snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

The snoRNA-LBME-db is a dedicated database containing human C/D box and H/ACA box small nucleolar RNAs (snoRNAs), and small Cajal body-specific RNAs (scaRNAs). C/D box and H/ACA box snoRNAs are part of ribonucleoparticles that guide 2′-O-ribose methylation and pseudouridilation, respectively, of selected residues of 28S, 18S or 5.8S rRNAs or of the spliceosomal U6 RNA. Similarly, scaRNAs guide modifications of the spliceosomal RNAs transcribed by RNA polymerase II (U1, U2, U4, U5 and U12) and are often composed of both C/D box and H/ACA box domains. However, some snoRNAs do not function as modification guide RNAs, but rather as RNA chaperones during the maturation of pre-rRNA. The database was built by a compilation of the literature, and comprises human sno/scaRNAs that were experimentally verified, as well as the human orthologs of snoRNAs that were cloned in other vertebrate species, and some snoRNAs that are predicted by bioinformatics search in loci submitted to genomic imprinting, but have not all been experimentally verified. For each entry, the database identifies the modified nucleotide(s) in the target RNA(s), indicates the corresponding predicted base pairing, gives a few pertinent references and provides a link to the position of the sno/scaRNA on the UCSC Genome Browser. The ‘Find guide RNA’ function allows one to find the sno/scaRNAs predicted to guide the modification of a particular nucleotide in the rRNA and spliceosomal RNA sequences. The ‘Browse’ function allows one to download the sequences of selected sno/scaRNAs in the FASTA format. The database is available online at . It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track

VLBA determination of the distance to nearby star-forming regions II. Hubble 4 and HDE 283572 in Taurus

The non-thermal 3.6 cm radio continuum emission from the naked T Tauri stars Hubble 4 and HDE 283572 in Taurus has been observed with the Very Long Baseline Array (VLBA) at 6 epochs between September 2004 and December 2005 with a typical separation between successive observations of 3 months. Thanks to the remarkably accurate astrometry delivered by the VLBA, the trajectory described by both stars on the plane of the sky could be traced very precisely, and modeled as the superposition of their trigonometric parallax and uniform proper motion. The best fits yield distances to Hubble 4 and HDE 283572 of 132.8 +/- 0.5 and 128.5 +/- 0.6 pc, respectively. Combining these results with the other two existing VLBI distance determinations in Taurus, we estimate the mean distance to the Taurus association to be 137 pc with a dispersion (most probably reflecting the depth of the complex) of about 20 pc.Comment: 21 pages, 4 figues, accepted in ApJ (Dec 20, 2007 issue

Autecology of broadleaved species

Anyone involved in timber production needs some knowledge of autecology. With the renewed interest in hardwoods in the last 20 years, they are increasingly being introduced by planting or encouraged in natural stands. The results in terms of growth have not always met foresters’ expectations, due to technical problems and especially because the species are not always suited to the different sites. While the principle of establishing hardwoods is not in question, it is important to be aware of the conditions they need for their growth. This is why the first component of the Pirinoble programme is about improving knowledge on the ecology and adaptation of valuable hardwood species. To support this, a wide-ranging bibliographic analysis was made of scientific publications in French, English, Spanish and Italian on the main hardwood species that can be established as plantations: - Wild Cherry (Prunus avium l.), - Common Ash (Fraxinus SSP.), - Wild service tree (Sorbus torminalis l.), service tree (Sorbus domestica L.) and other sorbus species. - Walnut (Juglans SSP.), - Common pear tree (Pyrus pyraster (l.) Du ROI) and the European Wild Apple tree (Malus sylvestris Mill.). - Lime (Tilia ssp.), - Maple (Acer SSP.). Favourable site conditions for hardwood trees are now better understood thanks to numerous observations carried out in stands and a number of scientific studies. Some species have been studied in more depth, including the wild cherry, wild service tree, common ash, maple and walnut. This guide is based on the results of these studies, supplemented by the expertise of the authors. It includes a series of autecology factsheets that describe the site conditions in which hardwoods will thrive and the minimum conditions required for rapid timber production. The factsheets were published on a regular basis in Forêt-entreprise in 2012 and 2013 (see footnote at the end of each of factsheet), and are now published together in this guide along with the bibliographical references consulted

A Surprising Dynamical Mass for V773~Tau~B

We report on new high-resolution imaging and spectroscopy on the multiple T Tauri star system V773 Tau over the 2003 -- 2009 period. With these data we derive relative astrometry, photometry between the A and B components, and radial velocity (RV) of the A-subsystem components. Combining these new data with previously published astrometry and RVs, we update the relative A-B orbit model. This updated orbit model, the known system distance, and A subsystem parameters yields a dynamical mass for the B component for the first time. Remarkably the derived B dynamical mass is in the range of 1.7 -- 3.0 M_\sun. This is much higher than previous estimates, and suggests that like A, B is also a multiple stellar system. Among these data, spatially-resolved spectroscopy provide new insight into the nature of the B component. Similar to A, these near-IR spectra indicate that the dominant source in B is of mid-K spectral type. If B is in fact a multiple star system as suggested by the dynamical mass estimate, the simplest assumption is that B is composed of similar $\sim$ 1.2 M_\sun PMS stars in a close ($<$ 1 AU) binary system. This inference is supported by line-shape changes in near-IR spectroscopy of B, tentatively interpreted as changing RV among components in V773 Tau B. Relative photometry indicate that B is highly variable in the near-IR. The most likely explanation for this variability is circum-B material resulting in variable line-of-sight extinction. The distribution of this material must be significantly affected by both the putative B multiplicity, and the A-B orbit.Comment: 22 pages, 7 figures, accepted for publication ApJ. Companion paper to R. Torres et al arXiv:1112.0114. Table 2 (RV Data Table) to appear in on-line versio

AzTEC millimeter survey of the COSMOS field - III. Source catalog over 0.72 sq. deg. and plausible boosting by large-scale structure

We present a 0.72 sq. deg. contiguous 1.1mm survey in the central area of the COSMOS field carried out to a 1sigma ~ 1.26 mJy/beam depth with the AzTEC camera mounted on the 10m Atacama Submillimeter Telescope Experiment (ASTE). We have uncovered 189 candidate sources at a signal-to-noise ratio S/N >= 3.5, out of which 129, with S/N >= 4, can be considered to have little chance of being spurious (< 2 per cent). We present the number counts derived with this survey, which show a significant excess of sources when compared to the number counts derived from the ~0.5 sq. deg. area sampled at similar depths in the Scuba HAlf Degree Extragalactic Survey (SHADES, Austermann et al. 2010). They are, however, consistent with those derived from fields that were considered too small to characterize the overall blank-field population. We identify differences to be more significant in the S > 5 mJy regime, and demonstrate that these excesses in number counts are related to the areas where galaxies at redshifts z < 1.1 are more densely clustered. The positions of optical-IR galaxies in the redshift interval 0.6 < z < 0.75 are the ones that show the strongest correlation with the positions of the 1.1mm bright population (S > 5 mJy), a result which does not depend exclusively on the presence of rich clusters within the survey sampled area. The most likely explanation for the observed excess in number counts at 1.1mm is galaxy-galaxy and galaxy-group lensing at moderate amplification levels, that increases in amplitude as one samples larger and larger flux densities. This effect should also be detectable in other high redshift populations.Comment: 21 pages, 17 figures, accepted for publication in MNRA

Detection of an ultra-bright submillimeter galaxy in the Subaru/XMM-Newton Deep Field using AzTEC/ASTE

We report the detection of an extremely bright ($\sim$37 mJy at 1100 $\mu$m and $\sim$91 mJy at 880 $\mu$m) submillimeter galaxy (SMG), AzTEC-ASTE-SXDF1100.001 (hereafter referred to as SXDF1100.001 or Orochi), discovered in 1100 $\mu$m observations of the Subaru/XMM-Newton Deep Field using AzTEC on ASTE. Subsequent CARMA 1300 $\mu$m and SMA 880 $\mu$m observations successfully pinpoint the location of Orochi and suggest that it has two components, one extended (FWHM of $\sim$ 4$^{\prime\prime}$) and one compact (unresolved). Z-Spec on CSO has also been used to obtain a wide band spectrum from 190 to 308 GHz, although no significant emission/absorption lines are found. The derived upper limit to the line-to-continuum flux ratio is 0.1--0.3 (2 $\sigma$) across the Z-Spec band. Based on the analysis of the derived spectral energy distribution from optical to radio wavelengths of possible counterparts near the SMA/CARMA peak position, we suggest that Orochi is a lensed, optically dark SMG lying at $z \sim 3.4$ behind a foreground, optically visible (but red) galaxy at $z \sim 1.4$. The deduced apparent (i.e., no correction for magnification) infrared luminosity ($L_{\rm IR}$) and star formation rate (SFR) are $6 \times 10^{13}$ $L_{\odot}$ and 11000 $M_{\odot}$ yr$^{-1}$, respectively, assuming that the $L_{\rm IR}$ is dominated by star formation. These values suggest that Orochi will consume its gas reservoir within a short time scale ($3 \times 10^{7}$ yr), which is indeed comparable to those in extreme starbursts like the centres of local ULIRGs.Comment: 18 pages, 13 figure

Dysregulation of Ribosome Biogenesis and Translational Capacity Is Associated with Tumor Progression of Human Breast Cancer Cells

Protein synthesis is a fundamental cell process and ribosomes - particularly through the ribosomal RNA that display ribozyme activity - are the main effectors of this process. Ribosome biogenesis is a very complex process involving transcriptional a

Autécologie des feuillus précieux

Pour la production de bois : l’autécologie1, un passage obligé ! Depuis une vingtaine d’années, le regain d’intérêt pour les feuillus a conduit bon nombre de sylviculteurs à les sélectionner dans les peuplements et à les introduire en plantation. Les résultats de croissance n’ont cependant pas toujours été à la hauteur des attentes, à cause de problèmes techniques et surtout par inadéquation de l’essence aux stations. L’installation de ces feuillus ne doit pas être remise en cause, mais il convient d’être attentif à leurs exigences stationnelles. C’est pour cette raison que le 1er axe du programme Pirinoble concerne l’amélioration des connaissances sur l'écologie et l'adaptation des essences de feuillus précieux. Pour cela, un vaste travail d’analyses bibliographiques des publications scientifiques multilingues (français, anglais, espagnol et italien) a été réalisé sur les principales essences feuillues pouvant être introduites en plantation : - Merisier (Prunus avium L.), - Frênes (Fraxinus ssp.), - Alisier torminal (Sorbus torminalis L.), Cormier (Sorbus domestica L.) et autres sorbiers, - Noyers (Juglans ssp.), - Poirier commun (Pyrus pyraster (L.) Du Roi) et Pommier sauvage (Malus sylvestris Mill.), - Tilleuls (Tilia ssp.), - Erables (Acer ssp.). Les conditions stationnelles favorables aux feuillus sont en effet mieux connues aujourd’hui, grâce à de nombreuses observations réalisées dans les peuplements et à quelques études scientifiques. Certaines essences ont cependant été plus étudiées, notamment le merisier, l’alisier torminal, le frêne commun, les érables, les noyers. Ce travail de synthèse, complété par l’expertise des auteurs, a débouché sur la rédaction de fiches autécologiques décrivant les situations stationnelles correspondant à une adaptation excellente et au minimum requis pour une production rapide de bois. Ces fiches ont été régulièrement publiées dans Forêt-entreprise en 2012 et 2013 (voir référence indiquée à la fin de chacune des fiches).Le présent ouvrage regroupe l’ensemble des fiches, avec également les références bibliographiques consultées.POCTEFA 93/08 "Pirinoble

Use of photoswitchable fluorescent proteins for droplet-based microfluidic screening

International audience11 Application of droplet-based microfluidics for the screening of microbial libraries is one of the 12 important ongoing development in functional genomics/metagenomics. In this article, we propose a 13 new method that can be employed for the high-throughput profiling of cell growth. It consists in light-14 driven labelling droplets that contain growing cells directly in microfluidics observation chamber, 15 followed by recovery of the labelled cells. This method is based on intracellular expression of green to 16 red switchable fluorescent proteins. The proof of concept is established here for two commonly used 17 biological models, E.coli and S.cerevisiae. Growth of cells in droplets was monitored under a 18 microscope and, depending on the targeted phenotype, the fluorescence of selected droplets was 19 switched from a "green" to a "red" state. Red fluorescent cells from labelled droplets were then 20 successfully detected, sorted with the Fluorescence Activated Cell Sorting machine and recovered. 21 Finally, the application of this method for different kind of screenings, in particular of metagenomic 22 libraries, is discussed and this idea is validated by the analysis of a model mini-library. 2