NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae

BACKGROUND: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications: a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. RESULTS: Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons. DISCUSSION: This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol. Availability: the program is freely available a

Narrow band selected high redshift galaxy candidates contaminated by lower redshift O[III] ultrastrong emitter line galaxies

Context. Lyman Break Galaxies (LBG) and Narrow Band (NB) surveys have been successful at detecting large samples of high-redshift galaxies. Both methods are subject to contamination from low-redshift interlopers. Aims. In this paper, our aim is to investigate the nature of low-redshift interlopers in NB Lyman-$\alpha$ emitters (LAE) searches. Methods. From previous HAWK-I NB imaging at z $\sim$7.7 we identify three objects that would have been selected as high-redshift LAEs had our optical data been one magnitude shallower (but still one to two magnitudes fainter than the near infrared data). We follow-up these objects in spectroscopy with XSHOOTER at the VLT. Results. Despite low quality data due to bad weather conditions, for each of the three objects we identify one, and only one emission line, in the spectra of the objects, that we identify as the O[III]5007A line. This result combined to spectral energy density fitting and tests based on line ratios of several populations of galaxies we infer that the 3 objects are ultrastrong line emitters at redshifts $\sim$1.1. Conclusions. From this work and the literature we remark that the O[III] line appears to be a common source of contamination in high-redshift LBG and LAE samples and we suggest that efforts be put to characterize with high accuracy the O[III] luminosity function out to redshift $\sim$3 or higher.Comment: 7 pages, 4 figures, accepted by A&

Panchromatic Study of the First Galaxies with Large ALMA Programs

Thanks to deep optical to near-IR imaging and spectroscopy, significant progress is made in characterizing the rest-frame UV to optical properties of galaxies in the early universe (z > 4). Surveys with Hubble, Spitzer, and ground-based facilities (Keck, Subaru, and VLT) provide spectroscopic and photometric redshifts, measurements of the spatial structure, stellar masses, and optical emission lines for large samples of galaxies. Recently, the Atacama Large (Sub) Millimeter Array (ALMA) has become a major player in pushing studies of high redshift galaxies to far-infrared wavelengths, hence making panchromatic surveys over many orders of frequencies possible. While past studies focused mostly on bright sub-millimeter galaxies, the sensitivity of ALMA now enables surveys like ALPINE, which focuses on measuring the gas and dust properties of a large sample of normal main-sequence galaxies at z > 4. Combining observations across different wavelengths into a single, panchromatic picture of galaxy formation and evolution is currently and in the future an important focus of the astronomical community.Comment: 4 pages, 2 figures. Submitted to Proceedings IAU Symposium No. 341, 201

ALMA reveals the molecular gas properties of five star-forming galaxies across the main sequence at 3

International audienceWe present the detection of CO(5-4) with S/N> 7 - 13 and a lower CO transition with S/N > 3 (CO(4-3) for 4 galaxies, and CO(3-2) for one) with ALMA in band 3 and 4 in five main sequence star-forming galaxies with stellar masses 3-6x10^10 M/M_sun at 3 < z < 3.5. We find a good correlation between the total far-infrared luminosity LFIR and the luminosity of the CO(5-4) transition L'CO(5-4), where L'CO(5-4) increases with SFR, indicating that CO(5-4) is a good tracer of the obscured SFR in these galaxies. The two galaxies that lie closer to the star-forming main sequence have CO SLED slopes that are comparable to other star-forming populations, such as local SMGs and BzK star-forming galaxies; the three objects with higher specific star formation rates (sSFR) have far steeper CO SLEDs, which possibly indicates a more concentrated episode of star formation. By exploiting the CO SLED slopes to extrapolate the luminosity of the CO(1-0) transition, and using a classical conversion factor for main sequence galaxies of alpha_CO = 3.8 M_sun(K km s^-1 pc^-2)^-1, we find that these galaxies are very gas rich, with molecular gas fractions between 60 and 80%, and quite long depletion times, between 0.2 and 1 Gyr. Finally, we obtain dynamical masses that are comparable with the sum of stellar and gas mass (at least for four out of five galaxies), allowing us to put a first constraint on the alpha_CO parameter for main sequence galaxies at an unprecedented redshift

Multi-Wavelength View of Kiloparsec-Scale Clumps in Star-Forming Galaxies at z~2

This paper studies the properties of kiloparsec-scale clumps in star-forming galaxies at z~2 through multi-wavelength broad band photometry. A sample of 40 clumps is identified through auto-detection and visual inspection from 10 galaxies with 1.5<z<2.5 in the Hubble Ultra Deep Field, where deep and high-resolution HST/WFC3 and ACS images enable us to resolve structures of z~2 galaxies down to kpc scale in the rest-frame UV and optical bands as well as to detect clumps toward the faint end. The physical properties of clumps are measured through fitting spatially resolved seven-band (BVizYJH) spectral energy distribution to models. On average, the clumps are blue and have similar median rest-frame UV--optical color as the diffuse components of their host galaxies, but the clumps have large scatter in their colors. Although the star formation rate (SFR)--stellar mass relation of galaxies is dominated by the diffuse components, clumps emerge as regions with enhanced specific SFRs, contributing individually ~10% and together ~50% of the SFR of the host galaxies. However, the contributions of clumps to the rest-frame UV/optical luminosity and stellar mass are smaller, typically a few percent individually and ~20% together. On average, clumps are younger by 0.2 dex and denser by a factor of 8 than diffuse components. Clump properties have obvious radial variations in the sense that central clumps are redder, older, more extincted, denser, and less active on forming stars than outskirts clumps. Our results are broadly consistent with a widely held view that clumps are formed through gravitational instability in gas-rich turbulent disks and would eventually migrate toward galactic centers and coalesce into bulges. Roughly 40% of the galaxies in our sample contain a massive clump that could be identified as a proto-bulge, which seems qualitatively consistent with such a bulge-formation scenario.Comment: Accepted by ApJ. This updated version matches the in-press one. 50 pages (single column), 10 figures, 3 table

Discovery Of Cold, Pristine Gas Possibly Accreting Onto An Overdensity Of Star-Forming Galaxies At Redshift z ~ 1.6

We report the discovery of large amounts of cold (T ~ 10^4 K), chemically young gas in an overdensity of galaxies at redshift z ~ 1.6 in the Great Observatories Origins Deep Survey southern field (GOODS-S). The gas is identified thanks to the ultra-strong Mg II absorption features it imprints in the rest-frame UV spectra of galaxies in the background of the overdensity. There is no evidence that the optically-thick gas is part of any massive galaxy (i.e. M_star > 4x10^9 M_sun), but rather is associated with the overdensity; less massive and fainter galaxies (25.5 < z_850 < 27.5 mag) have too large an impact parameter to be causing ultra-strong absorption systems, based on our knowledge of such systems. The lack of corresponding Fe II absorption features, not detected even in co-added spectra, suggests that the gas is chemically more pristine than the ISM and outflows of star-forming galaxies at similar redshift, including those in the overdensity itself, and comparable to the most metal-poor stars in the Milky Way halo. A crude estimate of the projected covering factor of the high-column density gas (N_H >~ 10^20 cm-2) based on the observed fraction of galaxies with ultra-strong absorbers is C_F ~ 0.04. A broad, continuum absorption profile extending to the red of the interstellar Mg II absorption line by <~ 2000 km/s is possibly detected in two independent co-added spectra of galaxies of the overdensity, consistent with a large-scale infall motion of the gas onto the overdensity and its galaxies. Overall, these findings provides the first tentative evidence of accretion of cold, chemically young gas onto galaxies at high redshift, possibly feeding their star formation activity. The fact that the galaxies are members of a large structure, as opposed to field galaxies, might play a significant role in our ability to detect the accreting gas.Comment: 57 pages, 17 figures, 1 table; accepted for publication by ApJ (Aug 9, 2011); minor modifications to match the accepted versio

Rest-Frame UV-Optical Selected Galaxies at 2.3 ≾ z ≾ 3.5: Searching for Dusty Star-forming and Passively Evolving Galaxies

A new set of color selection criteria (VJL) analogous with the BzK method is designed to select both star-forming galaxies (SFGs) and passively evolving galaxies (PEGs) at 2.3 ≾ z ≾ 3.5 by using rest-frame UV-optical (V – J versus J – L) colors. The criteria are thoroughly tested with theoretical stellar population synthesis models and real galaxies with spectroscopic redshifts to evaluate their efficiency and contamination. We apply the well-tested VJL criteria to the HST/WFC3 Early Release Science field and study the physical properties of selected galaxies. The redshift distribution of selected SFGs peaks at z ~ 2.7, slightly lower than that of Lyman break galaxies at z ~ 3. Comparing the observed mid-infrared fluxes of selected galaxies with the prediction of pure stellar emission, we find that our VJL method is effective at selecting massive dusty SFGs that are missed by the Lyman break technique. About half of the star formation in massive (M_(star) > 10^(10) M_☉) galaxies at 2.3 ≾ z ≾ 3.5 is contributed by dusty (extinction E(B – V) > 0.4) SFGs, which, however, only account for ~20% of the number density of massive SFGs. We also use the mid-infrared fluxes to clean our PEG sample and find that galaxy size can be used as a secondary criterion to effectively eliminate the contamination of dusty SFGs. The redshift distribution of the cleaned PEG sample peaks at z ~ 2.5. We find six PEG candidates at z > 3 and discuss possible methods to distinguish them from dusty contamination. We conclude that at least part of our candidates are real PEGs at z ~ 3, implying that these types of galaxies began to form their stars at z ≳ 5. We measure the integrated stellar mass density (ISMD) of PEGs at z ~ 2.5 and set constraints on it at z > 3. We find that the ISMD grows by at least about a factor of 10 in 1 Gyr at 3 < z <5 and by another factor of 10 in the next 3.5 Gyr (1 < z < 3)

The Progenitors of the Compact Early-Type Galaxies at High-Redshift

We use GOODS and CANDELS images to identify progenitors of massive (log M > 10 Msun) compact "early-type" galaxies (ETGs) at z~1.6. Since merging and accretion increase the size of the stellar component of galaxies, if the progenitors are among known star-forming galaxies, these must be compact themselves. We select candidate progenitors among compact Lyman-break galaxies at z~3 based on their mass, SFR and central stellar density and find that these account for a large fraction of, and possibly all, compact ETGs at z~1.6. We find that the average far-UV SED of the candidates is redder than that of the non-candidates, but the optical and mid-IR SED are the same, implying that the redder UV of the candidates is inconsistent with larger dust obscuration, and consistent with more evolved (aging) star-formation. This is in line with other evidence that compactness is a sensitive predictor of passivity among high-redshift massive galaxies. We also find that the light distribution of both the compact ETGs and their candidate progenitors does not show any extended "halos" surrounding the compact "core", both in individual images and in stacks. We argue that this is generally inconsistent with the morphology of merger remnants, even if gas-rich, as predicted by N-body simulations. This suggests that the compact ETGs formed via highly dissipative, mostly gaseous accretion of units whose stellar components are very small and undetected in the HST images, with their stellar mass assembling in-situ, and that they have not experienced any major merging until the epoch of observations at z~1.6.Comment: 25 pages, 20 figures; Accepted for publication in Ap