Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

Background Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation

Non-destructive cavity QED probe of Bloch oscillations in a gas of ultracold atoms

We describe a scheme for probing a gas of ultracold atoms trapped in an optical lattice and moving in the presence of an external potential. The probe is non-destructive and uses the existing lattice fields as the measurement device. Two counter-propagating cavity fields simultaneously set up a conservative lattice potential and a weak quantum probe of the atomic motion. Balanced heterodyne detection of the probe field at the cavity output along with integration in time and across the atomic cloud yield information about the atomic dynamics in a single run. The scheme is applied to a measurement of the Bloch oscillation frequency for atoms moving in the presence of the local gravitational potential. Signal-to-noise ratios are estimated to be as high as $10^4$.Comment: 8 pages, 6 figures, submitted to Phys. Rev.

The Hidden Child: Analyzing the Cyclical Nature of Statelessness and Violations of Reproductive Autonomy

Statelessness is a reproductive justice issue. When states explicitly or implicitly regulate or restrict reproduction, it results in children being born into statelessness. When there is a risk that a child will be born into statelessness, it both impacts the parents’ ability to parent with dignity and can have a chilling effect on the parents’ decision to have a child in the first place. In this way, statelessness results both in and from violations of reproductive autonomy. To combat statelessness, the international human rights community must use a reproductive justice lens to examine the ways that policies related to regulating nationality result in reproductive oppression. And, to combat reproductive oppression, the international human rights legal community must reckon with the national and international policies (and lack thereof) that cause statelessness. This paper aims to begin this process by examining statelessness through a reproductive justice framework, in particular the ways that national laws related to reproductive decision-making (including child limitation, surrogacy, and marriage regulations) result in statelessness and create reproductive oppression

Anomalous Behavior of Ru for Catalytic Oxidation: A Theoretical Study of the Catalytic Reaction CO + 1/2 O_2 --> CO_2

Recent experiments revealed an anomalous dependence of carbon monoxide oxidation at Ru(0001) on oxygen pressure and a particularly high reaction rate. Below we report density functional theory calculations of the energetics and reaction pathways of the speculated mechanism. We will show that the exceptionally high rate is actuated by a weakly but nevertheless well bound (1x1) oxygen adsorbate layer. Furthermore it is found that reactions via scattering of gas-phase CO at the oxygen covered surface may play an important role. Our analysis reveals, however, that reactions via adsorbed CO molecules (the so-called Langmuir-Hinshelwood mechanism) dominate.Comment: 5 pages, 4 figures, Phys. Rev. Letters, Feb. 1997, in prin

Closing the gap for drowning prevention across Europe

[No abstract available