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

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

Large-Scale Correlations in the Lyman-alpha Forest at z = 3-4

We present a study of the spatial coherence of the intergalactic medium toward two pairs of high-redshift quasars with moderate angular separations observed with Keck/ESI, Q1422+2309A/Q1424+2255 (z_em = 3.63, theta = 39") and Q1439-0034A/B (z_em = 4.25, theta = 33"). The crosscorrelation of transmitted flux in the Lyman-alpha forest shows a 5-7 sigma peak at zero velocity lag for both pairs. This strongly suggests that at least some of the absorbing structures span the 230-300/h_70 proper kpc transverse separation between sightlines. We also statistically examine the similarity between paired spectra as a function of transmitted flux, a measure which may be useful for comparison with numerical simulations. In investigating the dependence of the correlation functions on spectral characteristics, we find that photon noise has little impact for S/N >~ 10 per resolution element. However, the agreement between the autocorrelation along the line sight and the crosscorrelation between sightlines, a potential test of cosmological geometry, depends significantly on instrumental resolution. Finally, we present an inventory of metal lines. These include a a pair of strong C IV systems at z ~ 3.4 appearing only toward Q1439B, and a Mg II + Fe II system present toward Q1439 A and B at z = 1.68.Comment: 33 pages, 13 figures, submitted to Ap

Application of OCT to examination of easel paintings

We present results of applying low coherence interferometry to gallery paintings. Infrared low coherence interferometry is capable of non-destructive examination of paintings in 3D, which shows not only the structure of the varnish layer but also the paint layers