Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations

Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of Rhizobium etli CFN42 in a collection of 87 Rhizobium strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in R. etli CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (glyA and dnaB) and three symbiotic sequences (nodC and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the R. etli populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion

Active galactic nuclei synapses: X-ray versus optical classifications using artificial neural networks

(Abridged) Many classes of active galactic nuclei (AGN) have been defined entirely throughout optical wavelengths while the X-ray spectra have been very useful to investigate their inner regions. However, optical and X-ray results show many discrepancies that have not been fully understood yet. The aim of this paper is to study the "synapses" between the X-ray and optical classifications. For the first time, the new EFLUXER task allowed us to analyse broad band X-ray spectra of emission line nuclei (ELN) without any prior spectral fitting using artificial neural networks (ANNs). Our sample comprises 162 XMM-Newton/pn spectra of 90 local ELN in the Palomar sample. It includes starbursts (SB), transition objects (T2), LINERs (L1.8 and L2), and Seyferts (S1, S1.8, and S2). The ANNs are 90% efficient at classifying the trained classes S1, S1.8, and SB. The S1 and S1.8 classes show a wide range of S1- and S1.8-like components. We suggest that this is related to a large degree of obscuration at X-rays. The S1, S1.8, S2, L1.8, L2/T2/SB-AGN (SB with indications of AGN), and SB classes have similar average X-ray spectra within each class, but these average spectra can be distinguished from class to class. The S2 (L1.8) class is linked to the S1.8 (S1) class with larger SB-like component than the S1.8 (S1) class. The L2, T2, and SB-AGN classes conform a class in the X-rays similar to the S2 class albeit with larger fractions of SB-like component. This SB-like component is the contribution of the star-formation in the host galaxy, which is large when the AGN is weak. An AGN-like component seems to be present in the vast majority of the ELN, attending to the non-negligible fraction of S1-like or S1.8-like component. This trained ANN could be used to infer optical properties from X-ray spectra in surveys like eRosita.Comment: 15 pages, 7 figures, accepted for publication in A&A. Appendix B only in the full version of the paper here: https://dl.dropboxusercontent.com/u/3484086/AGNSynapsis_OGM_online.pd

3D molecular line formation in dwarf carbon-enhanced metal-poor stars

We present a detailed analysis of the carbon and nitrogen abundances of two dwarf carbon-enhanced metal-poor (CEMP) stars: SDSS J1349-0229 and SDSS J0912+0216. We also report the oxygen abundance of SDSS J1349-0229. These stars are metal-poor, with [Fe/H] < -2.5, and were selected from our ongoing survey of extremely metal-poor dwarf candidates from the Sloan Digital SkySurvey (SDSS). The carbon, nitrogen and oxygen abundances rely on molecular lines which form in the outer layers of the stellar atmosphere. It is known that convection in metal-poor stars induces very low temperatures which are not predicted by `classical' 1D stellar atmospheres. To obtain the correct temperature structure, one needs full 3D hydrodynamical models. Using CO5BOLD 3D hydrodynamical model atmospheres and the Linfor3D line formation code, molecular lines of CH, NH, OH and C2 were computed, and 3D carbon, nitrogen and oxygen abundances were determined. The resulting carbon abundances were compared to abundances derived using atomic CI lines in 1D LTE and NLTE. There is not a good agreement between the carbon abundances determined from C2 bands and from the CH band, and molecular lines do not agree with the atomic CI lines. Although this may be partly due to uncertainties in the transition probabilities of the molecular bands it certainly has to do with the temperature structure of the outer layers of the adopted model atmosphere. We explore the influence of the 3D model properties on the molecular abundance determination. In particular, the choice of the number of opacity bins used in the model calculations and its subsequent effects on the temperature structure and molecular line formation is discussed. (Abridged)Comment: Poster presented at IAU JD 10, Rio de Janeiro, 10-11 August 2009, published in Memorie della Societa' Astronomica Italiana, Vol. 80 n.3 P.735. One reference corrected, matches the published versio

No surviving evolved companions to the progenitor of supernova SN 1006

Type Ia supernovae are thought to occur as a white dwarf made of carbon and oxygen accretes sufficient mass to trigger a thermonuclear explosion$^{1}$. The accretion could occur slowly from an unevolved (main-sequence) or evolved (subgiant or giant) star$^{2,3}$, that being dubbed the single-degenerate channel, or rapidly as it breaks up a smaller orbiting white dwarf (the double- degenerate channel)$^{3,4}$. Obviously, a companion will survive the explosion only in the single-degenerate channel$^{5}$. Both channels might contribute to the production of type Ia supernovae$^{6,7}$ but their relative proportions still remain a fundamental puzzle in astronomy. Previous searches for remnant companions have revealed one possible case for SN 1572$^{8,9}$, though that has been criticized$^{10}$. More recently, observations have restricted surviving companions to be small, main-sequence stars$^{11,12,13}$, ruling out giant companions, though still allowing the single-degenerate channel. Here we report the result of a search for surviving companions to the progenitor of SN 1006$^{14}$. None of the stars within 4' of the apparent site of the explosion is associated with the supernova remnant, so we can firmly exclude all giant and subgiant companions to the progenitor. Combined with the previous results, less than 20 per cent of type Iae occur through the single degenerate channel.Comment: Published as a letter in Nature (2012 September 27

No surviving companion in Kepler's supernova

We have surveyed Kepler's supernova remnant in search of the companion star of the explosion. We have gone as deep as 2.6 solar luminosities in the stars within 20% of the radius of the remnant. We use FLAMES at the VLT-UT2 telescope to obtain high resolution spectra of the stellar candidates selected from HST images. The resulting set of stellar parameters suggests that these stars come from a rather ordinary mixture of field stars (mostly giants). A few of the stars seem to have low [Fe/H] (< -1) and they are consistent with being metal-poor giants. The radial velocities and rotational velocities vrot sin i are very well determined. There are no fast rotating stars as vrot sin i < 20 km/s. The radial velocities from the spectra and the proper motions determined from HST images are compatible with those expected from the Besan\c{c}on model of the Galaxy. The strong limits placed on luminosity suggest that this supernova could have arisen either from the core-degenerate scenario or from the double-degenerate scenario.Comment: ApJ accepted, 7 figures and 7 table

Solar analogs with and without planets: Tc_c trends and galactic evolution

We explore a sample of 148 solar-like stars to search for a possible correlation between the slopes of the abundance trends versus condensation temperature (known as the Tc slope) both with stellar parameters and Galactic orbital parameters in order to understand the nature of the peculiar chemical signatures of these stars and the possible connection with planet formation. We find that the Tc slope correlates at a significant level with the stellar age and the stellar surface gravity. We also find tentative evidence that the Tc slope correlates with the mean galactocentric distance of the stars (Rmean), suggesting that stars that originated in the inner Galaxy have fewer refractory elements relative to the volatile ones. We found that the chemical peculiarities (small refractory-to-volatile ratio) of planet-hosting stars is probably a reflection of their older age and their inner Galaxy origin. We conclude that the stellar age and probably Galactic birth place are key to establish the abundances of some specific elements.Comment: Proceedings of the GREAT-ITN conference: The Milky Way Unravelled by Gaia. Will be published in the "EAS Publications Series