Reef-building corals are keystone species that are threatened by anthropogenic stresses including climate change. To investigate corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating many hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals or closely related cnidarians. CRISPR technology seems likely to alleviate this problem. Indeed, we show here that microinjection of single-guide RNA/Cas9 ribonucleoprotein complexes into fertilized eggs of the coral Acropora millepora can produce a sufficiently high frequency of mutations to detect a clear phenotype in the injected generation. Based in part on experiments in a sea-anemone model system, we targeted the gene encoding Heat Shock Transcription Factor 1 (HSF1) and obtained larvae in which >90% of the gene copies were mutant. The mutant larvae survived well at 27 degrees C but died rapidly at 34 degrees C, a temperature that did not produce detectable mortality over the duration of the experiment in wild-type (WT) larvae or larvae injected with Cas9 alone. We conclude that HSF1 function (presumably its induction of genes in response to heat stress) plays an important protective role in corals. More broadly, we conclude that CRISPR mutagenesis in corals should allow wide-ranging and rigorous tests of gene function in both larval and adult corals.

Loss of endosymbiotic algae ("bleaching") under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to an-alyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NF kappa B and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.

Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is "coral bleaching," usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral.

Degradation and loss of coral reefs due to climate change and other anthropogenic stressors has fueled genomics, proteomics, and genetics research to investigate coral stress response pathways and to identify resilient species, genotypes, and populations to restore these biodiverse ecosystems. Much of the research and conservation effort has understandably focused on the most taxonomically rich regions, such as the Great Barrier Reef in Australia and the Coral Triangle in the western Pacific. These ecosystems are analogous to tropical rainforests that also house enormous biodiversity and complex biotic interactions among different trophic levels. An alternative model ecosystem for studying coral reef biology is the relatively species poor but abundant coral reefs in the Hawaiian Archipelago that exist at the northern edge of the Indo-Pacific coral distribution. The Hawaiian Islands are the world's most isolated archipelago, geographically isolated from other Pacific reef systems. This region houses about 80 species of scleractinian corals in three dominant genera (Porites, Montipora, and Pocillopora). Here we briefly review knowledge about the Hawaiian coral fauna with a focus on our model species, the rice coral Montipora capitata. We suggest that this simpler, relatively isolated reef system provides an ideal platform for advancing coral biology and conservation using multi-omics and genetic tools.

We present optical, near-IR, and radio follow-up of 16 Swift bursts, including our discovery of nine afterglows and a redshift determination for three. These observations, supplemented by data from the literature, provide an afterglow recovery rate of 52% in the optical/near-IR, much higher than in previous missions (BeppoSAX, HETE-2, INTEGRAL, and IPN). The optical/near-IR afterglows of Swift events are on average 1.8 mag fainter at t = 12 hr than those of previous missions. The X-ray afterglows are similarly fainter than those of pre-Swift bursts. In the radio the limiting factor is the VLA threshold, and the detection rate for Swift bursts is similar to that for past missions. The redshift distribution of pre-Swift bursts peaked at z similar to 1, whereas the six Swift bursts with measured redshifts are distributed evenly between 0.7 and 3.2. From these results we conclude that ( 1) the pre-Swift distributions were biased in favor of bright events and low-redshift events, ( 2) the higher sensitivity and accurate positions of Swift result in a better representation of the true burst redshift and brightness distributions ( which are higher and dimmer, respectively), and (3) similar to 10% of the bursts are optically dark, as a result of a high redshift and/or dust extinction. We remark that the apparent lack of low-redshift, low-luminosity Swift bursts and the lower event rate than prelaunch estimates ( 90 vs. 150 per year) are the result of a threshold that is similar to that of BATSE. In view of these inferences, afterglow observers may find it advisable to make significant changes in follow-up strategies of Swift events. The faintness of the afterglows means that large telescopes should be employed as soon as the burst is localized. Sensitive observations in RIz and near-IR bands will be needed to discriminate between a typical z similar to 2 burst with modest extinction and a high-redshift event. Radio observations will be profitable for a small fraction (similar to 10%) of events. Finally, we suggest that a search for bright host galaxies in untriggered BAT localizations may increase the chance of finding nearby low-luminosity GRBs.

Despite a rich phenomenology, gamma-ray bursts (GRBs) are divided(1) into two classes based on their duration and spectral hardness the long-soft and the short-hard bursts. The discovery of afterglow emission from long GRBs was a watershed event, pinpointing(2) their origin to star-forming galaxies, and hence the death of massive stars, and indicating(3) an energy release of about 10(51) erg. While theoretical arguments(4) suggest that short GRBs are produced in the coalescence of binary compact objects ( neutron stars or black holes), the progenitors, energetics and environments of these events remain elusive despite recent(5-8) localizations. Here we report the discovery of the first radio afterglow from the short burst GRB 050724, which unambiguously associates it with an elliptical galaxy at a redshift(9) z = 0.257. We show that the burst is powered by the same relativistic fireball mechanism as long GRBs, with the ejecta possibly collimated in jets, but that the total energy release is 10 - 1,000 times smaller. More importantly, the nature of the host galaxy demonstrates that short GRBs arise from an old (> 1 Gyr) stellar population, strengthening earlier suggestions(5,6) and providing support for coalescing compact object binaries as the progenitors.

We present a new compilation of Type Ia supernovae (SNe Ia), a new data set of low-redshift nearby-Hubble-flow SNe, and new analysis procedures to work with these heterogeneous compilations. This "Union'' compilation of 414 SNe Ia, which reduces to 307 SNe after selection cuts, includes the recent large samples of SNe Ia from the Supernova Legacy Survey and ESSENCE Survey, the older data sets, as well as the recently extended data set of distant supernovae observed with the Hubble Space Telescope (HST). A single, consistent, and blind analysis procedure is used for all the various SN Ia subsamples, and a new procedure is implemented that consistently weights the heterogeneous data sets and rejects outliers. We present the latest results from this Union compilation and discuss the cosmological constraints from this new compilation and its combination with other cosmological measurements (CMB and BAO). The constraint we obtain from supernovae on the dark energy density is Omega(Lambda) = 0.713(-0.029)(+0.027)(stat)(-0.039)(+0.036)(sys), for a flat, Lambda CDM universe. Assuming a constant equation of state parameter, w, the combined constraints from SNe, BAO, and CMB give w = -0.969(-0.063)(+0.059)(stat)(-0.066)(+0.063)(sys). While our results are consistent with a cosmological constant, we obtain only relatively weak constraints on a w that varies with redshift. In particular, the current SN data do not yet significantly constrain w at z > 1. With the addition of our new nearby Hubble-flow SNe Ia, these resulting cosmological constraints are currently the tightest available.

The Great Observatories All-Sky LIRG Survey (GOALS(20)) combines data from NASA's Spitzer Space Telescope, Chandra X-Ray Observatory, Hubble Space Telescope (HST), and Galaxy Evolution Explorer (GALEX) observatories, together with ground-based data, into a comprehensive imaging and spectroscopic survey of over 200 low-redshift (z < 0.088), Luminous Infrared Galaxies (LIRGs). The LIRGs are a complete subset of the IRAS Revised Bright Galaxy Sample (RBGS), which comprises 629 extragalactic objects with 60 mu m flux densities above 5.24 Jy, and Galactic latitudes above five degrees. The LIRGs targeted in GOALS span the full range of nuclear spectral types defined via traditional optical line-ratio diagrams (type-1 and type-2 AGN, LINERs, and starbursts) as well as interaction stages (major mergers, minor mergers, and isolated galaxies). They provide an unbiased picture of the processes responsible for enhanced infrared emission in galaxies in the local Universe. As an example of the analytic power of the multiwavelength GOALS data set, we present Spitzer, Chandra, HST, and GALEX images and spectra for the interacting system VV 340 (IRAS F14547 + 2449). The Spitzer MIPS imaging data indicates that between 80-95% of the total far-infrared emission (or about 5 x 10(11) L(circle dot)) originates in VV 340 north. While the Spitzer IRAC colors of VV 340 north and south are consistent with star-forming galaxies, both the Spitzer IRS and Chandra ACIS data indicate the presence of an AGN in VV 340 north. The observed line fluxes, without correction for extinction, imply that the AGN accounts for less than 10%-20% of the observed infrared emission. The X-ray data are consistent with a heavily absorbed (N(H) >= 10(24) cm(-2)) AGN. The GALEX far and near-UV fluxes imply a extremely large infrared "excess" (IRX) for the system (F(IR)/F(fuv) similar to 81) which is well above the correlation seen in starburst galaxies. Most of this excess is driven by VV 340 N, which has an IR excess of nearly 400. The VV 340 system seems to be comprised of two very different galaxies: an infrared luminous edge-on galaxy (VV 340 north) that dominates the long-wavelength emission from the system, which hosts a buried AGN; and a face-on starburst (VV 340 south) that dominates the short-wavelength emission.

An analysis of data from the Spitzer Space Telescope, Hubble Space Telescope, Chandra X-ray Observatory, and AKARI Infrared Astronomy Satellite is presented for the z = 0.036 merging galaxy system II Zw 096 (CGCG 448-020). Because II Zw 096 has an infrared luminosity of log(L-IR/L-circle dot) = 11.94, it is classified as a Luminous Infrared Galaxy (LIRG), and was observed as part of the Great Observatories All-sky LIRG Survey (GOALS). The Spitzer data suggest that 80% of the total infrared luminosity comes from an extremely compact, red source not associated with the nuclei of the merging galaxies. The Spitzer mid-infrared spectra indicate no high-ionization lines from a buried active galactic nucleus in this source. The strong detection of the 3.3 mu m and 6.2 mu m polycyclic aromatic hydrocarbon emission features in the AKARI and Spitzer spectra also implies that the energy source of II Zw 096 is a starburst. Based on Spitzer infrared imaging and AKARI near-infrared spectroscopy, the star formation rate is estimated to be 120 M-circle dot yr(-1) and >45 M-circle dot yr(-1), respectively. Finally, the high-resolution B-, I-, and H-band images show many star clusters in the interacting system. The colors of these clusters suggest at least two populations-one with an age of 1-5 Myr and one with an age of 20-500 Myr, reddened by 0-2 mag of visual extinction. The masses of these clusters span a range between 10(6) and 10(8) M-circle dot. This starburst source is reminiscent of the extranuclear starburst seen in NGC 4038/9 (the Antennae Galaxies) and Arp 299 but approximately an order of magnitude more luminous than the Antennae. The source is remarkable in that the off-nuclear infrared luminosity dominates the entire system.

The Great Observatories All-Sky LIRG Survey (GOALS) is a comprehensive, multiwavelength study of luminous infrared galaxies (LIRGs) in the local universe. Here we present low resolution Spitzer Infrared Spectrograph spectra covering 5-38 mu m and provide a basic analysis of the mid-IR spectral properties observed for nearby LIRGs. In a companion paper, we discuss detailed fits to the spectra and compare the LIRGs to other classes of galaxies. The GOALS sample of 244 nuclei in 180 luminous (10(11) <= L-IR/L-circle dot < 10(12)) and 22 ultraluminous (L-IR/L-circle dot >= 10(12)) IR galaxies represents a complete subset of the IRAS Revised Bright Galaxy Sample and covers a range of merger stages, morphologies, and spectral types. The majority (>60%) of the GOALS LIRGs have high 6.2 mu m polycyclic aromatic hydrocarbon (PAH) equivalent widths (EQW(6.2 mu m) > 0.4 mu m) and low levels of silicate absorption (s(9.7 mu m) > -1.0). There is a general trend among the U/LIRGs for both silicate depth and mid-infrared (MIR) slope to increase with increasing L-IR. U/LIRGs in the late to final stages of a merger also have, on average, steeper MIR slopes and higher levels of dust obscuration. Together, these trends suggest that as gas and dust is funneled toward the center of a coalescing merger, the nuclei become more compact and more obscured. As a result, the dust temperature increases also leading to a steeper MIR slope. The sources that depart from these correlations have very low PAH equivalent width (EQW(6.2 mu m) < 0.1 mu m) consistent with their emission being dominated by an active galactic nucleus (AGN) in the MIR. These extremely low PAH EQW sources separate into two distinct types: relatively unobscured sources with a very hot dust component (and thus very shallow MIR slopes) and heavily dust obscured nuclei with a steep temperature gradient. The most heavily dust obscured sources are also the most compact in their MIR emission, suggesting that the obscuring (cool) dust is associated with the outer regions of the starburst and not simply a measure of the dust along the line of sight through a large, dusty disk. A marked decline is seen for the fraction of high EQW (star formation dominated) sources as the merger progresses. The decline is accompanied by an increase in the fraction of composite sources while the fraction of sources where an AGN dominates the MIR emission remains low. When compared to the MIR spectra of submillimeter galaxies (SMGs) at z similar to 2, both the average GOALS LIRG and ULIRG spectra are more absorbed at 9.7 mu m and the average GOALS LIRG has more PAH emission. However, when the AGN contributions to both the local GOALS LIRGs and the high-z SMGs are removed, the average local starbursting LIRG closely resembles the starburst-dominated SMGs.