Discrepancies between the [O III] and [S III] temperatures in H II regions

Context. Analysis of published [O iii] and [S iii] temperatures measurements of emission line objects consisting of Hii galaxies, giant extragalactic Hii regions, Galactic Hii regions, and Hii regions from the Magellanic Clouds reveal that the [O iii] temperatures are higher than the corresponding values from [S iii] in most objects with gas metallicities in excess of 0.2 solar. For the coolest nebulae (the highest metallicities), the [O iii] temperature excess can reach ∼3000 K. Aims. We look for an explanation for these temperature differences and explore the parameter space of models with the aim of reproducing the observed trend of T O iii > T S iii in Hii regions with temperatures below 14 000 K. Methods. Using standard photoionization models, we varied the ionization parameter, the hardness of the ionizing continuum, and the gas metallicities in order to characterize how models behave with respect to the observations. We introduced temperature inhomogeneities and varied their mean squared amplitude t 2. We explored the possibility of inhomogeneities in abundances by combining two models of widely different metallicity. We calculated models that consider the possibility of a non-Maxwell-Boltzmann energy distribution (a κ-distribution) for the electron energies. We also considered shock heating within the photoionized nebula. Results. Simple photoionization calculations yield nearly equal [O iii] and [S iii] temperatures in the domain of interest. Hence these models fail to reproduce the [O iii] temperature excess. Models that consider temperature inhomogeneities, as measured by the mean squared amplitude t 2, also fail in the regime where T O iii < 14 000 K. Three options remain that can reproduce the observed excess in T O iii temperatures: (1) large metallicity inhomogeneities in the nebula; a (2) κ-distribution for the electron energies; and (3) shock waves that propagate in the photoionized plasma at velocities ∼60 km s -1. Conclusions. The observed nebular temperatures are not reproduced by varying the input parameters in the pure photoionization case nor by assuming local temperature inhomogeneities. We find that (1) metallicity inhomogeneities of the nebular gas; (2) shock waves of velocities 60 km s -1 propagating in a photoionized plasma; and (3) an electron energy distribution given by a κ-distribution are successful in reproducing the observed excess in the [O iii] temperatures. However, shock models require proper 3D hydrodynamical simulations to become a fully developed alternative while models with metallicity inhomogeneities appear to fail in metal-poor nebulae, since they result in T rec O++ T O iii T rec O++ ≳ TO iii.Facultad de Ciencias Astronómicas y Geofísica

Galaxy properties from J-PAS narrow-band photometry

We study the consistency of the physical properties of galaxies retrieved from SED-fitting as a function of spectral resolution and signal-to-noise ratio (SNR). Using a selection of physically motivated star formation histories, we set up a control sample of mock galaxy spectra representing observations of the local universe in high-resolution spectroscopy, and in 56 narrow-band and 5 broad-band photometry. We fit the SEDs at these spectral resolutions and compute their corresponding the stellar mass, the mass- and luminosity-weighted age and metallicity, and the dust extinction. We study the biases, correlations, and degeneracies affecting the retrieved parameters and explore the r\^ole of the spectral resolution and the SNR in regulating these degeneracies. We find that narrow-band photometry and spectroscopy yield similar trends in the physical properties derived, the former being considerably more precise. Using a galaxy sample from the SDSS, we compare more realistically the results obtained from high-resolution and narrow-band SEDs (synthesized from the same SDSS spectra) following the same spectral fitting procedures. We use results from the literature as a benchmark to our spectroscopic estimates and show that the prior PDFs, commonly adopted in parametric methods, may introduce biases not accounted for in a Bayesian framework. We conclude that narrow-band photometry yields the same trend in the age-metallicity relation in the literature, provided it is affected by the same biases as spectroscopy; albeit the precision achieved with the latter is generally twice as large as with the narrow-band, at SNR values typical of the different kinds of data.Comment: 26 pages, 15 figures. Accepted for publication in MNRA

In silico analysis of gene expression in V3a and the superior occipital gyrus. Relevance for migraine

Introduction: Visual manifestations are the most prominent non-painful features of migraine. During the last decades, visual area V3a has gathered attention of headache scientists because of its apparent implication on aura initiation, photophobia and cortical hyper-responsiveness related to visual motion perception. In this hypothesis-generating study, we performed an in silico analysis of gene expression in left V3a and the cerebral gyrus that harbours it (left superior occipital gyrus (lSOG)) searching for transcriptomic patterns that could be linked with migraine’s pathophysiology. Materials and methods: Neurotransmitter receptor gene expression levels in left V3a were extracted from validated brain mRNA expression models using a probabilistic volumetric mask of this region. The primary visual cortex and other sensory cortices (auditory, olfactory and somatosensory) were used as comparators. Genome-wide transcriptomic differences between the gyrus harbouring left V3a (lSOG) and the rest of the cerebral cortex were assessed using the Allen Brain Institute Human RNA micro array atlas/database. Results: Adrenergic receptor β1, dopaminergic receptor D3 and serotoninergic receptors 1B, 1F and 2A, which have been previously implicated in migraine’s pathophysiology and/or treatment, showed significantly higher expression levels on left V3a. Transcriptomic differences between the lSOG harbouring V3a and the rest of the cortex comprise genes whose products are involved in neuronal excitability (SLC17A6, KCNS1, KCNG1 and GABRQ), activation of multiple signal transduction pathways (MET) and cell metabolism (SPHKAP via its interaction with cAMP-dependent protein kinase). Conclusions: Focal gene expression analysis of V3a suggests some clues about its implication in migraine. Further studies are warranted

Shrimp ponds lead to massive loss of soil carbon and greenhouse gas emissions in northeastern Brazilian mangroves

Mangroves of the semiarid Caatinga region of northeastern Brazil are being rapidly converted to shrimp pond aquaculture. To determine ecosystem carbon stocks and potential greenhouse gas emissions from this widespread land use, we measured carbon stocks of eight mangrove forests and three shrimp ponds in the Acaraú and Jaguaribe watersheds in Ceará state, Brazil. The shrimp ponds were paired with adjacent intact mangroves to ascertain carbon losses and potential emissions from land conversion. The mean total ecosystem carbon stock of mangroves in this semiarid tropical landscape was 413 ± 94 Mg C/ha. There were highly significant differences in the ecosystem carbon stocks between the two sampled estuaries suggesting caution when extrapolating carbon stock across different estuaries even in the same landscape. Conversion of mangroves to shrimp ponds resulted in losses of 58%–82% of the ecosystem carbon stocks. The mean potential emissions arising from mangrove conversion to shrimp ponds was 1,390 Mg CO2e/ha. Carbon losses were largely from soils which accounted for 81% of the total emission. Losses from soils \u3e 100 cm in depth accounted for 33% of the total ecosystem carbon loss. Soil carbon losses from shrimp pond conversion are equivalent to about 182 years of soil carbon accumulation. Losses from mangrove conversion are about 10-fold greater than emissions from conversion of upland tropical dry forest in the Brazilian Caatinga underscoring the potential value for their inclusion in climate change mitigation activities

The QUEST RR Lyrae Survey: Confirmation of the Clump at 50 kpc and Other Over-Densities in the Outer Halo

We have measured the periods and light curves of 148 RR Lyrae variables from V=13.5 to 19.7 from the first 100 sq. degrees of the QUEST RR Lyrae survey. Approximately 55% of these stars belong to the clump of stars detected earlier by the Sloan Digital Sky Survey. According to our measurements, this feature has ~10 times the background density of halo stars, spans at least 37.5 deg by 3.5 deg in right ascension and declination (>=30 by >=3 kpc), lies ~50 kpc from the Sun, and has a depth along the line of sight of ~5 kpc (1 sigma). These properties are consistent with the recent models that suggest it is a tidal stream from the Sgr dSph galaxy. The mean period of the type ab variables, 0.58 d, is also consistent. In addition, we have found two smaller over-densities in the halo, one of which may be related to the globular cluster Pal 5.Comment: 12 pages (including 4 figures). Accepted for publication in the ApJ Letter

Exploring the gene regulatory networks of WRKY family in grapevine (Vitis vinifera L.) using DAP-Seq

The recent development of regulatory genomics has raised increasing interest in plant research since transcriptional regulation of genes plays a pivotal role in many biological processes. By shedding light on the target genes of the various transcription factors (TFs), it is therefore possible to infer the influence they exert on the different molecular mechanisms. In this regard, the attention was focused on WRKYs, a family of TFs almost exclusively found in plant species. In grapevine, WRKYs are involved in several biological processes, playing a key role in berry development, hormonal balance and signalling, biotic and abiotic stresses responses, and secondary metabolites biosynthesis. In this study, DAP-Seq was used to investigate the regulatory activity of the whole WRKY family in gDNA from young leaves of Cabernet Franc. This approach allowed the definition of the WRKYs cistrome (i.e., the set of bound genes). 46 out of 59 WRKYs gave results, outlining a total number of 674,407 binding events along whole grapevine genome, of which 459,791 (68%) are localized in the perigenic region, according to its intense regulatory activity. Cistrome maps were integrated with gene centred co-expression networks based on a large transcriptomics dataset, and with the results of an ATAC-Seq. This allowed to isolate some High Confidence Targets, characterized by high degree of co-expression with the related TF and laying down in genomic regions of open chromatin. The networks generated can be used to provide a complete regulatory map of WRKY family, shedding light on its biological role in grapevine

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors