Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo

We dissect the transcriptional regulatory relationships coordinating the dynamic expression patterns of two signaling genes, wnt8 and delta, which are central to specification of the sea urchin embryo endomesoderm. cis-Regulatory analysis shows that transcription of the gene encoding the Notch ligand Delta is activated by the widely expressed Runx transcription factor, but spatially restricted by HesC-mediated repression through a site in the delta 5′UTR. Spatial transcription of the hesC gene, however, is controlled by Blimp1 repression. Blimp1 thus represses the repressor of delta, thereby permitting its transcription. The blimp1 gene is itself linked into a feedback circuit that includes the wnt8 signaling ligand gene, and we showed earlier that this circuit generates an expanding torus of blimp1 and wnt8 expression. The finding that delta expression is also controlled at the cis-regulatory level by the blimp1-wnt8 torus-generating subcircuit now explains the progression of Notch signaling from the mesoderm to the endoderm of the developing embryo. Thus the specific cis-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo

Simulated Galaxy Interactions as Probes of Merger Spectral Energy Distributions

We present the first systematic comparison of ultraviolet-millimeter spectral energy distributions (SEDs) of observed and simulated interacting galaxies. Our sample is drawn from the Spitzer Interacting Galaxy Survey, and probes a range of galaxy interaction parameters. We use 31 galaxies in 14 systems which have been observed with Herschel, Spitzer, GALEX, and 2MASS. We create a suite of GADGET-3 hydrodynamic simulations of isolated and interacting galaxies with stellar masses comparable to those in our sample of interacting galaxies. Photometry for the simulated systems is then calculated with the SUNRISE radiative transfer code for comparison with the observed systems. For most of the observed systems, one or more of the simulated SEDs match reasonably well. The best matches recover the infrared luminosity and the star formation rate of the observed systems, and the more massive systems preferentially match SEDs from simulations of more massive galaxies. The most morphologically distorted systems in our sample are best matched to simulated SEDs close to coalescence, while less evolved systems match well with SEDs over a wide range of interaction stages, suggesting that an SED alone is insufficient to identify interaction stage except during the most active phases in strongly interacting systems. This result is supported by our finding that the SEDs calculated for simulated systems vary little over the interaction sequence.Comment: 24 pages, 16 figures, 2 tables, accepted for publication in ApJ. Animations of the evolution of the simulated SEDs can be found at http://www.cfa.harvard.edu/~llanz/sigs_sim.htm

Variations of the ISM Compactness Across the Main Sequence of Star-Forming Galaxies: Observations and Simulations

(abridged) The majority of star-forming galaxies follow a simple empirical correlation in the star formation rate (SFR) versus stellar mass ($M_*$) plane, usually referred to as the star formation Main Sequence (MS). Here we combine a set of hydro-dynamical simulations of interacting galactic disks with state-of-the-art radiative transfer codes to analyze how the evolution of mergers is reflected upon the properties of the MS. We present \textsc{Chiburst}, a Markov Chain Monte Carlo (MCMC) Spectral Energy Distribution (SED) code that fits the multi-wavelength, broad-band photometry of galaxies and derives stellar masses, star formation rates, and geometrical properties of the dust distribution. We apply this tool to the SEDs of simulated mergers and compare the derived results with the reference output from the simulations. Our results indicate that changes in the SEDs of mergers as they approach coalescence and depart from the MS are related to an evolution of dust geometry in scales larger than a few hundred parsecs. This is reflected in a correlation between the specific star formation rate (sSFR), and the compactness parameter $\mathcal{C}$, that parametrizes this geometry and hence the evolution of dust temperature ($T_{\rm{dust}}$) with time. As mergers approach coalescence, they depart from the MS and increase their compactness, which implies that moderate outliers of the MS are consistent with late-type mergers. By further applying our method to real observations of Luminous Infrared Galaxies (LIRGs), we show that the merger scenario is unable to explain these extreme outliers of the MS. Only by significantly increasing the gas fraction in the simulations are we able to reproduce the SEDs of LIRGs.Comment: 18 pages, 10 figures, accepted in Ap

The AGN Luminosity Fraction in Merging Galaxies

Galaxy mergers are key events in galaxy evolution, often causing massive starbursts and fueling active galactic nuclei (AGN). In these highly dynamic systems, it is not yet precisely known how much starbursts and AGN respectively contribute to the total luminosity, at what interaction stages they occur, and how long they persist. Here we estimate the fraction of the bolometric infrared (IR) luminosity that can be attributed to AGN by measuring and modeling the full ultraviolet to far-infrared spectral energy distributions (SEDs) in up to 33 broad bands for 24 merging galaxies with the Code for Investigating Galaxy Emission. In addition to a sample of 12 confirmed AGN in late-stage mergers, found in the $Infrared$ $Array$ $Satellite$ Revised Bright Galaxy Sample or Faint Source Catalog, our sample includes a comparison sample of 12 galaxy mergers from the $Spitzer$ Interacting Galaxies Survey, mostly early-stage. We perform identical SED modeling of simulated mergers to validate our methods, and we supplement the SED data with mid-IR spectra of diagnostic lines obtained with $Spitzer$ InfraRed Spectrograph. The estimated AGN contributions to the IR luminosities vary from system to system from 0% up to 91% but are significantly greater in the later-stage, more luminous mergers, consistent with what is known about galaxy evolution and AGN triggering.Comment: 26 pages, 10 figure

SpBase: the sea urchin genome database and web site

SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided

The Spitzer Interacting Galaxies Survey: A Mid-infrared Atlas of Star Formation

The Spitzer Interacting Galaxies Survey is a sample of 103 nearby galaxies in 48 systems, selected using association likelihoods and therefore free from disturbed morphology biases. All galaxies have been observed with Infrared Array Camera and MIPS 24 μm bands from the Spitzer Space Telescope. This catalog presents the global flux densities and colors of all systems and correlations between the interacting systems and their specific star formation rate (sSFR). This sample contains a wide variety of galaxy interactions with systems ranging in mass, mass ratios, and gas-content as well as interaction strength. This study seeks to identify the process of triggering star formation in galaxy interactions, therefore, we focus on the non-active galactic nucleus spiral galaxies only. From this subset of 70 spiral galaxies we have determined that this sample has enhanced sSFR compared to a sample of non-interacting field galaxies. Through optical data we have classified each system by "interaction strength"; the strongly interacting (Stage 4) galaxies have higher sSFR values than the weakly (Stage 2) and moderately (Stage 3) interacting systems. However, the Stage 2 and 3 systems have statistically identical sSFR properties, despite the lack of optical interaction signatures exhibited by the Stage 2 galaxies. We suggest that the similarity of sSFR in these stages could be a consequence of some of these Stage 2 systems actually being post-perigalactic and having had sufficient time for their tidal features to fade to undetectable levels. This interpretation is consistent with the correlation of sSFR with separation, which we have determined to have little variation up to 100 kpc

High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution

A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total “regulome” of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity

Merger Signatures in the Dynamics of Star-forming Gas

The recent advent of integral field spectrographs and millimeter interferometers has revealed the internal dynamics of many hundreds of star-forming galaxies. Spatially resolved kinematics have been used to determine the dynamical status of star-forming galaxies with ambiguous morphologies, and constrain the importance of galaxy interactions during the assembly of galaxies. However, measuring the importance of interactions or galaxy merger rates requires knowledge of the systematics in kinematic diagnostics and the visible time with merger indicators. We analyze the dynamics of star-forming gas in a set of binary merger hydrodynamic simulations with stellar mass ratios of 1:1 and 1:4. We find that the evolution of kinematic asymmetries traced by star-forming gas mirrors morphological asymmetries derived from mock optical images, in which both merger indicators show the largest deviation from isolated disks during strong interaction phases. Based on a series of simulations with various initial disk orientations, orbital parameters, gas fractions, and mass ratios, we find that the merger signatures are visible for ~0.2–0.4 Gyr with kinematic merger indicators but can be approximately twice as long for equal-mass mergers of massive gas-rich disk galaxies designed to be analogs of z ~ 2–3 submillimeter galaxies. Merger signatures are most apparent after the second passage and before the black holes coalescence, but in some cases they persist up to several hundred Myr after coalescence. About 20%–60% of the simulated galaxies are not identified as mergers during the strong interaction phase, implying that galaxies undergoing violent merging process do not necessarily exhibit highly asymmetric kinematics in their star-forming gas. The lack of identifiable merger signatures in this population can lead to an underestimation of merger abundances in star-forming galaxies, and including them in samples of star-forming disks may bias the measurements of disk properties such as intrinsic velocity dispersion

High-excitation OH and H_2O lines in Markarian 231: the molecular signatures of compact far-infrared continuum sources

The ISO/LWS far-infrared spectrum of the ultraluminous galaxy Mkn 231 shows OH and H_2O lines in absorption from energy levels up to 300 K above the ground state, and emission in the [O I] 63 micron and [C II] 158 micron lines. Our analysis shows that OH and H_2O are radiatively pumped by the far-infrared continuum emission of the galaxy. The absorptions in the high-excitation lines require high far-infrared radiation densities, allowing us to constrain the properties of the underlying continuum source. The bulk of the far-infrared continuum arises from a warm (T_dust=70-100 K), optically thick (tau_100micron=1-2) medium of effective diameter 200-400 pc. In our best-fit model of total luminosity L_IR, the observed OH and H2O high-lying lines arise from a luminous (L/L_IR~0.56) region with radius ~100 pc. The high surface brightness of this component suggests that its infrared emission is dominated by the AGN. The derived column densities N(OH)>~10^{17} cm^{-2} and N(H_2O)>~6x10^{16} cm^{-2} may indicate XDR chemistry, although significant starburst chemistry cannot be ruled out. The lower-lying OH, [C II] 158 micron, and [O I] 63 micron lines arise from a more extended (~350 pc) starburst region. We show that the [C II] deficit in Mkn 231 is compatible with a high average abundance of C+ because of an extreme overall luminosity to gas mass ratio. Therefore, a [C II] deficit may indicate a significant contribution to the luminosity by an AGN, and/or by extremely efficient star formation.Comment: 16 pages, 6 figures, accepted for publication in The Astrophysical Journa