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4. Supplementary File S4 from Conservation and turnover of miRNAs and their highly complementary targets in early branching animals

Author

Praher, Daniela, Zimmermann, Bob, Dnyansagar, Rohit, Miller, David J., Moya, Aurelie, Modepalli, Vengamanaidu, Fridrich, Arie, Sher, Daniel, Friis-M��ller, Lene, Sundberg, Per, F��ret, Sylvain, Ashby, Regan, Moran, Yehu, and Technau, Ulrich

Abstract

Scenarios of the evolution of miRNA target sites in Cnidaria

Published
2021
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8. Molecular techniques and their limitations shape our view of the holobiont

Author

Cooke, Ira, Mead, Oliver, Whalen, Casey, Boote, Chloë, Moya, Aurelie, Ying, Hua, Robbins, Steven, Strugnell, Jan M., Darling, Aaron, Miller, David, Voolstra, Christian R., Adamska, Maja, Ainsworth, Tracy, Andrade, Natalia R., Arnold, A. Elizabeth, Ball, Eldon, Bourne, David, Bosch, Thomas, Butterfield, Nicholas J., Chan, Cheong Xin, Cowman, Peter E., Davy, Simon K., Fabricius, Katharina, Fortunato, Sofia V., Fraune, Sebastian, Hernandez, Alejandra, Hoogenboom, Mia, Jaspers, Cornelia, Mohamed, Amin, Pita, Lucia, Ragan, Mark A., Sakamaki, Kazuhiro, Schoepf, Verena, Seemann, Torsten, Shinzato, Chuya, Stolarski, Jaroslaw, Takahashi, Shunichi, Tang, Sen-Lin, Webster, Nicole, and Whitelaw, Brooke

Subjects
0106 biological sciences, 0301 basic medicine, Microbial diversity, Microbiota, Inference, Molecular Technique, Holobiont, Imaging, Metagenomic sequencing, Evolutionary inference, Model system, Multi-omics, Biology, 010603 evolutionary biology, 01 natural sciences, Holobiont, 03 medical and health sciences, 030104 developmental biology, Functional importance, Evolutionary biology, ddc:570, Amplicon sequencing, Environmental Microbiology, Animal Science and Zoology, Identification (biology), Symbiosis, Organism
Abstract

It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA gene amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont. published

Published
2019

9. Primary Life Stage Boron Isotope and Trace Elements Incorporation in Aposymbiotic Acropora millepora Coral under Ocean Acidification and Warming

Author

Wu, Henry C., Dissard, Delphine, Le Cornec, Florence, Thil, François, Tribollet, Aline, Moya, Aurelie, Douville, Eric, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biogéochimie-Traceurs-Paléoclimat (BTP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ARC Centre of Excellence for Coral Reef Studies (CoralCoE), James Cook University (JCU), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Subjects
Global and Planetary Change, fungi, technology, industry, and agriculture, sea surface temperature proxies, Ocean Engineering, ocean acidification, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Aquatic Science, Acropora millepora, Oceanography, Sr/Ca, δ 11 B, δ11B, laser ablation, Marine Science, scleractinian corals, geographic locations, Water Science and Technology, pH proxy
Abstract

International audience; Early-life stages of reef-building corals are vital to coral existence and reef maintenance. It is therefore crucial to study juvenile coral response to future climate change pressures. Moreover, corals are known to be reliable recorders of environmental conditions in their skeletal materials. Aposymbiotic Acropora millepora larvae were cultured in different seawater temperature (27 and 29 • C) and pCO 2 (390 and 750 µatm) conditions to understand the impacts of "end of century" ocean acidification (OA) and ocean warming (OW) conditions on skeletal morphology and geochemistry. The experimental conditions impacted primary polyp juvenile coral skeletal morphology and growth resulting in asymmetric translucent appearances with brittle skeleton features. The impact of OA resulted in microstructure differences with decreased precipitation or lengthening of fasciculi and disorganized aragonite crystals that led to more concentrations of centers of calcifications. The coral skeletal δ 11 B composition measured by laser ablation MC-ICP-MS was significantly affected by pCO 2 (p = 0.0024) and water temperature (p = 1.46 × 10 −5). Reconstructed pH of the primary polyp skeleton using the δ 11 B proxy suggests a difference in coral calcification site and seawater pH consistent with previously observed coral pH up-regulation. Similarly, trace element results measured by laser ablation ICP-MS indicate the impact of pCO 2. Primary polyp juvenile Sr/Ca ratio indicates a bias in reconstructed sea surface temperature (SST) under higher pCO 2 conditions. Coral microstructure content changes (center of calcification and fasciculi) due to OA possibly contributed to the variability in B/Ca ratios. Our results imply that increasing OA and OW may lead to coral acclimation issues and species-specific inaccuracies of the commonly used Sr/Ca-SST proxy.

Published
2017

10. Additional file 4: of Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora

Author

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin, Huisman, Lotte, Forêt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David, Ball, Eldon, and Miller, David

Abstract

Phylogenetic analysis of caspase domains identifed in A. millepora inferred by Maximum Likelihood method. PhyML 3.0 starting from a random tree was used to obtain ML trees under a concatenated model assuming the WAG + G + F (G = 1.523) amino acid substitution matrix model. The ML bootstrap proportion was obtained after 500 bootstraps replicates. Background colouring is as in Fig. 6. (PDF 361 kb)

Published
2016
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11. Additional file 1: of Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora

Author

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin, Huisman, Lotte, Forêt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David, Ball, Eldon, and Miller, David

Abstract

Phylogenetic analysis of Bcl-2 proteins identifed in A. millepora inferred by the Maximum Likelihood method. PhyML 3.0 starting from a random tree was used to obtain ML trees under a concatenated model assuming the LG + G (G = 1.957) amino acid substitution matrix model. The ML bootstraps proportion was obtained after 1000 bootstrap replicates. (PDF 267 kb)

Published
2016
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12. Additional file 3: of Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora

Author

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin, Huisman, Lotte, Forêt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David, Ball, Eldon, and Miller, David

Abstract

Plasmid constructs and immunoblot analyses of A. millepora Bcl-2 family proteins. (A) A schematic diagram of the EGFP-fused A. millepora Bcl-2 family proteins. Figures in parentheses are the number of amino acid residues in each construct. (B) Microscopic observation of transfected cells expressing EGFP and mCherry together with or without tX1Bid. Plasmid constructs pEGFP-C1 and pCAG-mCherry were co-transfected into HeLa cells either with pCS2-tX1Bid or control pCS2 empty vector. After 2 days of growth, cultures were washed to remove floating cells, and then fixed. The phase-contrast and both green and red fluorescent images of the remaining attached cells were captured for each field under the microscope. Scale bars represent 100 μm. (C, D) Immunoblot analysis of fusion proteins. Plasmids encoding each fusion protein were transiently transfected into HEK293T cells. In the case of EGFP/AmBax and EGFP/AmBokA proteins, the plasmid construct pCAG-FLAG/XlBclXL was cotransfected to prevent cell death. After culture for 2 days, transgene products were analyzed with control cell extracts by immunoblotting with appropriate antibodies. Arrowheads indicate the positions of immunoreactive proteins. Additional details of reagents and immunoblot analysis are provided as Additional file 8. Abbreviation: MWM, molecular weight marker. (PDF 2361 kb)

Published
2016
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13. Additional file 2: of Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora

Author

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin, Huisman, Lotte, ForĂŞt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David, Ball, Eldon, and Miller, David

Subjects
fungi
Abstract

Alignment of A. millepora AmBclWA and AmBclWD with Human Bcl-W. Red indicates identical amino acids, blue similar amino acids. (PDF 236 kb)

Published
2016
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14. Additional file 5: of Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora

Author

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin, Huisman, Lotte, Forêt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David, Ball, Eldon, and Miller, David

Abstract

Similarity of caspase-X paralogs and immunoblot analysis of A. millepora caspase-X constructs. (A) Alignment of the caspase-X paralogs from A. millepora. The red underlined section is a typical caspase domain, with the catalytic residues (H and C) highlighted. The blue underlined section is an additional caspase-like domain, but lacking the catalytic residues (highlight indicates positions where the catalytic residues should be, based on the alignment). Numbering at left refers to residue position in the caspase-X sequence; note that, in the region shown, the caspase-X sequence (derived from cDNA clone D038-A5, GenBank:KR351289) differs at only one position (V266I) from the genomic prediction AmCaspase Xa. (B) Immunoblot analysis of FLAG/CaspX and its truncated form. Plasmids encoding intact or truncated forms of caspase-X with a FLAG-tag were transiently cotransfected into HEK293T cells together with the pCAG-p35 plasmid. After culture for 2 days, transgene products were analyzed with control cell extracts by immunoblotting with appropriate antibodies. The asterisk indicates a non-specific reaction. Abbreviation: MWM, molecular weight marker. (C) The assignments of α-helix and β-sheet secondary structure elements are based on a previous study [52]. Residues predicted to form H bonds between the two domains are indicated by asterisks. (PDF 1084 kb)

Published
2016
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15. Carbonic anhydrase in the scleractinian coral Stylophora pistillata - Characterization, localization, and role in biomineralization

Author

Moya, Aurelie, Tambutte, Sylvie, Bertucci, Anthony, Tambutte, Eric, Lotto, Severine, Vullo, Daniela, Supuran, Claudiu T., Allemand, Denis, and Zoccola, Didier

Abstract

Carbonic anhydrases (CA) play an important role in biomineralization from invertebrates to vertebrates. Previous experiments have investigated the role of CA in coral calcification, mainly by pharmacological approaches. This study reports the molecular cloning, sequencing, and immunolocalization of a CA isolated from the scleractinian coral Stylophora pistillata, named STPCA. Results show that STPCA is a secreted form of alpha-CA, which possesses a CA catalytic function, similar to the secreted human CAVI. We localized this enzyme at the calico-blastic ectoderm level, which is responsible for the precipitation of the skeleton. This localization supports the role of STPCA in the calcification process. In symbiotic scleractinian corals, calcification is stimulated by light, a phenomenon called "light-enhanced calcification" (LEC). The mechanism by which symbiont photosynthesis stimulates calcification is still enigmatic. We tested the hypothesis that coral genes are differentially expressed under light and dark conditions. By real-time PCR, we investigated the differential expression of STPCA to determine its role in the LEC phenomenon. Results show that the STPCA gene is expressed 2-fold more during the dark than the light. We suggest that in the dark, up-regulation of the STPCA gene represents a mechanism to cope with night acidosis.

Published
2008

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