A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance

Star Formation and Dynamics in the Galactic Centre

The centre of our Galaxy is one of the most studied and yet enigmatic places in the Universe. At a distance of about 8 kpc from our Sun, the Galactic centre (GC) is the ideal environment to study the extreme processes that take place in the vicinity of a supermassive black hole (SMBH). Despite the hostile environment, several tens of early-type stars populate the central parsec of our Galaxy. A fraction of them lie in a thin ring with mild eccentricity and inner radius ~0.04 pc, while the S-stars, i.e. the ~30 stars closest to the SMBH (<0.04 pc), have randomly oriented and highly eccentric orbits. The formation of such early-type stars has been a puzzle for a long time: molecular clouds should be tidally disrupted by the SMBH before they can fragment into stars. We review the main scenarios proposed to explain the formation and the dynamical evolution of the early-type stars in the GC. In particular, we discuss the most popular in situ scenarios (accretion disc fragmentation and molecular cloud disruption) and migration scenarios (star cluster inspiral and Hills mechanism). We focus on the most pressing challenges that must be faced to shed light on the process of star formation in the vicinity of a SMBH.Comment: 68 pages, 35 figures; invited review chapter, to be published in expanded form in Haardt, F., Gorini, V., Moschella, U. and Treves, A., 'Astrophysical Black Holes'. Lecture Notes in Physics. Springer 201

Herschel observations of EXtra-Ordinary Sources (HEXOS): Observations of H2O and its isotopologues towards Orion KL

We report the detection of more than 48 velocity-resolved ground rotational state transitions of H 16 2 O, H 18 2 O, and H 17 2 O – most for the first time – in both emission and absorption toward Orion KL using Herschel/HIFI. We show that a simple fit, constrained to match the known emission and absorption components along the line of sight, is in excellent agreement with the spectral profiles of all the water lines. Using the measured H 18 2 O line fluxes, which are less affected by line opacity than their H 16 2 O counterparts, and an escape probability method, the column densities of H 18 2 O associated with each emission component are derived. We infer total water abundances of 7.4 × 10−5, 1.0× 10−5, and 1.6 × 10−5 for the plateau, hot core, and extended warm gas, respectively. In the case of the plateau, this value is consistent with previous measures of the Orion-KL water abundance as well as those of other molecular outflows. In the case of the hot core and extended warm gas, these values are somewhat higher than water abundances derived for other quiescent clouds, suggesting that these regions are likely experiencing enhanced water-ice sublimation from (and reduced freeze-out onto) grain surfaces due to the warmer dust in these sources

Herschel observations of deuterated water towards Sgr B2(M)

Observations of HDO are an important complement for studies of water, because they give strong constraints on the formation processes – grain surfaces versus energetic process in the gas phase, e.g. in shocks. The HIFI observations of multiple transitions of HDO in Sgr B2(M) presented here allow the determination of the HDO abundance throughout the envelope, which has not been possible before with ground-based observations only. The abundance structure has been modeled with the spherical Monte Carlo radiative transfer code RATRAN, which also takes radiative pumping by continuum emission from dust into account. The modeling reveals that the abundance of HDO rises steeply with temperature from a low abundance (2.5 × 10−11) in the outer envelope at temperatures below 100 K through a medium abundance (1.5 × 10−9) in the inner envelope/outer core at temperatures between 100 and 200 K, and finally a high abundance ( 3.5 × 10−9) at temperatures above 200 K in the hot core

Herschel observations of EXtra-Ordinary Sources (HEXOS): Detection of hydrogen fluoride in absorption towards Orion KL

We report a detection of the fundamental rotational transition of hydrogen fluoride in absorption towards Orion KL using Herschel/HIFI. After the removal of contaminating features associated with common molecules (“weeds”), the HF spectrum shows a P-Cygni profile, with weak redshifted emission and strong blue-shifted absorption, associated with the low-velocity molecular outflow. We derive an estimate of 2.9 × 1013 cm−2 for the HF column density responsible for the broad absorption component. Using our best estimate of the H2 column density within the low-velocity molecular outflow, we obtain a lower limit of ∼1.6 × 10−10 for the HF abundance relative to hydrogen nuclei, corresponding to ∼0.6% of the solar abundance of fluorine. This value is close to that inferred from previous ISO observations of HF J = 2−1 absorption towards Sgr B2, but is in sharp contrast to the lower limit of 6 × 10−9 derived by Neufeld et al. for cold, foreground clouds on the line of sight towards G10.6-0.4

Herschel observations of EXtra-Ordinary Sources (HEXOS): The present and future of spectral surveys with Herschel/HIFI

We present initial results from the Herschel GT key program: Herschel observations of EXtra-Ordinary Sources (HEXOS) and outline the promise and potential of spectral surveys with Herschel/HIFI. The HIFI instrument offers unprecedented sensitivity, as well as continuous spectral coverage across the gaps imposed by the atmosphere, opening up a largely unexplored wavelength regime to high-resolution spectroscopy. We show the spectrum of Orion KL between 480 and 560 GHz and from 1.06 to 1.115 THz. From these data, we confirm that HIFI separately measures the dust continuum and spectrally resolves emission lines in Orion KL. Based on this capability we demonstrate that the line contribution to the broad-band continuum in this molecule-rich source is ∼20−40% below 1 THz and declines to a few percent at higher frequencies. We also tentatively identify multiple transitions of HD18O in the spectra. The first detection of this rare isotopologue in the interstellar medium suggests that HDO emission is optically thick in the Orion hot core with HDO/H2O ∼ 0.02. We discuss the implications of this detection for the water D/H ratio in hot cores

Reversal of infall in SgrB2(M) revealed by Herschel/HIFI observations of HCN lines at THz frequencies

Aims. To investigate the accretion and feedback processes in massive star formation, we analyze the shapes of emission lines from hot molecular cores, whose asymmetries trace infall and expansion motions. Methods. The high-mass star forming region SgrB2(M) was observed with Herschel/HIFI (HEXOS key project) in various lines of HCN and its isotopologues, complemented by APEX data. The observations are compared to spherically symmetric, centrally heated models with density power-law gradient and different velocity fields (infall or infall+expansion), using the radiative transfer code RATRAN. Results. The HCN line profiles are asymmetric, with the emission peak shifting from blue to red with increasing J and decreasing line opacity (HCN to H13CN). This is most evident in the HCN 12–11 line at 1062 GHz. These line shapes are reproduced by a model whose velocity field changes from infall in the outer part to expansion in the inner part. Conclusions. The qualitative reproduction of the HCN lines suggests that infall dominates in the colder, outer regions, but expansion dominates in the warmer, inner regions. We are thus witnessing the onset of feedback in massive star formation, starting to reverse the infall and finally disrupting the whole molecular cloud. To obtain our result, the THz lines uniquely covered by HIFI were critically important

Herschel observations of EXtra-Ordinary Sources (HEXOS): The Terahertz spectrum of Orion KL seen at high spectral resolution

We present the first high spectral resolution observations of Orion KL in the frequency ranges 1573.4–1702.8 GHz (band 6b) and 1788.4–1906.8 GHz (band 7b) obtained using the HIFI instrument on board the Herschel Space Observatory. We characterize the main emission lines found in the spectrum, which primarily arise from a range of components associated with Orion KL including the hot core, but also see widespread emission from components associated with molecular outflows traced by H2O, SO2, and OH. We find that the density of observed emission lines is significantly diminished in these bands compared to lower frequency Herschel/HIFI bands

Herschel observations of EXtra-Ordinary Sources (HEXOS): detecting spiral arm clouds by CH absorption lines

We have observed CH absorption lines (J = 3/2, N = 1 ← J = 1/2, N = 1) against the continuum source Sgr B2(M) using the Herschel/HIFI instrument. With the high spectral resolution and wide velocity coverage provided by HIFI, 31 CH absorption features with different radial velocities and line widths are detected and identified. The narrower line width and lower column density clouds show “spiral arm” cloud characteristics, while the absorption component with the broadest line width and highest column density corresponds to the gas from the Sgr B2 envelope. The observations show that each “spiral arm” harbors multiple velocity components, indicating that the clouds are not uniform and that they have internal structure. This line-of-sight through almost the entire Galaxy offers unique possibilities to study the basic chemistry of simple molecules in diffuse clouds, as a variety of different cloud classes are sampled simultaneously. We find that the linear relationship between CH and H2 column densities found at lower AV by UV observations does not continue into the range of higher visual extinction. There, the curve flattens, which probably means that CH is depleted in the denser cores of these clouds

Herschel/HIFI measurements of the ortho/para ratio in water towards Sagittarius B2(M) and W31C

We present Herschel/HIFI observations of the fundamental rotational transitions of ortho- and para-H16 2 O and H18 2 O in absorption towards Sagittarius B2(M) and W31C. The ortho/para ratio in water in the foreground clouds on the line of sight towards these bright continuum sources is generally consistent with the statistical high-temperature ratio of 3, within the observational uncertainties. However, somewhat unexpectedly, we derive a low ortho/para ratio of 2.35±0.35, corresponding to a spin temperature of ∼27 K, towards Sagittarius B2(M) at velocities of the expanding molecular ring. Water molecules in this region appear to have formed with, or relaxed to, an ortho/para ratio close to the value corresponding to the local temperature of the gas and dust