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

Persistence Characteristics of Latin American Financial Markets

The financial rates of return from Latin American stock and currency markets are found to be non-normal, non-stationary, non-ergodic and long-term dependent, i.e., they have long memory. The degree of long- term dependence is measured by monofractal (global) Hurst exponents from wavelet multiresolution analysis (MRA). Scalograms and scalegrams provide the respective visualizations of these wavelet coefficients and the power spectrum of the rates of return. The slope of the power spectrum identifies the Hurst exponent and thereby the degree of scaling dependence that cannot be determined by Box-Jenkins type time series analysis. Our dependency and time and frequency scaling results are consistent with similar empirical findings from American, European, and Asian financial markets, extending the domain of the empirical investigation of the dynamics and risk characteristics of financial markets and refuting the hypothesis of perfectly efficient markets.financial markets, long memory, Hurst exponent, scalegram, wavelets, multiresolution analysis, measurement accuracy

Slow-roll inflation with a Gauss-Bonnet correction

We consider slow-roll inflation for a single scalar field with an arbitrary potential and an arbitrary nonminimal coupling to the Gauss-Bonnet term. By introducing a combined hierarchy of Hubble and Gauss-Bonnet flow functions, we analytically derive the power spectra of scalar and tensor perturbations. The standard consistency relation between the tensor-to-scalar ratio and the spectral index of tensor perturbations is broken. We apply this formalism to a specific model with a monomial potential and an inverse monomial Gauss-Bonnet coupling and constrain it by the 7-year Wilkinson Microwave Anisotropy Probe data. The Gauss-Bonnet term with a positive (or negative) coupling may lead to a reduction (or enhancement) of the tensor-to-scalar ratio and hence may revive the quartic potential ruled out by recent cosmological data.Comment: 7 pages, 2 figures, RevTeX, references added, published versio

Parametrizations of the Dark Energy Density and Scalar Potentials

We develop a theoretical method of constructing the scalar (quintessence or phantom) potential directly from the dimensionless dark energy function X(z), the dark energy density in units of its present value. We apply our method to two parametrizations of the dark energy density, the quiessence-Lambda ansatz and the generalized Chaplygin gas model, and discuss some features of the constructed potentials.Comment: 8 pages, 2 figures, ws-mpla.cls, Accepted for publication in Mod. Phys. Lett.

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence

Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This evolution-development discordance is possibly caused by erroneous inference based on phylogenetic signals with low neutrality and/or high saturation. Here we show that the 3rd codon transversion (P3Tv), with high neutrality and low saturation, is a robust high-resolution phylogenetic signal for such divergences and that the P3Tv-based land plant phylogeny cautiously identifies _Nymphaea_, followed by _Amborella_, as the most basal among the angiosperm species examined in this study. This P3Tv-based phylogeny contributes insights to the origin of angiosperms with concordance to fossil and stomata development evidence

Parametrization of Quintessence and Its Potential

We develop a theoretical method of constructing the quintessence potential directly from the effective equation of state function $w(z)$, which describes the properties of the dark energy. We apply our method to four parametrizations of equation of state parameter and discuss the general features of the resulting potentials. In particular, it is shown that the constructed quintessence potentials are all in the form of a runaway type.Comment: 6 pages, 2 figures, LaTeX2

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