42 was in a complicated context and the mobilisation of blaCMY-42 was due to the transposition of IS Ecp1 by misidentifying its right-end boundary. Genetic context of blaNDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of blaNDM among Enterobacteriaceae in China

Gravitational Lensing Statistics as a Probe of Dark Energy

By using the comoving distance, we derive an analytic expression for the optical depth of gravitational lensing, which depends on the redshift to the source and the cosmological model characterized by the cosmic mass density parameter $\Omega_m$, the dark energy density parameter $\Omega_x$ and its equation of state $\omega_x = p_x/\rho_x$. It is shown that, the larger the dark energy density is and the more negative its pressure is, the higher the gravitational lensing probability is. This fact can provide an independent constraint for dark energy.Comment: 9 pages, 2 figure

The Equation of State and Quark Number Susceptibility in Hard-Dense-Loop Approximation

Based on the method proposed in [ H. S. Zong, W. M. Sun, Phys. Rev. \textbf{D 78}, 054001 (2008)], we calculate the equation of state (EOS) of QCD at zero temperature and finite quark chemical potential under the hard-dense-loop (HDL) approximation. A comparison between the EOS under HDL approximation and the cold, perturbative EOS of QCD proposed by Fraga, Pisarski and Schaffner-Bielich is made. It is found that the pressure under HDL approximation is generally smaller than the perturbative result. In addition, we also calculate the quark number susceptibility (QNS) at finite temperature and finite chemical potential under hard-thermal/dense-loop (HTL/HDL) approximation and compare our results with the corresponding ones in the previous literature.Comment: 12 pages, 3 figure

Relativistic description of J/\psi dissociation in hot matter

The mass spectra and binding radii of heavy quark bound states are studied on the basis of the reduced Bethe-Salpeter equation. The critical values of screening masses for $c\bar{c}$ and $b\bar{b}$ bound states at a finite temperature are obtained and compared with the previous results given by non-relativistic models.Comment: 13 latex pages, 2 figure

Gravitational lensing statistical properties in general FRW cosmologies with dark energy component(s): analytic results

Various astronomical observations have been consistently making a strong case for the existence of a component of dark energy with negative pressure in the universe. It is now necessary to take the dark energy component(s) into account in gravitational lensing statistics and other cosmological tests. By using the comoving distance we derive analytic but simple expressions for the optical depth of multiple image, the expected value of image separation and the probability distribution of image separation caused by an assemble of singular isothermal spheres in general FRW cosmological models with dark energy component(s). We also present the kinematical and dynamical properties of these kinds of cosmological models and calculate the age of the universe and the distance measures, which are often used in classical cosmological tests. In some cases we are able to give formulae that are simpler than those found elsewhere in the literature, which could make the cosmological tests for dark energy component(s) more convenient.Comment: 14 pages, no figure, Latex fil

Measuring Dark Energy with Gamma-Ray Bursts and Other Cosmological Probes

It has been widely shown that the cosmological parameters and dark energy can be constrained by using data from type-Ia supernovae (SNe Ia), the cosmic microwave background (CMB) anisotropy, the baryon acoustic oscillation (BAO) peak from Sloan Digital Sky Survey (SDSS), the X-ray gas mass fraction in clusters, and the linear growth rate of perturbations at z=0.15 as obtained from the 2dF Galaxy Redshift Survey. Recently, gamma-ray bursts (GRBs) have also been argued to be promising standard candles for cosmography. In this paper, we present constraints on the cosmological parameters and dark energy by combining a recent GRB sample including 69 events with the other cosmological probes. First, we find that for the LambdaCDM cosmology this combination makes the constraints stringent and the best fit is close to the flat universe. Second, we fit the flat Cardassian expansion model and find that this model is consistent with the LambdaCDM cosmology. Third, we present constraints on several two-parameter dark energy models and find that these models are also consistent with the LambdaCDM cosmology. Finally, we reconstruct the dark energy equation-of-state parameter w(z) and the deceleration parameter q(z). We see that the acceleration could have started at a redshift from z_T=0.40_{-0.08}^{+0.14} to z_T=0.65_{-0.05}^{+0.10}. This difference in the transition redshift is due to different dark energy models that we adopt. The most stringent constraint on w(z) lies in the redshift range z\sim 0.3-0.6.Comment: 28 pages, 13 figures, accepted for publication in ApJ. One reference added, one minor change in the final paragraph of section