RSAT 2011: regulatory sequence analysis tools

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/

Genome Biol.

With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome

Semiclassical description of multiphoton processes

We analyze strong field atomic dynamics semiclassically, based on a full time-dependent description with the Hermann-Kluk propagator. From the properties of the exact classical trajectories, in particular the accumulation of action in time, the prominent features of above threshold ionization (ATI) and higher harmonic generation (HHG) are proven to be interference phenomena. They are reproduced quantitatively in the semiclassical approximation. Moreover, the behavior of the action of the classical trajectories supports the so called strong field approximation which has been devised and postulated for strong field dynamics.Comment: 10 pages, 11 figure

The mass distribution of a moderate redshift galaxy group and brightest group galaxy from gravitational lensing and kinematics

The gravitational lens system CLASS B2108+213 has two radio-loud lensed images separated by 4.56 arcsec. The relatively large image separation implies that the lensing is caused by a group of galaxies. In this paper, new optical imaging and spectroscopic data for the lensing galaxies of B2108+213 and the surrounding field galaxies are presented. These data are used to investigate the mass and composition of the lensing structure. The redshift and stellar velocity dispersion of the main lensing galaxy (G1) are found to be z = 0.3648 +/- 0.0002 and sigma_v = 325 +/- 25 km/s, respectively. The optical spectrum of the lensed quasar shows no obvious emission or absorption features and is consistent with a BL Lac type radio source. However, the tentative detection of the G-band and Mg-b absorption lines, and a break in the spectrum of the host galaxy of the lensed quasar gives a likely source redshift of z = 0.67. Spectroscopy of the field around B2108+213 finds 51 galaxies at a similar redshift to G1, thus confirming that there is a much larger structure at z ~ 0.365 associated with this system. The width of the group velocity distribution is 694 +/- 93 km/s, but is non-Gaussian, implying that the structure is not yet viralized. The main lensing galaxy is also the brightest group member and has a surface brightness profile consistent with a typical cD galaxy. A lensing and dynamics analysis of the mass distribution, which also includes the newly found group members, finds that the logarithmic slope of the mass density profile is on average isothermal inside the Einstein radius, but steeper at the location of the Einstein radius. This apparent change in slope can be accounted for if an external convergence gradient, representing the underlying parent halo of the galaxy group, is included in the mass model.Comment: 18 pages, 14 figures, 5 tables, accepted for publication in MNRA

The Cluster Lensing and Supernova Survey with Hubble (CLASH): Strong Lensing Analysis of Abell 383 from 16-Band HST WFC3/ACS Imaging

We examine the inner mass distribution of the relaxed galaxy cluster Abell 383 in deep 16-band HST/ACS+WFC3 imaging taken as part of the CLASH multi-cycle treasury program. Our program is designed to study the dark matter distribution in 25 massive clusters, and balances depth with a wide wavelength coverage to better identify lensed systems and generate precise photometric redshifts. This information together with the predictive strength of our strong-lensing analysis method identifies 13 new multiply-lensed images and candidates, so that a total of 27 multiple-images of 9 systems are used to tightly constrain the inner mass profile, $d\log \Sigma/d\log r\simeq -0.6\pm 0.1$ (r<160 kpc). We find consistency with the standard distance-redshift relation for the full range spanned by the lensed images, 1.01<z<6.03, with the higher redshift sources deflected through larger angles as expected. The inner mass profile derived here is consistent with the results of our independent weak-lensing analysis of wide-field Subaru images, with good agreement in the region of overlap. The overall mass profile is well fitted by an NFW profile with M_{vir}=(5.37^{+0.70}_{-0.63}\pm 0.26) x 10^{14}M_{\odot}/h and a relatively high concentration, c_{vir}=8.77^{+0.44}_{-0.42}\pm 0.23, which lies above the standard c-M relation similar to other well-studied clusters. The critical radius of Abell 383 is modest by the standards of other lensing clusters, r_{E}\simeq16\pm2\arcsec (for z_s=2.55), so the relatively large number of lensed images uncovered here with precise photometric redshifts validates our imaging strategy for the CLASH survey. In total we aim to provide similarly high-quality lensing data for 25 clusters, 20 of which are X-ray selected relaxed clusters, enabling a precise determination of the representative mass profile free from lensing bias. (ABRIDGED)Comment: 15 pages, 14 figures, 2 tabels; V3 matches the submitted version later published in Ap

Extensive HST Ultraviolet Spectra and Multi-wavelength Observations of SN 2014J in M82 Indicate Reddening and Circumstellar Scattering by Typical Dust

SN 2014J in M82 is the closest detected Type Ia supernova (SN Ia) in at least 28 years and perhaps in 410 years. Despite its small distance of 3.3 Mpc, SN 2014J is surprisingly faint, peaking at V = 10.6 mag, and assuming a typical SN Ia luminosity, we infer an observed visual extinction of A_V = 2.0 +/- 0.1 mag. But this picture, with R_V = 1.6 +/- 0.2, is too simple to account for all observations. We combine 10 epochs (spanning a month) of HST/STIS ultraviolet through near-infrared spectroscopy with HST/WFC3, KAIT, and FanCam photometry from the optical to the infrared and 9 epochs of high-resolution TRES spectroscopy to investigate the sources of extinction and reddening for SN 2014J. We argue that the wide range of observed properties for SN 2014J is caused by a combination of dust reddening, likely originating in the interstellar medium of M82, and scattering off circumstellar material. For this model, roughly half of the extinction is caused by reddening from typical dust (E(B-V ) = 0.45 mag and R_V = 2.6) and roughly half by scattering off LMC-like dust in the circumstellar environment of SN 2014J.Comment: 17 pages (excluding references and tables), 15 figures, accepted to MNRAS. A high-resolution HST image of SN 2014J in M82 is available upon reques

The effect of loading on disturbance sounds of the Atlantic croaker Micropogonius undulatus: Air versus water

Physiological work on fish sound production may require exposure of the swimbladder to air, which will change its loading (radiation mass and resistance) and could affect parameters of emitted sounds. This issue was examined in Atlantic croaker Micropogonius chromis by recording sounds from the same individuals in air and water. Although sonograms appear relatively similar in both cases, pulse duration is longer because of decreased damping, and sharpness of tuning (Q factor) is higher in water. However, pulse repetition rate and dominant frequency are unaffected. With appropriate caution it is suggested that sounds recorded in air can provide a useful tool in understanding the function of various swimbladder adaptations and provide reasonable approximation of natural sounds. Further, they provide an avenue for experimentally manipulating the sonic system, which can reveal details of its function not available from intact fish underwater

LBT and Spitzer Spectroscopy of Star-Forming Galaxies at 1 < z < 3: Extinction and Star Formation Rate Indicators

We present spectroscopic observations in the rest-frame optical and near- to mid-infrared wavelengths of four gravitationally lensed infrared (IR) luminous star-forming galaxies at redshift 1 < z < 3 from the LUCIFER instrument on the Large Binocular Telescope and the Infrared Spectrograph on Spitzer. The sample was selected to represent pure, actively star-forming systems, absent of active galactic nuclei. The large lensing magnifications result in high signal-to-noise spectra that can probe faint IR recombination lines, including Pa-alpha and Br-alpha at high redshifts. The sample was augmented by three lensed galaxies with similar suites of unpublished data and observations from the literature, resulting in the final sample of seven galaxies. We use the IR recombination lines in conjunction with H-alpha observations to probe the extinction, Av, of these systems, as well as testing star formation rate (SFR) indicators against the SFR measured by fitting spectral energy distributions to far-IR photometry. Our galaxies occupy a range of Av from ~0 to 5.9 mag, larger than previously known for a similar range of IR luminosities at these redshifts. Thus, estimates of SFR even at z ~ 2 must take careful count of extinction in the most IR luminous galaxies. We also measure extinction by comparing SFR estimates from optical emission lines with those from far-IR measurements. The comparison of results from these two independent methods indicates a large variety of dust distribution scenarios at 1 < z < 3. Without correcting for dust extinction, the H-alpha SFR indicator underestimates the SFR; the size of the necessary correction depends on the IR luminosity and dust distribution scenario. Individual SFR estimates based on the 6.2 micron PAH emission line luminosity do not show a systematic discrepancy with extinction, although a considerable, ~0.2 dex scatter is observed.Comment: Accepted for publication in The Astrophysical Journal; 14 pages, 8 figure