Observational evidence of the formation of cyanopolyynes in CRL618 through the polimerization of HCN

The abundance ratio of consecutive members of the cyanopolyynes family has been explored in CRL618 using data acquired in a complete line survey covering the frequency range 81-356 GHz. The Jup range explored for the different molecules is the following: 1 to 4 for HCN and HNC, 9 to 39 for HC3N, 31 to 133 for HC5N, and 72 to 85 for HC7N (not detected beyond Jup=85). The lowest vibrationally excited state of HC7N (nu_15 at 62 cm^-1) has been tentatively detected. Data analysis has been performed by extending our previous geometrical and radiative transfer model of the slowly expanding envelope (SEE) surrounding the compact central continuum source of CRL 618, that was established from the study of rotational lines in several vibrationally excited states of HC_3N. The new lines analyzed here require to model the high velocity wind (HVW) component and the colder circumstellar gas, remnant of the AGB phase of CRL618. The derived HC3N/HC5N and HC5N/HC7N abundance ratios from this set of uniformly calibrated lines are between 3 and 6 in the different regions, similar to standard values in the CSM and ISM, and consistent with previous estimates obtained from ISO observations and chemical models. However, the abundance ratios of HC3N, HC5N and HC7N with respect to HCN are at least two orders of magnitude larger than those typical for AGB C-rich stars, such as IRC+10216. This fact indicates that, in the short transition toward the Planetary Nebula phase, HCN is quickly reprocessed into longer cyanopolyyne chains. A similar behavior was previously found in this object for the polyacetylenic chains (C(2n)H2).Comment: 8 figures, accepted in ApJ main journa

Dissimilar esponses of ancient grapevines recovered in Navarra (Spain) to arbuscular mycorrhizal symbiosis in terms of berry quality

The exploitation of genetic diversity within agricultural plants, including grapevine, is suggested as a valuable tool to cope with the negative impacts of climate change on yield and crop quality. In some winegrowing regions of Europe, there is a renewed interest in knowing the grapevine genetic resources available, focusing on the prospection, recovery, and study of ancient cultivars typical of every zone. Grapevines are naturally associated with arbuscular mycorrhizal fungi (AMF), which provide some benefits to the host plant, although such effects depending on many factors, including variety. Therefore, the aim of this research was to characterize the potential fruit quality of eight old grapevine varieties recovered in Navarre (northeastern of the Iberian Peninsula), associated or not with AMF. The study was carried out on fruit-bearing cuttings grown under controlled conditions (greenhouse). Overall, AMF inoculation reduced bunch and berry mass, as well as phenolic content in fruits. In some varieties, AMF association improved some berry traits by increasing the concentrations of soluble solids and anthocyanins; in others, berry colour, total phenolic and anthocyanin content were diminished in AMF-inoculated plants. The results, therefore, suggest that intraspecific diversity of old grapevines could include different abilities to respond to arbuscular mycorrhizal symbiosis

Far-IR Excited OH Lines from Orion KL Outflows

Accepted in ApJ letters, 2006 March 2As part of the first far-IR line survey towards Orion KL, we present the detection of seven new rotationally excited OH Lambda-doublets (at 48, 65, 71, 79, 98 and 115 um). Observations were performed with the Long Wavelength Spectrometer (LWS) Fabry-Perots on board the Infrared Space Observatory (ISO). In total, more than 20 resolved OH rotational lines, with upper energy levels up to 620 K, have been detected at an angular and velocity resolutions of 80$'' and 33 km s^-1 respectively. OH line profiles show a complex behavior evolving from pure absorption, P-Cygni type to pure emission. We also present a large scale 6' declination raster in the OH ^2\Pi_3/2 J=5/2^+-3/2^- and ^2\Pi_3/2 J=7/2^-5/2^+ lines (at 119.441 and 84.597 um) revealing the decrease of excitation outside the core of the cloud. From the observed profiles, mean intrinsic line widths and velocity offsets between emission and absorption line peaks we conclude that most of the excited OH arises from Orion outflow(s), i.e. the ``plateau'' component. We determine an averaged OH abundance relative to H_2 of X(OH)=(0.5-1.0)x10^-6, a kinetic temperature of 100 K and a density of n(H_2)=5x10^5 cm^-3. Even with these conditions, the OH excitation is heavily coupled with the strong dust continuum emission from the inner hot core regions and from the expanding flow itself.Peer reviewe

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

BACKGROUND: With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago. RESULTS: Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa. CONCLUSION: The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies

Treatment-limiting renal tubulopathy in patients treated with tenofovir disoproxil fumarate.

OBJECTIVES: Tenofovir disoproxil fumarate (TDF) is widely used in the treatment or prevention of HIV and hepatitis B infection. TDF may cause renal tubulopathy in a small proportion of recipients. We aimed to study the risk factors for developing severe renal tubulopathy. METHODS: We conducted an observational cohort study with retrospective identification of cases of treatment-limiting tubulopathy during TDF exposure. We used multivariate Poisson regression analysis to identify risk factors for tubulopathy, and mixed effects models to analyse adjusted estimated glomerular filtration rate (eGFR) slopes. RESULTS: Between October 2002 and June 2013, 60 (0.4%) of 15,983 patients who had received TDF developed tubulopathy after a median exposure of 44.1 (IQR 20.4, 64.4) months. Tubulopathy cases were predominantly male (92%), of white ethnicity (93%), and exposed to antiretroviral regimens that contained boosted protease inhibitors (PI, 90%). In multivariate analysis, age, ethnicity, CD4 cell count and use of didanosine or PI were significantly associated with tubulopathy. Tubulopathy cases experienced significantly greater eGFR decline while receiving TDF than the comparator group (-6.60 [-7.70, -5.50] vs. -0.34 [-0.43, -0.26] mL/min/1.73 m2/year, p < 0.0001). CONCLUSIONS: Older age, white ethnicity, immunodeficiency and co-administration of ddI and PI were risk factors for tubulopathy in patients who received TDF-containing antiretroviral therapy. The presence of rapid eGFR decline identified TDF recipients at increased risk of tubulopathy

PDRs4All IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar

(Abridged) Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 $\mu$m. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR, the atomic PDR, and the HII region. We use JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extract five template spectra to represent the morphology and environment of the Orion Bar PDR. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. While the spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 $\mu$m, a wealth of weaker features and sub-components are present. We report trends in the widths and relative strengths of AIBs across the five template spectra. These trends yield valuable insight into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 $\mu$m AIB emission from class B$_{11.2}$ in the molecular PDR to class A$_{11.2}$ in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a "weeding out" of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called 'grandPAHs'.Comment: 25 pages, 10 figures, to appear in A&