Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence

The PELskin project—part I: fluid–structure interaction for a row of flexible flaps: a reference study in oscillating channel flow

Previous studies of flexible flaps attached to the aft part of a cylinder have demonstrated a favourable effect on the drag and lift force fluctuation. This observation is thought to be linked to the excitation of travelling waves along the flaps and as a consequence of that, periodic shedding of the von Kármán vortices is altered in phase. A more general case of such interaction is studied herein for a limited row of flaps in an oscillating flow; representative of the cylinder case since the transversal flow in the wake-region shows oscillating character. This reference case is chosen to qualify recently developed numerical methods for the simulation of fluid–structure interaction in the context of the EU funded ‘PELskin’ project. The simulation of the two-way coupled dynamics of the flexible elements is achieved via a structure model for the flap motion, which was implemented and coupled to two different fluid solvers via the immersed boundary method. The results show the waving behaviour observed at the tips of the flexible elements in interaction with the fluid flow and the formation of vortices in the gaps between the flaps. In addition, formation of vortices upstream of the leading and downstream of the trailing flap is seen, which interact with the formation of the shear-layer on top of the row. This leads to a phase shift in the wave-type motion along the row that resembles the observation in the cylinder case

The PELskin project: part II—investigating the physical coupling between flexible filaments in an oscillating flow

The fluid-structure interaction mechanisms of a coating composed of flexible flaps immersed in a periodically oscillating channel flow is here studied by means of numerical simulation, employing the Euler-Bernoulli equations to account for the flexibility of the structures. A set of passively actuated flaps have previously been demonstrated to deliver favourable aerodynamic impact when attached to a bluff body undergoing periodic vortex shedding. As such, the present configuration is identified to provide a useful test-bed to better understand this mechanism, thought to be linked to experimentally observed travelling waves. Having previously validated and elucidated the flow mechanism in Paper 1 of this series, we hereby undertake a more detailed analysis of spectra obtained for different natural frequency of structures and different configurations, in order to better characterize the mechanisms involved in the organized motion of the structures. Herein, this wave-like behaviour, observed at the tips of flexible structures via interaction with the fluid flow, is characterized by examining the time history of the filaments motion and the corresponding effects on the fluid flow, in terms of dynamics and frequency of the fluid velocity. Results indicate that the wave motion behaviour is associated with the formation of vortices in the gaps between the flaps, which itself are a function of the structural resistance to the cross flow. In addition, formation of vortices upstream of the leading and downstream of the trailing flap is seen, which interact with the formation of the shear-layer on top of the row. This leads to a phase shift in the wave-type motion along the row that resembles the observation in the cylinder case

Semiclassical ionization dynamics of the hydrogen molecular ion in an electric field of arbitrary orientation

Quasi-static models of barrier suppression have played a major role in our understanding of the ionization of atoms and molecules in strong laser fields. Despite their success, in the case of diatomic molecules these studies have so far been restricted to fields aligned with the molecular axis. In this paper we investigate the locations and heights of the potential barriers in the hydrogen molecular ion in an electric field of arbitrary orientation. We find that the barriers undergo bifurcations as the external field strength and direction are varied. This phenomenon represents an unexpected level of intricacy even on this most elementary level of the dynamics. We describe the dynamics of tunnelling ionization through the barriers semiclassically and use our results to shed new light on the success of a recent theory of molecular tunnelling ionization as well as earlier theories that restrict the electric field to be aligned with the molecular axis

Subclinical infection of macaques and baboons with a baboon simarterivirus

Simarteriviruses (Arteriviridae: Simarterivirinae) are commonly found at high titers in the blood of African monkeys but do not cause overt disease in these hosts. In contrast, simarteriviruses cause severe disease in Asian macaques upon accidental or experimental transmission. Here, we sought to better understand the host-dependent drivers of simarterivirus pathogenesis by infecting olive baboons (n = 4) and rhesus monkeys (n = 4) with the simarterivirus Southwest baboon virus 1 (SWBV-1). Surprisingly, none of the animals in our study showed signs of disease following SWBV-1 inoculation. Three animals (two rhesus monkeys and one olive baboon) became infected and sustained high levels of SWBV-1 viremia for the duration of the study. The course of SWBV-1 infection was highly predictable: plasma viremia peaked between 1 × 107 and 1 × 108 vRNA copies/mL at 3–10 days post-inoculation, which was followed by a relative nadir and then establishment of a stable set-point between 1 × 106 and 1 × 107 vRNA copies/mL for the remainder of the study (56 days). We characterized cellular and antibody responses to SWBV-1 infection in these animals, demonstrating that macaques and baboons mount similar responses to SWBV-1 infection, yet these responses are ineffective at clearing SWBV-1 infection. SWBV-1 sequencing revealed the accumulation of non-synonymous mutations in a region of the genome that corresponds to an immunodominant epitope in the simarterivirus major envelope glycoprotein GP5, which likely contribute to viral persistence by enabling escape from host antibodies

Statistical Mechanics for Unstable States in Gel'fand Triplets and Investigations of Parabolic Potential Barriers

Free energies and other thermodynamical quantities are investigated in canonical and grand canonical ensembles of statistical mechanics involving unstable states which are described by the generalized eigenstates with complex energy eigenvalues in the conjugate space of Gel'fand triplet. The theory is applied to the systems containing parabolic potential barriers (PPB's). The entropy and energy productions from PPB systems are studied. An equilibrium for a chemical process described by reactions $A+CB\rightleftarrows AC+B$ is also discussed.Comment: 14 pages, AmS-LaTeX, no figur

On the new economic philosophy of crisis management in the European Union

This essay attempts to go beyond presenting the bits and pieces of still ongoing crisis management in the EU. Instead it attempts at finding the ‘red thread’ behind a series of politically improvised decisions. Our fundamental research question asks whether basic economic lessons learned in the 1970s are still valid. Namely, that a crises emanating from either structural or regulatory weaknesses cannot and should not be remedied by demand management. Our second research question is the following: Can lacking internal commitment and conviction in any member state be replaced or substituted by external pressure or formalized procedures and sanctions? Under those angles we analyze the project on establishing a fiscal and banking union in the EU, as approved by the Council in December 2012

Accuracy of Trace Formulas

Using quantum maps we study the accuracy of semiclassical trace formulas. The role of chaos in improving the semiclassical accuracy, in some systems, is demonstrated quantitatively. However, our study of the standard map cautions that this may not be most general. While studying a sawtooth map we demonstrate the rather remarkable fact that at the level of the time one trace even in the presence of fixed points on singularities the trace formula may be exact, and in any case has no logarithmic divergences observed for the quantum bakers map. As a byproduct we introduce fantastic periodic curves akin to curlicues.Comment: 20 pages, uuencoded and gzipped, 1 LaTex text file and 9 PS files for figure

Stationary Flows of the Parabolic Potential Barrier in Two Dimensions

In the two-dimensional isotropic parabolic potential barrier $V(x, y)=V_0 -m\gamma^2 (x^2+y^2)/2$, though it is a model of an unstable system in quantum mechanics, we can obtain the stationary states corresponding to the real energy eigenvalue $V_0$. Further, they are infinitely degenerate. For the first few eigenstates, we will find the stationary flows round a right angle that are expressed by the complex velocity potentials $W=\pm\gamma z^2/2$.Comment: 12 pages, AmS-LaTeX, 4 figure

Zeeman smearing of the Coulomb blockade

Charge fluctuations of a large quantum dot coupled to a two-dimensional lead via a single-mode good Quantum Point Contact (QPC) and capacitively coupled to a back-gate, are investigated in the presence of a parallel magnetic field. The Zeeman term induces an asymmetry between transmission probabilities for the spin-up and spin-down channels at the QPC, producing noticeable effects on the quantization of the grain charge already at low magnetic fields. Performing a quantitative analysis, I show that the capacitance between the gate and the lead exhibits - instead of a logarithmic singularity - a reduced peak as a function of gate voltage. Experimental applicability is discussed.Comment: 5 pages, 3 figures (Final version