Identification of WRKY transcription factors associated with leaf and corolla senescence in Petunia hybrida

Several families of transcription factors (TFs) control the progression of senescence. Many key TFs belonging to the WRKY family have been described to play crucial roles in the regulation of leaf senescence, mainly in Arabidopsis. However, little is known about senescence-associated WRKY members in floricultural species. Delay of senescence in leaves and petals of Petunia hybrida, a worldwide ornamental crop are highly appreciated traits. In this work, starting from 28 differentially expressed WRKY genes of Arabidopsis during the progression of leaf senescence, we identified the orthologous in P. hybrida and explored the expression profiles of 20 PhWRKY genes during the progression of natural (age-related) leaf and corolla senescence as well as in the corollas of flowers undergoing pollination-induced senescence. Simultaneous visualization showed consistent and similar expression profiles of PhWRKYs during natural leaf and corolla senescence, although weak expression changes were observed during pollination-induced senescence. Comparable expression trends between PhWRKYs and the corresponding genes of Arabidopsis were observed during leaf senescence, although more divergences were found in petals of pollinated petunia flowers. Integration of expression data with phylogenetics, conserved motif and cis-regulatory element analyses were used to establish a list of solid candidates that could regulate more than one senescence process. Our results suggest that several members of the WRKY family of TFs are tightly linked to the regulation of senescence in P. hybrida.Fil: Astigueta, Francisco Horacio. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Baigorria, Amilcar H.. Universidad Nacional de San Martín; ArgentinaFil: Garcia, Martín Nahuel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Delfosse, Verónica Cecilia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: González, Sergio Alejandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Perez de la Torre, Mariana Cecilia. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Moschen, Sebastián Nicolás. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Lia, Verónica Viviana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Fernandez, Paula del Carmen. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Trupkin, Santiago Ariel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentin

zCOSMOS 20k: Satellite galaxies are the main drivers of environmental effects in the galaxy population at least to z~0.7

We explore the role of environment in the evolution of galaxies over 0.1<z<0.7 using the final zCOSMOS-bright data set. Using the red fraction of galaxies as a proxy for the quenched population, we find that the fraction of red galaxies increases with the environmental overdensity and with the stellar mass, consistent with previous works. As at lower redshift, the red fraction appears to be separable in mass and environment, suggesting the action of two processes: mass and environmental quenching. The parameters describing these appear to be essentially the same at z~0.7 as locally. We explore the relation between red fraction, mass and environment also for the central and satellite galaxies separately, paying close attention to the effects of impurities in the central-satellite classification and using carefully constructed samples matched in stellar mass. There is little evidence for a dependence of the red fraction of centrals on overdensity. Satellites are consistently redder at all overdensities, and the satellite quenching efficiency increases with overdensity at 0.1<z<0.4. This is less marked at higher redshift, but both are nevertheless consistent with the equivalent local measurements. At a given stellar mass, the fraction of galaxies that are satellites also increases with the overdensity. At a given overdensity and mass, the obtained relation between the environmental quenching and the satellite fraction agrees well with the satellite quenching efficiency, demonstrating that the environmental quenching in the overall population is consistent with being entirely produced through the satellite quenching process at least up to z=0.7. However, despite the unprecedented size of our high redshift samples, the associated statistical uncertainties are still significant and our statements should be understood as approximations to physical reality, rather than physically exact formulae.Comment: 22 pages, 19 figures, submitted to MNRA

Smelling the dark proteome: Functional characterization of PITH domain-containing protein 1 (C1orf128) in olfactory metabolism

The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer’s disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1–/– mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634

The VIMOS VLT Deep Survey :Evolution of the major merger rate since z~1 from spectroscopicaly confirmed galaxy pairs

From the VIMOS VLT Deep Survey we use a sample of 6447 galaxies with I_{AB} < 24 to identify 251 pairs of galaxies, each member with a secure spectroscopic redshift, which are close in both projected separation and in velocity. We find that at z ~ 0.9, 10.9 +/- 3.2 % of galaxies with M_B(z) < -18-Qz are in pairs with separations dr < 20 kpc/h, dv < 500 km/s, and with dM_B < 1.5, significantly larger than 3.76 +/- 1.71 % at z ~ 0.5; we find that the pair fraction evolves as (1+z)^m with m = 2.49 +/- 0.56. For brighter galaxies with M_B(z=0) < -18.77, the pair fraction is higher and its evolution with redshift is somewhat flatter with m=1.88 \pm 0.40, a property also observed for galaxies with increasing stellar masses. Early type, dry mergers, pairs increase their relative fraction from 3 % at z ~ 0.9 to 12 % at z ~ 0.5. We find that the merger rate evolves as N_{mg}=(9.05 +/- 3.76) * 10^{-4}) * (1+z)^{2.43 +/- 0.76}. We find that the merger rate of galaxies with M_B(z) < -18-Qz has significantly evolved since z ~ 1. The merger rate is increasing more rapidly with redshift for galaxies with decreasing luminosities, indicating that the flat evolution found for bright samples is not universal. The merger rate is also strongly dependent on the spectral type of galaxies involved, late type mergers being more frequent in the past, while early type mergers are more frequent today, contributing to the rise in the local density of early type galaxies. About 20 % of the stellar mass in present day galaxies with log(M/M_{sun}) > 9.5 has been accreted through major merging events since z ~ 1, indicating that major mergers have contributed significantly to the growth in stellar mass density of bright galaxies over the last half of the life of the Universe.Comment: 22 pages, 19 figures, accepted in A&

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016.

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Obscured AGN at z~1 from the zCOSMOS-Bright Survey I. Selection and Optical Properties of a [Ne v]-selected sample

A sample of 94 narrow line AGN with 0.65<z<1.20 has been selected from the 20k-Bright zCOSMOS galaxy sample by detection of the high-ionization [NeV]3426 line. Taking advantage of the large amount of data available in the COSMOS field, the properties of the [NeV]-selected Type-2 AGN have been investigated, focusing on their host galaxies, X-ray emission, and optical line flux ratios. Finally, the diagnostic developed by Gilli et al. (2010), based on the X-ray to [NeV] luminosity ratio, has been exploited to search for the more heavily obscured AGN. We found that [Ne v]-selected narrow line AGN have Seyfert 2-like optical spectra, although with emission line ratios diluted by a star-forming component. The ACS morphologies and stellar component in the optical spectra indicate a preference for our Type-2 AGN to be hosted in early-spirals with stellar masses greater than 10^(9.5-10)Msun, on average higher than those of the galaxy parent sample. The fraction of galaxies hosting [NeV]-selected obscured AGN increases with the stellar mass, reaching a maximum of about 3% at 2x10^11 Msun. A comparison with other selection techniques at z~1 shows that the detection of the [Ne v] line is an effective method to select AGN in the optical band, in particular the most heavily obscured ones, but can not provide by itself a complete census of AGN2. Finally, the high fraction of [NeV]-selected Type-2 AGN not detected in medium-deep Chandra observations (67%) is suggestive of the inclusion of Compton-thick sources in our sample. The presence of a population of heavily obscured AGN is corroborated by the X-ray to [NeV] ratio; we estimated, by mean of X-ray stacking technique and simulations, that the Compton-thick fraction in our sample of Type-2 AGN is 43+-4%, in good agreement with standard assumptions by the XRB synthesis models.Comment: 14 pages, 12 figures, accepted for publication in A&

A group-galaxy cross-correlation function analysis in zCOSMOS

We present a group-galaxy cross-correlation analysis using a group catalog produced from the 16,500 spectra from the optical zCOSMOS galaxy survey. Our aim is to perform a consistency test in the redshift range 0.2 < z < 0.8 between the clustering strength of the groups and mass estimates that are based on the richness of the groups. We measure the linear bias of the groups by means of a group-galaxy cross-correlation analysis and convert it into mass using the bias-mass relation for a given cosmology, checking the systematic errors using realistic group and galaxy mock catalogs. The measured bias for the zCOSMOS groups increases with group richness as expected by the theory of cosmic structure formation and yields masses that are reasonably consistent with the masses estimated from the richness directly, considering the scatter that is obtained from the 24 mock catalogs. An exception are the richest groups at high redshift (estimated to be more massive than 10^13.5 M_sun), for which the measured bias is significantly larger than for any of the 24 mock catalogs (corresponding to a 3-sigma effect), which is attributed to the extremely large structure that is present in the COSMOS field at z ~ 0.7. Our results are in general agreement with previous studies that reported unusually strong clustering in the COSMOS field.Comment: 13 pages, 9 figures, published in Ap

The zCOSMOS 20k Group Catalog

We present an optical group catalog between 0.1 < z < 1 based on 16,500 high-quality spectroscopic redshifts in the completed zCOSMOS-bright survey. The catalog published herein contains 1498 groups in total and 192 groups with more than five observed members. The catalog includes both group properties and the identification of the member galaxies. Based on mock catalogs, the completeness and purity of groups with three and more members should be both about 83% with respect to all groups that should have been detectable within the survey, and more than 75% of the groups should exhibit a one-to-one correspondence to the "real" groups. Particularly at high redshift, there are apparently more galaxies in groups in the COSMOS field than expected from mock catalogs. We detect clear evidence for the growth of cosmic structure over the last seven billion years in the sense that the fraction of galaxies that are found in groups (in volume-limited samples) increases significantly with cosmic time. In the second part of the paper, we develop a method for associating galaxies that only have photo-z to our spectroscopically identified groups. We show that this leads to improved definition of group centers, improved identification of the most massive galaxies in the groups, and improved identification of central and satellite galaxies, where we define the former to be galaxies at the minimum of the gravitational potential wells. Subsamples of centrals and satellites in the groups can be defined with purities up to 80%, while a straight binary classification of all group and non-group galaxies into centrals and satellites achieves purities of 85% and 75%, respectively, for the spectroscopic sample.Comment: 26 pages, 21 figures, published in ApJ (along with machine-readable tables

The XMM-Newton Wide-Field Survey in the COSMOS field (XMM-COSMOS): demography and multiwavelength properties of obscured and unobscured luminous AGN

We report the final optical identifications of the medium-depth (~60 ksec), contiguous (2 deg^2) XMM-Newton survey of the COSMOS field. XMM-Newton has detected ~800 X-ray sources down to limiting fluxes of ~5x10^{-16}, ~3x10^{-15}, and ~7x10^{-15} erg/cm2/s in the 0.5-2 keV, 2-10 keV and 5-10 keV bands, respectively. The work is complemented by an extensive collection of multi-wavelength data from 24 micron to UV, available from the COSMOS survey, for each of the X-ray sources, including spectroscopic redshifts for ~50% of the sample, and high-quality photometric redshifts for the rest. The XMM and multiwavelength flux limits are well matched: 1760 (98%) of the X-ray sources have optical counterparts, 1711 (~95%) have IRAC counterparts, and 1394 (~78%) have MIPS 24micron detections. Thanks to the redshift completeness (almost 100%) we were able to constrain the high-luminosity tail of the X-ray luminosity function confirming that the peak of the number density of logL_X>44.5 AGN is at z~2. Spectroscopically-identified obscured and unobscured AGN, as well as normal and starforming galaxies, present well-defined optical and infrared properties. We devised a robust method to identify a sample of ~150 high redshift (z>1), obscured AGN candidates for which optical spectroscopy is not available. We were able to determine that the fraction of the obscured AGN population at the highest (L_X>10^{44} erg s^{-1}) X-ray luminosity is ~15-30% when selection effects are taken into account, providing an important observational constraint for X-ray background synthesis. We studied in detail the optical spectrum and the overall spectral energy distribution of a prototypical Type 2 QSO, caught in a stage transitioning from being starburst dominated to AGN dominated, which was possible to isolate only thanks to the combination of X-ray and infrared observations.Comment: ApJ, in press. 59 pages, 14 figures, 2 Tables. A few typos corrected and a reference added. Table 2 is also available at http://www.mpe.mpg.de/XMMCosmos/xmm53_release ; a version of the paper in ApJ format (27 pages) is available at http://www.mpe.mpg.de/XMMCosmos/xmm53_release/brusa_xmmcosmos_optid.pd