A-to-I RNA editing in the earliest-diverging Eumetazoan phyla

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14)

Impact of catchment-derived nutrients and sediments on marine water quality on the Great Barrier Reef: an application of the eReefs marine modelling system

Water quality of the Great Barrier Reef (GBR) is determined by a range of natural and anthropogenic drivers that are resolved in the eReefs coupled hydrodynamic - biogeochemical marine model forced by a process-based catchment model, GBR Dynamic SedNet. Model simulations presented here quantify the impact of anthropogenic catchment loads of sediments and nutrients on a range of marine water quality variables. Simulations of 2011–2018 show that reduction of anthropogenic catchment loads results in improved water quality, especially within river plumes. Within the 16 resolved river plumes, anthropogenic loads increased chlorophyll concentration by 0.10 (0.02–0.25) mg Chl m−3. Reductions of anthropogenic loads following proposed Reef 2050 Water Quality Improvement Plan targets reduced chlorophyll concentration in the plumes by 0.04 (0.01–0.10) mg Chl m−3. Our simulations demonstrate the impact of anthropogenic loads on GBR water quality and quantify the benefits of improved catchment management

Major Cellular and Physiological Impacts of Ocean Acidification on a Reef Building Coral

As atmospheric levels of CO2 increase, reef-building corals are under greater stress from both increased sea surface temperatures and declining sea water pH. To date, most studies have focused on either coral bleaching due to warming oceans or declining calcification due to decreasing oceanic carbonate ion concentrations. Here, through the use of physiology measurements and cDNA microarrays, we show that changes in pH and ocean chemistry consistent with two scenarios put forward by the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, before affects on biomineralisation are apparent at the phenotype level. Under high CO2 conditions corals at the phenotype level lost over half their Symbiodinium populations, and had a decrease in both photosynthesis and respiration. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrate upregulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur before impacts on calcification

Interactions between scleractinian coral morphology and light

The success of scleractinian corals can be attributed to a symbiotic relationship between the coral animal and a unicellular photosynthetic dinoflagellate Symbiodinium. The ability of the coral-symbiont to form highly complex aragonite structures provides the framework for coral reefs and habitat for a diverse range of marine organisms. Due to the photosynthetic nature of this symbiosis, light is an important resource for reef-building corals. The marine light environment can be highly variable and corals similar to terrestrial plants have adopted a range of photoacclimatory mechanisms. These can range from pigment concentration and cell density manipulation to polyp behaviour, tissue retraction and expansion, as well as interaction with skeletal properties. Intra-specific phenotypic plasticity is a common trait among scleractinian corals. Biomechanical and physiological photoacclimatory mechanisms have been studied to some detail, while there is less information on photoacclimatory morphological adaptations at the colony level. This project focused on unravelling photoacclimatory mechanisms, involving changes in colony morphology for branching reef-building corals. Changes in simple morphological parameters for Acropora humilis and Stylophora pistillata across a depth gradient with ambient flow and light conditions varying, were investigated. For both branching species changes in colony morphology resulted in optimization of within-colony surface irradiances. Exploring variability in coral surface irradiances, across colonies of Acropora humilis, along a depth gradient revealed bathymetric differences. Within-colony heterogeneity of surface irradiance correlated with variability in photosynthetic activity at the coral surface. Although overall colonies at shallower depths (5 m) had greater photosynthetic performance compared to colonies in the deep (18 m), morphological variation maximised energy acquisition. Actual irradiance levels reaching the photosynthetic Symbiodinium were investigated for two coral species of varying colony growth forms, one branching Stylophora pistillata and one massive Lobophyllia corymbosa, at 5 m. High light attenuation was observed for both species and they had similar within tissue irradiances. For Stylophora pistillata high light attenuationwas observed at the colony level, as a result of branch to branch self shading, while in Lobophyllia corymbosa high light attenuation was occurring within the coral tissue. To explore environmental cues affecting branch initiation, the beginning of morphological change in branching corals, axial polyp development in Acropora pulchra was investigated. Both aquaria and field experiments revealed that light was an important factor in axial polyp differentiation. Axial polyp structures would only develop above a light intensity threshold and with the presence of light from the blue wavelength spectrum. In order to gain a further understanding into possible molecular mechanisms responsible for axial polyp development, gene expression differences were explored between axial and radial polyps. Several putative genes were isolated, and their homologies indicate that a negative feedback mechanism may be involved in axial polyp differentiation. Successful identification of genes in a genomic library provides possibilities of future work characterizing genes and promoter regions. The results of this project have revealed how phenotypic plasticity associates with branching reef-building corals acclimating to light. The present study has identified the irradiance levels reaching the photosynthetic unit as opposed to the more normally measured ambient irradiances. Molecular mechanisms for branch initiation in response to environmental cues appear to play important roles in modifying these irradiances and thereby represent another set of strategies for branching scleractinian corals to acclimate to marine light fields

Coral skeletons defend against ultraviolet radiation

Background: Many coral reef organisms are photosynthetic or have evolved in tight symbiosis with photosynthetic symbionts. As such, the tissues of reef organisms are often exposed to intense solar radiation in clear tropical waters and have adapted to trap and harness photosynthetically active radiation (PAR). High levels of ultraviolet radiation (UVR) associated with sunlight, however, represent a potential problem in terms of tissue damage

Low-FODMAP Diet for the Management of Irritable Bowel Syndrome in Remission of IBD

Approximately 30% of patients with quiescent inflammatory bowel disease (IBD) meet the diagnostic criteria for irritable bowel syndrome (IBS). The aim of this study was to evaluate the effectiveness of a low-FODMAP diet in patients who meet the diagnostic criteria for IBS whilst in IBD remission. A total of 200 patients in remission of IBD were included in the study. Sixty-five of these patients (32.5%) were diagnosed with IBS according to the R4DQ. On the patients who met the IBS diagnostic criteria, anthropometric measurements, laboratory tests and lactulose hydrogen breath tests were performed. A low-FODMAP diet was introduced for 6 weeks. Of the 59 patients with IBS diagnosed at baseline for whom data were collected at the end of follow-up, after the low-FODMAP intervention IBS-like symptoms were not present in 66.1% (n = 39) (95% CI (53.4%; 76.9%)). The difference between the two groups (with SIBO at baseline (33 of 48 patients) and without SIBO at baseline (6 of 11 patients)) in the low-FODMAP diet’s effectiveness was not statistically significant (p = 0.586). The low-FODMAP diet improved the gut symptoms of flatulence and diarrhea. It had no effect on the occurrence of constipation. In IBD patients in remission who meet the IBS criteria, the dietary intervention of a low-FODMAP diet is effective for a reduction in IBS-like symptoms, regardless of the coexistence of bacterial overgrowth

Schematic of the reflectance light measured from the different substrates.

<p>Reflectance collected and measured off a coral skeleton (S), a reflector (R), and the anemones on top of the skeleton (AS) and the reflector (AR). Measurements were made in the UV range (250–400 nm) as well as the visible (558–595 nm). The irradiance source was one or two 4 W UV-B lamps (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007995#pone-0007995-g004" target="_blank">Fig. 4</a>).</p

Luminescence of the coral skeleton.

<p>A) A long exposure photograph of a <i>Stylophora pistillata</i> skeleton irradiated with mid range UVR, photographed through a barrier UV filter, showing characteristic yellow fluorescence A photograph of an (B ..skeleton taken in the same manner .sp Echinopora.</p

Derived absorbance of the coral skeleton.

<p>A) Derived absorbance spectrum of the white <i>Echinopora sp.</i> skeleton under full sunlight. Shaded areas correspond to the UVR (250–400 nm) and visible (558–595 nm) peaks used in this study. Maximal absorption occurred at 330 nm. R is reflectance measured from the PTFE reflector and S is reflectance from the skeleton. Slightly negative absorbance values >600 nm are due to a lower reflectivity of PTFE in that range (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007995#pone-0007995-g005" target="_blank">Fig. 5</a>). B) Average (<i>n</i> = 10) reflectance of downwelling UVR (AU, arbitrary units) measured from PTFE (blue), <i>Stylophora pistillata</i> skeletons (green) and <i>S. pistillata</i> skeletons crushed to a fine powder (grey). Error bars are standard deviations from the mean.</p

New-old hemoglobin-like proteins of symbiotic dinoflagellates

Symbiotic dinoflagellates are unicellular photosynthetic algae that live in mutualistic symbioses with many marine organisms. Within the transcriptome of coral endosymbionts Symbiodinium sp. (type C3), we discovered the sequences of two novel and highly polymorphic hemoglobin-like genes and proposed their 3D protein structures. At the protein level, four isoforms shared between 87 and 97% sequence identity for Hb-1 and 7899% for Hb-2, whereas between Hb-1 and Hb-2 proteins, only 1521% sequence homology has been preserved. Phylogenetic analyses of the dinoflagellate encoding Hb sequences have revealed a separate evolutionary origin of the discovered globin genes and indicated the possibility of horizontal gene transfer. Transcriptional regulation of the Hb-like genes was studied in the reef-building coral Acropora aspera exposed to elevated temperatures (67 degrees C above average sea temperature) over a 24-h period and a 72-h period, as well as to nutrient stress. Exposure to elevated temperatures resulted in an increased Hb-1 gene expression of 31% after 72h only, whereas transcript abundance of the Hb-2 gene was enhanced by up to 59% by both 1-day and 3-day thermal stress conditions. Nutrient stress also increased gene expression of Hb-2 gene by 70%. Our findings describe the differential expression patterns of two novel Hb genes from symbiotic dinoflagellates and their polymorphic nature. Furthermore, the inducible nature of Hb-2 gene by both thermal and nutrient stressors indicates a prospective role of this form of hemoglobin in the initial coralalgal responses to changes in environmental conditions. This novel hemoglobin has potential use as a stress biomarker