Predicting global habitat suitability for stony corals on seamounts

Aim Globally, species distribution patterns in the deep sea are poorly resolved, with spatial coverage being sparse for most taxa and true absence data missing. Increasing human impacts on deep-sea ecosystems mean that reaching a better understanding of such patterns is becoming more urgent. Cold-water stony corals (Order Scleractinia) form structurally complex habitats (dense thickets or reefs) that can support a diversity of other associated fauna. Despite their widely accepted ecological importance, records of scleractinian corals on seamounts are patchy and simply not available for most of the global ocean. The objective of this paper is to model the global distribution of suitable habitat for stony corals on seamounts. Location Seamounts worldwide. Methods We compiled a database containing all accessible records of scleractinian corals on seamounts. Two modelling approaches developed for presence-only data were used to predict global habitat suitability for seamount scleractinians: maximum entropy modelling (Maxent) and environmental niche factor analysis (ENFA). We generated habitat-suitability maps and used a cross-validation process with a threshold-independent metric to evaluate the performance of the models. Results Both models performed well in cross-validation, although the Maxent method consistently outperformed ENFA. Highly suitable habitat for seamount stony corals was predicted to occur at most modelled depths in the North Atlantic, and in a circumglobal strip in the Southern Hemisphere between 20° and 50° S and shallower than around 1500 m. Seamount summits in most other regions appeared much less likely to provide suitable habitat, except for small near-surface patches. The patterns of habitat suitability largely reflect current biogeographical knowledge. Environmental variables positively associated with high predicted habitat suitability included the aragonite saturation state, and oxygen saturation and concentration. By contrast, low levels of dissolved inorganic carbon, nitrate, phosphate and silicate were associated with high predicted suitability. High correlation among variables made assessing individual drivers difficult. Main conclusions Our models predict environmental conditions likely to play a role in determining large-scale scleractinian coral distributions on seamounts, and provide a baseline scenario on a global scale. These results present a first-order hypothesis that can be tested by further sampling. Given the high vulnerability of cold-water corals to human impacts, such predictions are crucial tools in developing worldwide conservation and management strategies for seamount ecosystems. © 2009 Blackwell Publishing Ltd

Multimodal tandem mass spectrometry techniques for the analysis of phosphopeptides

Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging

Baryon content in a sample of 91 galaxy clusters selected by the South Pole Telescope at 0.2 <z < 1.25

We estimate total mass (M500), intracluster medium (ICM) mass (MICM), and stellar mass (M) in a Sunyaev–Zel’dovich effect (SZE) selected sample of 91 galaxy clusters with masses M500 2.5 × 1014 M and redshift 0.2 < z < 1.25 from the 2500 deg2 South Pole Telescope SPT-SZ survey. The total masses M500 are estimated from the SZE observable, the ICM masses MICM are obtained from the analysis of Chandra X-ray observations, and the stellar masses M are derived by fitting spectral energy distribution templates to Dark Energy Survey griz optical photometry and WISE or Spitzer near-infrared photometry. We study trends in the stellar mass, the ICM mass, the total baryonic mass, and the cold baryonic fraction with cluster halo mass and redshift. We find significant departures from self-similarity in the mass scaling for all quantities, while the redshift trends are all statistically consistent with zero, indicating that the baryon content of clusters at fixed mass has changed remarkably little over the past ≈9 Gyr. We compare our results to the mean baryon fraction (and the stellar mass fraction) in the field, finding that these values lie above (below) those in cluster virial regions in all but the most massive clusters at low redshift. Using a simple model of the matter assembly of clusters from infalling groups with lower masses and from infalling material from the low-density environment or field surrounding the parent haloes, we show that the measured mass trends without strong redshift trends in the stellar mass scaling relation could be explained by a mass and redshift dependent fractional contribution from field material. Similar analyses of the ICM and baryon mass scaling relations provide evidence for the so-called ‘missing baryons’ outside cluster virial regions

Characterization of anti-mineralocorticoid receptor antibody (SC-11412) and its use in chromatin immunoprecipitation (ChIP) assay.

<p>[<b>A</b>] <i>Characterization of SC-11412 antibody</i>: The CHOK1 cells were transfected with vector (<b>lane-1</b>) or the vector containing a mineralocorticoid receptor (MR) (<b>lane-2</b>), labeled with ³⁵S-methionine, immunoprecipitated with SC-11412 antibody to MR, resolved on SDS-PAGE, and the gel used to expose X-ray film. [<b>B</b>] <i>Immunoprecipitation of MR-like proteins from rat colonic epithelial cells</i>: Protein extracts of the colonic epithelial cells from an aldosterone rat was immunoprecipitated with the control (<b>lane-1</b>) or the SC-11412 (<b>lane-2</b>) antibody. The immnoprecipitated proteins were resolved on SDS-PAGE and transferred to the nitrocellulose membrane and probed with the SC-11412 antibody. [<b>C</b>] <i>ChIP assay of MR</i>: Numbers on the X-axis represent primer pairs directed to 1 kb blocks starting at approximately 20 kb upstream (number-1) of the Kcnn4 presumed transcript start site (TSS) and extending to 10 kb downstream (number-29) of the presumed TSS (located in block 21). The Y-axis represents fold enrichment in the RT-PCR comparing the specific to the control antibody. Data presented represents mean ± SE of 4 independent experiments using distal colon epithelial cells from aldosterone (<b>closed bars</b>) and normal rats (<b>open bars</b>). The RNA transcript is indicated by an arrow. The presumed promoter region is immediately to the left of the arrow. Exons 1 and 2 are indicated by blocks. Genomic regions cloned in pGL4.23 are indicated by bars and are numbered.</p

Sub-localization of mineralocorticoid hormone responsive element (MRE) in clone 1.

<p>Sub-clones of clone-1 were made and tested for MR/aldosterone responsiveness in HEK 293T cells. Clone-1 was sub-cloned into thirds, clone-1A, clone-1B and clone-1C representing the left, middle and right thirds, respectively. Clone-1B and clone-1C exhibited enhanced luciferase activity. Putative MREs were identified in clone-1B and clone-1C using TESS and MatInspector bioinformatics tools. The sequence <u>TCTTGA</u>GTG<u>TGTTCT</u> in clone-1B (candidate MRE underlined) was mutated to <u>TCTTGc</u>GTG<u>cacgac (clone-1B_mut)</u> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098695#pone.0098695.s001" target="_blank">Figure S1</a> for sequence). The candidate MRE <u>GGCTCT</u>GCG<u>TGTTCT</u> in clone-1C was mutated to <u>GGCTgT</u>GCG<u>cacgac (clone-1C_mut).</u> The absence of the enhanced luciferase activity in the HEK293T cells transfected with c<u>lone-1B_mut</u> and <u>clone-1C_mut</u> showed a loss of function, thus demonstrating functionality of the MREs localized in clone-1B and clone-1C. Data presented represent mean ± SE of triplicate assays from 3 different experiments. *<i>p</i><0.05– compared to pGL4.23.</p

Functional activity of clone-1, clone-5 and clone-6 expressed in CaCo2 cells.

<p>The CaCo-2 cells were transfected with either a vector (pGL4.23), clone-1, clone-5, or clone-6. After the transfection, the luciferase activity was measured in the presence and absence of aldosterone (10 nM) treatment. Relative luciferase activity was normalized to the luciferase activity present in the vector transfected cell (pGL4.23; considered 1.0). Data presented represent mean ± SE, from triplicate assays from 3 different experiments). *<i>p</i><0.05– compared to pGL4.23.</p

Effect of mineralocorticoid receptor (MR) and aldosterone in HEK293T cells expressing Kcnn4 genomic clone.

<p>Regions of the Kcnn4 genes showing positive response in a ChIP assay and indicated by bars in Figure-1C (clone-1, clone-3, clone-5, clone-6, clone-7 and clone-8) were sub-cloned in pGL4.23 and tested for the presence of MR/aldosterone (mineralocorticoid)-responsive enhancers (MRE). The HEK293T cells were transfected with pGL4.23 or pGL4.23 containing Kcnn4 genomic clones. The cells transfected with Kcnn4 genomic clones were also transfected with MR. Luciferase activity was measured in the cells transfected with the Kcnn4 genomic clones with (<b>hatched bars</b>) and without (<b>grey bars</b>) MR transfection. The luciferase activity in the cells transfected with the Kcnn4 genomic clones and MR was also measured in the presence of 10 nM aldosterone (<b>black bars</b>). For clarity, luciferase activity measured in the presence of a plasmid, MR and aldosterone are shown in cells transfected with pGL-4.23, clones-3, -5 and -6. Results presented represent mean ± SE from 3 different experiments. *<i>p</i><0.05– compared to pGL4.23.</p

Sub-localization of mineralocorticoid response elements (MRE) in clone-5 and clone-6.

<p>The clone-5 was sub-cloned into thirds, clone-5A, clone-5B and clone-5C representing the left, middle and right thirds of clone-5, respectively. Clone-5A, -5B and -5C were tested for MRE/aldosterone responsiveness in the HEK293T cells. The HEK293T cells transfected with clone-5A and clone-5B exhibited a significantly higher luciferase activity compared to the pGL4.23 vector transfected cells. Neither clone-5A nor clone-5B contained candidate MREs as analyzed using the Transcription Element Search System (TESS) or MatInspector. Further sub-clones of clone-5B were made (clone-5Ba and clone-5Bb that represent the left and right half of clone-5B, respectively). (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098695#pone.0098695.s001" target="_blank">Figure S1</a> for the sequences). Luciferase activity was not significantly altered in the HEK239T cells transfected with clone-5Ba and clone-5Bb, compared to the cells transfected with a vector (pGL4.23). Clone-6 was also sub-cloned into thirds (clone-6A, clone-6B, and clone-6C). Similar to the clone-5Ba and clone-5Bb transfected cells, luciferase activity was also not significantly altered in the HECK293T cells transfected with clone-6A, clone-6B and clone-6C compared that of cells transfected with a vector (pGL4.23). Data presented represent mean ± SE of triplicate assays of 3 different experiments. *<i>p</i><0.05– compared to pGL4.23.</p