Genomic analysis of eight native plasmids of the phytopathogen Pseudomonas syringae

Comunicación a conferenciaThe pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences from PFPs from three different P. syringae pathovars and perform a comparative genomic analysis. In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were used to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs. Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic basis of the role of PFPs in different P. syringae lifestyles.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Quantum control on entangled bipartite qubits

Ising interaction between qubits could produce distortion in entangled pairs generated for engineering purposes (as in quantum computation) in presence of parasite magnetic fields, destroying or altering the expected behavior of process in which is projected to be used. Quantum control could be used to correct that situation in several ways. Sometimes the user should be make some measurement upon the system to decide which is the best control scheme; other posibility is try to reconstruct the system using similar procedures without perturbate it. In the complete pictures both schemes are present. We will work first with pure systems studying advantages of different procedures. After, we will extend these operations when time of distortion is uncertain, generating a mixed state, which needs to be corrected by suposing the most probably time of distortion.Comment: 10 pages, 5 figure

Phantom energy traversable wormholes

It has been suggested that a possible candidate for the present accelerated expansion of the Universe is ''phantom energy''. The latter possesses an equation of state of the form $\omega\equiv p/\rho<-1$, consequently violating the null energy condition. As this is the fundamental ingredient to sustain traversable wormholes, this cosmic fluid presents us with a natural scenario for the existence of these exotic geometries. Due to the fact of the accelerating Universe, macroscopic wormholes could naturally be grown from the submicroscopic constructions that originally pervaded the quantum foam. One could also imagine an advanced civilization mining the cosmic fluid for phantom energy necessary to construct and sustain a traversable wormhole. In this context, we investigate the physical properties and characteristics of traversable wormholes constructed using the equation of state $p=\omega \rho$, with $\omega<-1$. We analyze specific wormhole geometries, considering asymptotically flat spacetimes and imposing an isotropic pressure. We also construct a thin shell around the interior wormhole solution, by imposing the phantom energy equation of state on the surface stresses. Using the ''volume integral quantifier'' we verify that it is theoretically possible to construct these geometries with vanishing amounts of averaged null energy condition violating phantom energy. Specific wormhole dimensions and the traversal velocity and time are also deduced from the traversability conditions for a particular wormhole geometry. These phantom energy traversable wormholes have far-reaching physical and cosmological implications. For instance, an advanced civilization may use these geometries to induce closed timelike curves, consequently violating causality.Comment: 9 pages, Revtex4. V2: Considerable comments and references added, no physics changes, now 10 pages. Accepted for publication in Physical Review

Decoherence induced by Smith-Purcell radiation

The interaction between charged particles and the vacuum fluctuations of the electromagnetic field induces decoherence, and therefore affects the contrast of fringes in an interference experiment. In this article we show that if a double slit experiment is performed near a conducting grating, the fringe visibility is reduced. We find that the reduction of contrast is proportional to the number of grooves in the conducting surface, and that for realistic values of the parameters it could be large enough to be observed. The effect can be understood in terms of the Smith-Purcell radiation produced by the surface currents induced in the conductor.Comment: 10 pages, 3 figures. Improved discussion on experimental perspectives. References added. Version to appear in Phys. Rev.

Comparative genomic analysis of native pseudomonas syringae plasmids belonging to the ppt23 a family reveals their role in p. Syringae epiphytic and pathogenic lifestyles

Backgrounds The pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. Objectives Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences of PFPs from three different P. syringae pathovars and perform a comprehensive comparative genomic analysis. Methods In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were carried out to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs. Conclusions Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic bases of the role of PFPs in different P. syringae lifestyles. This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch.This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch; Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Fourth order perturbative expansion for the Casimir energy with a slightly deformed plate

We apply a perturbative approach to evaluate the Casimir energy for a massless real scalar field in 3+1 dimensions, subject to Dirichlet boundary conditions on two surfaces. One of the surfaces is assumed to be flat, while the other corresponds to a small deformation, described by a single function $\eta$, of a flat mirror. The perturbative expansion is carried out up to the fourth order in the deformation $\eta$, and the results are applied to the calculation of the Casimir energy for corrugated mirrors in front of a plane. We also reconsider the proximity force approximation within the context of this expansion.Comment: 10 pages, 3 figures. Version to appear in Phys. Rev.

High order analysis of the limit cycle of the van der Pol oscillator

We have applied the Lindstedt-Poincaré method to study the limit cycle of the van der Pol oscillator, obtaining the numerical coefficients of the series for the period and for the amplitude to order 859. Hermite-Padé approximants have been used to extract the location of the branch cut of the series with unprecedented accuracy (100 digits). Both series have then been resummed using an approach based on Padé approximants, where the exact asymptotic behaviors of the period and the amplitude are taken into account. Our results improve drastically all previous results obtained on this subject.Fil: Amore, Paolo. Universidad de Colima; MéxicoFil: Boyd, John P.. University of Michigan; Estados UnidosFil: Fernández, Francisco Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentin

Soliton pinning by long-range order in aperiodic systems

We investigate propagation of a kink soliton along inhomogeneous chains with two different constituents, arranged either periodically, aperiodically, or randomly. For the discrete sine-Gordon equation and the Fibonacci and Thue-Morse chains taken as examples, we have found that the phenomenology of aperiodic systems is very peculiar: On the one hand, they exhibit soliton pinning as in the random chain, although the depinning forces are clearly smaller. In addition, solitons are seen to propagate differently in the aperiodic chains than on periodic chains with large unit cells, given by approximations to the full aperiodic sequence. We show that most of these phenomena can be understood by means of simple collective coordinate arguments, with the exception of long range order effects. In the conclusion we comment on the interesting implications that our work could bring about in the field of solitons in molecular (e.g., DNA) chains.Comment: 4 pages, REVTeX 3.0 + epsf, 3 figures in accompanying PostScript file (Submitted to Phys Rev E Rapid Comm

Derivative expansion of the electromagnetic Casimir energy for two thin mirrors

We extend our previous work on a derivative expansion for the Casimir energy, to the case of the electromagnetic field coupled to two thin, imperfect mirrors. The latter are described by means of vacuum polarization tensors localized on the mirrors. We apply the results so obtained to compute the first correction to the proximity force approximation to the static Casimir effect.Comment: Version to appear in Phys. Rev.