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

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

Study of Atmospheric Pollution Scavenging: Sixteenth Progress Report

published or submitted for publicationis peer reviewedOpe

Variation in the strength of selected codon usage bias among bacteria

Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min

Theoretical study of O adlayers on Ru(0001)

Recent experiments performed at high pressures indicate that ruthenium can support unusually high concentrations of oxygen at the surface. To investigate the structure and stability of high coverage oxygen structures, we performed density functional theory calculations, within the generalized gradient approximation, for O adlayers on Ru(0001) from low coverage up to a full monolayer. We achieve quantitative agreement with previous low energy electron diffraction intensity analyses for the (2x2) and (2x1) phases and predict that an O adlayer with a (1x1) periodicity and coverage of 1 monolayer can form on Ru(0001), where the O adatoms occupy hcp-hollow sites.Comment: RevTeX, 6 pages, 4 figure

Artificial intelligence methods for a Bayesian epistemology-powered evidence evaluation

Rationale, aims and objectives: The diversity of types of evidence (eg, case reports, animal studies and observational studies) makes the assessment of a drug's safety profile into a formidable challenge. While frequentist uncertain inference struggles i

Surface Core Level Shifts of Clean and Oxygen Covered Ru(0001)

We have performed high resolution XPS experiments of the Ru(0001) surface, both clean and covered with well-defined amounts of oxygen up to 1 ML coverage. For the clean surface we detected two distinct components in the Ru 3d_{5/2} core level spectra, for which a definite assignment was made using the high resolution Angle-Scan Photoelectron Diffraction approach. For the p(2x2), p(2x1), (2x2)-3O and (1x1)-O oxygen structures we found Ru 3d_{5/2} core level peaks which are shifted up to 1 eV to higher binding energies. Very good agreement with density functional theory calculations of these Surface Core Level Shifts (SCLS) is reported. The overriding parameter for the resulting Ru SCLSs turns out to be the number of directly coordinated O atoms. Since the calculations permit the separation of initial and final state effects, our results give valuable information for the understanding of bonding and screening at the surface, otherwise not accessible in the measurement of the core level energies alone.Comment: 16 pages including 10 figures. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Dental treatment and risk of variant CJD - a case control study

Abstract Objective: Knowledge of risk factors for variant CJD (vCJD) remains limited, but transmission of prion proteins via re-useable medical devices, including dental instruments, or enhanced susceptibility following trauma to the oral cavity is a concern. This study aimed to identify whether previous dental treatment is a risk factor for development of vCJD. Design: Case control study Methods: Risk factor questionnaires completed by interview with relatives of 130 vCJD patients and with relatives of 66 community and 53 hospital controls were examined by a dental surgeon. Responses regarding dental treatments were analysed. Results: We did not find a statistically significant excess of risk of vCJD associated with dental treatments with the exception of extractions in an unmatched analysis of vCJD cases with community controls (p=0.02). However, this result may be explained by multiple testing. Conclusions: This is the first published study to date to examine potential links between vCJD and dental treatment. There was no convincing evidence found of an increased risk of variant CJD associated with reported dental treatment. However, the power of the study is restricted by the number of vCJD cases to date and does not preclude the possibility that some cases have resulted from secondary transmission via dental procedures. Due to the limitations of the data available, more detailed analyses of dental records are required to fully exclude the possibility of transmission via dental treatment

Impact of metabolic syndrome on the outcomes of superficial femoral artery interventions

BackgroundMetabolic syndrome (MetSyn) is an epidemic in the United States and is associated with early onset of atherosclerosis, increased thrombotic events, and increased complications after cardiovascular intervention. MetSyn is found in ∼50% of patients with peripheral vascular disease. However, its impact on peripheral interventions is unknown. The aim of this study is to determine the outcomes of superficial femoral artery (SFA) interventions in patients with and without MetSyn.MethodsA database of patients undergoing endovascular treatment of SFA disease between 1999 and 2009 was retrospectively queried. MetSyn was defined as the presence of ≥3 of the following criteria: blood pressure ≥130 mm Hg/≥85 mm Hg; triglycerides ≥150 mg/dL; high-density lipoprotein ≤50 mg/dL for women and ≤40 mg/dL for men; fasting blood glucose ≥110 mg/dL; or body mass index ≥30 kg/m2. Kaplan-Meier survival analyses were performed to assess time-dependent outcomes. Factor analyses were performed using a Cox proportional hazard model for time-dependent variables.ResultsA total of 1018 limbs in 738 patients (64% male, average age 67 years) underwent endovascular treatment for symptomatic SFA disease with 45% of patients meeting the criteria for MetSyn. MetSyn patients were more likely to be female (P = .001), to present with critical ischemia (rest pain/tissue loss: 55% MetSyn vs 45% non-MetSyn; P = .001), have poorer ambulatory status (P = .001), and have more advanced SFA lesions (TransAtlantic Inter-Society Consensus II C/D: 51% vs 11%; P = .001) and worse tibial runoff (P = .001). MetSyn patients required more complex interventions (P = .0001). There was no difference in mortality and major adverse cardiac events, but systemic complications (4% vs 1%; P = .001) and major adverse limb events (12% vs 7%; P = .0009) were significantly higher in the MetSyn group. Immediate postprocedural hemodynamic improvement, resolved or improved symptoms, and restoration of impaired ambulation were equivalent in both groups. Early failure (<6 months) was more common in those with MetSyn. At 5 years, primary, assisted primary, and secondary patencies were not affected by the presence of MetSyn. The presence of MetSyn was associated with a decrease in clinical efficacy, decreased freedom from recurrent symptoms, and decreased freedom from major amputation at 5 years.ConclusionsMetSyn is present in nearly half of the patients presenting with SFA disease. These patients present with more advanced disease and have poorer symptomatic and functional outcomes compared with those patients without MetSyn