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Sample records for sea anemone genome

  1. Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: Lesson learned from Anemonia viridis.

    Science.gov (United States)

    Chi, Sylvia Ighem; Urbarova, Ilona; Johansen, Steinar D

    2018-04-30

    The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Concerted evolution of sea anemone neurotoxin genes is revealed through analysis of the Nematostella vectensis genome.

    Science.gov (United States)

    Moran, Yehu; Weinberger, Hagar; Sullivan, James C; Reitzel, Adam M; Finnerty, John R; Gurevitz, Michael

    2008-04-01

    Gene families, which encode toxins, are found in many poisonous animals, yet there is limited understanding of their evolution at the nucleotide level. The release of the genome draft sequence for the sea anemone Nematostella vectensis enabled a comprehensive study of a gene family whose neurotoxin products affect voltage-gated sodium channels. All gene family members are clustered in a highly repetitive approximately 30-kb genomic region and encode a single toxin, Nv1. These genes exhibit extreme conservation at the nucleotide level which cannot be explained by purifying selection. This conservation greatly differs from the toxin gene families of other animals (e.g., snakes, scorpions, and cone snails), whose evolution was driven by diversifying selection, thereby generating a high degree of genetic diversity. The low nucleotide diversity at the Nv1 genes is reminiscent of that reported for DNA encoding ribosomal RNA (rDNA) and 2 hsp70 genes from Drosophila, which have evolved via concerted evolution. This evolutionary pattern was experimentally demonstrated in yeast rDNA and was shown to involve unequal crossing-over. Through sequence analysis of toxin genes from multiple N. vectensis populations and 2 other anemone species, Anemonia viridis and Actinia equina, we observed that the toxin genes for each sea anemone species are more similar to one another than to those of other species, suggesting they evolved by manner of concerted evolution. Furthermore, in 2 of the species (A. viridis and A. equina) we found genes that evolved under diversifying selection, suggesting that concerted evolution and accelerated evolution may occur simultaneously.

  3. The genome of Aiptasia, a sea anemone model for coral symbiosis

    KAUST Repository

    Baumgarten, Sebastian

    2015-08-31

    The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal–algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal–algal pair also with its prokaryotic microbiome.

  4. Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing.

    Science.gov (United States)

    Urbarova, Ilona; Patel, Hardip; Forêt, Sylvain; Karlsen, Bård Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M; Johansen, Steinar D

    2018-02-01

    Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping-pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia. The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Genomic organization of a receptor from sea anemones, structurally and evolutionary related to glycoprotein hormone receptors from mamals

    DEFF Research Database (Denmark)

    Vibede, N; Hauser, Frank; Williamson, M

    1998-01-01

    organization of this sea anemone receptor. The receptor gene contains eight introns that are all localized within a region coding for the large extracellular N terminus. These introns occur at the same positions and have the same intron phasing as eight introns in the genes coding for the mammalian...

  6. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis

    Directory of Open Access Journals (Sweden)

    Deleury Emeline

    2009-07-01

    Full Text Available Abstract Background Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zooxanthellae. These algae are photosynthetic and the cnidarian-zooxanthellae association is based on nutritional exchanges. Maintenance of such an intimate cellular partnership involves many crosstalks between the partners. To better characterize symbiotic relationships between a cnidarian host and its dinoflagellate symbionts, we conducted a large-scale EST study on a symbiotic sea anemone, Anemonia viridis, in which the two tissue layers (epiderm and gastroderm can be easily separated. Results A single cDNA library was constructed from symbiotic tissue of sea anemones A. viridis in various environmental conditions (both normal and stressed. We generated 39,939 high quality ESTs, which were assembled into 14,504 unique sequences (UniSeqs. Sequences were analysed and sorted according to their putative origin (animal, algal or bacterial. We identified many new repeated elements in the 3'UTR of most animal genes, suggesting that these elements potentially have a biological role, especially with respect to gene expression regulation. We identified genes of animal origin that have no homolog in the non-symbiotic starlet sea anemone Nematostella vectensis genome, but in other symbiotic cnidarians, and may therefore be involved in the symbiosis relationship in A. viridis. Comparison of protein domain occurrence in A. viridis with that in N. vectensis demonstrated an increase in abundance of some molecular functions, such as protein binding or antioxidant activity, suggesting that these functions are essential for the symbiotic state and may be specific adaptations. Conclusion This large dataset of sequences provides a valuable resource for future studies on symbiotic interactions in Cnidaria. The comparison with the closest

  7. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis.

    Science.gov (United States)

    Sabourault, Cécile; Ganot, Philippe; Deleury, Emeline; Allemand, Denis; Furla, Paola

    2009-07-23

    Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zooxanthellae. These algae are photosynthetic and the cnidarian-zooxanthellae association is based on nutritional exchanges. Maintenance of such an intimate cellular partnership involves many crosstalks between the partners. To better characterize symbiotic relationships between a cnidarian host and its dinoflagellate symbionts, we conducted a large-scale EST study on a symbiotic sea anemone, Anemonia viridis, in which the two tissue layers (epiderm and gastroderm) can be easily separated. A single cDNA library was constructed from symbiotic tissue of sea anemones A. viridis in various environmental conditions (both normal and stressed). We generated 39,939 high quality ESTs, which were assembled into 14,504 unique sequences (UniSeqs). Sequences were analysed and sorted according to their putative origin (animal, algal or bacterial). We identified many new repeated elements in the 3'UTR of most animal genes, suggesting that these elements potentially have a biological role, especially with respect to gene expression regulation. We identified genes of animal origin that have no homolog in the non-symbiotic starlet sea anemone Nematostella vectensis genome, but in other symbiotic cnidarians, and may therefore be involved in the symbiosis relationship in A. viridis. Comparison of protein domain occurrence in A. viridis with that in N. vectensis demonstrated an increase in abundance of some molecular functions, such as protein binding or antioxidant activity, suggesting that these functions are essential for the symbiotic state and may be specific adaptations. This large dataset of sequences provides a valuable resource for future studies on symbiotic interactions in Cnidaria. The comparison with the closest available genome, the sea anemone N. vectensis, as well as

  8. MODIFICATION OF SEA ANEMONE BEHAVIOR BY SYMBIOTIC ZOOXANTHELLAE: PHOTOTAXIS.

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    Pearse, Vicki Buchsbaum

    1974-12-01

    The sea anemone Anthopleura elegantissima, with and without endosymbiotic zooxanthellae, was tested for evidence of phototactic behavior. Anemones with zooxanthellae always displayed phototaxis, either positive or negative depending on the experimental light intensity and the light intensity of the habitat from which the animals were taken. Anemones without zooxanthellae-even those that had previously harbored zooxanthellae and that were genetically identical clone-mates of phototactic individuals-never displayed phototaxis, appearing completely indifferent to light and shade. The results indicate that phototaxis in this sea anemone depends directly on the presence of its symbiotic algae. It is suggested that the flexible phototactic behavior of the anemone may play an important role in favorably regulating the amount of light to which the zooxanthellae are exposed.

  9. Ectosymbionts of the Sea Anemone Stichodactyla gigantea at Kosrae, Micronesia

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    Hayes, Floyd E.

    2016-04-01

    Full Text Available We studied the ectosymbionts associating with the sea anemone Stichodactyla gigantea at Kosrae, Micronesia. Ectosymbionts of seven species associated with 60.7% of S. gigantea (n=28, with a mean of 2.4 per anemone and 3.9 per occupied anemone. Anemones hosting one or more ectosymbionts did not differ significantly in size from anemones lacking ectosymbionts and there was no significant correlation between anemone size and the number of ectosymbionts. Of 67 ectosymbionts observed, the sea cucumber Stichopus vastus comprised 23.9%, followed by the shrimp Thor amboinensis (20.9%, unidentified hermit crabs (Paguroidea; 20.9%, the cardinalfish Ostorhinchus novemfasciatus (20.9%, the shrimp Periclimenes brevicarpalis (9.0%, the sea cucumber Holothuria hilla (3.0%, and an unidentified brachyuran crab (1.5%. This study documents the first records of S. vastus, H. hilla, and O. novemfasciatus associating with S. gigantea, and the first locality records of S. gigantea, T. amboinensis, P. brevicarpalis, and S. vastus for Kosrae. Because humans often harvest S. gigantea for food at Kosrae, we recommend protecting the symbiotic assemblage of S. gigantea by establishing a sustainable system of harvesting.

  10. Sea anemone Radianthus macrodactylus--a new source of palytoxin.

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    Mahnir, V M; Kozlovskaya, E P; Kalinovsky, A I

    1992-11-01

    A very potent non-protein toxin was isolated from the sea anemone Radianthus macrodactylus with the use of chromatography on polytetrafluoroethylene, CM-Sephadex C-25 and by cation and anion exchange HPLC. The toxin was identified as palytoxin by u.v.-, i.r.- and 500 MHz 1H NMR spectroscopy. Its LD50 was 0.74 +/- 0.29 micrograms/kg by i.v. injection into mice. So far, palytoxin has been associated with zoanthids only. The toxin caused the loss of haemoglobin from erythrocytes but only in about 2 hr after the beginning of incubation, which is characteristic for palytoxin from zoanthids. Sea anemone palytoxin was divided into major and minor components by HPLC. The latter proved to be a product of degradation of palytoxin.

  11. Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft

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    Yisrael Schnytzer

    2017-01-01

    Full Text Available Crabs of the genus Lybia have the remarkable habit of holding a sea anemone in each of their claws. This partnership appears to be obligate, at least on the part of the crab. The present study focuses on Lybia leptochelis from the Red Sea holding anemones of the genus Alicia (family Aliciidae. These anemones have not been found free living, only in association with L. leptochelis. In an attempt to understand how the crabs acquire them, we conducted a series of behavioral experiments and molecular analyses. Laboratory observations showed that the removal of one anemone from a crab induces a “splitting” behavior, whereby the crab tears the remaining anemone into two similar parts, resulting in a complete anemone in each claw after regeneration. Furthermore, when two crabs, one holding anemones and one lacking them, are confronted, the crabs fight, almost always leading to the “theft” of a complete anemone or anemone fragment by the crab without them. Following this, crabs “split” their lone anemone into two. Individuals of Alicia sp. removed from freshly collected L. leptochelis were used for DNA analysis. By employing AFLP (Fluorescence Amplified Fragments Length Polymorphism it was shown that each pair of anemones from a given crab is genetically identical. Furthermore, there is genetic identity between most pairs of anemone held by different crabs, with the others showing slight genetic differences. This is a unique case in which one animal induces asexual reproduction of another, consequently also affecting its genetic diversity.

  12. Molecular cloning of a peptidylglycine alpha-hydroxylating monooxygenase from sea anemones

    DEFF Research Database (Denmark)

    Hauser, F; Williamson, M; Grimmelikhuijzen, C J

    1997-01-01

    conserved regions of PHM, we have now cloned a PHM from the sea anemone Calliactis parasitica showing 42% amino acid sequence identity with rat PHM. Among the conserved (identical) amino acid residues are five histidine and one methionine residue, which bind two Cu2+ atoms that are essential for PHM...... activity. No cDNA coding for PAL could be identified, suggesting that sea anemone PAL is coded for by a gene that is different from the sea anemone PHM gene, a situation similar to the one found in insects. This is the first report on the molecular cloning of a cnidarian PHM. Udgivelsesdato: 1997-Dec-18...

  13. DNA extraction from sea anemone (Cnidaria: Actiniaria tissues for molecular analyses

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    Pinto S.M.

    2000-01-01

    Full Text Available A specific DNA extraction method for sea anemones is described in which extraction of total DNA from eight species of sea anemones and one species of corallimorpharian was achieved by changing the standard extraction protocols. DNA extraction from sea anemone tissue is made more difficult both by the tissue consistency and the presence of symbiotic zooxanthellae. The technique described here is an efficient way to avoid problems of DNA contamination and obtain large amounts of purified and integral DNA which can be used in different kinds of molecular analyses.

  14. Fusion and retrotransposition events in the evolution of the sea anemone Anemonia viridis neurotoxin genes.

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    Moran, Yehu; Weinberger, Hagar; Lazarus, Nimrod; Gur, Maya; Kahn, Roy; Gordon, Dalia; Gurevitz, Michael

    2009-08-01

    Sea anemones are sessile predators that use a variety of toxins to paralyze prey and foe. Among these toxins, Types I, II and III are short peptides that affect voltage-gated sodium channels. Anemonia viridis is the only sea anemone species that produces both Types I and III neurotoxin. Although the two toxin types are unrelated in sequence and three-dimensional structure, cloning and comparative analysis of their loci revealed a highly similar sequence at the 5' region, which encodes a signal peptide. This similarity was likely generated by gene fusion and could be advantageous in transcript stability and intracellular trafficking and secretion. In addition, these analyses identified the processed pseudogenes of the two gene families in the genome of A. viridis, probably resulting from retrotransposition events. As presence of processed pseudogenes in the genome requires transcription in germ-line cells, we analyzed oocyte-rich ovaries and found that indeed they contain Types I and III transcripts. This result raises questions regarding the role of toxin transcripts in these tissues. Overall, the retrotransposition and gene fusion events suggest that the genes of both Types I and III neurotoxins evolved in a similar fashion and share a partial common ancestry.

  15. New records of Decapod Crustaceans (Decapoda: Pontoniinae and Inachidae associated with sea anemones in Turkish waters

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    Z. DURIS

    2013-10-01

    Full Text Available Three anemone-associated decapod crustaceans, two shrimp species, Periclimenes amethysteus and P. aegylios (Caridea: Palaemonidae: Pontoniinae, and the crab Inachus phalangium (Brachyura: Inachidae, all collected from the Dardanelles, are reported for the first time from Turkish coasts. Another inachid crab, Macropodia czernjawskii is also reported for the first time to occur in association with the sea anemone, Anemonia viridis. Periclimenes scriptus was the fifth decapod species recorded associated with sea anemones within the present study, and while this species has already been reported from Turkish waters, this is the first time it is recorded from the Dardanelles (the Turkish Straits System.

  16. Neurotoxin localization to ectodermal gland cells uncovers an alternative mechanism of venom delivery in sea anemones

    OpenAIRE

    Moran, Yehu; Genikhovich, Grigory; Gordon, Dalia; Wienkoop, Stefanie; Zenkert, Claudia; Özbek, Suat; Technau, Ulrich; Gurevitz, Michael

    2011-01-01

    Jellyfish, hydras, corals and sea anemones (phylum Cnidaria) are known for their venomous stinging cells, nematocytes, used for prey and defence. Here we show, however, that the potent Type I neurotoxin of the sea anemone Nematostella vectensis, Nv1, is confined to ectodermal gland cells rather than nematocytes. We demonstrate massive Nv1 secretion upon encounter with a crustacean prey. Concomitant discharge of nematocysts probably pierces the prey, expediting toxin penetration. Toxin efficie...

  17. MODIFICATION OF SEA ANEMONE BEHAVIOR BY SYMBIOTIC ZOOXANTHELLAE: EXPANSION AND CONTRACTION.

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    Pearse, Vicki Buchsbaum

    1974-12-01

    The pattern of expansion and contraction by the sea anemone Anthopleura elegantissima differs in individuals with or without endosymbiotic zooxanthellae. Anemones without zooxanthellae, found in dark habitats, do not regularly expand or contract under changes in light. Anemones with zooxanthellae expand in moderate light and contract in intense light or in darkness, with striking uniformity. However, this behavior does not always depend directly on the presence of zooxanthellae. Anemones that have previously had endosymbiotic zooxanthellae subsequently expand and contract with changes in light in the absence of these algae. Thus, conditioned responses may be involved. It is suggested that expansion and contraction of the anemones may play an important role in favorably regulating the amount of light to which their zooxanthellae are exposed.

  18. Neurotoxin localization to ectodermal gland cells uncovers an alternative mechanism of venom delivery in sea anemones.

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    Moran, Yehu; Genikhovich, Grigory; Gordon, Dalia; Wienkoop, Stefanie; Zenkert, Claudia; Ozbek, Suat; Technau, Ulrich; Gurevitz, Michael

    2012-04-07

    Jellyfish, hydras, corals and sea anemones (phylum Cnidaria) are known for their venomous stinging cells, nematocytes, used for prey and defence. Here we show, however, that the potent Type I neurotoxin of the sea anemone Nematostella vectensis, Nv1, is confined to ectodermal gland cells rather than nematocytes. We demonstrate massive Nv1 secretion upon encounter with a crustacean prey. Concomitant discharge of nematocysts probably pierces the prey, expediting toxin penetration. Toxin efficiency in sea water is further demonstrated by the rapid paralysis of fish or crustacean larvae upon application of recombinant Nv1 into their medium. Analysis of other anemone species reveals that in Anthopleura elegantissima, Type I neurotoxins also appear in gland cells, whereas in the common species Anemonia viridis, Type I toxins are localized to both nematocytes and ectodermal gland cells. The nematocyte-based and gland cell-based envenomation mechanisms may reflect substantial differences in the ecology and feeding habits of sea anemone species. Overall, the immunolocalization of neurotoxins to gland cells changes the common view in the literature that sea anemone neurotoxins are produced and delivered only by stinging nematocytes, and raises the possibility that this toxin-secretion mechanism is an ancestral evolutionary state of the venom delivery machinery in sea anemones.

  19. Molecular characterization of two CuZn-superoxide dismutases in a sea anemone.

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    Plantivaux, Amandine; Furla, Paola; Zoccola, Didier; Garello, Ginette; Forcioli, Didier; Richier, Sophie; Merle, Pierre-Laurent; Tambutté, Eric; Tambutté, Sylvie; Allemand, Denis

    2004-10-15

    Cnidarians living in symbiosis with photosynthetic cells--called zooxanthellae--are submitted to high oxygen levels generated by photosynthesis. To cope with this hyperoxic state, symbiotic cnidarians present a high diversity of superoxide dismutases (SOD) isoforms. To understand better the mechanism of resistance of cnidarian hosts to hyperoxia, we studied copper- and zinc-containing SOD (CuZnSOD) from Anemonia viridis, a temperate symbiotic sea anemone. We cloned two CuZnSOD genes that we call AvCuZnSODa and AvCuZnSODb. Their molecular analysis suggests that the AvCuZnSODa transcript encodes an extracellular form of CuZnSOD, whereas the AvCuZnSODb transcript encodes an intracellular form. Using in situ hybridization, we showed that both AvCuZnSODa and AvCuZnSODb transcripts are expressed in the endodermal and ectodermal cells of the sea anemone, but not in the zooxanthellae. The genomic flanking sequences of AvCuZnSODa and AvCuZnSODb revealed different putative binding sites for transcription factors, suggesting different modes of regulation for the two genes. This study represents a first step in the understanding of the molecular mechanisms of host animal resistance to permanent hyperoxia status resulting from the photosynthetic symbiosis. Moreover, AvCuZnSODa and AvCuZnSODb are the first SODs cloned from a diploblastic animal, contributing to the evolutionary understanding of SODs.

  20. Sea anemones may thrive in a high CO2 world.

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    Suggett, David J; Hall-Spencer, Jason M; Rodolfo-Metalpa, Riccardo; Boatman, Toby G; Payton, Ross; Tye Pettay, D; Johnson, Vivienne R; Warner, Mark E; Lawson, Tracy

    2012-10-01

    Increased seawater pCO 2 , and in turn 'ocean acidification' (OA), is predicted to profoundly impact marine ecosystem diversity and function this century. Much research has already focussed on calcifying reef-forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA-like conditions can simultaneously enhance the ecological success of non-calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft-bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone (Anemonia viridis) population was observed along a natural CO 2 gradient at Vulcano, Italy. Both gross photosynthesis (P G ) and respiration (R) increased with pCO 2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO 2 stimulation) of metabolism. The increase of P G outweighed that of R and the genetic identity of the symbiotic microalgae (Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO 2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with pCO 2 , which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non-calcifying anthozoans to thrive in future environments, i.e. higher seawater pCO 2 . Understanding how CO 2 -enhanced productivity of non- (and less-) calcifying anthozoans applies more widely to tropical ecosystems is a priority where such organisms can dominate benthic ecosystems, in particular following localized anthropogenic stress. © 2012 Blackwell Publishing Ltd.

  1. Pore formation by actinoporins, cytolysins from sea anemones.

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    Rojko, Nejc; Dalla Serra, Mauro; Maček, Peter; Anderluh, Gregor

    2016-03-01

    Actinoporins (APs) from sea anemones are ~20 kDa pore forming toxins with a β-sandwich structure flanked by two α-helices. The molecular mechanism of APs pore formation is composed of several well-defined steps. APs bind to membrane by interfacial binding site composed of several aromatic amino acid residues that allow binding to phosphatidylcholine and specific recognition of sphingomyelin. Subsequently, the N-terminal α-helix from the β-sandwich has to be inserted into the lipid/water interphase in order to form a functional pore. Functional studies and single molecule imaging revealed that only several monomers, 3-4, oligomerise to form a functional pore. In this model the α-helices and surrounding lipid molecules build toroidal pore. In agreement, AP pores are transient and electrically heterogeneous. On the contrary, crystallized oligomers of actinoporin fragaceatoxin C were found to be composed of eight monomers with no lipids present between the adjacent α-helices. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Maur Dalla Serra and Franco Gambale. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Repair of traumatized mammalian hair cells via sea anemone repair proteins.

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    Tang, Pei-Ciao; Smith, Karen Müller; Watson, Glen M

    2016-08-01

    Mammalian hair cells possess only a limited ability to repair damage after trauma. In contrast, sea anemones show a marked capability to repair damaged hair bundles by means of secreted repair proteins (RPs). Previously, it was found that recovery of traumatized hair cells in blind cavefish was enhanced by anemone-derived RPs; therefore, the ability of anemone RPs to assist recovery of damaged hair cells in mammals was tested here. After a 1 h incubation in RP-enriched culture media, uptake of FM1-43 by experimentally traumatized murine cochlear hair cells was restored to levels comparable to those exhibited by healthy controls. In addition, RP-treated explants had significantly more normally structured hair bundles than time-matched traumatized control explants. Collectively, these results indicate that anemone-derived RPs assist in restoring normal function and structure of experimentally traumatized hair cells of the mouse cochlea. © 2016. Published by The Company of Biologists Ltd.

  3. Masquerade, mimicry and crypsis of the polymorphic sea anemone Phyllodiscus semoni and its aggregations in South Sulawesi

    NARCIS (Netherlands)

    Hoeksema, B.; Crowther, A.L.

    2011-01-01

    Phyllodiscus semoni is a morphologically variable sea anemone species from the Indo-Pacific with morphotypes ranging from upright and branched to low-lying and rounded. The apparent camouflage strategies of this sea anemone allow it to resemble other species or objects in its environment, such as

  4. Characterization of circadian behavior in the starlet sea anemone, Nematostella vectensis.

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    William D Hendricks

    Full Text Available Although much is known about how circadian systems control daily cycles in the physiology and behavior of Drosophila and several vertebrate models, marine invertebrates have often been overlooked in circadian rhythms research. This study focuses on the starlet sea anemone, Nematostella vectensis, a species that has received increasing attention within the scientific community for its potential as a model research organism. The recently sequenced genome of N. vectensis makes it an especially attractive model for exploring the molecular evolution of circadian behavior. Critical behavioral data needed to correlate gene expression patterns to specific behaviors are currently lacking in N. vectensis.To detect the presence of behavioral oscillations in N. vectensis, locomotor activity was evaluated using an automated system in an environmentally controlled chamber. Animals exposed to a 24 hr photoperiod (12 hr light: 12 hr dark exhibited locomotor behavior that was both rhythmic and predominantly nocturnal. The activity peak occurred in the early half of the night with a 2-fold increase in locomotion. Upon transfer to constant lighting conditions (constant light or constant dark, an approximately 24 hr rhythm persisted in most animals, suggesting that the rhythm is controlled by an endogenous circadian mechanism. Fourier analysis revealed the presence of multiple peaks in some animals suggesting additional rhythmic components could be present. In particular, an approximately 12 hr oscillation was often observed. The nocturnal increase in generalized locomotion corresponded to a 24 hr oscillation in animal elongation.These data confirm the presence of a light-entrainable circadian clock in Nematostella vectensis. Additional components observed in some individuals indicate that an endogenous clock of approximately 12 hr frequency may also be present. By describing rhythmic locomotor behavior in N. vectensis, we have made important progress in developing

  5. Cadherin-23 may be dynamic in hair bundles of the model sea anemone Nematostella vectensis.

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    Pei-Ciao Tang

    Full Text Available Cadherin 23 (CDH23, a component of tip links in hair cells of vertebrate animals, is essential to mechanotransduction by hair cells in the inner ear. A homolog of CDH23 occurs in hair bundles of sea anemones. Anemone hair bundles are located on the tentacles where they detect the swimming movements of nearby prey. The anemone CDH23 is predicted to be a large polypeptide featuring a short exoplasmic C-terminal domain that is unique to sea anemones. Experimentally masking this domain with antibodies or mimicking this domain with free peptide rapidly disrupts mechanotransduction and morphology of anemone hair bundles. The loss of normal morphology is accompanied, or followed by a decrease in F-actin in stereocilia of the hair bundles. These effects were observed at very low concentrations of the reagents, 0.1-10 nM, and within minutes of exposure. The results presented herein suggest that: (1 the interaction between CDH23 and molecular partners on stereocilia of hair bundles is dynamic and; (2 the interaction is crucial for normal mechanotransduction and morphology of hair bundles.

  6. Digestion rates of prey eaten by intertidal sea anemones from the ...

    African Journals Online (AJOL)

    Digestion rates were determined for natural prey items offered to each of seven species of sea anemones found at Wooley's Pool in False Say and to the single species (Bunodactis reynaudl) recorded at Siouberg on the Atlantic coast of the south-western Cape, South Africa.This was done by examining prey items removed ...

  7. Early development and acquisition of Zooxanthellae in the temperate symbiotic sea anemone Anthopleura ballii (Cocks).

    Science.gov (United States)

    Davy, Simon K; Turner, John R

    2003-08-01

    The ova of Anthopleura ballii become infected with zooxanthellae (endosymbiotic dinoflagellates) of maternal origin just prior to spawning. After fertilization, the zygotes undergo radial, holoblastic cleavage, and then gastrulate by invagination to form ciliated planulae. Because the zooxanthellae are localized on one side of the ovum-and later, within the blastomeres at one end of the embryo-invagination leads to the zooxanthellae being restricted to the planular endoderm and hence to the gastrodermal cells of the adult anemone. We propose that maternal inheritance of zooxanthellae plays an important part in the success of these temperate sea anemones, which live in regions where potential sources of zooxanthellae are scarce.

  8. Juvenile Thalassoma amblycephalum Bleeker (Labridae, Teleostei) dwelling among the tentacles of sea anemones

    DEFF Research Database (Denmark)

    Arvedlund, Michael; Iwao, Kenji; Brolund, Thea Marie

    2006-01-01

    each) of the juvenile wrasse Thalassoma amblycephalum dwelling among the tentacles of the two sea anemones Entacmaea quadricolor (clonal type), and Heteractis magnifica at a coral reef in southern Japan during 16 months in daylight hours. There are only two past records of this facultative association......, one from east Africa and one from Indonesia. The wrasse remained close to and was occasionally in physical contact with the host when foraging amongst the tentacles. When frightened, they took shelter among corals, away from the host anemone. The wrasse co-existed with the anemonefishes Amphiprion...

  9. Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues.

    Science.gov (United States)

    Nicosia, Aldo; Bennici, Carmelo; Biondo, Girolama; Costa, Salvatore; Di Natale, Marilena; Masullo, Tiziana; Monastero, Calogera; Ragusa, Maria Antonietta; Tagliavia, Marcello; Cuttitta, Angela

    2018-01-11

    Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis . The release of the genome sequence of Acropora digitifera , Exaiptasia pallida , Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure. The pattern of mRNA expression profile was also defined in A. viridis . These analyses revealed a constitutive mRNA expression especially in tissues with active proliferation. Additionally, the transcriptional profile of A. viridis TCTP ( AvTCTP ) after challenges with different abiotic/biotic stresses showed induction by extreme temperatures, heavy metals exposure and immune stimulation. These results suggest the involvement of AvTCTP in the sea anemone defensome taking part in environmental stress and immune responses.

  10. Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues

    Directory of Open Access Journals (Sweden)

    Aldo Nicosia

    2018-01-01

    Full Text Available Gene family encoding translationally controlled tumour protein (TCTP is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure. The pattern of mRNA expression profile was also defined in A. viridis. These analyses revealed a constitutive mRNA expression especially in tissues with active proliferation. Additionally, the transcriptional profile of A. viridis TCTP (AvTCTP after challenges with different abiotic/biotic stresses showed induction by extreme temperatures, heavy metals exposure and immune stimulation. These results suggest the involvement of AvTCTP in the sea anemone defensome taking part in environmental stress and immune responses.

  11. Asexual propagation of sea anemones that host anemonefishes: implications for the marine ornamental aquarium trade and restocking programs.

    Science.gov (United States)

    Scott, Anna; Hardefeldt, Jannah M; Hall, Karina C

    2014-01-01

    Anemonefishes and their host sea anemones form an iconic symbiotic association in reef environments, and are highly sought after in the marine aquarium trade. This study examines asexual propagation as a method for culturing a geographically widespread and commonly traded species of host sea anemone, Entacmaea quadricolor. Two experiments were done: the first to establish whether size or colour morph influenced survival after cutting into halves or quarters; and the second to see whether feeding was needed to maximise survival and growth after cutting. Survival rates were high in both experiments, with 89.3 and 93.8% of the anemones cut in half, and 62.5 and 80.4% cut in quarters surviving in experiments 1 and 2, respectively. Anemones that were cut in half were larger in size, and healed and grew quicker than those cut in quarters. However, even though survival was lower when the individuals were cut in quarters, this treatment produced the greatest number of anemones. Feeding increased oral disc diameter growth and reduced wet weight loss, but did not significantly influence pedal disc diameter. Given that the anemones took up to 56 d to form an off-centre mouth, it is highly likely that feeding may have produced greater effect if the experiment was run for longer. This low technology method of propagation could be used to produce individuals throughout the year and the anemones could then be used to supply the aquarium trade or restock depleted habitats, thus supporting biodiversity conservation in coral reef areas.

  12. Differential accumulation of heavy metals in the sea anemone Anthopleura elegantissima as a function of symbiotic state

    International Nuclear Information System (INIS)

    Mitchelmore, Carys L.; Alan Verde, E.; Ringwood, Amy H.; Weis, Virginia M.

    2003-01-01

    The accumulation of metals by the North American Pacific Coast temperate sea anemone Anthopleura elegantissima, and its dinoflagellate-algal symbiont Symbiodinium muscatinei was examined following laboratory metal exposures. Both, naturally occurring symbiotic and symbiont-free (aposymbiotic) anemones were used in this study to investigate differences in metal uptake due to the symbiotic state of the animal. The effects of metal exposures on the anemone-algal symbiosis were determined using measures of algal cell density and mitotic index (MI). Anemones were exposed to either cadmium, copper, nickel or zinc chloride (0, 10, 100 μg l -1 for Cd, Cu and Ni; 0, 100, 1000 μg l -1 for Zn) for 42 days followed by a 42-day recovery period in ambient seawater. Anemones were analyzed for metal content using inductively coupled plasma mass spectroscopy (ICP-MS) at various time points during the study. Symbiotic anemones accumulated Cd, Ni and Zn to a greater extent than aposymbiotic anemones. A dramatically different pattern of Cu accumulation was observed, with aposymbiotic anemones accumulating higher levels than symbiotic anemones. Following recovery in ambient seawater, all tissue metal levels were reduced to near pre-exposure control levels in most cases. No changes in algal cell density or MI were observed in symbiotic anemone tentacle clips at any dose or time point in the Cd and Cu exposures. However, significant reductions in algal cell densities were observed in the Ni-exposed and some Zn-exposed animals, although levels returned to control values following recovery. There were no changes in mitotic index (MI) following Ni or Zn exposures. These results demonstrate that the extent of heavy metal accumulation depends upon cnidarian symbiotic state and the heavy metal in question

  13. Observations on a population of the sea anemone Anemonia viridis (Forskal, 1775) in the North Aegean Sea

    Energy Technology Data Exchange (ETDEWEB)

    Chariton Chintiroglou, C. [Thessaloniki, Aristotle Univ. (Greece). Dept. of Zoology

    1996-12-31

    The present paper is concerned with the structural aspects of Anemonia viridis populations found in the North Aegean Sea. It was found that mean wet weight and density of anemone populations increases with depth and distance from shore. Differences in the structure of the Anemonia viridis populations were attributed both to the specific hydrodynamic characteristics of the biotopes and to a number biotic interactions. From our results and t previous investigations the adoption of three different lifestyles by the anemones was assumed.: (1) a colonial form, with population densities around 650 individuals per m{sup 2}, found in substrates exposed to increased hydrodynamism; (2) a colonial form, with lower densities (90 indiv. per m{sup 2}), found in less exposed sites; (3) finally, large individuals in deeper waters chose a solitary lifestyle, as mechanical stresses were much lower.

  14. Three New Indole Diterpenoids from the Sea-Anemone-Derived Fungus Penicillium sp. AS-79.

    Science.gov (United States)

    Hu, Xue-Yi; Meng, Ling-Hong; Li, Xin; Yang, Sui-Qun; Li, Xiao-Ming; Wang, Bin-Gui

    2017-05-12

    Three new indolediterpenoids, namely, 22-hydroxylshearinine F ( 1 ), 6-hydroxylpaspalinine ( 2 ), and 7- O -acetylemindole SB ( 3 ), along with eight related known analogs ( 4 - 11 ), were isolated from the sea-anemone-derived fungus Penicillium sp. AS-79. The structures and relative configurations of these compounds were determined by a detailed interpretation of the spectroscopic data, and their absolute configurations were determined by ECD calculations ( 1 and 2 ) and single-crystal X-ray diffraction ( 3 ). Some of these compounds exhibited prominent activity against aquatic and human pathogenic microbes.

  15. Indole Alkaloids from the Sea Anemone Heteractis aurora and Homarine from Octopus cyanea.

    Science.gov (United States)

    Shaker, Kamel H; Göhl, Matthias; Müller, Tobias; Seifert, Karlheinz

    2015-11-01

    The two new indole alkaloids 2-amino-1,5-dihydro-5-(1H-indol-3-ylmethyl)-4H-imidazol-4-one (1), 2-amino-5-[(6-bromo-1H-indol-3-yl)methyl]-3,5-dihydro-3-methyl-4H-imidazol-4-one (2), and auramine (3) have been isolated from the sea anemone Heteractis aurora. Both indole alkaloids were synthesized for the confirmation of the structures. Homarine (4), along with uracil (5), hypoxanthine (6), and inosine (7) have been obtained from Octopus cyanea. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

  16. Asexual propagation of sea anemones that host anemonefishes: implications for the marine ornamental aquarium trade and restocking programs.

    Directory of Open Access Journals (Sweden)

    Anna Scott

    Full Text Available Anemonefishes and their host sea anemones form an iconic symbiotic association in reef environments, and are highly sought after in the marine aquarium trade. This study examines asexual propagation as a method for culturing a geographically widespread and commonly traded species of host sea anemone, Entacmaea quadricolor. Two experiments were done: the first to establish whether size or colour morph influenced survival after cutting into halves or quarters; and the second to see whether feeding was needed to maximise survival and growth after cutting. Survival rates were high in both experiments, with 89.3 and 93.8% of the anemones cut in half, and 62.5 and 80.4% cut in quarters surviving in experiments 1 and 2, respectively. Anemones that were cut in half were larger in size, and healed and grew quicker than those cut in quarters. However, even though survival was lower when the individuals were cut in quarters, this treatment produced the greatest number of anemones. Feeding increased oral disc diameter growth and reduced wet weight loss, but did not significantly influence pedal disc diameter. Given that the anemones took up to 56 d to form an off-centre mouth, it is highly likely that feeding may have produced greater effect if the experiment was run for longer. This low technology method of propagation could be used to produce individuals throughout the year and the anemones could then be used to supply the aquarium trade or restock depleted habitats, thus supporting biodiversity conservation in coral reef areas.

  17. Field experiments on individual adaptation of the spider crab Inachus phalangium to its sea anemone host Anemonia viridis in the northern Adriatic Sea

    Directory of Open Access Journals (Sweden)

    S. LANDMANN

    2015-02-01

    Full Text Available We studied the adaptation of the spider crab Inachus phalangium (Fabricius, 1755 to one of its sea anemone host species, Anemonia viridis (Forsskål, 1775 in the coastal region of Rovinj, Croatia. Similar to other brachyuran species, Inachus spp. generally lives within the anemone to obtain protection from possible predators. Using removal and reintroduction experiments, this study investigates the protection mechanism and shows a loss of adaptation after a period of 10 days when the crabs are taken out of their host and kept solitary. Thirty-nine anemones from two different trial sites were marked individually and the inhabiting crabs were isolated to be released back into their individual hosts later. The reactions of the anemones were closely observed and characterized to determine the respective state of crab adaptation. As 35 out of 39 individuals provoked a defense /attack reaction of the anemone, it is concluded that the crabs possessed some sort of non-permanent protection mechanism that was lost during the test run (chi-square test, p < 0.00014. All tested crabs re-inhabited their host anemones within a maximum of 20 minutes after they had been reintroduced and stung by the anemones. Therefore, habituation to the host’s defense / attack mechanism is acquired individually and not genetically inherent to the species. The results are compared to adaptation and protection data on other decapod crustaceans and some anemonefishes.

  18. Catalase characterization and implication in bleaching of a symbiotic sea anemone.

    Science.gov (United States)

    Merle, Pierre-Laurent; Sabourault, Cécile; Richier, Sophie; Allemand, Denis; Furla, Paola

    2007-01-15

    Symbiotic cnidarians are marine invertebrates harboring photosynthesizing microalgae (named zooxanthellae), which produce great amounts of oxygen and free radicals upon illumination. Studying antioxidative balance is then crucial to understanding how symbiotic cnidarians cope with ROS production. In particular, it is suspected that oxidative stress triggers cnidarian bleaching, i.e., the expulsion of zooxanthellae from the animal host, responsible for symbiotic cnidarian mass mortality worldwide. This study therefore investigates catalase antioxidant enzymes and their role in bleaching of the temperate symbiotic sea anemone Anemonia viridis. Using specific separation of animal tissues (ectoderm and endoderm) from the symbionts (zooxanthellae), spectrophotometric assays and native PAGE revealed both tissue-specific and activity pattern distribution of two catalase electrophoretypes, E1 and E2. E1, expressed in all three tissues, presents high sensitivity to the catalase inhibitor aminotriazole (ATZ) and elevated temperatures. The ectodermal E1 form is responsible for 67% of total catalase activity. The E2 form, expressed only within zooxanthellae and their host endodermal cells, displays low sensitivity to ATZ and relative thermostability. We further cloned an ectodermal catalase, which shares 68% identity with mammalian monofunctional catalases. Last, 6 days of exposure of whole sea anemones to ATZ (0.5 mM) led to effective catalase inhibition and initiated symbiont expulsion. This demonstrates the crucial role of this enzyme in cnidarian bleaching, a phenomenon responsible for worldwide climate-change-induced mass mortalities, with catastrophic consequences for marine biodiversity.

  19. Comparative effects of dissolved copper and copper oxide nanoparticle exposure to the sea anemone, Exaiptasia pallida

    Energy Technology Data Exchange (ETDEWEB)

    Siddiqui, Samreen; Goddard, Russell H.; Bielmyer-Fraser, Gretchen K., E-mail: gkbielmyer@valdosta.edu

    2015-03-15

    Highlights: • Differences between CuO NP and CuCl{sub 2} exposure were characterized. • Copper accumulation in E. pallida was concentration-dependent. • E. pallida exposed to CuCl{sub 2} accumulated higher copper tissue burdens. • The oxidative stress response was greater in E. pallida exposed to CuO NP. • Both forms of copper inhibited CA activity in E. pallida. - Abstract: Increasing use of metal oxide nanoparticles (NP) by various industries has resulted in substantial output of these NP into aquatic systems. At elevated concentrations, NP may interact with and potentially affect aquatic organisms. Environmental implications of increased NP use are largely unknown, particularly in marine systems. This research investigated and compared the effects of copper oxide (CuO) NP and dissolved copper, as copper chloride (CuCl{sub 2}), on the sea anemone, Exaiptasia pallida. Sea anemones were collected over 21 days and tissue copper accumulation and activities of the enzymes: catalase, glutathione peroxidase, glutathione reductase, and carbonic anhydrase were quantified. The size and shape of CuO NP were observed using a ecanning electron microscope (SEM) and the presence of copper was confirmed by using Oxford energy dispersive spectroscopy systems (EDS/EDX). E. pallida accumulated copper in their tissues in a concentration- and time-dependent manner, with the animals exposed to CuCl{sub 2} accumulating higher tissue copper burdens than those exposed to CuO NP. As a consequence of increased copper exposure, as CuO NP or CuCl{sub 2}, anemones increased activities of all of the antioxidant enzymes measured to some degree, and decreased the activity of carbonic anhydrase. Anemones exposed to CuO NP generally had higher anti-oxidant enzyme activities than those exposed to the same concentrations of CuCl{sub 2}. This study is useful in discerning differences between CuO NP and dissolved copper exposure and the findings have implications for exposure of aquatic

  20. Isolation of L-3-phenyllactyl-Phe-Lys-Ala-NH2 (Antho-KAamide), a novel neuropeptide from sea anemones

    DEFF Research Database (Denmark)

    Nothacker, H P; Rinehart, K L; Grimmelikhuijzen, C J

    1991-01-01

    sea anemones. We propose that the L-3-phenyllactyl residue renders Antho-KAamide resistant to nonspecific aminopeptidases, thereby increasing the stability of the neuropeptide after neuronal release. The existence of the L-3-phenyllactyl residue in 3 neuropeptides isolated so far suggests...

  1. INTERSPECIFIC AGGRESSIVE BEHAVIOR OF THE CORALLIMORPHARIAN CORYNACTIS CALIFORNICA (CNIDARIA: ANTHOZOA): EFFECTS ON SYMPATRIC CORALS AND SEA ANEMONES.

    Science.gov (United States)

    Chadwick, Nanette E

    1987-08-01

    Corallimorpharians are sessile cnidarians that are morphologically similar to the actiniarian sea anemones and scleractinian corals. This study describes for the first time the behavioral mechanism and effects of aggression by a corallimorpharian. Polyps of the temperate clonal corallimorpharian Corynactis californica extruded their mesenteries and associated filaments onto members of certain species of sea anemones and corals. They did not exhibit this behavior intraspecifically, and members of different clones of C. californica remained expanded upon contact. In contrast, members of four species of corals and zoanthids responded to contact with C. californica by contracting their tentacles, and members of three sea anemone species bent or moved away, detached from the substrate, or attacked using their aggressive structures. When interspecific contact was prolonged, individuals of C. californica extruded filaments onto, and killed polyps of, the sea anemones Anthopleura elegantissima and Metridium senile within 3 weeks, and the corals Astrangia lajollaensis and Balanophyllia elegans within 4-10 months under laboratory conditions. The use of extruded mesenterial filaments by C. californica to attack members of other anthozoan species is similar to the aggressive behavior exhibited by many scleractinian reef corals. Field observations suggest that C. californica may use this agonistic behavior during interspecific competition for space on hard marine substrate.

  2. Increased cell proliferation and mucocyte density in the sea anemone Aiptasia pallida recovering from bleaching.

    Directory of Open Access Journals (Sweden)

    David Fransolet

    Full Text Available Recovery of coral after bleaching episodes is a critical period for the health of the reef ecosystem. While events such as symbiont (genus Symbiodinium shifting/shuffling or tissue apoptosis have been demonstrated to occur following bleaching, little is known concerning tissue recovery or cell proliferation. Here, we studied the sea anemone Aiptasia pallida exposed to a transient elevation of water temperature combined with high illumination (33°C and 1900 µmol photons x m(-2 x s(-1 for 30 h. Following such treatment bleached anemones showed a significant reduction of their Symbiodinium density. Cell proliferation in the ectodermis and gastrodermis was determined by assessing the densities of cells labeled with a thymidine analogue (EdU. Cell proliferation significantly increased during the first day following stress in both tissue types. This increased cell proliferation returned to pre-stress values after one week. Although cell proliferation was higher in the ectodermis in absence of stress, it was relatively more pronounced in the gastrodermis of stressed anemones. In addition, the ratio of ectodermal mucocytes significantly increased three weeks after induced stress. These results suggest that thermal/photic stress coupled with the loss of the symbionts is able to enhance cell proliferation in both gastrodermis and ectodermis of cnidarians. While new cells formed in the gastrodermis are likely to host new Symbiodinium, the fate of new cells in the ectodermis was only partially revealed. Some new ectodermal cells may, in part, contribute to the increased number of mucocytes which could eventually help strengthen the heterotrophic state until restoration of the symbiosis.

  3. Responses of the sea anemone, Exaiptasia pallida, to ocean acidification conditions and zinc or nickel exposure.

    Science.gov (United States)

    Duckworth, Christina G; Picariello, Codie R; Thomason, Rachel K; Patel, Krina S; Bielmyer-Fraser, Gretchen K

    2017-01-01

    Ocean acidification, caused by increasing atmospheric carbon dioxide (CO 2 ), is a growing concern in marine environments. Land-based sources of pollution, such as metals, have also been a noted problem; however, little research has addressed the combined exposure of both pollutants to coral reef organisms. In this study we examined tissue metal accumulation and physiological effects (activity of anti-oxidant enzymes, catalase and glutathione reductase) in the sea anemone, Exaiptasia pallida after exposure to increased CO 2 , as well as zinc (Zn) or nickel (Ni). After exposure to four concentrations (nominal values=control, 10, 50, 100μg/L) of Zn or Ni over 7days, both metals accumulated in the tissues of E. pallida in a concentration-dependent manner. Anemones exposed to elevated CO 2 (1000ppm) accumulated significant tissue burdens of Zn or Ni faster (by 48h) than those exposed to the same metal concentrations at ambient CO 2 . No differences were observed in catalase activity due to Zn exposure; however, 50μg/L Ni caused a significant increase in catalase activity at ambient CO 2 . No significant effect on catalase activity from CO 2 exposure alone was observed. Glutathione reductase activity was affected by increased Zn or Ni exposure and those effects were influenced by increased CO 2 . Results of this study provide insight into the toxic mechanisms and environmental implications of CO 2 and Zn or Ni exposure to the cnidarian E. pallida. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    KAUST Repository

    Herrera Sarrias, Marcela; Ziegler, Maren; Voolstra, Christian R.; Aranda, Manuel

    2017-01-01

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  5. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    KAUST Repository

    Herrera Sarrias, Marcela

    2017-05-02

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  6. Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent.

    Science.gov (United States)

    Horwitz, Rael; Borell, Esther M; Fine, Maoz; Shaked, Yeala

    2014-01-01

    Ocean acidification (OA) is not an isolated threat, but acts in concert with other impacts on ecosystems and species. Coastal marine invertebrates will have to face the synergistic interactions of OA with other global and local stressors. One local factor, common in coastal environments, is trace element contamination. CO2 vent sites are extensively studied in the context of OA and are often considered analogous to the oceans in the next few decades. The CO2 vent found at Levante Bay (Vulcano, NE Sicily, Italy) also releases high concentrations of trace elements to its surrounding seawater, and is therefore a unique site to examine the effects of long-term exposure of nearby organisms to high pCO2 and trace element enrichment in situ. The sea anemone Anemonia viridis is prevalent next to the Vulcano vent and does not show signs of trace element poisoning/stress. The aim of our study was to compare A. viridis trace element profiles and compartmentalization between high pCO2 and control environments. Rather than examining whole anemone tissue, we analyzed two different body compartments-the pedal disc and the tentacles, and also examined the distribution of trace elements in the tentacles between the animal and the symbiotic algae. We found dramatic changes in trace element tissue concentrations between the high pCO2/high trace element and control sites, with strong accumulation of iron, lead, copper and cobalt, but decreased concentrations of cadmium, zinc and arsenic proximate to the vent. The pedal disc contained substantially more trace elements than the anemone's tentacles, suggesting the pedal disc may serve as a detoxification/storage site for excess trace elements. Within the tentacles, the various trace elements displayed different partitioning patterns between animal tissue and algal symbionts. At both sites iron was found primarily in the algae, whereas cadmium, zinc and arsenic were primarily found in the animal tissue. Our data suggests that A. viridis

  7. A Low Molecular Weight Protein from the Sea Anemone Anemonia viridis with an Anti-Angiogenic Activity.

    Science.gov (United States)

    Loret, Erwann P; Luis, José; Nuccio, Christopher; Villard, Claude; Mansuelle, Pascal; Lebrun, Régine; Villard, Pierre Henri

    2018-04-19

    Sea anemones are a remarkable source of active principles due to a decentralized venom system. New blood vessel growth or angiogenesis is a very promising target against cancer, but the few available antiangiogenic compounds have limited efficacy. In this study, a protein fraction, purified from tentacles of Anemonia viridis , was able to limit endothelial cells proliferation and angiogenesis at low concentration (14 nM). Protein sequences were determined with Edman degradation and mass spectrometry in source decay and revealed homologies with Blood Depressing Substance (BDS) sea anemones. The presence of a two-turn alpha helix observed with circular dichroism and a trypsin activity inhibition suggested that the active principle could be a Kunitz-type inhibitor, which may interact with an integrin due to an Arginine Glycin Aspartate (RGD) motif. Molecular modeling showed that this RGD motif was well exposed to solvent. This active principle could improve antiangiogenic therapy from existing antiangiogenic compounds binding on the Vascular Endothelial Growth Factor (VEGF).

  8. Partially Purified Extracts of Sea Anemone Anemonia viridis Affect the Growth and Viability of Selected Tumour Cell Lines

    OpenAIRE

    Bulati, Matteo; Longo, Alessandra; Masullo, Tiziana; Vlah, Sara; Bennici, Carmelo; Bonura, Angela; Salamone, Monica; Tagliavia, Marcello; Nicosia, Aldo; Mazzola, Salvatore; Colombo, Paolo; Cuttitta, Angela

    2016-01-01

    In the last few years, marine species have been investigated for the presence of natural products with anticancer activity. Using reversed phase chromatography, low molecular weight proteins were fractionated from the sea anemone Anemonia viridis. Four different fractions were evaluated for their cytotoxic activity by means of erythrocyte haemolysis test, MTS, and LDH assays. Finally, the antiproliferative activities of three of these fractions were studied on PC3, PLC/PRF/5, and A375 human c...

  9. Development and characterization of new polymorphic microsatellite markers in four sea anemones: Entacmaea quadricolor, Heteractis magnifica, Stichodactyla gigantea, and Stichodactyla mertensii

    KAUST Repository

    Gatins, Remy

    2016-10-08

    Relatively few studies have investigated the genetic population structure of sea anemones. This is particularly true for sea anemones that host some of the most iconic fishes on coral reefs, the anemonefishes. One of the main reasons for this knowledge gap is the lack of appropriate genetic markers. We developed and characterized a total of 47 novel polymorphic microsatellite markers for four host sea anemone species from the Indo-Pacific: Entacmaea quadricolor (n = 16 microsatellite markers), Heteractis magnifica (n = 8), Stichodactyla mertensii (n = 13), and Stichodactyla gigantea (n = 10). Here, we report genetic diversity statistics from two different sampling locations for each anemone species. Overall, we found that most markers were highly polymorphic. On average, we found a mean of seven alleles per locus. Observed and expected heterozygosities displayed high variation among loci, ranging from 0.033 to 0.980 and from 0.038 to 0.927, respectively. Only four loci showed deviations of Hardy–Weinberg equilibrium in both populations and were identified as having null alleles. Additionally, two pairs of loci were identified to be in linkage disequilibrium in only one population. Host anemones are highly sought after in the marine aquarium trade and are susceptible to thermal bleaching. Although most studies focus on their obligate symbionts (the anemonefish), genetic analyses of host sea anemones can expand our understanding of the biology, connectivity, and population structure of these organisms and potentially help develop conservation strategies that will aid both the host and its symbionts.

  10. Development and characterization of new polymorphic microsatellite markers in four sea anemones: Entacmaea quadricolor, Heteractis magnifica, Stichodactyla gigantea, and Stichodactyla mertensii

    KAUST Repository

    Gatins, Remy; Saenz-Agudelo, Pablo; Scott, Anna; Berumen, Michael L.

    2016-01-01

    Relatively few studies have investigated the genetic population structure of sea anemones. This is particularly true for sea anemones that host some of the most iconic fishes on coral reefs, the anemonefishes. One of the main reasons for this knowledge gap is the lack of appropriate genetic markers. We developed and characterized a total of 47 novel polymorphic microsatellite markers for four host sea anemone species from the Indo-Pacific: Entacmaea quadricolor (n = 16 microsatellite markers), Heteractis magnifica (n = 8), Stichodactyla mertensii (n = 13), and Stichodactyla gigantea (n = 10). Here, we report genetic diversity statistics from two different sampling locations for each anemone species. Overall, we found that most markers were highly polymorphic. On average, we found a mean of seven alleles per locus. Observed and expected heterozygosities displayed high variation among loci, ranging from 0.033 to 0.980 and from 0.038 to 0.927, respectively. Only four loci showed deviations of Hardy–Weinberg equilibrium in both populations and were identified as having null alleles. Additionally, two pairs of loci were identified to be in linkage disequilibrium in only one population. Host anemones are highly sought after in the marine aquarium trade and are susceptible to thermal bleaching. Although most studies focus on their obligate symbionts (the anemonefish), genetic analyses of host sea anemones can expand our understanding of the biology, connectivity, and population structure of these organisms and potentially help develop conservation strategies that will aid both the host and its symbionts.

  11. Oxidative stress and apoptotic events during thermal stress in the symbiotic sea anemone, Anemonia viridis.

    Science.gov (United States)

    Richier, Sophie; Sabourault, Cécile; Courtiade, Juliette; Zucchini, Nathalie; Allemand, Denis; Furla, Paola

    2006-09-01

    Symbiosis between cnidarian and photosynthetic protists is widely distributed over temperate and tropical seas. These symbioses can periodically breakdown, a phenomenon known as cnidarian bleaching. This event can be irreversible for some associations subjected to acute and/or prolonged environmental disturbances, and leads to the death of the animal host. During bleaching, oxidative stress has been described previously as acting at molecular level and apoptosis is suggested to be one of the mechanisms involved. We focused our study on the role of apoptosis in bleaching via oxidative stress in the association between the sea anemone Anemonia viridis and the dinoflagellates Symbiodinium species. Characterization of caspase-like enzymes were conducted at the biochemical and molecular level to confirm the presence of a caspase-dependent apoptotic phenomenon in the cnidarian host. We provide evidence of oxidative stress followed by induction of caspase-like activity in animal host cells after an elevated temperature stress, suggesting the concomitant action of these components in bleaching.

  12. Heat stress induces different forms of cell death in sea anemones and their endosymbiotic algae depending on temperature and duration.

    Science.gov (United States)

    Dunn, S R; Thomason, J C; Le Tissier, M D A; Bythell, J C

    2004-11-01

    Bleaching of reef building corals and other symbiotic cnidarians due to the loss of their dinoflagellate algal symbionts (=zooxanthellae), and/or their photosynthetic pigments, is a common sign of environmental stress. Mass bleaching events are becoming an increasingly important cause of mortality and reef degradation on a global scale, linked by many to global climate change. However, the cellular mechanisms of stress-induced bleaching remain largely unresolved. In this study, the frequency of apoptosis-like and necrosis-like cell death was determined in the symbiotic sea anemone Aiptasia sp. using criteria that had previously been validated for this symbiosis as indicators of programmed cell death (PCD) and necrosis. Results indicate that PCD and necrosis occur simultaneously in both host tissues and zooxanthellae subject to environmentally relevant doses of heat stress. Frequency of PCD in the anemone endoderm increased within minutes of treatment. Peak rates of apoptosis-like cell death in the host were coincident with the timing of loss of zooxanthellae during bleaching. The proportion of apoptosis-like host cells subsequently declined while cell necrosis increased. In the zooxanthellae, both apoptosis-like and necrosis-like activity increased throughout the duration of the experiment (6 days), dependent on temperature dose. A stress-mediated PCD pathway is an important part of the thermal stress response in the sea anemone symbiosis and this study suggests that PCD may play different roles in different components of the symbiosis during bleaching.

  13. Algal genotype and photoacclimatory responses of the symbiotic alga Symbiodinium in natural populations of the sea anemone Anemonia viridis

    Science.gov (United States)

    Bythell, J. C.; Douglas, A. E.; Sharp, V. A.; Searle, J. B.; Brown, B. E.

    1997-01-01

    As an approach to investigate the impact of solar radiation on an alga–invertebrate symbiosis, the genetic variation and photosynthetic responses of the dinoflagellate algal symbiosis in an intertidal and a subtidal population of the sea anemone Anemonia viridis were explored. Allozyme analysis of the anemones indicated that the two populations were genetically very similar, with a Nei's index value of genetic identity (I) of 0.998. The algae in all animals examined were identified as Symbiodinium of clade a by PCR-RFLP analysis of the small subunit ribosomal RNA gene. The symbiosis in the two populations did not differ significantly in algal population density, chlorophyll a content per algal cell or any photosynthetic parameter obtained from studies of the relationship between photosynthesis and irradiance. We conclude that there is not necessarily genetic variation or photosynthetic plasticity of the symbiotic algae in Anemonia viridis inhabiting environments characterized by the different solar irradiances of the subtidal and intertidal habitats.

  14. The gastropod-symbiotic sea anemone genus Isosicyonis Carlgren, 1927 (Actiniaria: Actiniidae: a new species from the Weddell Sea (Antarctica that clarifies the taxonomic position of the genus

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    Estefanía Rodríguez

    2008-03-01

    Full Text Available A second species of the sea anemone genus Isosicyonis is described and illustrated from 16 specimens collected in the Weddell Sea (Antarctica on the Polarstern cruises ANT XVII/3, ANT XXI/2 and ANT XXIII/8. Isosicyonis striata n. sp. is easily distinguishable externally from the other species of the genus Isosicyonis alba by its pattern: white longitudinal stripes on the column, oral disc, and tentacles. It is also distinguished by internal features including the retractor muscles, parietobasilar muscles, marginal sphincter muscles, number of mesenteries, and cnidae. The genus Isosycionis is currently only known from the Southern Ocean. Both species of Isosicyonis live in association with a gastropod, with a single sea anemone occupying almost the whole shell of its gastropod host. The description of this new species, and our re-examination of Isosicyonis alba, resolves the controversial higher taxonomic position of the genus, confirming its placement within the Endomyaria.

  15. The sea anemone Bunodactis octoradiata (Anthozoa: Actiniaria from southern Patagonia: morphological study and new records

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    Agustín Garese

    2014-10-01

    Full Text Available Bunodactis Verril, 1899 comprises at present 19 nominal species of sea anemones. The validity of the genus is under discussion. The description of the species, Bunodactis octoradiata Carlgren, 1899, is insufficient for reliable identification, and although subsequent works have provided additional information on the species, its description still needs to be complemented. Herein we describe B. octoradiata based on histological sections of the internal anatomy, and give a complete and detailed description of the external anatomy. The cnidom is composed of spirocysts, basitrichs and microbasic p-mastigophores; their distribution in the organism, sizes and relative abundances are provided. The presence of zooxanthellae is reported for the first time. Bunodactis octoradiata is distributed in groups that vary from 5.6 to 45 ind./m² in the field. Additionally, our data extends the distribution of the species along the coast of southern Patagonia (47°44'36"-49°15'13"S and 65°50'26"-67°39'45"W.

  16. Germ-layer commitment and axis formation in sea anemone embryonic cell aggregates.

    Science.gov (United States)

    Kirillova, Anastasia; Genikhovich, Grigory; Pukhlyakova, Ekaterina; Demilly, Adrien; Kraus, Yulia; Technau, Ulrich

    2018-02-20

    Robust morphogenetic events are pivotal for animal embryogenesis. However, comparison of the modes of development of different members of a phylum suggests that the spectrum of developmental trajectories accessible for a species might be far broader than can be concluded from the observation of normal development. Here, by using a combination of microsurgery and transgenic reporter gene expression, we show that, facing a new developmental context, the aggregates of dissociated embryonic cells of the sea anemone Nematostella vectensis take an alternative developmental trajectory. The self-organizing aggregates rely on Wnt signals produced by the cells of the original blastopore lip organizer to form body axes but employ morphogenetic events typical for normal development of distantly related cnidarians to re-establish the germ layers. The reaggregated cells show enormous plasticity including the capacity of the ectodermal cells to convert into endoderm. Our results suggest that new developmental trajectories may evolve relatively easily when highly plastic embryonic cells face new constraints. Copyright © 2018 the Author(s). Published by PNAS.

  17. Interactions between the tropical sea anemone Aiptasia pallida and Serratia marcescens, an opportunistic pathogen of corals.

    Science.gov (United States)

    Krediet, Cory J; Meyer, Julie L; Gimbrone, Nicholas; Yanong, Roy; Berzins, Ilze; Alagely, Ali; Castro, Herman; Ritchie, Kim B; Paul, Valerie J; Teplitski, Max

    2014-06-01

    Coral reefs are under increasing stress caused by global and local environmental changes, which are thought to increase the susceptibility of corals to opportunistic pathogens. In the absence of an easily culturable model animal, the understanding of the mechanisms of disease progression in corals remains fairly limited. In the present study, we tested the susceptibility of the tropical sea anemone Aiptasia pallida to an opportunistic coral pathogen (Serratia marcescens). A. pallida was susceptible to S. marcescens PDL100 and responded to this opportunistic coral pathogen with darkening of the tissues and retraction of tentacles, followed by complete disintegration of polyp tissues. Histological observations revealed loss of zooxanthellae and structural changes in eosinophilic granular cells in response to pathogen infection. A screen of S. marcescens mutants identified a motility and tetrathionate reductase mutants as defective in virulence in the A. pallida infection model. In co-infections with the wild-type strain, the tetrathionate reductase mutant was less fit within the surface mucopolysaccharide layer of the host coral Acropora palmata. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Diffusion Limitation and Hyperoxic Enhancement of Oxygen Consumption in Zooxanthellate Sea Anemones, Zoanthids, and Corals.

    Science.gov (United States)

    Shick, J M

    1990-08-01

    Depending on their size and morphology, anthozoan polyps and colonies may be diffusion-limited in their oxygen consumption, even under well-stirred, air-saturated conditions. This is indicated by an enhancement of oxygen consumption under steady-state hyperoxic conditions that simulate the levels of O2 produced photosynthetically by zooxanthellae in the hosts' tissues. Such hyperoxia in the tissues of zooxanthellate species negates the effect of the diffusive boundary layer, and increases the rate of oxygen consumption; thus, in many cases, the rate of respiration measured under normoxia in the dark may not be representative of the rate during the day when the zooxanthellae are photosynthesizing and when the supply of oxygen for respiration is in the tissues themselves, not from the environment. These results have implications in respirometric methodology and in calculating the rate of gross photosynthesis in energetic studies. The activity of cytochrome c oxidase is higher in aposymbiotic than in zooxanthellate specimens of the sea anemone Aiptasia pulchella, and this may indicate a compensation for the relative hypoxia in the tissues of the former, enhancing the delivery of oxygen to the mitochondria from the environment.

  19. Characterization of Morphological and Cellular Events Underlying Oral Regeneration in the Sea Anemone, Nematostella vectensis

    Directory of Open Access Journals (Sweden)

    Aldine R. Amiel

    2015-12-01

    Full Text Available Cnidarians, the extant sister group to bilateria, are well known for their impressive regenerative capacity. The sea anemone Nematostella vectensis is a well-established system for the study of development and evolution that is receiving increased attention for its regenerative capacity. Nematostella is able to regrow missing body parts within five to six days after its bisection, yet studies describing the morphological, cellular, and molecular events underlying this process are sparse and very heterogeneous in their experimental approaches. In this study, we lay down the basic framework to study oral regeneration in Nematostella vectensis. Using various imaging and staining techniques we characterize in detail the morphological, cellular, and global molecular events that define specific landmarks of this process. Furthermore, we describe in vivo assays to evaluate wound healing success and the initiation of pharynx reformation. Using our described landmarks for regeneration and in vivo assays, we analyze the effects of perturbing either transcription or cellular proliferation on the regenerative process. Interestingly, neither one of these experimental perturbations has major effects on wound closure, although they slightly delay or partially block it. We further show that while the inhibition of transcription blocks regeneration in a very early step, inhibiting cellular proliferation only affects later events such as pharynx reformation and tentacle elongation.

  20. Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent

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    Rael Horwitz

    2014-09-01

    Full Text Available Ocean acidification (OA is not an isolated threat, but acts in concert with other impacts on ecosystems and species. Coastal marine invertebrates will have to face the synergistic interactions of OA with other global and local stressors. One local factor, common in coastal environments, is trace element contamination. CO2 vent sites are extensively studied in the context of OA and are often considered analogous to the oceans in the next few decades. The CO2 vent found at Levante Bay (Vulcano, NE Sicily, Italy also releases high concentrations of trace elements to its surrounding seawater, and is therefore a unique site to examine the effects of long-term exposure of nearby organisms to high pCO2 and trace element enrichment in situ. The sea anemone Anemonia viridis is prevalent next to the Vulcano vent and does not show signs of trace element poisoning/stress. The aim of our study was to compare A. viridis trace element profiles and compartmentalization between high pCO2 and control environments. Rather than examining whole anemone tissue, we analyzed two different body compartments—the pedal disc and the tentacles, and also examined the distribution of trace elements in the tentacles between the animal and the symbiotic algae. We found dramatic changes in trace element tissue concentrations between the high pCO2/high trace element and control sites, with strong accumulation of iron, lead, copper and cobalt, but decreased concentrations of cadmium, zinc and arsenic proximate to the vent. The pedal disc contained substantially more trace elements than the anemone’s tentacles, suggesting the pedal disc may serve as a detoxification/storage site for excess trace elements. Within the tentacles, the various trace elements displayed different partitioning patterns between animal tissue and algal symbionts. At both sites iron was found primarily in the algae, whereas cadmium, zinc and arsenic were primarily found in the animal tissue. Our data

  1. Fatty acid and phospholipid syntheses are prerequisites for the cell cycle of Symbiodinium and their endosymbiosis within sea anemones.

    Directory of Open Access Journals (Sweden)

    Li-Hsueh Wang

    Full Text Available Lipids are a source of metabolic energy, as well as essential components of cellular membranes. Although they have been shown to be key players in the regulation of cell proliferation in various eukaryotes, including microalgae, their role in the cell cycle of cnidarian-dinoflagellate (genus Symbiodinium endosymbioses remains to be elucidated. The present study examined the effects of a lipid synthesis inhibitor, cerulenin, on the cell cycle of both cultured Symbiodinium (clade B and those engaged in an endosymbiotic association with the sea anemone Aiptasia pulchella. In the former, cerulenin exposure was found to inhibit free fatty acid (FFA synthesis, as it does in other organisms. Additionally, while it also significantly inhibited the synthesis of phosphatidylethanolamine (PE, it did not affect the production of sterol ester (SE or phosphatidylcholine (PC. Interestingly, cerulenin also significantly retarded cell division by arresting the cell cycles at the G0/G1 phase. Cerulenin-treated Symbiodinium were found to be taken up by anemone hosts at a significantly depressed quantity in comparison with control Symbiodinium. Furthermore, the uptake of cerulenin-treated Symbiodinium in host tentacles occurred much more slowly than in untreated controls. These results indicate that FFA and PE may play critical roles in the recognition, proliferation, and ultimately the success of endosymbiosis with anemones.

  2. Visible-light-assisted SLCs template synthesis of sea anemone-like Pd/PANI nanocomposites with high electrocatalytic activity for methane oxidation in acidic medium

    Science.gov (United States)

    Tan, De-Xin; Wang, Yan-Li

    2018-03-01

    Sea anemone-like palladium (Pd)/polyaniline (PANI) nanocomposites were synthesized via visible-light-assisted swollen liquid crystals (SLCs) template method. The resulting samples were characterized by transmission electron microscopy (TEM), selected area electron diffraction (SAED), energy dispersive spectrometer (EDS), x-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), ultraviolet-visible (UV–vis) absorption spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, respectively. The electrocatalytic properties of Pd/PANI nanocomposites modified glass carbon electrode (GCE) for methane oxidation were investigated by cycle voltammetry (CV) and chronoamperometry. Those dispersed sea anemone-like Pd/PANI nanocomposites had an average diameter of 320 nm. The obtained Pd nanoparticles with an average diameter of about 45 nm were uniformly distributed in PANI matrix. Sea anemone-like Pd/PANI nanocomposites exhibited excellent electrocatalytic activity and stability for oxidation of methane (CH4).

  3. Uptake and Persistence of Homologous and Heterologous Zooxanthellae in the Temperate Sea Anemone Cereus pedunculatus (Pennant).

    Science.gov (United States)

    Davy, S K; Lucas, I A N; Turner, J R

    1997-04-01

    The uptake and persistence of symbiotic dinoflagellates (zooxanthellae) were measured in the temperate sea anemone Cereus pedunculatus (Pennant). Aposymbiotic specimens of C. pedunculatus were inoculated with zooxanthellae freshly isolated from a range of temperate and subtropical Anthozoa. Each inoculate consisted of zooxanthellae from a single host species and was either homologous (zooxanthellae from a host of the same species as the one being inoculated) or heterologous (from a host of a different species than the one being inoculated). The densities of zooxanthellae in host tissues were determined at regular intervals. C. pedunculatus took up homologous and heterologous zooxanthellae to similar degrees, except for zooxanthellae from the temperate Anthopleura ballii, which were taken up to a lesser extent. The densities of all zooxanthellae declined between 4 hours and 4 days after uptake, indicating that zooxanthellae were expelled, digested, or both during this period. The densities of all zooxanthellae increased between 2 and 8 weeks after inoculation, indicating zooxanthella growth. Over the entire 8-week period after uptake, densities of homologous zooxanthellae were always greater than those of heterologous zooxanthellae. Between 8 and 36 weeks after infection, densities of homologous zooxanthellae declined markedly and densities of some heterologous zooxanthellae increased further, resulting in homologous and heterologous zooxanthella densities being the same at 36 weeks. These densities were the same as those in naturally infected C. pedunculatus of similar size. The results suggest that zooxanthellae from a range of host species and environments can establish symbioses with C. pedunculatus and that, over long periods under laboratory conditions, heterologous zooxanthellae may populate C. pedunculatus to the same extent as homologous zooxanthellae.

  4. Functional polarity of the tentacle of the sea anemone Anemonia viridis: role in inorganic carbon acquisition.

    Science.gov (United States)

    Furla, P; Bénazet-Tambutté, S; Jaubert, J; Allemand, D

    1998-02-01

    The oral epithelial layers of anthozoans have a polarized morphology: photosynthetic endosymbionts live within endodermal cells facing the coelenteric cavity and are separated from the external seawater by the ectodermal layer and the mesoglea. To study if this morphology plays a role in the supply of inorganic carbon for symbiont photosynthesis, we measured the change in pH and the rate of OH- (H+) fluxes induced by each cell layer on a tentacle of the sea anemone Anemonia viridis. Light-induced pH increase of the medium bathing the endodermal layers led to the generation of a transepithelial pH gradient of approximately 0.8 pH units across the tentacle, whereas darkness induced acidification of this medium. The light-induced pH change was associated with an increase of total alkalinity. Only the endodermal layer was able to induce a net OH- secretion (H+ absorption). The light-induced OH- secretion by the endodermal cell layer was dependent on the presence of HCO3- in the compartment facing the ectoderm and was sensitive to several inhibitors of ion transport. [14C] HCO3- incorporation into photosynthates confirmed the ectodermal supply, the extent of which varied from 25 to > 90%, according to HCO3- availability. Our results suggest that the light-induced OH- secretion by the endodermal cell layer followed the polarized transport of HCO3- and its subsequent decarboxylation within the endodermal cell layer. This polarity may play a significant role both in inorganic carbon absorption and in the control of light-enhanced calcification in scleractinian corals.

  5. Differential distribution of lipids in epidermis, gastrodermis and hosted Symbiodinium in the sea anemone Anemonia viridis.

    Science.gov (United States)

    Revel, Johana; Massi, Lionel; Mehiri, Mohamed; Boutoute, Marc; Mayzaud, Patrick; Capron, Laure; Sabourault, Cécile

    2016-01-01

    Cnidarian-dinoflagellate symbiosis mainly relies on nutrient recycling, thus providing both partners with a competitive advantage in nutrient-poor waters. Essential processes related to lipid metabolism can be influenced by various factors, including hyperthermal stress. This can affect the lipid content and distribution in both partners, while contributing to symbiosis disruption and bleaching. In order to gain further insight into the role and distribution of lipids in the cnidarian metabolism, we investigated the lipid composition of the sea anemone Anemonia viridis and its photosynthetic dinoflagellate endosymbionts (Symbiodinium). We compared the lipid content and fatty acid profiles of the host cellular layers, non-symbiotic epidermal and symbiont-containing gastrodermal cells, and those of Symbiodinium, in a mass spectrometry-based assessment. Lipids were more concentrated in Symbiodinium cells, and the lipid class distribution was dominated by polar lipids in all tissues. The fatty acid distribution between host cell layers and Symbiodinium cells suggested potential lipid transfers between the partners. The lipid composition and distribution was modified during short-term hyperthermal stress, mainly in Symbiodinium cells and gastrodermis. Exposure to elevated temperature rapidly caused a decrease in polar lipid C18 unsaturated fatty acids and a strong and rapid decrease in the abundance of polar lipid fatty acids relative to sterols. These lipid indicators could therefore be used as sensitive biomarkers to assess the physiology of symbiotic cnidarians, especially the effect of thermal stress at the onset of cnidarian bleaching. Overall, the findings of this study provide some insight on key lipids that may regulate maintenance of the symbiotic interaction. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Comparative anatomy and histology of developmental and parasitic stages in the life cycle of the lined sea anemone Edwardsiella lineata.

    Science.gov (United States)

    Reitzel, Adam M; Daly, Marymegan; Sullivan, James C; Finnerty, John R

    2009-02-01

    The evolution of parasitism is often accompanied by profound changes to the developmental program. However, relatively few studies have directly examined the developmental evolution of parasitic species from free-living ancestors. The lined sea anemone Edwardsiella lineata is a relatively recently evolved parasite for which closely related free-living outgroups are known, including the starlet sea anemone Nematostella vectensis. The larva of E. lineata parasitizes the ctenophore Mnemiopsis leidyi, and, once embedded in its host, the anemone assumes a novel vermiform body plan. That we might begin to understand how the developmental program of this species has been transformed during the evolution of parasitism, we characterized the gross anatomy, histology, and cnidom of the parasitic stage, post-parasitic larval stage, and adult stage of the E. lineata life cycle. The distinct parasitic stage of the life cycle differs from the post-parasitic larva with respect to overall shape, external ciliation, cnida frequency, and tissue architecture. The parasitic stage and planula both contain holotrichs, a type of cnida not previously reported in Edwardsiidae. The internal morphology of the post-parasitic planula is extremely similar to the adult morphology, with a complete set of mesenterial tissue and musculature despite this stage having little external differentiation. Finally, we observed 2 previously undocumented aspects of asexual reproduction in E. lineata: (1) the parasitic stage undergoes transverse fission via physal pinching, the first report of asexual reproduction in a pre-adult stage in the Edwardsiidae; and (2) the juvenile polyp undergoes transverse fission via polarity reversal, the first time this form of fission has been reported in E. lineata.

  7. A Low Molecular Weight Protein from the Sea Anemone Anemonia viridis with an Anti-Angiogenic Activity

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    Erwann P. Loret

    2018-04-01

    Full Text Available Sea anemones are a remarkable source of active principles due to a decentralized venom system. New blood vessel growth or angiogenesis is a very promising target against cancer, but the few available antiangiogenic compounds have limited efficacy. In this study, a protein fraction, purified from tentacles of Anemonia viridis, was able to limit endothelial cells proliferation and angiogenesis at low concentration (14 nM. Protein sequences were determined with Edman degradation and mass spectrometry in source decay and revealed homologies with Blood Depressing Substance (BDS sea anemones. The presence of a two-turn alpha helix observed with circular dichroism and a trypsin activity inhibition suggested that the active principle could be a Kunitz-type inhibitor, which may interact with an integrin due to an Arginine Glycin Aspartate (RGD motif. Molecular modeling showed that this RGD motif was well exposed to solvent. This active principle could improve antiangiogenic therapy from existing antiangiogenic compounds binding on the Vascular Endothelial Growth Factor (VEGF.

  8. Evolutionary conserved mechanisms pervade structure and transcriptional modulation of allograft inflammatory factor-1 from sea anemone Anemonia viridis.

    Science.gov (United States)

    Cuttitta, Angela; Ragusa, Maria Antonietta; Costa, Salvatore; Bennici, Carmelo; Colombo, Paolo; Mazzola, Salvatore; Gianguzza, Fabrizio; Nicosia, Aldo

    2017-08-01

    Gene family encoding allograft inflammatory factor-1 (AIF-1) is well conserved among organisms; however, there is limited knowledge in lower organisms. In this study, the first AIF-1 homologue from cnidarians was identified and characterised in the sea anemone Anemonia viridis. The full-length cDNA of AvAIF-1 was of 913 bp with a 5' -untranslated region (UTR) of 148 bp, a 3'-UTR of 315 and an open reading frame (ORF) of 450 bp encoding a polypeptide with149 amino acid residues and predicted molecular weight of about 17 kDa. The predicted protein possesses evolutionary conserved EF hand Ca 2+ binding motifs, post-transcriptional modification sites and a 3D structure which can be superimposed with human members of AIF-1 family. The AvAIF-1 transcript was constitutively expressed in all tested tissues of unchallenged sea anemone, suggesting that AvAIF-1 could serve as a general protective factor under normal physiological conditions. Moreover, we profiled the transcriptional activation of AvAIF-1 after challenges with different abiotic/biotic stresses showing induction by warming conditions, heavy metals exposure and immune stimulation. Thus, mechanisms associated to inflammation and immune challenges up-regulated AvAIF-1 mRNA levels. Our results suggest its involvement in the inflammatory processes and immune response of A. viridis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Locomotory behaviour and functional morphology of Nematostella vectensis (Anthozoa: Actiniaria: Edwardsiidae): a contribution to a comparative study of burrowing behaviour in athenarian sea anemones

    NARCIS (Netherlands)

    Williams, R.B.

    2003-01-01

    The locomotory behaviour and functional morphology of English populations of a small (<2 cm long), burrowing athenarian sea anemone, Nematostella vectensis Stephenson, 1935 (= N. pellucida Crowell, 1946), which lives in soft mud in salt marshes and creeks, are described. Objectives were to ascertain

  10. Expression and mutagenesis of the sea anemone toxin Av2 reveals key amino acid residues important for activity on voltage-gated sodium channels.

    Science.gov (United States)

    Moran, Yehu; Cohen, Lior; Kahn, Roy; Karbat, Izhar; Gordon, Dalia; Gurevitz, Michael

    2006-07-25

    Type I sea anemone toxins are highly potent modulators of voltage-gated Na-channels (Na(v)s) and compete with the structurally dissimilar scorpion alpha-toxins on binding to receptor site-3. Although these features provide two structurally different probes for studying receptor site-3 and channel fast inactivation, the bioactive surface of sea anemone toxins has not been fully resolved. We established an efficient expression system for Av2 (known as ATX II), a highly insecticidal sea anemone toxin from Anemonia viridis (previously named A. sulcata), and mutagenized it throughout. Each toxin mutant was analyzed in toxicity and binding assays as well as by circular dichroism spectroscopy to discern the effects derived from structural perturbation from those related to bioactivity. Six residues were found to constitute the anti-insect bioactive surface of Av2 (Val-2, Leu-5, Asn-16, Leu-18, and Ile-41). Further analysis of nine Av2 mutants on the human heart channel Na(v)1.5 expressed in Xenopus oocytes indicated that the bioactive surfaces toward insects and mammals practically coincide but differ from the bioactive surface of a structurally similar sea anemone toxin, Anthopleurin B, from Anthopleura xanthogrammica. Hence, our results not only demonstrate clear differences in the bioactive surfaces of Av2 and scorpion alpha-toxins but also indicate that despite the general conservation in structure and importance of the Arg-14 loop and its flanking residues Gly-10 and Gly-20 for function, the surface of interaction between different sea anemone toxins and Na(v)s varies.

  11. Experimentally Induced Bleaching in the Sea Anemone Exaiptasia Supports Glucose as a Main Metabolite Associated with Its Symbiosis

    Directory of Open Access Journals (Sweden)

    Víctor Hugo Molina

    2017-01-01

    Full Text Available Our current understanding of carbon exchange between partners in the Symbiodinium-cnidarian symbioses is still limited, even though studies employing carbon isotopes have made us aware of the metabolic complexity of this exchange. We examined glycerol and glucose metabolism to better understand how photosynthates are exchanged between host and symbiont. The levels of these metabolites were compared between symbiotic and bleached Exaiptasia pallida anemones, assaying enzymes directly involved in their metabolism. We measured a significant decrease of glucose levels in bleached animals but a significant increase in glycerol and G3P pools, suggesting that bleached animals degrade lipids to compensate for the loss of symbionts and seem to rely on symbiotic glucose. The lower glycerol 3-phosphate dehydrogenase but higher glucose 6-phosphate dehydrogenase specific activities measured in bleached animals agree with a metabolic deficit mainly due to the loss of glucose from the ruptured symbiosis. These results corroborate previous observations on carbon translocation from symbiont to host in the sea anemone Exaiptasia, where glucose was proposed as a main translocated metabolite. To better understand photosynthate translocation and its regulation, additional research with other symbiotic cnidarians is needed, in particular, those with calcium carbonate skeletons.

  12. Broad-scale Population Genetics of the Host Sea Anemone, Heteractis magnifica

    KAUST Repository

    Emms, Madeleine

    2015-12-01

    Broad-scale population genetics can reveal population structure across an organism’s entire range, which can enable us to determine the most efficient population-wide management strategy depending on levels of connectivity. Genetic variation and differences in genetic diversity on small-scales have been reported in anemones, but nothing is known about their broad-scale population structure, including that of “host” anemone species, which are increasingly being targeted in the aquarium trade. In this study, microsatellite markers were used as a tool to determine the population structure of a sessile, host anemone species, Heteractis magnifica, across the Indo-Pacific region. In addition, two rDNA markers were used to identify Symbiodinium from the samples, and phylogenetic analyses were used to measure diversity and geographic distribution of Symbiodinium across the region. Significant population structure was identified in H. magnifica across the Indo-Pacific, with at least three genetic breaks, possibly the result of factors such as geographic distance, geographic isolation and environmental variation. Symbiodinium associations were also affected by environmental variation and supported the geographic isolation of some regions. These results suggests that management of H. magnifica must be implemented on a local scale, due to the lack of connectivity between clusters. This study also provides further evidence for the combined effects of geographic distance and environmental distance in explaining genetic variance.

  13. Partially Purified Extracts of Sea Anemone Anemonia viridis Affect the Growth and Viability of Selected Tumour Cell Lines

    Directory of Open Access Journals (Sweden)

    Matteo Bulati

    2016-01-01

    Full Text Available In the last few years, marine species have been investigated for the presence of natural products with anticancer activity. Using reversed phase chromatography, low molecular weight proteins were fractionated from the sea anemone Anemonia viridis. Four different fractions were evaluated for their cytotoxic activity by means of erythrocyte haemolysis test, MTS, and LDH assays. Finally, the antiproliferative activities of three of these fractions were studied on PC3, PLC/PRF/5, and A375 human cancer cell lines. Our analysis revealed that the four fractions showed different protein contents and diverse patterns of activity towards human PBMC and cancer cell lines. Interestingly, fractions III and IV exerted cytotoxic effects on human cells. Conversely, fractions I and II displayed very low toxic effects associated with antiproliferative activities on cancer cell lines.

  14. Partially Purified Extracts of Sea Anemone Anemonia viridis Affect the Growth and Viability of Selected Tumour Cell Lines.

    Science.gov (United States)

    Bulati, Matteo; Longo, Alessandra; Masullo, Tiziana; Vlah, Sara; Bennici, Carmelo; Bonura, Angela; Salamone, Monica; Tagliavia, Marcello; Nicosia, Aldo; Mazzola, Salvatore; Colombo, Paolo; Cuttitta, Angela

    2016-01-01

    In the last few years, marine species have been investigated for the presence of natural products with anticancer activity. Using reversed phase chromatography, low molecular weight proteins were fractionated from the sea anemone Anemonia viridis . Four different fractions were evaluated for their cytotoxic activity by means of erythrocyte haemolysis test, MTS, and LDH assays. Finally, the antiproliferative activities of three of these fractions were studied on PC3, PLC/PRF/5, and A375 human cancer cell lines. Our analysis revealed that the four fractions showed different protein contents and diverse patterns of activity towards human PBMC and cancer cell lines. Interestingly, fractions III and IV exerted cytotoxic effects on human cells. Conversely, fractions I and II displayed very low toxic effects associated with antiproliferative activities on cancer cell lines.

  15. In silico assessment of interaction of sea anemone toxin APETx2 and acid sensing ion channel 3

    International Nuclear Information System (INIS)

    Rahman, Taufiq; Smith, Ewan St. John

    2014-01-01

    Highlights: • We have made a reasonable model of rat ASIC3 using published structure of chicken ASIC1. • We have docked sea anemone toxin APETx2 on the model. • We have identified two putative sites for toxin binding. • We have argued for plausibility one site over the other. • We have identified the residues that are likely to be critical for APETx2–ASIC3 interaction. - Abstract: Acid sensing ion channels (ASICs) are proton-gated cation channels that are expressed throughout the nervous system and have been implicated in mediating sensory perception of noxious stimuli. Amongst the six ASIC isoforms, ASIC1a, 1b, 2a and 3 form proton-gated homomers, which differ in their activation and inactivation kinetics, expression profiles and pharmacological modulation; protons do not gate ASIC2b and ASIC4. As with many other ion channels, structure-function studies of ASICs have been greatly aided by the discovery of some toxins that act in isoform-specific ways. ASIC3 is predominantly expressed by sensory neurons of the peripheral nervous system where it acts to detect acid as a noxious stimulus and thus plays an important role in nociception. ASIC3 is the only ASIC subunit that is inhibited by the sea anemone (Anthopleura elegantissima)-derived toxin APETx2. However, the molecular mechanism by which APETx2 interacts with ASIC3 remains largely unknown. In this study, we made a homology model of ASIC3 and used extensive protein–protein docking to predict for the first time, the probable sites of APETx2 interaction on ASIC3. Additionally, using computational alanine scanning, we also suggest the ‘hot-spots’ that are likely to be critical for ASIC3–APETx2 interaction

  16. In silico assessment of interaction of sea anemone toxin APETx2 and acid sensing ion channel 3

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Taufiq, E-mail: mtur2@cam.ac.uk; Smith, Ewan St. John

    2014-07-18

    Highlights: • We have made a reasonable model of rat ASIC3 using published structure of chicken ASIC1. • We have docked sea anemone toxin APETx2 on the model. • We have identified two putative sites for toxin binding. • We have argued for plausibility one site over the other. • We have identified the residues that are likely to be critical for APETx2–ASIC3 interaction. - Abstract: Acid sensing ion channels (ASICs) are proton-gated cation channels that are expressed throughout the nervous system and have been implicated in mediating sensory perception of noxious stimuli. Amongst the six ASIC isoforms, ASIC1a, 1b, 2a and 3 form proton-gated homomers, which differ in their activation and inactivation kinetics, expression profiles and pharmacological modulation; protons do not gate ASIC2b and ASIC4. As with many other ion channels, structure-function studies of ASICs have been greatly aided by the discovery of some toxins that act in isoform-specific ways. ASIC3 is predominantly expressed by sensory neurons of the peripheral nervous system where it acts to detect acid as a noxious stimulus and thus plays an important role in nociception. ASIC3 is the only ASIC subunit that is inhibited by the sea anemone (Anthopleura elegantissima)-derived toxin APETx2. However, the molecular mechanism by which APETx2 interacts with ASIC3 remains largely unknown. In this study, we made a homology model of ASIC3 and used extensive protein–protein docking to predict for the first time, the probable sites of APETx2 interaction on ASIC3. Additionally, using computational alanine scanning, we also suggest the ‘hot-spots’ that are likely to be critical for ASIC3–APETx2 interaction.

  17. Ocurrence of the sea anemone Telmatactis panamensis (Verrill, 1869 (Cnidaria: Anthozoa: Actiniaria at Isla del Coco National Park, Costa Rica

    Directory of Open Access Journals (Sweden)

    Fabián H. Acuña

    2012-11-01

    Full Text Available The sea anemone fauna of Isla del Coco National Park (also known as Cocos Island Nacional Park, Pacific Costa Rica is poorly known. In the present work we report the first occurrence of the species Telmatactis panamensis. Individuals of this sea anemone (n=24 were collected at Chatham Bay intertidal and at 15m depth in Punta Ulloa, in both cases attached to rocks; during the expedition UCR-UNA-COCO-I in April 2010. We provide photographs of live individuals, external anatomy and an inventory of cnidae of the studied specimens. Possibly this species is extended to greater depth as observed by other authors in the Galápagos Islands.La fauna de anémonas de mar es prácticamente desconocida para el Parque Nacional Isla del Coco (Costa Rica. En el presente trabajo se reporta por primera vez la presencia de la especie Telmatactis panamensis. Individuos de esta anémona de mar fueron colectados en el intermareal de Bahía Chatham y a 15m de profundidad en Punta Ulloa, en ambos casos adheridas a rocas; durante la expedición UCR-UNA-COCO-I en Abril de 2010. Se proveen fotografías de ejemplares vivos, datos de su anatomía externa y un inventario del cnidae de los especímenes estudiados. Posiblemente esta especie se extienda a mayor profundidad, tal como fue observado por otros autores para ejemplares de las Islas Galápagos.

  18. The 60-kDa heat shock protein (HSP60) of the sea anemone Anemonia viridis: a potential early warning system for environmental changes.

    Science.gov (United States)

    Choresh, O; Ron, E; Loya, Y

    2001-09-01

    Expression of heat shock proteins (HSPs) is often correlated with adaptation to environmental stress. We examined the role of HSP60 (60 kDa) in acclimatization to thermal stress in the sea anemone Anemonia viridis. Using monoclonal antibodies, we identified HSP60 in sea anemones for the first time, and showed that its expression varied with changes in seawater temperature (SWT). Anemonia viridis displayed high levels of HSP60 when extreme temperatures prevailed in stressful habitats such as tidal pools. Specimens sampled from different temperature layers in the same tidal pool differed in their levels of HSP60. Specimens from subtidal zones exhibited a seasonal pattern of expression of HSP60, according to the seasonal SWT. The level of HSP60 was significantly higher in the summer (SWT, 31 degrees C) than in other seasons throughout the year. This study suggests the use of HSP60 expression as a tool for stress detection in marine invertebrates.

  19. PhcrTx2, a New Crab-Paralyzing Peptide Toxin from the Sea Anemone Phymanthus crucifer

    Science.gov (United States)

    Garateix, Anoland; Salceda, Emilio; Zaharenko, André Junqueira; Pons, Tirso; Santos, Yúlica; Arreguín, Roberto; Ständker, Ludger; Forssmann, Wolf-Georg; Tytgat, Jan; Vega, Rosario

    2018-01-01

    Sea anemones produce proteinaceous toxins for predation and defense, including peptide toxins that act on a large variety of ion channels of pharmacological and biomedical interest. Phymanthus crucifer is commonly found in the Caribbean Sea; however, the chemical structure and biological activity of its toxins remain unknown, with the exception of PhcrTx1, an acid-sensing ion channel (ASIC) inhibitor. Therefore, in the present work, we focused on the isolation and characterization of new P. crucifer toxins by chromatographic fractionation, followed by a toxicity screening on crabs, an evaluation of ion channels, and sequence analysis. Five groups of toxic chromatographic fractions were found, and a new paralyzing toxin was purified and named PhcrTx2. The toxin inhibited glutamate-gated currents in snail neurons (maximum inhibition of 35%, IC50 4.7 µM), and displayed little or no influence on voltage-sensitive sodium/potassium channels in snail and rat dorsal root ganglion (DRG) neurons, nor on a variety of cloned voltage-gated ion channels. The toxin sequence was fully elucidated by Edman degradation. PhcrTx2 is a new β-defensin-fold peptide that shares a sequence similarity to type 3 potassium channels toxins. However, its low activity on the evaluated ion channels suggests that its molecular target remains unknown. PhcrTx2 is the first known paralyzing toxin in the family Phymanthidae. PMID:29414882

  20. PhcrTx2, a New Crab-Paralyzing Peptide Toxin from the Sea Anemone Phymanthus crucifer

    Directory of Open Access Journals (Sweden)

    Armando Alexei Rodríguez

    2018-02-01

    Full Text Available Sea anemones produce proteinaceous toxins for predation and defense, including peptide toxins that act on a large variety of ion channels of pharmacological and biomedical interest. Phymanthus crucifer is commonly found in the Caribbean Sea; however, the chemical structure and biological activity of its toxins remain unknown, with the exception of PhcrTx1, an acid-sensing ion channel (ASIC inhibitor. Therefore, in the present work, we focused on the isolation and characterization of new P. crucifer toxins by chromatographic fractionation, followed by a toxicity screening on crabs, an evaluation of ion channels, and sequence analysis. Five groups of toxic chromatographic fractions were found, and a new paralyzing toxin was purified and named PhcrTx2. The toxin inhibited glutamate-gated currents in snail neurons (maximum inhibition of 35%, IC50 4.7 µM, and displayed little or no influence on voltage-sensitive sodium/potassium channels in snail and rat dorsal root ganglion (DRG neurons, nor on a variety of cloned voltage-gated ion channels. The toxin sequence was fully elucidated by Edman degradation. PhcrTx2 is a new β-defensin-fold peptide that shares a sequence similarity to type 3 potassium channels toxins. However, its low activity on the evaluated ion channels suggests that its molecular target remains unknown. PhcrTx2 is the first known paralyzing toxin in the family Phymanthidae.

  1. Comparative analysis and culturing of the microbial community of Aiptasia pallida, A Sea Anemone Model for Coral Biology

    KAUST Repository

    Binsarhan, Mohammad

    2016-01-01

    Recent works has highlighted the contribution of microbes to animal function. In this regard, the microbial community associated with corals has become a growing field of research in order to understand how microbes contribute to the host organisms’ response to environmental changes. It has been shown that microbes associated with corals have important functions in the coral holobiont such as immunity and nutrient assimilation. However, corals are notoriously difficult to work with. To this end, the sea anemone Aiptasia is becoming a model organism for coral symbiosis. Given the importance of host-­microbiome interactions, the topic of this thesis is to assess microbial structure of Aiptasia, culture prominent bacterial members, and compare bacterial community structure to corals. Different molecular methods have been applied using 16S rRNA bacterial gene fragments to characterize the microbial composition of Aiptasia. 16S rRNA gene sequence derived from cultured bacteria was compared to 16S rRNA gene sequences retrieved from native Red Sea Aiptasia. Inter-­individual as well as methodological differences were found to account for variance in microbiome composition. However, all approaches showed a highly abundant microbial taxon belonging to the genus Alteromonas in all samples. The Alteromonas species was successfully isolated for further research targeting microbiome selection mechanisms in Aiptasia. Future investigations by using different molecular tools will help to define the functions and relationship between the Aiptasia and its complex microbiome.

  2. Quantification of dimethyl sulfide (DMS production in the sea anemone Aiptasia sp. to simulate the sea-to-air flux from coral reefs

    Directory of Open Access Journals (Sweden)

    F. Franchini

    2017-12-01

    Full Text Available The production of dimethyl sulfide (DMS is poorly quantified in tropical reef environments but forms an essential process that couples marine and terrestrial sulfur cycles and affects climate. Here we quantified net aqueous DMS production and the concentration of its cellular precursor dimethylsulfoniopropionate (DMSP in the sea anemone Aiptasia sp., a model organism to study coral-related processes. Bleached anemones did not show net DMS production whereas symbiotic anemones produced DMS concentrations (mean ± standard error of 160.7 ± 44.22 nmol g−1 dry weight (DW after 48 h incubation. Symbiotic and bleached individuals showed DMSP concentrations of 32.7 ± 6.00 and 0.6 ± 0.19 µmol g−1 DW, respectively. We applied these findings to a Monte Carlo simulation to demonstrate that net aqueous DMS production accounts for only 20 % of gross aqueous DMS production. Monte Carlo-based estimations of sea-to-air fluxes of gaseous DMS showed that reefs may release 0.1 to 26.3 µmol DMS m−2 coral surface area (CSA d−1 into the atmosphere with 40 % probability for rates between 0.5 and 1.5 µmol m−2 CSA d−1. These predictions were in agreement with directly quantified fluxes in previous studies. Conversion to a flux normalised to sea surface area (SSA (range 0.1 to 17.4, with the highest probability for 0.3 to 1.0 µmol DMS m−2 SSA d−1 suggests that coral reefs emit gaseous DMS at lower rates than the average global oceanic DMS flux of 4.6 µmol m−2 SSA d−1 (19.6 Tg sulfur per year. The large difference between simulated gross and quantified net aqueous DMS production in corals suggests that the current and future potential for its production in tropical reefs is critically governed by DMS consumption processes. Hence, more research is required to assess the sensitivity of DMS-consumption pathways to ongoing environmental change in order to address the impact of predicted

  3. Quantification of dimethyl sulfide (DMS) production in the sea anemone Aiptasia sp. to simulate the sea-to-air flux from coral reefs

    Science.gov (United States)

    Franchini, Filippo; Steinke, Michael

    2017-12-01

    The production of dimethyl sulfide (DMS) is poorly quantified in tropical reef environments but forms an essential process that couples marine and terrestrial sulfur cycles and affects climate. Here we quantified net aqueous DMS production and the concentration of its cellular precursor dimethylsulfoniopropionate (DMSP) in the sea anemone Aiptasia sp., a model organism to study coral-related processes. Bleached anemones did not show net DMS production whereas symbiotic anemones produced DMS concentrations (mean ± standard error) of 160.7 ± 44.22 nmol g-1 dry weight (DW) after 48 h incubation. Symbiotic and bleached individuals showed DMSP concentrations of 32.7 ± 6.00 and 0.6 ± 0.19 µmol g-1 DW, respectively. We applied these findings to a Monte Carlo simulation to demonstrate that net aqueous DMS production accounts for only 20 % of gross aqueous DMS production. Monte Carlo-based estimations of sea-to-air fluxes of gaseous DMS showed that reefs may release 0.1 to 26.3 µmol DMS m-2 coral surface area (CSA) d-1 into the atmosphere with 40 % probability for rates between 0.5 and 1.5 µmol m-2 CSA d-1. These predictions were in agreement with directly quantified fluxes in previous studies. Conversion to a flux normalised to sea surface area (SSA) (range 0.1 to 17.4, with the highest probability for 0.3 to 1.0 µmol DMS m-2 SSA d-1) suggests that coral reefs emit gaseous DMS at lower rates than the average global oceanic DMS flux of 4.6 µmol m-2 SSA d-1 (19.6 Tg sulfur per year). The large difference between simulated gross and quantified net aqueous DMS production in corals suggests that the current and future potential for its production in tropical reefs is critically governed by DMS consumption processes. Hence, more research is required to assess the sensitivity of DMS-consumption pathways to ongoing environmental change in order to address the impact of predicted degradation of coral reefs on DMS production in tropical coastal ecosystems and its impact on

  4. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.

    Science.gov (United States)

    Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

    2014-11-11

    For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer.

  5. Acid-sensing ion channel (ASIC) structure and function: Insights from spider, snake and sea anemone venoms.

    Science.gov (United States)

    Cristofori-Armstrong, Ben; Rash, Lachlan D

    2017-12-01

    Acid-sensing ion channels (ASICs) are proton-activated cation channels that are expressed in a variety of neuronal and non-neuronal tissues. As proton-gated channels, they have been implicated in many pathophysiological conditions where pH is perturbed. Venom derived compounds represent the most potent and selective modulators of ASICs described to date, and thus have been invaluable as pharmacological tools to study ASIC structure, function, and biological roles. There are now ten ASIC modulators described from animal venoms, with those from snakes and spiders favouring ASIC1, while the sea anemones preferentially target ASIC3. Some modulators, such as the prototypical ASIC1 modulator PcTx1 have been studied in great detail, while some of the newer members of the club remain largely unstudied. Here we review the current state of knowledge on venom derived ASIC modulators, with a particular focus on their molecular interaction with ASICs, what they have taught us about channel structure, and what they might still reveal about ASIC function and pathophysiological roles. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.' Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Breaking up and getting together: evolution of symbiosis and cloning by fission in sea anemones (Genus Anthopleura).

    Science.gov (United States)

    Geller, J B; Walton, E D

    2001-09-01

    Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura, a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.

  7. The transcriptomic response to thermal stress is immediate, transient and potentiated by ultraviolet radiation in the sea anemone Anemonia viridis.

    Science.gov (United States)

    Moya, A; Ganot, P; Furla, P; Sabourault, C

    2012-03-01

    Among the environmental threats to coral reef health, temperature and ultraviolet increases have been proposed as major agents, although the relative contribution of each in the cnidarian/zooxanthellae symbiosis breakdown has been poorly addressed. We have investigated the transcriptomic response to thermal stress, with and without ultraviolet radiation (UVR), in the symbiotic sea anemone Anemonia viridis. Using the Oligo2K A. viridis microarray, dedicated to genes potentially involved in the symbiosis interaction, we monitored the gene expression profiles after 1, 2 and 5 days of stresses that further lead to massive losses of zooxanthellae. Each stress showed a specific gene expression profile with very little overlap. We showed that the major response to thermal stress is immediate (24 h) but returns to the baseline gene expression profile after 2 days. UVR alone has little effect but potentiates thermal stress, as a second response at 5 days was observed when the two stresses were coupled. Several pathways were highlighted, such as mesoglea loosening, cell death and calcium homeostasis and described in more details. Finally, we showed that the dermatopontin gene family, potentially involved in collagen fibrillogenesis, issued from actinarian-specific duplication events, with one member preferentially expressed in the gastroderm and specifically responding to stress. Anemonia viridis EST sequences have been deposited into GenBank dbEST ([GenBank:FK719875–FK759813]. © 2012 Blackwell Publishing Ltd.

  8. Changes in microbial communities associated with the sea anemone Anemonia viridis in a natural pH gradient.

    Science.gov (United States)

    Meron, Dalit; Buia, Maria-Cristina; Fine, Maoz; Banin, Ehud

    2013-02-01

    Ocean acidification, resulting from rising atmospheric carbon dioxide concentrations, is a pervasive stressor that can affect many marine organisms and their symbionts. Studies which examine the host physiology and microbial communities have shown a variety of responses to the ocean acidification process. Recently, several studies were conducted based on field experiments, which take place in natural CO(2) vents, exposing the host to natural environmental conditions of varying pH. This study examines the sea anemone Anemonia viridis which is found naturally along the pH gradient in Ischia, Italy, with an aim to characterize whether exposure to pH impacts the holobiont. The physiological parameters of A. viridis (Symbiodinium density, protein, and chlorophyll a+c concentration) and its microbial community were monitored. Although reduction in pH was seen to have had an impact on composition and diversity of associated microbial communities, no significant changes were observed in A. viridis physiology, and no microbial stress indicators (i.e., pathogens, antibacterial activity, etc.) were detected. In light of these results, it appears that elevated CO(2) does not have a negative influence on A. viridis that live naturally in the site. This suggests that natural long-term exposure and dynamic diverse microbial communities may contribute to the acclimation process of the host in a changing pH environment.

  9. Primary structure of the precursor for the sea anemone neuropeptide Antho-RFamide (less than Glu-Gly-Arg-Phe-NH2)

    DEFF Research Database (Denmark)

    Darmer, D; Schmutzler, C; Diekhoff, D

    1991-01-01

    Neuropeptides containing the carboxylterminal sequence Arg-Phe-NH2 are found throughout the animal kingdom and are important substances mediating neuronal communication. Here, we have cloned the cDNA coding for the precursor protein of the sea anemone neuropeptide (Antho-RFamide) less than Glu...... harbors four other putative neuropeptides that are much less related to Antho-RFamide. This report shows that the biosynthetic machinery for neuropeptides in coelenterates, the lowest animal group having a nervous system, is already very efficient and similar to that of higher invertebrates...

  10. Molecular cloning of a preprohormone from sea anemones containing numerous copies of a metamorphosis-inducing neuropeptide: a likely role for dipeptidyl aminopeptidase in neuropeptide precursor processing

    DEFF Research Database (Denmark)

    Leviev, I; Grimmelikhuijzen, C J

    1995-01-01

    a polyp, a medusa, and a planula larva stage. Recently, a neuropeptide, metamorphosis in a hydroid planula larva to become a hydropolyp [Leitz, T., Morand, K. & Mann, M. (1994) Dev. Biol. 163, 440-446]. Here, we have cloned...... the precursor protein for this metamorphosis-inducing neuropeptide from sea anemones. The precursor protein is 514-amino acid residues long and contains 10 copies of the immature, authentic neuropeptide (Gln-Gln-Pro-Gly-Leu-Trp-Gly). All neuropeptide copies are preceded by Xaa-Pro or Xaa-Ala sequences...

  11. Molecular cloning of a novel, putative G protein-coupled receptor from sea anemones structurally related to members of the FSH, TSH, LH/CG receptor family from mammals

    DEFF Research Database (Denmark)

    Nothacker, H P; Grimmelikhuijzen, C J

    1993-01-01

    hormone (FSH, TSH, LH/CG) receptor family from mammals, including a very large, extracellular N terminus (18-25% sequence identity) and a 7 transmembrane region (44-48% sequence identity). As with the mammalian glycoprotein hormone receptor genes, the sea anemone receptor gene yields transcripts which can...... be alternatively spliced, thereby yielding a shortened receptor variant only containing the large extracellular (soluble) N terminus. All this is strong evidence that the putative glycoprotein hormone receptor from sea anemones is evolutionarily related to those from mammals. This is the first report showing...

  12. Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis

    Directory of Open Access Journals (Sweden)

    Botman Daniel

    2012-10-01

    Full Text Available Abstract Background Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly Drosophila melanogaster is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom. In the sea anemone Nematostella vectensis the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans. Nematostella is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques. Findings Our new quantification method produces standardized gene expression profiles from raw or annotated Nematostella in situ hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation. Conclusions We created a standard format for gene expression data, which enables quantitative analysis of in situ hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar Nematostella morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.

  13. Notes on the genus Amphiprion Bloch & Schneider, 1801 (Teleostei: Pomacentridae) and its host sea anemones in the Seychelles

    NARCIS (Netherlands)

    Hartog, den J.C.

    1997-01-01

    The genus Amphiprion Bloch & Schneider, 1801, is represented in the Seychelles by two species, A. akallopisos Bleeker, 1853, and the endemic A. fuscocaudatus Allen, 1972. Throughout its distributional range Amphiprion akallopisos has exclusively been recorded to associate with the clownfish anemones

  14. An assemblage of the host anemone Heteractis magnifica in the northern Red Sea, and distribution of the resident anemonefish

    DEFF Research Database (Denmark)

    Tychsen, Anders; Brolund, T. M.; Nielsen, L. E.

    2004-01-01

    The Heteractis magnifica assemblage at the tip of the Sinai Peninsula was examined. The actinian size, location, and number of resident anemonefishes were recorded. The anemones were found at depths down to approximately 40 m and the sizes of clustering H. magnifica and clusters were positively c...

  15. On a case of commensalism of a Fish (Amphiprion intermedius Schleg.) and a large Sea-Anemone (Discosoma-spec.)

    NARCIS (Netherlands)

    Horst, R.

    1903-01-01

    Among an interesting collection of Invertebrate animals from Sabang-bay (Poeloe Weh) brought together by Mr. G. A. J. van der Sande, Surgeon in the Dutch naval service, and presented by him to the Leyden Museum, there is a large Anemone, belonging to the genus Discosoma. About this specimen Mr. van

  16. Menthol-induced bleaching rapidly and effectively provides experimental aposymbiotic sea anemones (Aiptasia sp.) for symbiosis investigations.

    Science.gov (United States)

    Matthews, Jennifer L; Sproles, Ashley E; Oakley, Clinton A; Grossman, Arthur R; Weis, Virginia M; Davy, Simon K

    2016-02-01

    Experimental manipulation of the symbiosis between cnidarians and photosynthetic dinoflagellates (Symbiodinium spp.) is crucial to advancing the understanding of the cellular mechanisms involved in host-symbiont interactions, and overall coral reef ecology. The anemone Aiptasia sp. is a model for cnidarian-dinoflagellate symbiosis, and notably it can be rendered aposymbiotic (i.e. dinoflagellate-free) and re-infected with a range of Symbiodinium types. Various methods exist for generating aposymbiotic hosts; however, they can be hugely time consuming and not wholly effective. Here, we optimise a method using menthol for production of aposymbiotic Aiptasia. The menthol treatment produced aposymbiotic hosts within just 4 weeks (97-100% symbiont loss), and the condition was maintained long after treatment when anemones were held under a standard light:dark cycle. The ability of Aiptasia to form a stable symbiosis appeared to be unaffected by menthol exposure, as demonstrated by successful re-establishment of the symbiosis when anemones were experimentally re-infected. Furthermore, there was no significant impact on photosynthetic or respiratory performance of re-infected anemones. © 2016. Published by The Company of Biologists Ltd.

  17. Redescription of Oulactis concinnata (Drayton in Dana, 1846) (Cnidaria: Anthozoa: Actiniidae), an actiniid sea anemone from Chile and Perú with special fighting tentacles; with a preliminary revision of the genera with a “frond-like” marginal ruff

    NARCIS (Netherlands)

    Häussermann, V.

    2003-01-01

    Two species of sea anemones with a conspicuous marginal ruff of frond-like structures encompassing the tentacular crown occur on the Chilean coast. Oulactis concinnata (= Isoulactis chilensis) (Drayton in Dana, 1846) is re-described in detail and further information is provided for Oulactis

  18. Development of Highly Selective Kv1.3-Blocking Peptides Based on the Sea Anemone Peptide ShK

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    Michael W. Pennington

    2015-01-01

    Full Text Available ShK, from the sea anemone Stichodactyla helianthus, is a 35-residue disulfide-rich peptide that blocks the voltage-gated potassium channel Kv1.3 at ca. 10 pM and the related channel Kv1.1 at ca. 16 pM. We developed an analog of this peptide, ShK-186, which is currently in Phase 1b-2a clinical trials for the treatment of autoimmune diseases such as multiple sclerosis and rheumatoid arthritis. While ShK-186 displays a >100-fold improvement in selectivity for Kv1.3 over Kv1.1 compared with ShK, there is considerable interest in developing peptides with an even greater selectivity ratio. In this report, we describe several variants of ShK that incorporate p-phophono-phenylalanine at the N-terminus coupled with internal substitutions at Gln16 and Met21. In addition, we also explored the combinatorial effects of these internal substitutions with an alanine extension at the C-terminus. Their selectivity was determined by patch-clamp electrophysiology on Kv1.3 and Kv1.1 channels stably expressed in mouse fibroblasts. The peptides with an alanine extension blocked Kv1.3 at low pM concentrations and exhibited up to 2250-fold selectivity for Kv1.3 over Kv1.1. Analogs that incorporates p-phosphono-phenylalanine at the N-terminus blocked Kv1.3 with IC50s in the low pM range and did not affect Kv1.1 at concentrations up to 100 nM, displaying a selectivity enhancement of >10,000-fold for Kv1.3 over Kv1.1. Other potentially important Kv channels such as Kv1.4 and Kv1.6 were only partially blocked at 100 nM concentrations of each of the ShK analogs.

  19. The role of complement in cnidarian-dinoflagellate symbiosis and immune challenge in the sea anemone Aiptasia pallida

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    Angela ePoole

    2016-04-01

    Full Text Available The complement system is an innate immune pathway that in vertebrates, is responsible for initial recognition and ultimately phagocytosis and destruction of microbes. Several complement molecules including C3, Factor B, and mannose binding lectin associated serine proteases (MASP have been characterized in invertebrates and while most studies have focused on their conserved role in defense against pathogens, little is known about their role in managing beneficial microbes. The purpose of this study was to (1 characterize complement pathway genes in the symbiotic sea anemone A. pallida, (2 investigate the evolution of complement genes in invertebrates, and (3 examine the potential dual role of complement genes Factor B and MASP in the onset and maintenance of cnidarian-dinoflagellate symbiosis and immune challenge using qPCR based studies. The results demonstrate that A. pallida has multiple Factor B genes (Ap_Bf-1, Ap_Bf-2a, and Ap_Bf-2b and one MASP gene (Ap_MASP. Phylogenetic analysis indicates that the evolutionary history of complement genes is complex, and there have been many gene duplications or gene loss events, even within members of the same phylum. Gene expression analyses revealed a potential role for complement in both onset and maintenance of cnidarian-dinoflagellate symbiosis and immune challenge. Specifically, Ap_Bf-1 and Ap_MASP are significantly upregulated in the light at the onset of symbiosis and in response to challenge with the pathogen Serratia marcescens suggesting that they play a role in the initial recognition of both beneficial and harmful microbes. Ap_Bf-2b in contrast was generally downregulated during the onset and maintenance of symbiosis and in response to challenge with S. marcescens. Therefore the exact role of Ap_Bf-2b in response to microbes remains unclear, but the results suggests that the presence of microbes leads to repressed expression. Together these results indicate functional divergence between Ap

  20. Different Principles of ADP-Ribose-Mediated Activation and Opposite Roles of the NUDT9 Homology Domain in the TRPM2 Orthologs of Man and Sea Anemone

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    Frank Kühn

    2017-10-01

    Full Text Available A decisive element in the human cation channel TRPM2 is a region in its cytosolic C-terminus named NUDT9H because of its homology to the NUDT9 enzyme, a pyrophosphatase degrading ADP-ribose (ADPR. In hTRPM2, however, the NUDT9H domain has lost its enzymatic activity but serves as a binding domain for ADPR. As consequence of binding, gating of the channel is initiated. Since ADPR is produced after oxidative DNA damage, hTRPM2 mediates Ca2+ influx in response to oxidative stress which may lead to cell death. In the genome of the sea anemone Nematostella vectensis (nv, a preferred model organism for the evolution of key bilaterian features, a TRPM2 ortholog has been identified that contains a NUDT9H domain as well. Heterologous expression of nvTRPM2 in HEK-293 cells reveals a cation channel with many close similarities to the human counterpart. Most notably, nvTRPM2 is activated by ADPR, and Ca2+ is a co-agonist. However, the intramolecular mechanisms of ADPR gating as well as the role of NUDT9H are strikingly different in the two species. Whereas already subtle changes of NUDT9H abolish ADPR gating in hTRPM2, the region can be completely removed from nvTRPM2 without loss of responses to ADPR. An alternative ADPR binding site seems to be present but has not yet been characterized. The ADP-ribose pyrophosphatase (ADPRase function of nvNUDT9H has been preserved but can be abolished by numerous genetic manipulations. All these manipulations create channels that are sensitive to hydrogen peroxide which fails to induce channel activity in wild-type nvTRPM2. Therefore, the function of NUDT9H in nvTRPM2 is the degradation of ADPR, thereby reducing agonist concentration in the presence of oxidative stress. Thus, the two TRPM2 orthologs have evolved divergently but nevertheless gained analogous functional properties, i.e., gating by ADPR with Ca2+ as co-factor. Opposite roles are played by the respective NUDT9H domains, either binding of ADPR and mediating

  1. Characterization of glutathione peroxidase diversity in the symbiotic sea anemone Anemonia viridis.

    Science.gov (United States)

    Pey, Alexis; Zamoum, Thamilla; Christen, Richard; Merle, Pierre-Laurent; Furla, Paola

    2017-01-01

    Cnidarians living in symbiosis with photosynthetic dinoflagellates (commonly named zooxanthellae) are exposed to high concentrations of reactive oxygen species (ROS) upon illumination. To quench ROS production, both the cnidarian host and zooxanthellae express a full suite of antioxidant enzymes. Studying antioxidative balance is therefore crucial to understanding how symbiotic cnidarians cope with ROS production. We characterized glutathione peroxidases (GPx) in the symbiotic cnidarian Anemonia viridis by analysis of their isoform diversity, their activity distribution in the three cellular compartments (ectoderm, endoderm and zooxanthellae) and their involvement in the response to thermal stress. We identified a GPx repertoire through a phylogenetic analysis showing 7 GPx transcripts belonging to the A. viridis host and 4 GPx transcripts strongly related to Symbiodinium sp. The biochemical approach, used for the first time with a cnidarian species, allowed the identification of GPx activity in the three cellular compartments and in the animal mitochondrial fraction, and revealed a high GPx electrophoretic diversity. The symbiotic lifestyle of zooxanthellae requires more GPx activity and diversity than that of free-living species. Heat stress induced no modification of GPx activities. We highlight a high GPx diversity in A. viridis tissues by genomic and biochemical approaches. GPx activities represent an overall constitutive enzymatic pattern inherent to symbiotic lifestyle adaptation. This work allows the characterization of the GPx family in a symbiotic cnidarian and establishes a foundation for future studies of GPx in symbiotic cnidarians. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  2. Biophysical and biochemical strategies to understand membrane binding and pore formation by sticholysins, pore-forming proteins from a sea anemone.

    Science.gov (United States)

    Alvarez, Carlos; Ros, Uris; Valle, Aisel; Pedrera, Lohans; Soto, Carmen; Hervis, Yadira P; Cabezas, Sheila; Valiente, Pedro A; Pazos, Fabiola; Lanio, Maria E

    2017-10-01

    Actinoporins constitute a unique class of pore-forming toxins found in sea anemones that are able to bind and oligomerize in membranes, leading to cell swelling, impairment of ionic gradients and, eventually, to cell death. In this review we summarize the knowledge generated from the combination of biochemical and biophysical approaches to the study of sticholysins I and II (Sts, StI/II), two actinoporins largely characterized by the Center of Protein Studies at the University of Havana during the last 20 years. These approaches include strategies for understanding the toxin structure-function relationship, the protein-membrane association process leading to pore formation and the interaction of toxin with cells. The rational combination of experimental and theoretical tools have allowed unraveling, at least partially, of the complex mechanisms involved in toxin-membrane interaction and of the molecular pathways triggered upon this interaction. The study of actinoporins is important not only to gain an understanding of their biological roles in anemone venom but also to investigate basic molecular mechanisms of protein insertion into membranes, protein-lipid interactions and the modulation of protein conformation by lipid binding. A deeper knowledge of the basic molecular mechanisms involved in Sts-cell interaction, as described in this review, will support the current investigations conducted by our group which focus on the design of immunotoxins against tumor cells and antigen-releasing systems to cell cytosol as Sts-based vaccine platforms.

  3. The sea anemone Bunodosoma caissarum toxin BcIII modulates the sodium current kinetics of rat dorsal root ganglia neurons and is displaced in a voltage-dependent manner.

    Science.gov (United States)

    Salceda, Emilio; López, Omar; Zaharenko, André J; Garateix, Anoland; Soto, Enrique

    2010-03-01

    Sea anemone toxins bind to site 3 of the sodium channels, which is partially formed by the extracellular linker connecting S3 and S4 segments of domain IV, slowing down the inactivation process. In this work we have characterized the actions of BcIII, a sea anemone polypeptide toxin isolated from Bunodosoma caissarum, on neuronal sodium currents using the patch clamp technique. Neurons of the dorsal root ganglia of Wistar rats (P5-9) in primary culture were used for this study (n=65). The main effects of BcIII were a concentration-dependent increase in the sodium current inactivation time course (IC(50)=2.8 microM) as well as an increase in the current peak amplitude. BcIII did not modify the voltage at which 50% of the channels are activated or inactivated, nor the reversal potential of sodium current. BcIII shows a voltage-dependent action. A progressive acceleration of sodium current fast inactivation with longer conditioning pulses was observed, which was steeper as more depolarizing were the prepulses. The same was observed for other two anemone toxins (CgNa, from Condylactis gigantea and ATX-II, from Anemonia viridis). These results suggest that the binding affinity of sea anemone toxins may be reduced in a voltage-dependent manner, as has been described for alpha-scorpion toxins. (c) 2009 Elsevier Inc. All rights reserved.

  4. Molecular analysis of the sea anemone toxin Av3 reveals selectivity to insects and demonstrates the heterogeneity of receptor site-3 on voltage-gated Na+ channels.

    Science.gov (United States)

    Moran, Yehu; Kahn, Roy; Cohen, Lior; Gur, Maya; Karbat, Izhar; Gordon, Dalia; Gurevitz, Michael

    2007-08-15

    Av3 is a short peptide toxin from the sea anemone Anemonia viridis shown to be active on crustaceans and inactive on mammals. It inhibits inactivation of Na(v)s (voltage-gated Na+ channels) like the structurally dissimilar scorpion alpha-toxins and type I sea anemone toxins that bind to receptor site-3. To examine the potency and mode of interaction of Av3 with insect Na(v)s, we established a system for its expression, mutagenized it throughout, and analysed it in toxicity, binding and electrophysiological assays. The recombinant Av3 was found to be highly toxic to blowfly larvae (ED50=2.65+/-0.46 pmol/100 mg), to compete well with the site-3 toxin LqhalphaIT (from the scorpion Leiurus quinquestriatus) on binding to cockroach neuronal membranes (K(i)=21.4+/-7.1 nM), and to inhibit the inactivation of Drosophila melanogaster channel, DmNa(v)1, but not that of mammalian Na(v)s expressed in Xenopus oocytes. Moreover, like other site-3 toxins, the activity of Av3 was synergically enhanced by ligands of receptor site-4 (e.g. scorpion beta-toxins). The bioactive surface of Av3 was found to consist mainly of aromatic residues and did not resemble any of the bioactive surfaces of other site-3 toxins. These analyses have portrayed a toxin that might interact with receptor site-3 in a different fashion compared with other ligands of this site. This assumption was corroborated by a D1701R mutation in DmNa(v)1, which has been shown to abolish the activity of all other site-3 ligands, except Av3. All in all, the present study provides further evidence for the heterogeneity of receptor site-3, and raises Av3 as a unique model for design of selective anti-insect compounds.

  5. Hidden among Sea Anemones: The First Comprehensive Phylogenetic Reconstruction of the Order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) Reveals a Novel Group of Hexacorals

    Science.gov (United States)

    Rodríguez, Estefanía; Barbeitos, Marcos S.; Brugler, Mercer R.; Crowley, Louise M.; Grajales, Alejandro; Gusmão, Luciana; Häussermann, Verena; Reft, Abigail; Daly, Marymegan

    2014-01-01

    Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders

  6. Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia reveals a novel group of hexacorals.

    Directory of Open Access Journals (Sweden)

    Estefanía Rodríguez

    Full Text Available Sea anemones (order Actiniaria are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae. Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein. We also erect subgroups within these two newly

  7. Increasing pCO2 correlates with low concentrations of intracellular dimethylsulfoniopropionate in the sea anemone Anemonia viridis.

    Science.gov (United States)

    Borell, Esther M; Steinke, Michael; Horwitz, Rael; Fine, Maoz

    2014-02-01

    Marine anthozoans maintain a mutualistic symbiosis with dinoflagellates that are prolific producers of the algal secondary metabolite dimethylsulfoniopropionate (DMSP), the precursor of the climate-cooling trace gas dimethyl sulfide (DMS). Surprisingly, little is known about the physiological role of DMSP in anthozoans and the environmental factors that regulate its production. Here, we assessed the potential functional role of DMSP as an antioxidant and determined how future increases in seawater pCO2 may affect DMSP concentrations in the anemone Anemonia viridis along a natural pCO2 gradient at the island of Vulcano, Italy. There was no significant difference in zooxanthellae genotype and characteristics (density of zooxanthellae, and chlorophyll a) as well as protein concentrations between anemones from three stations along the gradient, V1 (3232 μatm CO2), V2 (682 μatm) and control (463 μatm), which indicated that A. viridis can acclimate to various seawater pCO2. In contrast, DMSP concentrations in anemones from stations V1 (33.23 ± 8.30 fmol cell(-1)) and V2 (34.78 ± 8.69 fmol cell(-1)) were about 35% lower than concentrations in tentacles from the control station (51.85 ± 12.96 fmol cell(-1)). Furthermore, low tissue concentrations of DMSP coincided with low activities of the antioxidant enzyme superoxide dismutase (SOD). Superoxide dismutase activity for both host (7.84 ± 1.37 U·mg(-1) protein) and zooxanthellae (2.84 ± 0.41 U·mg(-1) protein) at V1 was 40% lower than at the control station (host: 13.19 ± 1.42; zooxanthellae: 4.72 ± 0.57 U·mg(-1) protein). Our results provide insight into coastal DMSP production under predicted environmental change and support the function of DMSP as an antioxidant in symbiotic anthozoans.

  8. APETx4, a Novel Sea Anemone Toxin and a Modulator of the Cancer-Relevant Potassium Channel KV10.1

    Directory of Open Access Journals (Sweden)

    Lien Moreels

    2017-09-01

    Full Text Available The human ether-à-go-go channel (hEag1 or KV10.1 is a cancer-relevant voltage-gated potassium channel that is overexpressed in a majority of human tumors. Peptides that are able to selectively inhibit this channel can be lead compounds in the search for new anticancer drugs. Here, we report the activity-guided purification and electrophysiological characterization of a novel KV10.1 inhibitor from the sea anemone Anthopleura elegantissima. Purified sea anemone fractions were screened for inhibitory activity on KV10.1 by measuring whole-cell currents as expressed in Xenopus laevis oocytes using the two-microelectrode voltage clamp technique. Fractions that showed activity on Kv10.1 were further purified by RP-HPLC. The amino acid sequence of the peptide was determined by a combination of MALDI- LIFT-TOF/TOF MS/MS and CID-ESI-FT-ICR MS/MS and showed a high similarity with APETx1 and APETx3 and was therefore named APETx4. Subsequently, the peptide was electrophysiologically characterized on KV10.1. The selectivity of the toxin was investigated on an array of voltage-gated ion channels, including the cardiac human ether-à-go-go-related gene potassium channel (hERG or Kv11.1. The toxin inhibits KV10.1 with an IC50 value of 1.1 μM. In the presence of a similar toxin concentration, a shift of the activation curve towards more positive potentials was observed. Similar to the effect of the gating modifier toxin APETx1 on hERG, the inhibition of Kv10.1 by the isolated toxin is reduced at more positive voltages and the peptide seems to keep the channel in a closed state. Although the peptide also induces inhibitory effects on other KV and NaV channels, it exhibits no significant effect on hERG. Moreover, APETx4 induces a concentration-dependent cytotoxic and proapoptotic effect in various cancerous and noncancerous cell lines. This newly identified KV10.1 inhibitor can be used as a tool to further characterize the oncogenic channel KV10.1 or as a

  9. Anthopleura radians, a new species of sea anemone (Cnidaria: Actiniaria: Actiniidae from northern Chile, with comments on other species of the genus from the South Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Carlos Spano

    2017-05-01

    Full Text Available A new species of sea anemone, Anthopleura radians n. sp., is described from the intertidal zone of northern Chile and the taxonomic status of the other Anthopleura species from the South Pacific are discussed. A. radians n. sp. is characterized by a yellow-whitish and brown checkerboard-like pattern on the oral disc, adhesive verrucae along the entire column and a series of marginal projections, each bearing a brightly-colored acrorhagus on the oral surface. This is the seventh species of Anthopleura described from the South Pacific Ocean; each one distinguished by a particular combination of differences related to their coloration pattern, presence of zooxanthellae, cnidae, and mode of reproduction. Some of these species have not been reported since their original description and thus require to be taxonomically validated. A. hermaphroditica and A. aureoradiata are synonyms considering the lack of differences seen between live specimens, museum collections and published records. A. radians could also be a junior synonym of A. minima, however, no type material was found for testing this hypothesis. Furthermore, it is crucial to designate neotypes for A. inconspicua, A. rosea and A. minima since there are no name-bearing types reported for these species.

  10. Nutrients, signals, and photosynthetic release by symbiotic algae. The impact of taurine on the dinoflagellate alga Symbiodinium from the sea anemone Aiptasia pulchella

    International Nuclear Information System (INIS)

    Wang, J.T.; Douglas, A.E.

    1997-01-01

    Exogenous concentrations of 10 micromolar to 1 mM of the nonprotein amino acid taurine stimulated photosynthate release from the dinoflagellate alga Symbiodinium, which had been freshly isolated from the sea anemone Aiptasia pulchella. Photosynthate release, as induced by taurine and animal extract, was metabolically equivalent at both concentrations in that they (a) stimulated photosynthate release to the same extent and (b) induced the selective release of photosynthetically derived organic acids. A complex mixture of amino acids at 75 mM also promoted photosynthate release, but the release rate was reduced by 34% after the omission of taurine (3 mM) from the mixture, suggesting that much of the effect of amino acids was largely attributable to taurine. Exogenous 14C-labeled taurine was taken up by the cells, and more than 95% of the internalized 14C was recovered as taurine, indicating that taurine-induced photosynthate release was not dependent on taurine metabolism. Both taurine uptake and taurine-induced photosynthate release by Symbiodinium exhibited saturation kinetics, but with significantly different Km values of 68 and 21 micromolar, respectively. The difference in Km values is compatible with the hypothesis that Symbiodinium has a taurine signal transducer that is responsible for photosynthate release and is distinct from the taurine transporter

  11. Different visible colors and green fluorescence were obtained from the mutated purple chromoprotein isolated from sea anemone.

    Science.gov (United States)

    Chiang, Cheng-Yi; Chen, Yi-Lin; Tsai, Huai-Jen

    2014-08-01

    Green fluorescent protein (GFP)-like proteins have been studied with the aim of developing fluorescent proteins. Since the property of color variation is understudied, we isolated a novel GFP-like chromoprotein from the carpet anemone Stichodactyla haddoni, termed shCP. Its maximum absorption wavelength peak (λ(max)) is located at 574 nm, resulting in a purple color. The shCP protein consists of 227 amino acids (aa), sharing 96 % identity with the GFP-like chromoprotein of Heteractis crispa. We mutated aa residues to examine any alteration in color. When E63, the first aa of the chromophore, was replaced by serine (E63S), the λ(max) of the mutated protein shCP-E63S was shifted to 560 nm and exhibited a pink color. When Q39, T194, and I196, which reside in the surrounding 5 Å of the chromophore's microenvironment, were mutated, we found that (1) the λ(max) of the mutated protein shCP-Q39S was shifted to 518 nm and exhibited a red color, (2) shCP-T194I exhibited a purple-blue color, and (3) an additional mutation at I196H of the mutated protein shCP-E63L exhibited green fluorescence. In contrast, when the aa located neither at the chromophore nor within its microenvironment were mutated, the resultant proteins shCP-L122H, -E138G, -S137D, -T95I, -D129N, -T194V, -E138Q, -G75E, -I183V, and -I70V never altered their purple color, suggesting that mutations at the shCP chromophore and the surrounding 5 Å microenvironment mostly control changes in color expression or cause fluorescence to develop. Additionally, we found that the cDNAs of shCP and its mutated varieties are faithfully and stably expressed both in Escherichia coli and zebrafish embryos.

  12. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

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    Adam G Marsh

    Full Text Available Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera and an anemone (Nematostella vectensis. Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to

  13. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    Science.gov (United States)

    Marsh, Adam G; Hoadley, Kenneth D; Warner, Mark E

    2016-01-01

    Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in

  14. The genome of Aiptasia, a sea anemone model for coral symbiosis

    KAUST Repository

    Baumgarten, Sebastian; Simakov, Oleg; Esherick, Lisl Y.; Liew, Yi Jin; Lehnert, Erik M.; Michell, Craig; Li, Yong; Hambleton, Elizabeth A.; Guse, Annika; Oates, Matt E.; Gough, Julian; Weis, Virginia M.; Aranda, Manuel; Pringle, John R.; Voolstra, Christian R.

    2015-01-01

    The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying

  15. Genomic organization and splicing variants of a peptidylglycine alpha-hydroxylating monooxygenase from sea anemones

    DEFF Research Database (Denmark)

    Williamson, M; Hauser, F; Grimmelikhuijzen, C J

    2000-01-01

    Cnidarians are primitive animals that use neuropeptides as their transmitters. All the numerous cnidarian neuropeptides isolated, so far, have a carboxy-terminal amide group that is essential for their actions. This strongly suggests that alpha-amidating enzymes are essential for the functioning ...

  16. Evidence for participation of GCS1 in fertilization of the starlet sea anemone Nematostella vectensis: Implication of a common mechanism of sperm–egg fusion in plants and animals

    Energy Technology Data Exchange (ETDEWEB)

    Ebchuqin, Eerdundagula; Yokota, Naoto; Yamada, Lixy [Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba 517-0004 (Japan); Yasuoka, Yuuri [Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495 (Japan); Akasaka, Mari [Laboratory of Molecular Genetics, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8602 (Japan); Arakawa, Mio; Deguchi, Ryusaku [Department of Biology, Miyagi University of Education, Sendai, Miyagi 980-0845 (Japan); Mori, Toshiyuki [Waseda Institute for Advanced Study, Waseda University, Shinjuku, Tokyo 169-8050 (Japan); Sawada, Hitoshi, E-mail: hsawada@bio.nagoya-u.ac.jp [Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba 517-0004 (Japan)

    2014-09-05

    Highlights: • GCS1 is a sperm transmembrane protein that is essential for gamete fusion in flowering plants. • The GCS1 gene is present not only in angiosperms but also in unicellular organisms and animals. • NvGCS1 gene is expressed in the testis and GCS1 protein exists in sperm of a sea anemone. • Anti-GCS1 antibodies inhibited the fertilization, showing the participation in fertilization. - Abstract: It has been reported that GCS1 (Generative Cell Specific 1) is a transmembrane protein that is exclusively expressed in sperm cells and is essential for gamete fusion in flowering plants. The GCS1 gene is present not only in angiosperms but also in unicellular organisms and animals, implying the occurrence of a common or ancestral mechanism of GCS1-mediated gamete fusion. In order to elucidate the common mechanism, we investigated the role of GCS1 in animal fertilization using a sea anemone (Cnidaria), Nematostella vectensis. Although the existence of the GCS1 gene in N. vectensis has been reported, the expression of GCS1 in sperm and the role of GCS1 in fertilization are not known. In this study, we showed that the GCS1 gene is expressed in the testis and that GCS1 protein exists in sperm by in situ hybridization and proteomic analysis, respectively. Then we made four peptide antibodies against the N-terminal extracellular region of NvGCS1. These antibodies specifically reacted to NvGCS1 among sperm proteins on the basis of Western analysis and potently inhibited fertilization in a concentration-dependent manner. These results indicate that sperm GCS1 plays a pivotal role in fertilization, most probably in sperm–egg fusion, in a starlet sea anemone, suggesting a common gamete-fusion mechanism shared by eukaryotic organisms.

  17. Antifouling activity by sea anemone (Heteractis magnifica and H. aurora extracts against marine biofilm bacteria Actividades antiincrustantes de las extractos de las anémonas marinas Heteractis magnifica y H. aurora frente a biofilm de bacterias marinas

    Directory of Open Access Journals (Sweden)

    Subramanian Bragadeeswaran

    2011-07-01

    Full Text Available Sea anemones (Actiniaria are solitary, ocean-dwelling members of the phylum Cnidaria and the class Anthozoa. In this study, we screened antibacterial activity of two benthic sea anemones (Heteractis magnifica and H. aurora collected from the Mandapam coast of southeast India. Crude extracts of the sea anemone were assayed against seven bacterial biofilms isolated from three different test panels. The crude extract of H. magnifica showed a maximum inhibition zone of 18 mm against Pseudomonas sp. and Escherichia coli and a minimum inhibition zone of 3 mm against Pseudomonas aeruginosa, Micrococcus sp., and Bacillus cerens for methanol, acetone, and DCM extracts, respectively. The butanol extract of H. aurora showed a maximum inhibition zone of 23 mm against Vibrio parahaemolyticus, whereas the methanol extract revealed a minimum inhibition zone of 1 mm against V. parahaemolyticus. The present study revealed that the H. aurora extracts were more effective than those of H. magnifica and that the active compounds from the sea anemone can be used as antifouling compounds.Las anémonas de mar (Actiniaria son solitarias, habitantes oceánicos del phylum Cnidaria y de la clase Anthozoa. En este estudio se determina la actividad antibacteriana de dos anémonas bentónicas Heteractis magnifica y H. aurora recolectadas en la costa de Mandapam, sudeste de India. Los extractos crudos de estas anémonas fueron ensayados frente a siete biofilms bacterianos aislados de tres paneles de control distintos. El extracto crudo de la anémona H. magnifica mostró una zona inhibición máxima de 18 mm contra Psudomonas sp. y Escherichia coli y la zona de inhibición mínima de 3 mm fue encontrada frente a Pseudomonas aeruginosa, Micrococus sp. y Bacillus cerens de extractos de metanol, acetona y DCM respectivamente. El extracto de butanol de la anémona H. magnifica mostró una zona de inhibición máxima de 23 mm frente a Vibrio parahemolyticus, mientras que con el

  18. Prolonged exposure to elevated CO2 promotes growth of the algal symbiont Symbiodinium muscatinei in the intertidal sea anemone Anthopleura elegantissima

    Science.gov (United States)

    Towanda, Trisha; Thuesen, Erik V.

    2012-01-01

    Summary Some photosynthetic organisms benefit from elevated levels of carbon dioxide, but studies on the effects of elevated PCO2 on the algal symbionts of animals are very few. This study investigated the impact of hypercapnia on a photosynthetic symbiosis between the anemone Anthopleura elegantissima and its zooxanthella Symbiodinium muscatinei. Anemones were maintained in the laboratory for 1 week at 37 Pa PCO2 and pH 8.1. Clonal pairs were then divided into two groups and maintained for 6 weeks under conditions naturally experienced in their intertidal environment, 45 Pa PCO2, pH 8.1 and 231 Pa PCO2, pH 7.3. Respiration and photosynthesis were measured after the 1-week acclimation period and after 6 weeks in experimental conditions. Density of zooxanthellal cells, zooxanthellal cell size, mitotic index and chlorophyll content were compared between non-clonemate anemones after the 1-week acclimation period and clonal anemones at the end of the experiment. Anemones thrived in hypercapnia. After 6 weeks, A. elegantissima exhibited higher rates of photosynthesis at 45 Pa (4.2 µmol O2 g−1 h−1) and 231 Pa (3.30 µmol O2 g−1 h−1) than at the initial 37 Pa (1.53 µmol O2 g−1 h−1). Likewise, anemones at 231 Pa received more of their respiratory carbon from zooxanthellae (CZAR  = 78.2%) than those at 37 Pa (CZAR  = 66.6%) but less than anemones at 45 Pa (CZAR  = 137.3%). The mitotic index of zooxanthellae was significantly greater in the hypercapnic anemones than in anemones at lower PCO2. Excess zooxanthellae were expelled by their hosts, and cell densities, cell diameters and chlorophyll contents were not significantly different between the groups. The response of A. elegantissima to hypercapnic acidification reveals the potential adaptation of an intertidal, photosynthetic symbiosis for high PCO2. PMID:23213455

  19. Prolonged exposure to elevated CO2 promotes growth of the algal symbiont Symbiodinium muscatinei in the intertidal sea anemone Anthopleura elegantissima

    Directory of Open Access Journals (Sweden)

    Trisha Towanda

    2012-05-01

    Some photosynthetic organisms benefit from elevated levels of carbon dioxide, but studies on the effects of elevated PCO2 on the algal symbionts of animals are very few. This study investigated the impact of hypercapnia on a photosynthetic symbiosis between the anemone Anthopleura elegantissima and its zooxanthella Symbiodinium muscatinei. Anemones were maintained in the laboratory for 1 week at 37 Pa PCO2 and pH 8.1. Clonal pairs were then divided into two groups and maintained for 6 weeks under conditions naturally experienced in their intertidal environment, 45 Pa PCO2, pH 8.1 and 231 Pa PCO2, pH 7.3. Respiration and photosynthesis were measured after the 1-week acclimation period and after 6 weeks in experimental conditions. Density of zooxanthellal cells, zooxanthellal cell size, mitotic index and chlorophyll content were compared between non-clonemate anemones after the 1-week acclimation period and clonal anemones at the end of the experiment. Anemones thrived in hypercapnia. After 6 weeks, A. elegantissima exhibited higher rates of photosynthesis at 45 Pa (4.2 µmol O2 g−1 h−1 and 231 Pa (3.30 µmol O2 g−1 h−1 than at the initial 37 Pa (1.53 µmol O2 g−1 h−1. Likewise, anemones at 231 Pa received more of their respiratory carbon from zooxanthellae (CZAR  = 78.2% than those at 37 Pa (CZAR  = 66.6% but less than anemones at 45 Pa (CZAR  = 137.3%. The mitotic index of zooxanthellae was significantly greater in the hypercapnic anemones than in anemones at lower PCO2. Excess zooxanthellae were expelled by their hosts, and cell densities, cell diameters and chlorophyll contents were not significantly different between the groups. The response of A. elegantissima to hypercapnic acidification reveals the potential adaptation of an intertidal, photosynthetic symbiosis for high PCO2.

  20. Prolonged exposure to elevated CO(2) promotes growth of the algal symbiont Symbiodinium muscatinei in the intertidal sea anemone Anthopleura elegantissima.

    Science.gov (United States)

    Towanda, Trisha; Thuesen, Erik V

    2012-07-15

    Some photosynthetic organisms benefit from elevated levels of carbon dioxide, but studies on the effects of elevated PCO(2) on the algal symbionts of animals are very few. This study investigated the impact of hypercapnia on a photosynthetic symbiosis between the anemone Anthopleura elegantissima and its zooxanthella Symbiodinium muscatinei. Anemones were maintained in the laboratory for 1 week at 37 Pa PCO(2) and pH 8.1. Clonal pairs were then divided into two groups and maintained for 6 weeks under conditions naturally experienced in their intertidal environment, 45 Pa PCO(2), pH 8.1 and 231 Pa PCO(2), pH 7.3. Respiration and photosynthesis were measured after the 1-week acclimation period and after 6 weeks in experimental conditions. Density of zooxanthellal cells, zooxanthellal cell size, mitotic index and chlorophyll content were compared between non-clonemate anemones after the 1-week acclimation period and clonal anemones at the end of the experiment. Anemones thrived in hypercapnia. After 6 weeks, A. elegantissima exhibited higher rates of photosynthesis at 45 Pa (4.2 µmol O(2) g(-1) h(-1)) and 231 Pa (3.30 µmol O(2) g(-1) h(-1)) than at the initial 37 Pa (1.53 µmol O(2) g(-1) h(-1)). Likewise, anemones at 231 Pa received more of their respiratory carbon from zooxanthellae (CZAR  = 78.2%) than those at 37 Pa (CZAR  = 66.6%) but less than anemones at 45 Pa (CZAR  = 137.3%). The mitotic index of zooxanthellae was significantly greater in the hypercapnic anemones than in anemones at lower PCO(2). Excess zooxanthellae were expelled by their hosts, and cell densities, cell diameters and chlorophyll contents were not significantly different between the groups. The response of A. elegantissima to hypercapnic acidification reveals the potential adaptation of an intertidal, photosynthetic symbiosis for high PCO(2).

  1. Cooperativity in the two-domain arginine kinase from the sea anemone Anthopleura japonicus. II. Evidence from site-directed mutagenesis studies.

    Science.gov (United States)

    Tada, Hiroshi; Suzuki, Tomohiko

    2010-08-01

    The arginine kinase (AK) from the sea anemone Anthopleura japonicus has an unusual two-domain structure (contiguous dimer; denoted by D1-D2). In a previous report, we suggested cooperativity in the contiguous dimer, which may be a result of domain-domain interactions, using MBP-fused enzymes. To further understand this observation, we inserted six-Lys residues into the linker region of the two-domain AK (D1-K6-D2 mutant) using His-tagged enzyme. The dissociation constants, K(a) and K(ia), of the mutant were similar to those of the wild-type enzyme but the catalytic constant, k(cat), was decreased to 28% that of the wild-type, indicating that some of the domain-domain interactions are lost due to the six-Lys insertion. Y68 plays a major role in arginine binding in the catalytic pocket in Limulus AK, and introduction of mutation at the Y68 position virtually abolishes catalytic activity. Thus, the constructed D1(Y68G)-D2 and D1-D2(Y68G) mutants mimic the D1(inactive)-D2(active) and D1(active)-D2(inactive) enzymes, respectively. The k(cat) values of both Y68 mutants were decreased to 13-18% that of the wild-type enzyme, which is much less than the 50% level of the two-domain enzyme. Thus, it is clear that substrate-binding to both domains is necessary for full expression of activity. In other words, substrate-binding appears to act as the trigger of the functional cooperativity in two-domain AK. Copyright 2010 Elsevier B.V. All rights reserved.

  2. Antifouling Activity towards Mussel by Small-Molecule Compounds from a Strain of Vibrio alginolyticus Bacterium Associated with Sea Anemone Haliplanella sp.

    Science.gov (United States)

    Wang, Xiang; Huang, Yanqiu; Sheng, Yanqing; Su, Pei; Qiu, Yan; Ke, Caihuan; Feng, Danqing

    2017-03-28

    Mussels are major fouling organisms causing serious technical and economic problems. In this study, antifouling activity towards mussel was found in three compounds isolated from a marine bacterium associated with the sea anemone Haliplanella sp. This bacterial strain, called PE2, was identified as Vibrio alginolyticus using morphology, biochemical tests, and phylogenetic analysis based on sequences of 16S rRNA and four housekeeping genes ( rpoD, gyrB, rctB, and toxR ). Three small-molecule compounds (indole, 3-formylindole, and cyclo (Pro-Leu)) were purified from the ethyl acetate extract of V. alginolyticus PE2 using column chromatography techniques. They all significantly inhibited byssal thread production of the green mussel Perna viridis , with EC 50 values of 24.45 μg/ml for indole, 50.07 μg/ml for 3-formylindole, and 49.24 μg/ml for cyclo (Pro-Leu). Previous research on the antifouling activity of metabolites from marine bacteria towards mussels is scarce. Indole, 3-formylindole and cyclo (Pro-Leu) also exhibited antifouling activity against settlement of the barnacle Balanus albicostatus (EC 50 values of 8.84, 0.43, and 11.35 μg/ml, respectively) and the marine bacterium Pseudomonas sp. (EC 50 values of 42.68, 69.68, and 39.05 μg/ml, respectively). These results suggested that the three compounds are potentially useful for environmentally friendly mussel control and/or the development of new antifouling additives that are effective against several biofoulers.

  3. IncreasingpCO2correlates with low concentrations of intracellular dimethylsulfoniopropionate in the sea anemoneAnemonia viridis

    OpenAIRE

    Borell, Esther M.; Steinke, Michael; Horwitz, Rael; Fine, Maoz

    2014-01-01

    Marine anthozoans maintain a mutualistic symbiosis with dinoflagellates that are prolific producers of the algal secondary metabolite dimethylsulfoniopropionate (DMSP), the precursor of the climate-cooling trace gas dimethyl sulfide (DMS). Surprisingly, little is known about the physiological role of DMSP in anthozoans and the environmental factors that regulate its production. Here, we assessed the potential functional role of DMSP as an antioxidant and determined how future increases in sea...

  4. Parasitic anemone infects the invasive ctenophore Mnemiopsis leidyi in the North East Atlantic

    DEFF Research Database (Denmark)

    Selander, Erik; Møller, Lene Friis; Sundberg, Per

    2010-01-01

    We report of the first finding of parasitic sea anemone larvae infecting the invasive ctenophore Mnemiopsis leidyi in the North East Atlantic. Parasitic anemone larvae are common in the native habitat of Mnemiopsis, but have not previously been reported from any of the locations where Mnemiopsis ...

  5. Anemone bleaching increases the metabolic demands of symbiont anemonefish.

    Science.gov (United States)

    Norin, Tommy; Mills, Suzanne C; Crespel, Amélie; Cortese, Daphne; Killen, Shaun S; Beldade, Ricardo

    2018-04-11

    Increased ocean temperatures are causing mass bleaching of anemones and corals in the tropics worldwide. While such heat-induced loss of algal symbionts (zooxanthellae) directly affects anemones and corals physiologically, this damage may also cascade on to other animal symbionts. Metabolic rate is an integrative physiological trait shown to relate to various aspects of organismal performance, behaviour and locomotor capacity, and also shows plasticity during exposure to acute and chronic stressors. As climate warming is expected to affect the physiology, behaviour and life history of animals, including ectotherms such as fish, we measured if residing in bleached versus unbleached sea anemones ( Heteractis magnifica ) affected the standard (i.e. baseline) metabolic rate and behaviour (activity) of juvenile orange-fin anemonefish ( Amphiprion chrysopterus ) . Metabolic rate was estimated from rates of oxygen uptake [Formula: see text], and the standard metabolic rate [Formula: see text] of anemonefish from bleached anemones was significantly higher by 8.2% compared with that of fish residing in unbleached anemones, possibly due to increased stress levels. Activity levels did not differ between fish from bleached and unbleached anemones. As [Formula: see text] reflects the minimum cost of living, the increased metabolic demands may contribute to the negative impacts of bleaching on important anemonefish life history and fitness traits observed previously (e.g. reduced spawning frequency and lower fecundity). © 2018 The Author(s).

  6. Taxonomic, Spatial and Temporal Patterns of Bleaching in Anemones Inhabited by Anemonefishes

    KAUST Repository

    Hobbs, Jean-Paul A.; Frisch, Ashley J.; Ford, Benjamin M.; Thums, Michele; Saenz Agudelo, Pablo; Furby, Kathryn A.; Berumen, Michael L.

    2013-01-01

    Background:Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms.Methodology/Principal Findings:This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19-100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance.Conclusions/Significance:Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of host

  7. Taxonomic, Spatial and Temporal Patterns of Bleaching in Anemones Inhabited by Anemonefishes

    KAUST Repository

    Hobbs, Jean-Paul A.

    2013-08-08

    Background:Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms.Methodology/Principal Findings:This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19-100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance.Conclusions/Significance:Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of host

  8. The specificity of Av3 sea anemone toxin for arthropods is determined at linker DI/SS2-S6 in the pore module of target sodium channels.

    Science.gov (United States)

    Gur Barzilai, Maya; Kahn, Roy; Regev, Noa; Gordon, Dalia; Moran, Yehu; Gurevitz, Michael

    2014-10-15

    Av3 is a peptide neurotoxin from the sea anemone Anemonia viridis that shows specificity for arthropod voltage-gated sodium channels (Navs). Interestingly, Av3 competes with a scorpion α-toxin on binding to insect Navs and similarly inhibits the inactivation process, and thus has been classified as 'receptor site-3 toxin', although the two peptides are structurally unrelated. This raises questions as to commonalities and differences in the way both toxins interact with Navs. Recently, site-3 was partly resolved for scorpion α-toxins highlighting S1-S2 and S3-S4 external linkers at the DIV voltage-sensor module and the juxtaposed external linkers at the DI pore module. To uncover channel determinants involved in Av3 specificity for arthropods, the toxin was examined on channel chimaeras constructed with the external linkers of the mammalian brain Nav1.2a, which is insensitive to Av3, in the background of the Drosophila DmNav1. This approach highlighted the role of linker DI/SS2-S6, adjacent to the channel pore, in determining Av3 specificity. Point mutagenesis at DI/SS2-S6 accompanied by functional assays highlighted Trp404 and His405 as a putative point of Av3 interaction with DmNav1. His405 conservation in arthropod Navs compared with tyrosine in vertebrate Navs may represent an ancient substitution that explains the contemporary selectivity of Av3. Trp404 and His405 localization near the membrane surface and the hydrophobic bioactive surface of Av3 suggest that the toxin possibly binds at a cleft by DI/S6. A partial overlap in receptor site-3 of both toxins nearby DI/S6 may explain their binding competition capabilities.

  9. Severe Toxic Skin Reaction Caused by a Common Anemone and Identification of the Culprit Organism.

    Science.gov (United States)

    Tezcan, Özgür Deniz; Gözer, Özgür

    2015-01-01

    In a marine envenomation, identification of the culprit organism can be difficult. In this case report, we present our method to identify snakelocks anemone (Anemonia viridis or formerly Anemonia sulcata) as the culprit of a severe toxic skin reaction. A. viridis is one of the most common anemones of the Mediterranean Sea and the North Atlantic Ocean. It lives at a depth of up to 10 m. It is a member of the phylum Cnidaria, which includes jellyfish, anemones, hydroids, and corals. They have toxic organelles called cnidocysts that have the capacity to inject venom with microscopic harpoon-like structures. The cnidocysts of A. viridis may cause toxic and allergic reactions, and although its venom is one of the most studied cnidarian venoms, detailed case reports are rare. © 2015 International Society of Travel Medicine.

  10. Actiniarian Sea anemone fauna of India

    Digital Repository Service at National Institute of Oceanography (India)

    Parulekar, A.H.

    stream_size 11 stream_content_type text/plain stream_name Mar_Biofouling_Power_Plants_1990_218.pdf.txt stream_source_info Mar_Biofouling_Power_Plants_1990_218.pdf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset...

  11. The Effects of Ocean Acidification on Feeding and Contest Behaviour by the Beadlet Anemone Actinia equina

    Science.gov (United States)

    Bamber, Tess Olivia; Jackson, Angus Charles; Mansfield, Robert Philip

    2018-05-01

    Increasing concentrations of atmospheric carbon dioxide are causing oceanic pH to decline worldwide, a phenomenon termed ocean acidification. Mounting experimental evidence indicates that near-future levels of CO2 will affect calcareous invertebrates such as corals, molluscs and gastropods, by reducing their scope for calcification. Despite extensive research into ocean acidification in recent years, the effects on non-calcifying anthozoans, such as sea anemones, remain little explored. In Western Europe, intertidal anemones such as Actinia equina are abundant, lower trophic-level organisms that function as important ecosystem engineers. Changes to behaviours of these simple predators could have implications for intertidal assemblages. This investigation identified the effects of reduced seawater pH on feeding and contest behaviour by A. equina. Video footage was recorded for A. equina feeding at current-day seawater (pH 8.1), and the least (pH 7.9) and most (pH 7.6) severe end-of-century predictions. Footage was also taken of contests over ownership of space between anemones exposed to reduced pH and those that were not. No statistically significant differences were identified in feeding duration or various aspects of contest behaviour including initiating, winning, inflating acrorhagi, inflicting acrorhagial peels and contest duration. Multivariate analyses showed no effect of pH on a combination of these variables. This provides contrast with other studies where anemones with symbiotic algae thrive in areas of natural increased acidity. Thus, novel experiments using intraspecific contests and resource-holding potential may prove an effective approach to understand sub-lethal consequences of ocean acidification for A. equina, other sea anemones and more broadly for marine ecosystems.

  12. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

    KAUST Repository

    Othoum, Ghofran K; Bougouffa, Salim; Razali, Rozaimi; Bokhari, Ameerah; Alamoudi, Soha; Antunes, André ; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Lafi, Feras Fawzi; Essack, Magbubah

    2018-01-01

    are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked

  13. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed; Thompson, Luke R.; Stingl, Ulrich

    2016-01-01

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  14. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed

    2016-02-11

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  15. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    OpenAIRE

    Har, Jia Y.; Helbig, Tim; Lim, Ju H.; Fernando, Samodha C.; Reitzel, Adam M.; Penn, Kevin; Thompson, Janelle R.

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacter...

  16. Draft genome of bagasse-degrading bacteria Bacillus aryabhattai GZ03 from deep sea water.

    Science.gov (United States)

    Wen, Jian; Ren, Chong; Huang, Nan; Liu, Yang; Zeng, Runying

    2015-02-01

    Bacillus aryabhattai GZ03 was isolated from deep sea water of the South China Sea, which can produce glucose and fructose by degrading bagasse at 25 °C. Here we report the draft genome sequence of Bacillus aryabhattai GZ03. The data obtained revealed 37 contigs with genome size of 5,105,129 bp and G+C content of 38.09%. The draft genome of B. aryabhattai GZ03 may provide insights into the mechanism of microbial carbohydrate and lignocellulosic material degradation. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Evolution of genomic diversity and sex at extreme environments: Fungal life under hypersaline Dead Sea stress

    Science.gov (United States)

    Kis-Papo, Tamar; Kirzhner, Valery; Wasser, Solomon P.; Nevo, Eviatar

    2003-01-01

    We have found that genomic diversity is generally positively correlated with abiotic and biotic stress levels (1–3). However, beyond a high-threshold level of stress, the diversity declines to a few adapted genotypes. The Dead Sea is the harshest planetary hypersaline environment (340 g·liter–1 total dissolved salts, ≈10 times sea water). Hence, the Dead Sea is an excellent natural laboratory for testing the “rise and fall” pattern of genetic diversity with stress proposed in this article. Here, we examined genomic diversity of the ascomycete fungus Aspergillus versicolor from saline, nonsaline, and hypersaline Dead Sea environments. We screened the coding and noncoding genomes of A. versicolor isolates by using >600 AFLP (amplified fragment length polymorphism) markers (equal to loci). Genomic diversity was positively correlated with stress, culminating in the Dead Sea surface but dropped drastically in 50- to 280-m-deep seawater. The genomic diversity pattern paralleled the pattern of sexual reproduction of fungal species across the same southward gradient of increasing stress in Israel. This parallel may suggest that diversity and sex are intertwined intimately according to the rise and fall pattern and adaptively selected by natural selection in fungal genome evolution. Future large-scale verification in micromycetes will define further the trajectories of diversity and sex in the rise and fall pattern. PMID:14645702

  18. HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus.

    Science.gov (United States)

    Kinjo, Sonoko; Kiyomoto, Masato; Yamamoto, Takashi; Ikeo, Kazuho; Yaguchi, Shunsuke

    2018-04-01

    To understand the mystery of life, it is important to accumulate genomic information for various organisms because the whole genome encodes the commands for all the genes. Since the genome of Strongylocentrotus purpratus was sequenced in 2006 as the first sequenced genome in echinoderms, the genomic resources of other North American sea urchins have gradually been accumulated, but no sea urchin genomes are available in other areas, where many scientists have used the local species and reported important results. In this manuscript, we report a draft genome of the sea urchin Hemincentrotus pulcherrimus because this species has a long history as the target of developmental and cell biology in East Asia. The genome of H. pulcherrimus was assembled into 16,251 scaffold sequences with an N50 length of 143 kbp, and approximately 25,000 genes were identified in the genome. The size of the genome and the sequencing coverage were estimated to be approximately 800 Mbp and 100×, respectively. To provide these data and information of annotation, we constructed a database, HpBase (http://cell-innovation.nig.ac.jp/Hpul/). In HpBase, gene searches, genome browsing, and blast searches are available. In addition, HpBase includes the "recipes" for experiments from each lab using H. pulcherrimus. These recipes will continue to be updated according to the circumstances of individual scientists and can be powerful tools for experimental biologists and for the community. HpBase is a suitable dataset for evolutionary, developmental, and cell biologists to compare H. pulcherrimus genomic information with that of other species and to isolate gene information. © 2018 Japanese Society of Developmental Biologists.

  19. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Science.gov (United States)

    Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

    2013-01-01

    The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  20. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    Directory of Open Access Journals (Sweden)

    Intikhab Alam

    Full Text Available The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.We developed a data warehouse system (INDIGO that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

  1. Ecological genomics for coral and sea urchin conservation in times of climate change

    Science.gov (United States)

    Carpizo-Ituarte, E.; Hofmann, G.; Fangue, N.; Cupul-Magaña, A.; Rodríguez-Troncoso, A. P.; Díaz-Pérez, L.; Olivares Bañuelos, T.; Escobar Fernández, R.

    2010-03-01

    If atmospheric CO2 levels continue to increase, it is predicted that the average ocean sea surface temperature will also increase and ocean pH will decrease to levels not experienced by marine organisms for millions of years. Understanding the impact of these stressors will require the study of several marine organisms, and this knowledge will be fundamental to our ability to predict possible effects along large geographical regions and across phyla. Ecological genomics, defined as the use of molecular techniques to answer ecological questions, offers a set of tools that can help us better understand the responses of marine organisms to changes in their environment. In the present work we are using genomic tools to characterize the response of corals and sea urchins to environmental stress. On one side, coral species represent a useful model due to its functions as "environmental sentinels" in tropical ecosystems; on the other hand, species of sea urchins, with the recent sequence of the genome of the purple sea urchin S. purpuratus, offers important genomic resources. Recent results in corals and in sea urchins have shown that the response to stressful conditions can be detected using molecular genomic markers. Continued study of the mRNA expression patterns of several important gene families including calcification genes as well as genes involved in the cellular stress response such as heat shock proteins, will be valuable index of ecological stress in marine systems. These data can be integrated into better strategies of conservation and management of the oceans.

  2. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

    Science.gov (United States)

    Smith, Jeramiah J; Kuraku, Shigehiro; Holt, Carson; Sauka-Spengler, Tatjana; Jiang, Ning; Campbell, Michael S; Yandell, Mark D; Manousaki, Tereza; Meyer, Axel; Bloom, Ona E; Morgan, Jennifer R; Buxbaum, Joseph D; Sachidanandam, Ravi; Sims, Carrie; Garruss, Alexander S; Cook, Malcolm; Krumlauf, Robb; Wiedemann, Leanne M; Sower, Stacia A; Decatur, Wayne A; Hall, Jeffrey A; Amemiya, Chris T; Saha, Nil R; Buckley, Katherine M; Rast, Jonathan P; Das, Sabyasachi; Hirano, Masayuki; McCurley, Nathanael; Guo, Peng; Rohner, Nicolas; Tabin, Clifford J; Piccinelli, Paul; Elgar, Greg; Ruffier, Magali; Aken, Bronwen L; Searle, Stephen MJ; Muffato, Matthieu; Pignatelli, Miguel; Herrero, Javier; Jones, Matthew; Brown, C Titus; Chung-Davidson, Yu-Wen; Nanlohy, Kaben G; Libants, Scot V; Yeh, Chu-Yin; McCauley, David W; Langeland, James A; Pancer, Zeev; Fritzsch, Bernd; de Jong, Pieter J; Zhu, Baoli; Fulton, Lucinda L; Theising, Brenda; Flicek, Paul; Bronner, Marianne E; Warren, Wesley C; Clifton, Sandra W; Wilson, Richard K; Li, Weiming

    2013-01-01

    Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms. PMID:23435085

  3. The complete mitochondrial genome of the deep-sea sponge Poecillastra laminaris (Astrophorida, Vulcanellidae).

    Science.gov (United States)

    Zeng, Cong; Thomas, Leighton J; Kelly, Michelle; Gardner, Jonathan P A

    2016-05-01

    The complete mitochondrial genome of a New Zealand specimen of the deep-sea sponge Poecillastra laminaris (Sollas, 1886) (Astrophorida, Vulcanellidae), from the Colville Ridge, New Zealand, was sequenced using the 454 Life Science pyrosequencing system. To identify homologous mitochondrial sequences, the 454 reads were mapped to the complete mitochondrial genome sequence of Geodia neptuni (GeneBank No. NC_006990). The P. laminaris genome is 18,413 bp in length and includes 14 protein-coding genes, 24 transfer RNA genes and 2 ribosomal RNA genes. Gene order resembled that of other demosponges. The base composition of the genome is A (29.1%), T (35.2%), C (14.0%) and G (21.7%). This is the second published mitogenome for a sponge of the order Astrophorida and will be useful in future phylogenetic analysis of deep-sea sponges.

  4. Evolutionary Genomics of Life in (and from) the Sea

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Dehal, Paramvir; Fuerstenberg, Susan I.

    2006-01-09

    High throughput genome sequencing centers that were originally built for the Human Genome Project (Lander et al., 2001; Venter et al., 2001) have now become an engine for comparative genomics. The six largest centers alone are now producing over 150 billion nucleotides per year, more than 50 times the amount of DNA in the human genome, and nearly all of this is directed at projects that promise great insights into the pattern and processes of evolution. Unfortunately, this data is being produced at a pace far exceeding the capacity of the scientific community to provide insightful analysis, and few scientists with training and experience in evolutionary biology have played prominent roles to date. One of the consequences is that poor quality analyses are typical; for example, orthology among genes is generally determined by simple measures of sequence similarity, when this has been discredited by molecular evolutionary biologists decades ago. Here we discuss the how genomes are chosen for sequencing and how the scientific community can have input. We describe the PhIGs database and web tools (Dehal and Boore 2005a; http://PhIGs.org), which provide phylogenetic analysis of all gene families for all completely sequenced genomes and the associated 'Synteny Viewer', which allows comparisons of the relative positions of orthologous genes. This is the best tool available for inferring gene function across multiple genomes. We also describe how we have used the PhIGs methods with the whole genome sequences of a tunicate, fish, mouse, and human to conclusively demonstrate that two rounds of whole genome duplication occurred at the base of vertebrates (Dehal and Boore 2005b). This evidence is found in the large scale structure of the positions of paralogous genes that arose from duplications inferred by evolutionary analysis to have occurred at the base of vertebrates.

  5. The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

    Science.gov (United States)

    Zhang, Xiaojun; Sun, Lina; Yuan, Jianbo; Sun, Yamin; Gao, Yi; Zhang, Libin; Li, Shihao; Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng; Xiang, Jianhai

    2017-10-01

    Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

  6. The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

    Directory of Open Access Journals (Sweden)

    Xiaojun Zhang

    2017-10-01

    Full Text Available Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb, with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94-like gene family and a significantly expanded fibrinogen-related protein (FREP gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

  7. Recent advances in functional perturbation and genome editing techniques in studying sea urchin development.

    Science.gov (United States)

    Cui, Miao; Lin, Che-Yi; Su, Yi-Hsien

    2017-09-01

    Studies on the gene regulatory networks (GRNs) of sea urchin embryos have provided a basic understanding of the molecular mechanisms controlling animal development. The causal links in GRNs have been verified experimentally through perturbation of gene functions. Microinjection of antisense morpholino oligonucleotides (MOs) into the egg is the most widely used approach for gene knockdown in sea urchin embryos. The modification of MOs into a membrane-permeable form (vivo-MOs) has allowed gene knockdown at later developmental stages. Recent advances in genome editing tools, such as zinc-finger nucleases, transcription activator-like effector-based nucleases and the clustered regularly interspaced short palindromic repeat/clustered regularly interspaced short palindromic repeat-associated protein 9 (CRISPR/Cas9) system, have provided methods for gene knockout in sea urchins. Here, we review the use of vivo-MOs and genome editing tools in sea urchin studies since the publication of its genome in 2006. Various applications of the CRISPR/Cas9 system and their potential in studying sea urchin development are also discussed. These new tools will provide more sophisticated experimental methods for studying sea urchin development. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Genome editing in sea urchin embryos by using a CRISPR/Cas9 system.

    Science.gov (United States)

    Lin, Che-Yi; Su, Yi-Hsien

    2016-01-15

    Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

    NARCIS (Netherlands)

    Olsen, Jeanine; Rouzé, Pierre; Verhelst, Bram; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; De Paoli, Emanuele; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna; Lauritano, Chiara; Lohaus, Rolf; Töpel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Boström, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J; Pearson, Gareth A; Procaccini, Gabriele; Duarte, Carlos M; Schmutz, Jeremy; Reusch, Thorsten B H; Van de Peer, Yves

    2016-01-01

    Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals

  10. A catalogue of 136 microbial draft genomes from Red Sea metagenomes

    KAUST Repository

    Haroon, Mohamed; Thompson, Luke R.; Parks, Donovan H.; Hugenholtz, Philip; Stingl, Ulrich

    2016-01-01

    Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

  11. A catalogue of 136 microbial draft genomes from Red Sea metagenomes

    KAUST Repository

    Haroon, Mohamed

    2016-07-05

    Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

  12. A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

    Science.gov (United States)

    Haroon, Mohamed F; Thompson, Luke R; Parks, Donovan H; Hugenholtz, Philip; Stingl, Ulrich

    2016-07-05

    Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

  13. Changes in zooxanthellae density, morphology, and mitotic index in hermatypic corals and anemones exposed to cyanide.

    Science.gov (United States)

    Cervino, J M; Hayes, R L; Honovich, M; Goreau, T J; Jones, S; Rubec, P J

    2003-05-01

    Sodium cyanide (NaCN) is widely used for the capture of reef fish throughout Southeast Asia and causes extensive fish mortality, but the effect of NaCN on reef corals remains debated. To document the impact of cyanide exposure on corals, the species Acropora millepora, Goniopora sp., Favites abdita, Trachyphyllia geoffrio, Plerogyra sp., Heliofungia actinformis, Euphyllia divisa, and Scarophyton sp., and the sea anemone Aiptasia pallida were exposed to varying concentrations of cyanide for varying time periods. Corals were exposed to 50, 100, 300, and 600 mg/l of cyanide ion (CN(-)) for 1-2 min (in seawater, the CN(-) forms hydrocyanic acid). These concentrations are much lower than those reportedly used by fish collectors. Exposed corals and anemones immediately retracted their tentacles and mesenterial filaments, and discharged copious amounts of mucus containing zooxanthellae. Gel electrophoreses techniques found changes in protein expression in both zooxanthellae and host tissue. Corals and anemones exposed to cyanide showed an immediate increase in mitotic cell division of their zooxenthellae, and a decrease in zooxanthellae density. In contrast, zooxanthellae cell division and density remained constant in controls. Histopathological changes included gastrodermal disruption, mesogleal degradation, and increased mucus in coral tissues. Zooxanthellae showed pigment loss, swelling, and deformation. Mortality occurred at all exposure levels. Exposed specimens experienced an increase in the ratio of gram-negative to gram-positive bacteria on the coral surface. The results demonstrate that exposure cyanide causes mortality to corals and anemones, even when applied at lower levels than that used by fish collectors. Even brief exposure to cyanide caused slow-acting and long-term damage to corals and their zooxanthellae.

  14. AdE-1, a new inotropic Na(+) channel toxin from Aiptasia diaphana, is similar to, yet distinct from, known anemone Na(+) channel toxins.

    Science.gov (United States)

    Nesher, Nir; Shapira, Eli; Sher, Daniel; Moran, Yehu; Tsveyer, Liora; Turchetti-Maia, Ana Luiza; Horowitz, Michal; Hochner, Binyamin; Zlotkin, Eliahu

    2013-04-01

    Heart failure is one of the most prevalent causes of death in the western world. Sea anemone contains a myriad of short peptide neurotoxins affecting many pharmacological targets, several of which possess cardiotonic activity. In the present study we describe the isolation and characterization of AdE-1 (ion channel modifier), a novel cardiotonic peptide from the sea anemone Aiptasia diaphana, which differs from other cnidarian toxins. Although AdE-1 has the same cysteine residue arrangement as sea anemone type 1 and 2 Na(+) channel toxins, its sequence contains many substitutions in conserved and essential sites and its overall homology to other toxins identified to date is low (Anemonia viridis toxin II), AdE-1 markedly inhibits Na(+) current inactivation with no significant effect on current activation, suggesting a similar mechanism of action. However, its effects on twitch relaxation velocity, action potential amplitude and on the time to peak suggest that this novel toxin affects cardiomyocyte function via a more complex mechanism. Additionally, Av2's characteristic delayed and early after-depolarizations were not observed. Despite its structural differences, AdE-1 physiologic effectiveness is comparable with Av2 with a similar ED(50) value to blowfly larvae. This finding raises questions regarding the extent of the universality of structure-function in sea anemone Na(+) channel toxins.

  15. Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

    Institute of Scientific and Technical Information of China (English)

    SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

    2014-01-01

    The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

  16. Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.

    Science.gov (United States)

    Jo, Jihoon; Oh, Jooseong; Lee, Hyun-Gwan; Hong, Hyun-Hee; Lee, Sung-Gwon; Cheon, Seongmin; Kern, Elizabeth M A; Jin, Soyeong; Cho, Sung-Jin; Park, Joong-Ki; Park, Chungoo

    2017-01-01

    The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6-14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research. © The Author 2017. Published by Oxford University Press.

  17. Exploring Archaeal Communities And Genomes Across Five Deep-Sea Brine Lakes Of The Red Sea With A Focus On Methanogens

    KAUST Repository

    Guan, Yue

    2015-12-15

    The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

  18. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Volckaert Filip AM

    2010-01-01

    Full Text Available Abstract Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690 were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.

  19. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

    KAUST Repository

    Othoum, Ghofran K

    2018-05-22

    BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.

  20. Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.

    Science.gov (United States)

    Lehnert, Erik M; Burriesci, Matthew S; Pringle, John R

    2012-06-22

    Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can lead to a breakdown of the essential symbiotic relationship between the coral host and its endosymbiotic dinoflagellates, a process known as coral bleaching. Although the environmental stresses causing this breakdown are largely known, the cellular mechanisms of symbiosis establishment, maintenance, and breakdown are still largely obscure. Investigating the symbiosis using an experimentally tractable model organism, such as the small sea anemone Aiptasia, should improve our understanding of exactly how the environmental stressors affect coral survival and growth. We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. We demonstrated that many of these contigs represent full-length or near-full-length transcripts that encode proteins similar to those from a diverse array of pathways in other organisms, including various metabolic enzymes, cytoskeletal proteins, and neuropeptide precursors. The contigs were annotated by sequence similarity, assigned GO terms, and scanned for conserved protein domains. We analyzed the frequency and types of single-nucleotide variants and estimated the size of the Aiptasia genome to be ~421 Mb. The contigs and annotations are available through NCBI (Transcription Shotgun Assembly database, accession numbers JV077153-JV134524) and at http://pringlelab.stanford.edu/projects.html. The availability of an extensive transcriptome assembly for A. pallida will facilitate analyses of gene-expression changes, identification of proteins of interest, and other studies in this important emerging model system.

  1. Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida

    Directory of Open Access Journals (Sweden)

    Lehnert Erik M

    2012-06-01

    Full Text Available Abstract Background Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can lead to a breakdown of the essential symbiotic relationship between the coral host and its endosymbiotic dinoflagellates, a process known as coral bleaching. Although the environmental stresses causing this breakdown are largely known, the cellular mechanisms of symbiosis establishment, maintenance, and breakdown are still largely obscure. Investigating the symbiosis using an experimentally tractable model organism, such as the small sea anemone Aiptasia, should improve our understanding of exactly how the environmental stressors affect coral survival and growth. Results We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. We demonstrated that many of these contigs represent full-length or near-full-length transcripts that encode proteins similar to those from a diverse array of pathways in other organisms, including various metabolic enzymes, cytoskeletal proteins, and neuropeptide precursors. The contigs were annotated by sequence similarity, assigned GO terms, and scanned for conserved protein domains. We analyzed the frequency and types of single-nucleotide variants and estimated the size of the Aiptasia genome to be ~421 Mb. The contigs and annotations are available through NCBI (Transcription Shotgun Assembly database, accession numbers JV077153-JV134524 and at http://pringlelab.stanford.edu/projects.html. Conclusions The availability of an extensive transcriptome assembly for A. pallida will facilitate analyses of gene-expression changes, identification of proteins of interest, and other studies in this

  2. Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis.

    Science.gov (United States)

    Long, Kyle A; Nossa, Carlos W; Sewell, Mary A; Putnam, Nicholas H; Ryan, Joseph F

    2016-01-01

    There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water vascular system, mutable collagenous tissues, and endoskeletons of high magnesium calcite. To our knowledge, the only echinoderm species with a genome sequence available to date is Strongylocentrotus pupuratus (Echinoidea). The availability of additional echinoderm genome sequences is crucial for understanding the biology of these animals. Here we present assembled draft genomes of the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis from Illumina sequence data with coverages of 12.5x, 22.5x, and 21.4x, respectively. These data provide a resource for mining gene superfamilies, identifying non-coding RNAs, confirming gene losses, and designing experimental constructs. They will be important comparative resources for future genomic studies in echinoderms.

  3. Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

    Science.gov (United States)

    Wang, Guojun; Barrett, Nolan H; McCarthy, Peter J

    2017-02-02

    The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. Copyright © 2017 Wang et al.

  4. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

    KAUST Repository

    Wang, Yong

    2016-07-01

    Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

  5. Genome-scale Evaluation of the Biotechnological Potential of Red Sea Bacilli Strains

    KAUST Repository

    Othoum, Ghofran K.

    2018-02-01

    The increasing spectrum of multidrug-resistant bacteria has caused a major global public health concern, necessitating the discovery of novel antimicrobial agents. Additionally, recent advancements in the use of microbial cells for the scalable production of industrial enzymes has encouraged the screening of new environments for efficient microbial cell factories. The unique ecological niche of the Red Sea points to the promising metabolic and biosynthetic potential of its microbial system. Here, ten sequenced Bacilli strains, that are isolated from microbial mat and mangrove mud samples from the Red Sea, were evaluated for their use as platforms for protein production and biosynthesis of bioactive compounds. Two of the species (B.paralicheniformis Bac48 and B. litoralis Bac94) were found to secrete twice as much protein as Bacillus subtilis 168, and B. litoralis Bac94 had complete Tat and Sec protein secretion systems. Additionally, four Red Sea Species (B. paralicheniformis Bac48, Virgibacillus sp. Bac330, B. vallismortis Bac111, B. amyloliquefaciens Bac57) showed capabilities for genetic transformation and possessed competence genes. More specifically, the distinctive biosynthetic potential evident in the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 was assessed and compared to nine available complete genomes of B. licheniformis and three genomes of B. paralicheniformis. A uniquely-structured trans-acyltransferase (trans-AT) polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) cluster in strains of this species was identified in the genome of B. paralicheniformis 48. In total, the two B. paralicheniformis Red Sea strains were found to be more enriched in modular clusters compared to B. licheniformis strains and B. paralicheniformis strains from other environments. These findings provided more insights into the potential of B. paralicheniformis 48 as a microbial cell factory and encouraged further focus on the strain

  6. Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake.

    KAUST Repository

    Antunes, Andre

    2011-09-01

    We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever isolated from a deep-sea anoxic brine. Genome comparison with Halorhabdus utahensis revealed some striking differences, including a marked increase in genes associated with transmembrane transport and putative genes for a trehalose synthase and a lactate dehydrogenase.

  7. Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake.

    KAUST Repository

    Antunes, Andre; Alam, Intikhab; Bajic, Vladimir B.; Stingl, Ulrich

    2011-01-01

    We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever isolated from a deep-sea anoxic brine. Genome comparison with Halorhabdus utahensis revealed some striking differences, including a marked increase in genes associated with transmembrane transport and putative genes for a trehalose synthase and a lactate dehydrogenase.

  8. Body size and symbiotic status influence gonad development in Aiptasia pallida anemones.

    Science.gov (United States)

    Carlisle, Judith F; Murphy, Grant K; Roark, Alison M

    2017-01-01

    Pale anemones ( Aiptasia pallida ) coexist with dinoflagellates (primarily Symbiodinium minutum ) in a mutualistic relationship. The purpose of this study was to investigate the role of these symbionts in gonad development of anemone hosts. Symbiotic and aposymbiotic anemones were subjected to light cycles that induced gametogenesis. These anemones were then sampled weekly for nine weeks, and gonad development was analyzed histologically. Anemone size was measured as mean body column diameter, and oocytes or sperm follicles were counted for each anemone. Generalized linear models were used to evaluate the influence of body size and symbiotic status on whether gonads were present and on the number of oocytes or sperm follicles produced. Body size predicted whether gonads were present, with larger anemones being more likely than smaller anemones to develop gonads. Both body size and symbiotic status predicted gonad size, such that larger and symbiotic anemones produced more oocytes and sperm follicles than smaller and aposymbiotic anemones. Overall, only 22 % of aposymbiotic females produced oocytes, whereas 63 % of symbiotic females produced oocytes. Similarly, 6 % of aposymbiotic males produced sperm follicles, whereas 60 % of symbiotic males produced sperm follicles. Thus, while gonads were present in 62 % of symbiotic anemones, they were present in only 11 % of aposymbiotic anemones. These results indicate that dinoflagellate symbionts influence gonad development and thus sexual maturation in both female and male Aiptasia pallida anemones. This finding substantiates and expands our current understanding of the importance of symbionts in the development and physiology of cnidarian hosts.

  9. Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity.

    Science.gov (United States)

    Yang, Shanjun; Yu, Mingjia; Chen, Jianming

    Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  10. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications.

    Science.gov (United States)

    Smith, Jeramiah J; Keinath, Melissa C

    2015-08-01

    It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution. © 2015 Smith and Keinath; Published by Cold Spring Harbor Laboratory Press.

  11. Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum.

    Science.gov (United States)

    Kis-Papo, Tamar; Weig, Alfons R; Riley, Robert; Peršoh, Derek; Salamov, Asaf; Sun, Hui; Lipzen, Anna; Wasser, Solomon P; Rambold, Gerhard; Grigoriev, Igor V; Nevo, Eviatar

    2014-05-09

    The Dead Sea is one of the most hypersaline habitats on Earth. The fungus Eurotium rubrum (Eurotiomycetes) is among the few species able to survive there. Here we highlight its adaptive strategies, based on genome analysis and transcriptome profiling. The 26.2 Mb genome of E. rubrum shows, for example, gains in gene families related to stress response and losses with regard to transport processes. Transcriptome analyses under different salt growth conditions revealed, among other things differentially expressed genes encoding ion and metabolite transporters. Our findings suggest that long-term adaptation to salinity requires cellular and metabolic responses that differ from short-term osmotic stress signalling. The transcriptional response indicates that halophilic E. rubrum actively counteracts the salinity stress. Many of its genes encode for proteins with a significantly higher proportion of acidic amino acid residues. This trait is characteristic of the halophilic prokaryotes as well, supporting the theory of convergent evolution under extreme hypersaline stress.

  12. INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

    Science.gov (United States)

    Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

    2013-01-01

    Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID

  13. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

    Energy Technology Data Exchange (ETDEWEB)

    Scott, K M; Sievert, S M; Abril, F N; Ball, L A; Barrett, C J; Blake, R A; Boller, A J; Chain, P G; Clark, J A; Davis, C R; Detter, C; Do, K F; Dobrinski, K P; Faza, B I; Fitzpatrick, K A; Freyermuth, S K; Harmer, T L; Hauser, L J; Hugler, M; Kerfeld, C A; Klotz, M G; Kong, W W; Land, M; Lapidus, A; Larimer, F W; Longo, D L; Lucas, S; Malfatti, S A; Massey, S E; Martin, D D; McCuddin, Z; Meyer, F; Moore, J L; Ocampo Jr., L H; Paul, J H; Paulsen, I T; Reep, D K; Ren, Q; Ross, R L; Sato, P Y; Thomas, P; Tinkham, L E; Zerugh, G T

    2007-01-10

    Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 bp), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of CDSs encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. T. crunogena XCL-2 is unusual among obligate sulfur oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. A 38 kb prophage is present, and a high level of prophage induction was observed, which may play a role in keeping competing populations of close relatives in check. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

  14. Cascading effects of thermally-induced anemone bleaching on associated anemonefish hormonal stress response and reproduction.

    Science.gov (United States)

    Beldade, Ricardo; Blandin, Agathe; O'Donnell, Rory; Mills, Suzanne C

    2017-10-10

    Organisms can behaviorally, physiologically, and morphologically adjust to environmental variation via integrative hormonal mechanisms, ultimately allowing animals to cope with environmental change. The stress response to environmental and social changes commonly promotes survival at the expense of reproduction. However, despite climate change impacts on population declines and diversity loss, few studies have attributed hormonal stress responses, or their regulatory effects, to climate change in the wild. Here, we report hormonal and fitness responses of individual wild fish to a recent large-scale sea warming event that caused widespread bleaching on coral reefs. This 14-month monitoring study shows a strong correlation between anemone bleaching (zooxanthellae loss), anemonefish stress response, and reproductive hormones that decreased fecundity by 73%. These findings suggest that hormone stress responses play a crucial role in changes to population demography following climate change and plasticity in hormonal responsiveness may be a key mechanism enabling individual acclimation to climate change.Elevated temperatures can cause anemones to bleach, with unknown effects on their associated symbiotic fish. Here, Beldade and colleagues show that climate-induced bleaching alters anemonefish hormonal stress response, resulting in decreased reproductive hormones and severely impacted reproduction.

  15. Biogeography, Cultivation and Genomic Characterization of Prochlorococcus in the Red Sea

    KAUST Repository

    Shibl, Ahmed A.

    2015-12-16

    unusual features of the Red Sea, a Prochlorococcus strain of the HL II adapted clade from the euphotic zone was cultured, enabling morphological analyses and growth rates measurements for the strain. In addition, we successfully sequenced and annotated the genome of the strain, which was then used for genomic comparison with other ecotypes. Interestingly, the set of unique genes identified in the draft genome included genes encoding proteins involved in salt tolerance mechanisms. The expression level and pattern of these genes in the Red Sea water column was explored through metatranscriptomic mapping and revealed their occurrence throughout, independent of the diel cycle. This led to the hypothesis that Prochlorococcus populations in the highly saline Red Sea are able to biosynthesize additional compatible solutes via several pathways to counterbalance the effects of salt stress. The results presented in this dissertation provide the first glimpse on how the environmental parameters of the Red Sea can affect the evolution, diversity and distribution patterns of Prochlorococcus ecotypes.

  16. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

    KAUST Repository

    Olsen, Jeanine L.

    2016-01-27

    Seagrasses colonized the sea1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet2. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes3, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae4 and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming5, 6, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants7.

  17. Phytochemicals and bioactivities of Anemone raddeana Regel: a review.

    Science.gov (United States)

    Sun, Yong-Xu; Liu, Ji-Cheng; Liu, Da-You

    2011-11-01

    Anemone raddeana, usually called as'"Toujian Liang" in China, is an Anemone herb belonging to the Ranunculaceae family. Until now there are in total 67 of chemical components identified including triterpenoids, steroids, lactones, fats and oils, saccharide and alkaloids. A broad spectrum of pharmacological activity of A. raddeana compounds have been reported, such as antitumor, antimicrobial, anti-inflammatory, sedative and analgesic activites, as well as anti-convulsant and anti-histamine effects. In view of this, we initiated this short review to present the phytochemical and pharmacological profile of A. raddeana to support future studies in this discipline.

  18. Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

    Science.gov (United States)

    Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

    2009-01-01

    The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

  19. Blocking actions of the sea anemone, Bunodosoma cavernata ...

    African Journals Online (AJOL)

    It was also found to block acetylcholine (ACh) – induced contractions of the ileum of grass cutter (90 + 6.2% inhibition + SEM) and the contractile action induced by ACh (0.2mg and 0.4mg) (89 + 5.8% inhibition + SEM) and histamine (0.075mg and 0.15mg) on the rabbit ileum (80 + 4.6% inhibition + SEM) . The antagonism ...

  20. Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake.

    KAUST Repository

    Antunes, Andre; Alam, Intikhab; El Dorry, Hamza; Siam, Rania; Robertson, Anthony J.; Bajic, Vladimir B.; Stingl, Ulrich

    2011-01-01

    We present the draft genome of Haloplasma contractile, isolated from a deep-sea brine and representing a new order between Firmicutes and Mollicutes. Its complex morphology with contractile protrusions might be strongly influenced by the presence of seven MreB/Mbl homologs, which appears to be the highest copy number ever reported.

  1. Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake.

    KAUST Repository

    Antunes, Andre

    2011-09-01

    We present the draft genome of Haloplasma contractile, isolated from a deep-sea brine and representing a new order between Firmicutes and Mollicutes. Its complex morphology with contractile protrusions might be strongly influenced by the presence of seven MreB/Mbl homologs, which appears to be the highest copy number ever reported.

  2. Two new triterpenoid saponins from rhizome of Anemone raddeana Regel

    DEFF Research Database (Denmark)

    Fan, Li; Lu, Jincai; Wang, Jing

    2009-01-01

    Two new 27-hydroxyoleanolic acid-type triterpenoid saponins, raddeanoside Ra (1) and raddeanoside Rb (2), were isolated from the rhizome of Anemone raddeana Regel. The structures of the two compounds were elucidated to be 27-hydroxyoleanolic acid 3-O-beta-D: -glucopyranosyl-(1 --> 4)-alpha...

  3. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    Directory of Open Access Journals (Sweden)

    Jia Yi Har

    2015-09-01

    Full Text Available We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e. Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P, polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins. We hypothesize that such activities may mediate acclimation and persistence of bacteria in N. vectensis.

  4. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.

    Science.gov (United States)

    Har, Jia Y; Helbig, Tim; Lim, Ju H; Fernando, Samodha C; Reitzel, Adam M; Penn, Kevin; Thompson, Janelle R

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and

  5. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan

    2011-01-01

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  6. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  7. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  8. Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction

    Directory of Open Access Journals (Sweden)

    Wan-Nan U. Chen

    2016-08-01

    Full Text Available Anemones of genus Exaiptasia are used as model organisms for the study of cnidarian-dinoflagellate (genus Symbiodinium endosymbiosis. However, while most reef-building corals harbor Symbiodinium of clade C, Exaiptasia spp. anemones mainly harbor clade B Symbiodinium (ITS2 type B1 populations. In this study, we reveal for the first time that bleached Exaiptasia pallida anemones can establish a symbiotic relationship with a clade C Symbiodinium (ITS2 type C1. We further found that anemones can transmit the exogenously supplied clade C Symbiodinium cells to their offspring by asexual reproduction (pedal laceration. In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system.

  9. Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan.

    Science.gov (United States)

    Hiraoka, Koichi; Tomaru, Nobuhiro

    2009-05-01

    Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species' range. Although population differentiation was very low (F (ST) = 0.027; R (ST) = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H (E) = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.

  10. Keragaman genetik simbion alga Zooxanthellae pada anemone laut Stichodactyla gigantea (Forsskal 1775 hasil reproduksi aseksual

    Directory of Open Access Journals (Sweden)

    M. AHSIN RIFA’I

    2012-11-01

    Full Text Available Rifa’i MA. 2012. Keragaman genetik simbion alga Zooxanthellae pada anemone laut Stichodactyla gigantea (Forsskal 1775 hasil reproduksi aseksual. Bioteknologi 9: 49-56. Penelitian ini bertujuan untuk mengetahui keragaman genetik simbion alga zooxanthellae yang bersimbiosis dengan anemon laut Stichodactyla gigantea hasil reproduksi aseksual dengan teknik fragmentasi. Penelitian dilaksanakan selama 10 bulan, mulai Oktober 2011 – Juli 2012, bertempat di kolam pembibitan Universitas Hasanuddin di Pulau Barrang Lompo dan kawasan terumbu karang Pulau Barrang Lompo. Rangkaian penelitian meliputi koleksi induk anemon laut, aklimatisasi, fragmentasi tubuh, dan kultur anemon di kawasan terumbu karang, serta koleksi alga zooxanthellae untuk analisis PCR-ISSR. Keragaman genetik dianalisis menggunakan analisis pengelompokan data matriks (cluster analysis dan pembuatan dendrogram pohon kekerabatan menggunakan metode UPGMA melalui program NTSYS. Hasilnya menunjukkan bahwa seluruh primer menghasilkan pita polimorfis antara 16,67%-66,67%. Hasil analisis variasi genetik terhadap zooxanthellae yang ditemukan pada anemon uji menunjukkan polimorfisme sebesar 37,93%. Sedangkan berdasarkan analisis jarak genetik ditemukan tingkat ketidakmiripan sebesar 19% yang bersumber dari 2 kelompok anemon utama yaitu kelompok anemon hasil fragmentasi 4 bagian (AF4 yang terpisah dengan kelompok anemon alami (AA dan anemon hasil fragmentasi 2 bagian (AF2.

  11. Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics

    KAUST Repository

    DiBattista, Joseph

    2016-08-04

    Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high-quality protein-coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo-Pacific. © 2016 John Wiley & Sons Ltd.

  12. Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics

    KAUST Repository

    DiBattista, Joseph; Wang, Xin; Saenz Agudelo, Pablo; Piatek, Marek J.; Aranda, Manuel; Berumen, Michael L.

    2016-01-01

    Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high-quality protein-coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo-Pacific. © 2016 John Wiley & Sons Ltd.

  13. Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey.

    Science.gov (United States)

    Ren, Jianfeng; Chung-Davidson, Yu-Wen; Yeh, Chu-Yin; Scott, Camille; Brown, Titus; Li, Weiming

    2015-06-06

    Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates. We conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed. Thirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC

  14. High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

    KAUST Repository

    Ngugi, David

    2018-05-09

    Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

  15. High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

    KAUST Repository

    Ngugi, David; Stingl, Ulrich

    2018-01-01

    Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

  16. Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus.

    Science.gov (United States)

    Evans, Tyler G; Padilla-Gamiño, Jacqueline L; Kelly, Morgan W; Pespeni, Melissa H; Chan, Francis; Menge, Bruce A; Gaylord, Brian; Hill, Tessa M; Russell, Ann D; Palumbi, Stephen R; Sanford, Eric; Hofmann, Gretchen E

    2015-07-01

    Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Is dimethylsulfoniopropionate (DMSP) produced by the symbionts or the host in an anemone-zooxanthella symbiosis?

    Science.gov (United States)

    van Alstyne, K. L.; Dominique, V. J.; Muller-Parker, G.

    2009-03-01

    Many groups of tropical cnidarians including scleractinian corals, octocorals, corallimorphs, and anemones contain the tertiary sulfonium compound dimethylsulfoniopropionate (DMSP). It is not known if the compound is synthesized by the animals, their microalgal symbionts, or derived through their diet. We determined the source of the DMSP in several species of tropical and temperate anemones using three approaches: (1) conducting comparative measurements of DMSP in aposymbiotic and zooxanthellate anemones of three species that harbor zooxanthellae, and similar measurements in one species that can harbor both zooxanthellae and zoochlorellae, (2) manipulating the presence or absence of zooxanthellae by inoculating juvenile aposymbiotic anemones ( Aiptasia pallida) with their symbiont, Symbiodinium bermudense, and (3) manipulating the numbers of S. bermudense by growing aposymbiotic and zooxanthellate A. pallida in the light and the dark. DMSP was present in zooxanthellate anemones in concentrations of 3.4-15 μmol g-1 fresh mass (FM). In aposymbiotic Aiptasia spp. and Anthopleura elegantissima that lacked large numbers of zooxanthellae, concentrations ranged from being undetectable to 0.43 μmol g-1 FM. When aposymbiotic A. pallida were inoculated with zooxanthellae, concentrations of DMSP were an average of 4.24 μmol g-1 FM after 5 weeks; DMSP was undetectable in uninoculated control animals. Aposymbiotic anemones maintained in the light or the dark for 6 weeks contained no DMSP or zooxanthellae. Zooxanthellate anemones in the light contained five times as many zooxanthellae and approximately 7.5 times as much DMSP as zooxanthellate anemones maintained in the dark. Taken together, these data show that the zooxanthellae are the sole source of DMSP in A. pallida. The trends in DMSP concentrations in other species of zooxanthellate anemones suggest that this phenomenon is not limited to A. pallida but may be more generally true for other anemones or even other

  18. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    KAUST Repository

    Alam, Intikhab; Antunes, André ; Kamau, Allan; Ba Alawi, Wail; Kalkatawi, Manal M.; Stingl, Ulrich; Bajic, Vladimir B.

    2013-01-01

    The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.

  19. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

    KAUST Repository

    Alam, Intikhab

    2013-12-06

    The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.

  20. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe.

    Science.gov (United States)

    Triska, Petr; Chekanov, Nikolay; Stepanov, Vadim; Khusnutdinova, Elza K; Kumar, Ganesh Prasad Arun; Akhmetova, Vita; Babalyan, Konstantin; Boulygina, Eugenia; Kharkov, Vladimir; Gubina, Marina; Khidiyatova, Irina; Khitrinskaya, Irina; Khrameeva, Ekaterina E; Khusainova, Rita; Konovalova, Natalia; Litvinov, Sergey; Marusin, Andrey; Mazur, Alexandr M; Puzyrev, Valery; Ivanoshchuk, Dinara; Spiridonova, Maria; Teslyuk, Anton; Tsygankova, Svetlana; Triska, Martin; Trofimova, Natalya; Vajda, Edward; Balanovsky, Oleg; Baranova, Ancha; Skryabin, Konstantin; Tatarinova, Tatiana V; Prokhortchouk, Egor

    2017-12-28

    The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers

  1. Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp

    KAUST Repository

    Wang, Xin

    2017-04-13

    Corallimorpharia are the closest non-calcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp.. The draft genomes encompass 370 Mbp and 445 Mbp respectively and encode for 21,372 and 23,199 genes. To facilitate future studies using these resources, we provide annotations for the predicted gene models-not only at gene level, by annotating gene models with the function of the best-matching homolog, and GO terms when available; but also at protein domain level, where gene function can be better verified through the conservation of the sequence and order of protein domains. Further, we provide an online platform (http://corallimorpharia.reefgenomics.org), which includes a BLAST interface as well as a genome browser to facilitate the use of these resources. We believe that these two genomes are important resources for future studies on hexacorallian systematics and the evolutionary basis of their specific traits such as the symbiotic relationship with dinoflagellates of the genus Symbiodinium or the evolution of calcification in reef-building corals. This article is protected by copyright. All rights reserved.

  2. Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity.

    Science.gov (United States)

    Teikari, Jonna E; Hou, Shengwei; Wahlsten, Matti; Hess, Wolfgang R; Sivonen, Kaarina

    2018-01-01

    Salinity is an important abiotic factor controlling the distribution and abundance of Nodularia spumigena , the dominating diazotrophic and toxic phototroph, in the brackish water cyanobacterial blooms of the Baltic Sea. To expand the available genomic information for brackish water cyanobacteria, we sequenced the isolate Nodularia spumigena UHCC 0039 using an Illumina-SMRT hybrid sequencing approach, revealing a chromosome of 5,294,286 base pairs (bp) and a single plasmid of 92,326 bp. Comparative genomics in Nostocales showed pronounced genetic similarity among Nodularia spumigena strains evidencing their short evolutionary history. The studied Baltic Sea strains share similar sets of CRISPR-Cas cassettes and a higher number of insertion sequence (IS) elements compared to Nodularia spumigena CENA596 isolated from a shrimp production pond in Brazil. Nodularia spumigena UHCC 0039 proliferated similarly at three tested salinities, whereas the lack of salt inhibited its growth and triggered transcriptome remodeling, including the up-regulation of five sigma factors and the down-regulation of two other sigma factors, one of which is specific for strain UHCC 0039. Down-regulated genes additionally included a large genetic region for the synthesis of two yet unidentified natural products. Our results indicate a remarkable plasticity of the Nodularia salinity acclimation, and thus salinity strongly impacts the intensity and distribution of cyanobacterial blooms in the Baltic Sea.

  3. Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity

    Directory of Open Access Journals (Sweden)

    Jonna E. Teikari

    2018-03-01

    Full Text Available Salinity is an important abiotic factor controlling the distribution and abundance of Nodularia spumigena, the dominating diazotrophic and toxic phototroph, in the brackish water cyanobacterial blooms of the Baltic Sea. To expand the available genomic information for brackish water cyanobacteria, we sequenced the isolate Nodularia spumigena UHCC 0039 using an Illumina-SMRT hybrid sequencing approach, revealing a chromosome of 5,294,286 base pairs (bp and a single plasmid of 92,326 bp. Comparative genomics in Nostocales showed pronounced genetic similarity among Nodularia spumigena strains evidencing their short evolutionary history. The studied Baltic Sea strains share similar sets of CRISPR-Cas cassettes and a higher number of insertion sequence (IS elements compared to Nodularia spumigena CENA596 isolated from a shrimp production pond in Brazil. Nodularia spumigena UHCC 0039 proliferated similarly at three tested salinities, whereas the lack of salt inhibited its growth and triggered transcriptome remodeling, including the up-regulation of five sigma factors and the down-regulation of two other sigma factors, one of which is specific for strain UHCC 0039. Down-regulated genes additionally included a large genetic region for the synthesis of two yet unidentified natural products. Our results indicate a remarkable plasticity of the Nodularia salinity acclimation, and thus salinity strongly impacts the intensity and distribution of cyanobacterial blooms in the Baltic Sea.

  4. The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae: arthropod ground pattern of gene arrangement

    Directory of Open Access Journals (Sweden)

    Lee Yong-Seok

    2007-10-01

    Full Text Available Abstract Background The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae, was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis. Results The complete mitochondrial genome (15,474 bp of a sea spider (Achelia bituberculata belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes. The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile may be closely related to the clade of Acari and Araneae. Conclusion The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like, but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be

  5. Characterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea.

    Science.gov (United States)

    Li, Baolian; Zhang, Si; Long, Lijuan; Huang, Sijun

    2016-09-01

    Three bacteriophages (RD-1410W1-01, RD-1410Ws-07, and DS-1410Ws-06) were isolated from the surface water of Sanya Bay, northern South China Sea, on two marine bacteria type strains of the Roseobacter lineage. These phages have an isometric head and a short tail, morphologically belonging to the Podoviridae family. Two of these phages can infect four of seven marine roseobacter strains tested and the other one can infect three of them, showing relatively broader host ranges compared to known N4-like roseophages. One-step growth curves showed that these phages have similar short latent periods (1-2 h) but highly variable burst sizes (27-341 pfu cell(-1)). Their complete genomes show high level of similarities to known N4-like roseophages in terms of genome size, G + C content, gene content, and arrangement. The morphological and genomic features of these phages indicate that they belong to the N4likevirus genus. Moreover, comparative genomic analysis based on 43 N4-like phages (10 roseobacter phages and 33 phages infecting other lineages of bacteria) revealed a core genome of 18 genes shared by all the 43 phages and 38 genes shared by all the ten roseophages. The 38 core genes of N4-like roseophages nearly make up 70 % of each genome in length. Phylogenetic analysis based on the concatenated core gene products showed that our phage isolates represent two new phyletic branches, suggesting the broad genetic diversity of marine N4-like roseophages remains.

  6. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

    KAUST Repository

    Ngugi, David

    2014-08-08

    The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate \\'switch\\' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

  7. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

    Science.gov (United States)

    Kamanda Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba-Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas; Guan, Yue; Antunes, Andre; Siam, Rania; El Dorry, Hamza; Bajic, Vladimir; Stingl, Ulrich

    2015-01-01

    The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate ‘switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA. PMID:25105904

  8. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

    KAUST Repository

    Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas I.; Guan, Yue; Antunes, Andre; Siam, Rania; El-Dorry, Hamza A A; Bajic, Vladimir B.; Stingl, Ulrich

    2014-01-01

    The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

  9. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.

    Science.gov (United States)

    Kamanda Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba-Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas; Guan, Yue; Antunes, Andre; Siam, Rania; El Dorry, Hamza; Bajic, Vladimir; Stingl, Ulrich

    2015-02-01

    The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

  10. Spiral phyllotaxis underlies constrained variation in Anemone (Ranunculaceae) tepal arrangement.

    Science.gov (United States)

    Kitazawa, Miho S; Fujimoto, Koichi

    2018-05-01

    Stabilization and variation of floral structures are indispensable for plant reproduction and evolution; however, the developmental mechanism regulating their structural robustness is largely unknown. To investigate this mechanism, we examined positional arrangement (aestivation) of excessively produced perianth organs (tepals) of six- and seven-tepaled (lobed) flowers in six Anemone species (Ranunculaceae). We found that the tepal arrangement that occurred in nature varied intraspecifically between spiral and whorled arrangements. Moreover, among the studied species, variation was commonly limited to three types, including whorls, despite five geometrically possible arrangements in six-tepaled flowers and two types among six possibilities in seven-tepaled flowers. A spiral arrangement, on the other hand, was unique to five-tepaled flowers. A spiral phyllotaxis model with stochasticity on initiating excessive primordia accounted for these limited variations in arrangement in cases when the divergence angle between preexisting primordia was less than 144°. Moreover, interspecific differences in the frequency of the observed arrangements were explained by the change of model parameters that represent meristematic growth and differential organ growth. These findings suggest that the phyllotaxis parameters are responsible for not only intraspecific stability but interspecific difference of floral structure. Decreasing arrangements from six-tepaled to seven-tepaled Anemone flowers demonstrate that the stabilization occurs as development proceeds to increase the component (organ) number, in contrast from the intuition that the variation will be larger due to increasing number of possible states (arrangements).

  11. High in situ repeatability of behaviour indicates animal personality in the beadlet anemone Actinia equina (Cnidaria.

    Directory of Open Access Journals (Sweden)

    Mark Briffa

    Full Text Available 'Animal personality' means that individuals differ from one another in either single behaviours or suites of related behaviours in a way that is consistent over time. It is usually assumed that such consistent individual differences in behaviour are driven by variation in how individuals respond to information about their environment, rather than by differences in external factors such as variation in microhabitat. Since behavioural variation is ubiquitous in nature we might expect 'animal personality' to be present in diverse taxa, including animals with relatively simple nervous systems. We investigated in situ startle responses in a sea anemone, Actinia equina, to determine whether personalities might be present in this example of an animal with a simple nervous system. We found very high levels of repeatability among individuals that were re-identified in the same locations over a three week sampling period. In a subset of the data, where we used tide-pool temperature measurements to control for a key element of variation in microhabitat, these high levels of repeatability remained. Although a range of other consistent differences in micro-habitat features could have contributed to consistent differences between the behaviour of individuals, these data suggest the presence of animal personality in A. equina. Rather than being restricted to certain groups, personality may be a general feature of animals and may be particularly pronounced in species with simple nervous systems.

  12. Genome-scale Evaluation of the Biotechnological Potential of Red Sea Bacilli Strains

    KAUST Repository

    Othoum, Ghofran K.

    2018-01-01

    production of industrial enzymes has encouraged the screening of new environments for efficient microbial cell factories. The unique ecological niche of the Red Sea points to the promising metabolic and biosynthetic potential of its microbial system. Here

  13. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney

    Energy Technology Data Exchange (ETDEWEB)

    Copeland, A [U.S. Department of Energy, Joint Genome Institute; Gu, Wei [U.S. Department of Energy, Joint Genome Institute; Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2012-01-01

    Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1 T was the first isolate within the phylum ThermusDeinococcus to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1 T is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney.

    Science.gov (United States)

    Copeland, Alex; Gu, Wei; Yasawong, Montri; Lapidus, Alla; Lucas, Susan; Deshpande, Shweta; Pagani, Ioanna; Tapia, Roxanne; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Pan, Chongle; Brambilla, Evelyne-Marie; Rohde, Manfred; Tindall, Brian J; Sikorski, Johannes; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2012-03-19

    Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1(T) was the first isolate within the phylum "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1(T) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Pharmacological effects of two cytolysins isolated from the sea ...

    Indian Academy of Sciences (India)

    Sticholysins I and II (St I/II) are cytolysins purified from the sea anemone Stichodactyla helianthus. In this study, we show their pharmacological action on guinea-pig and snail models in native and pH-denatured conditions in order to correlate the pharmacological findings with the pore-forming activity of both isoforms.

  16. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus.

    Directory of Open Access Journals (Sweden)

    Juan Wang

    Full Text Available Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE for 30 individuals from two populations. The nucleotide diversity (π for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001 and the putatively neutral SNPs (FST = 0.0347, P < 0.001. However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001. Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40% significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

  17. Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea

    KAUST Repository

    Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Hikmawan, Tyas I.; Stingl, Ulrich

    2016-01-01

    Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface of Erba Deep in the Red Sea, Saudi Arabia. Here, we present the draft genome sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides for biofilm formation when grown in liquid culture.

  18. Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

    KAUST Repository

    Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2015-01-01

    We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

  19. Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

    KAUST Repository

    Barbato, Marta

    2015-12-10

    We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

  20. Draft Genome Sequences of TwoThiomicrospiraStrains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea

    KAUST Repository

    Zhang, Guishan

    2016-03-11

    Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater interface in the Red Sea, Saudi Arabia. Here, we present the draft genome sequences of these gammaproteobacteria, which both produce sulfuric acid from thiosulfate in culture.

  1. Draft Genome Sequences of TwoThiomicrospiraStrains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea

    KAUST Repository

    Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Hikmawan, Tyas I.; Stingl, Ulrich

    2016-01-01

    Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater interface in the Red Sea, Saudi Arabia. Here, we present the draft genome sequences of these gammaproteobacteria, which both produce sulfuric acid from thiosulfate in culture.

  2. Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone.

    Science.gov (United States)

    Wang, Xing; Lin, Danqiu; Jing, Xiaohuan; Zhu, Sidong; Yang, Jifang; Chen, Jigang

    2018-01-20

    Staphylococcus sp. AntiMn-1 is a deep-sea bacterium inhabiting seafloor sediment in the Clarion-Clipperton Zone (CCZ) that is highly tolerant to Mn(II) and displays efficient Mn(II) oxidation. Herein, we present the assembly and annotation of its genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea

    KAUST Repository

    Zhang, Guishan

    2016-03-10

    Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface of Erba Deep in the Red Sea, Saudi Arabia. Here, we present the draft genome sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides for biofilm formation when grown in liquid culture.

  4. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  5. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

    KAUST Repository

    Wang, Yong; Gao, Zhao-Ming; Li, Jiang-Tao; Bougouffa, Salim; Tian, Ren Mao; Bajic, Vladimir B.; Qian, Pei-Yuan

    2016-01-01

    and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross

  6. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospiracrunogena XCL-2

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Kathleen M.; Sievert, Stefan M.; Abril, Fereniki N.; Ball,Lois A.; Barrett, Chantell J.; Blake, Rodrigo A.; Boller, Amanda J.; Chain, Patrick S.G.; Clark, Justine A.; Davis, Carisa R.; Detter, Chris; Do, Kimberly F.; Dobrinski, Kimberly P.; Faza, BrandonI.; Fitzpatrick,Kelly A.; Freyermuth, Sharyn K.; Harmer, Tara L.; Hauser, Loren J.; Hugler, Michael; Kerfeld, Cheryl A.; Klotz, Martin G.; Kong, William W.; Land, Miriam; Lapidus, Alla; Larimer, Frank W.; Longo, Dana L.; Lucas,Susan; Malfatti, Stephanie A.; Massey, Steven E.; Martin, Darlene D.; McCuddin, Zoe; Meyer, Folker; Moore, Jessica L.; Ocampo, Luis H.; Paul,John H.; Paulsen, Ian T.; Reep, Douglas K.; Ren, Qinghu; Ross, Rachel L.; Sato, Priscila Y.; Thomas, Phaedra; Tinkham, Lance E.; Zeruth, Gary T.

    2006-08-23

    Presented here is the complete genome sequence ofThiomicrospira crunogena XCL-2, representative of ubiquitouschemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-seahydrothermal vents. This gammaproteobacterium has a single chromosome(2,427,734 bp), and its genome illustrates many of the adaptations thathave enabled it to thrive at vents globally. It has 14 methyl-acceptingchemotaxis protein genes, including four that may assist in positioningit in the redoxcline. A relative abundance of CDSs encoding regulatoryproteins likely control the expression of genes encoding carboxysomes,multiple dissolved inorganic nitrogen and phosphate transporters, as wellas a phosphonate operon, which provide this species with a variety ofoptions for acquiring these substrates from the environment. T. crunogenaXCL-2 is unusual among obligate sulfur oxidizing bacteria in relying onthe Sox system for the oxidation of reduced sulfur compounds. A 38 kbprophage is present, and a high level of prophage induction was observed,which may play a role in keeping competing populations of close relativesin check. The genome has characteristics consistent with an obligatelychemolithoautotrophic lifestyle, including few transporters predicted tohave organic allocrits, and Calvin-Benson-Bassham cycle CDSs scatteredthroughout the genome.

  7. How do Bacteria Adapt to the Red Sea? Cultivation and Genomic and Physiological Characterization of Oligotrophic Bacteria of the PS1, OM43, and SAR11 Clades

    KAUST Repository

    Jimenez Infante, Francy M.

    2015-05-01

    Given the high salinity, prevailing annual high temperatures, and ultra-oligotrophic conditions in the Red Sea isolation and characterization of important microbial groups thriving in this environment is important in understanding the ecological significance and metabolic capabilities of these communities. By using a high-­throughput cultivation technique in natural seawater amended with minute amounts of nutrients, members of the rare biosphere (PS1), methylotrophic Betaproteobacteria (OM43), and the ubiquitous and abundant SAR11 group (Pelagibacterales), were isolated in pure culture. Phylogenetic analyses of Red Sea isolates along with comparative genomics with close representatives from disparate provinces revealed ecotypes and genomic differentiation among the groups. Firstly, the PS1 alphaproteobacterial clade was found to be present in very low abundance in several metagenomic datasets form divergent environments. While strain RS24 (Red Sea) harbored genomic islands involved in polymer degradation, IMCC14465 (East (Japan) Sea) contained unique genes for degradation of aromatic compounds. Secondly, methylotrophic OM43 bacteria from the Red Sea (F5, G12 and H7) showed higher similarities with KB13 isolate from Hawaii, forming a ‘H-­RS’ (Hawaii-­Red Sea) cluster separate from HTCC2181 (Oregon isolate). HTCC2181 members were shown to prevail in cold, productive coastal environments and had an nqrA-­F system for energy generation by sodium motive force. On the contrary, H-­RS cluster members may be better adapted to warm and oligotrophic environments, and seem to generate energy by using a proton-­translocating NADH:Quinone oxidoreductase (complex I; nuoA-­N subunits). Moreover, F5, G12, and H7 had unique proteins related to resistance to UV, temperature and salinity, in addition to a heavy metal ‘resistance island’ as adaptive traits to cope with the environmental conditions in the Red Sea. Finally, description of the Red Sea Pelagibacterales

  8. Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

    Science.gov (United States)

    Lu, G. S.; Amend, J.

    2015-12-01

    Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken

  9. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    Directory of Open Access Journals (Sweden)

    Zhou Bai-Cheng

    2010-04-01

    Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

  10. Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis

    Science.gov (United States)

    Morrison, Cheryl L.; Iwanowicz, Luke R.; Work, Thierry M.; Fahsbender, Elizabeth; Breitbart, Mya; Adams, Cynthia; Iwanowicz, Deborah; Sanders, Lakyn; Ackermann, Mathias; Cornman, Robert S.

    2018-01-01

    Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.

  11. Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis.

    Science.gov (United States)

    Morrison, Cheryl L; Iwanowicz, Luke; Work, Thierry M; Fahsbender, Elizabeth; Breitbart, Mya; Adams, Cynthia; Iwanowicz, Deb; Sanders, Lakyn; Ackermann, Mathias; Cornman, Robert S

    2018-01-01

    Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.

  12. Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis

    Directory of Open Access Journals (Sweden)

    Cheryl L. Morrison

    2018-02-01

    Full Text Available Chelonid alphaherpesvirus 5 (ChHV5 is a herpesvirus associated with fibropapillomatosis (FP in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%, and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent co-infection of individuals by well-differentiated geographic variants.

  13. Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade.

    Science.gov (United States)

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Blom, Jochen; Alam, Intikhab; Bajic, Vladimir B; Stingl, Ulrich

    2017-07-01

    The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea: one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade

    KAUST Repository

    Jimenez Infante, Francy M.

    2017-06-22

    The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain-specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.

  15. Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade

    KAUST Repository

    Jimenez Infante, Francy M.; Ngugi, David; Vinu, Manikandan; Blom, Jochen; Alam, Intikhab; Bajic, Vladimir B.; Stingl, Ulrich

    2017-01-01

    The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain-specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.

  16. Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).

    Science.gov (United States)

    Dunlap, Paul V; Ast, Jennifer C

    2005-02-01

    Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of

  17. The mitochondrial genome of the deep-sea glass sponge Lophophysema eversa (Porifera, Hexacinellida, Hyalonematidae).

    Science.gov (United States)

    Zhang, Yanjie; Sun, Jin; Li, Xinzheng; Qiu, Jian-Wen

    2016-01-01

    We reported a nearly complete mitochondrial genome (mitogenome) from the glass sponge Lophophysema eversa, the second mitogenome in the order Amphidiscosida and the ninth in the class Hexactinellida. It is 20,651 base pairs in length and contains 39 genes including 13 protein-coding genes, 2 ribosomal RNA subunit genes and 24 tRNA genes. The gene content and order of L. eversa are identical to those of Tabachnickia sp., the other species with a sequenced mitogenome in Amphidiscosida, except with two additional tRNAs and three tRNA translocations. The cob gene has a +1 translational frameshift. These results will contribute to a better understanding of the phylogeny of glass sponges.

  18. Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes.

    Science.gov (United States)

    Sewell, Holly L; Kaster, Anne-Kristin; Spormann, Alfred M

    2017-12-19

    The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive

  19. Using Nematostella vectensis to study the interactions between genome, epigenome and bacteria in a changing environment

    Directory of Open Access Journals (Sweden)

    Sebastian Fraune

    2016-08-01

    Full Text Available The phenotype of an animal cannot be explained entirely by its genes. It is now clear that factors other than the genome contribute to the ecology and evolution of animals. Two fundamentally important factors are the associated microbiota and epigenetic regulations. Unlike the genes and regulatory regions of the genome, epigenetics and microbial composition can be rapidly modified, and may thus represent mechanisms for rapid acclimation to a changing environment. At present, the individual functions of epigenetics, microbiomes, and genomic mutations are largely studied in isolation, particularly for species in marine ecosystems. This single variable approach leaves significant questions open for how these mechanisms intersect in the acclimation and adaptation of organisms in different environments. Here, we propose that the starlet sea anemone, Nematostella vectensis, is a model of choice to investigate the complex interplay between adaptation as well as physiological and molecular plasticity in coastal ecosystems. N. vectensis’ geographic range spans four distinct coastlines, including a wide thermocline along the Atlantic coast of North America. N. vectensis is a particularly powerful invertebrate model for studying genome-environment interactions due to (1 the availability of a well-annotated genome, including preexisting data on genome methylation, histone modifications and miRNAs, (2 an extensive molecular toolkit including well-developed protocols for gene suppression and transgenesis, and (3 the simplicity of culture and experimentation in the laboratory. Taken together, N. vectensis has the tractability to connect the functional relationships between a host animal, microbes, and genome modifications to determine mechanisms underlying phenotypic plasticity and local adaptation.

  20. Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

    Science.gov (United States)

    Figueroa, Diego F.; Baco, Amy R.

    2014-01-01

    In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed

  1. Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification

    Science.gov (United States)

    Dorey, Narimane; Garfield, David A.; Stumpp, Meike; Dupont, Sam; Wray, Gregory A.

    2016-01-01

    Abstract Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms’ health and persistence, an understanding is needed of the 1) mechanisms underlying developmental and physiological tolerance and 2) potential populations have for rapid evolutionary adaptation. This is especially challenging in nonmodel species where targeted assays of metabolism and stress physiology may not be available or economical for large-scale assessments of genetic constraints. We used mRNA sequencing and a quantitative genetics breeding design to study mechanisms underlying genetic variability and tolerance to decreased seawater pH (-0.4 pH units) in larvae of the sea urchin Strongylocentrotus droebachiensis. We used a gene ontology-based approach to integrate expression profiles into indirect measures of cellular and biochemical traits underlying variation in larval performance (i.e., growth rates). Molecular responses to OA were complex, involving changes to several functions such as growth rates, cell division, metabolism, and immune activities. Surprisingly, the magnitude of pH effects on molecular traits tended to be small relative to variation attributable to segregating functional genetic variation in this species. We discuss how the application of transcriptomics and quantitative genetics approaches across diverse species can enrich our understanding of the biological impacts of climate change. PMID:28082601

  2. Correlation of Coral Bleaching Events and Remotely-Sensed Sea Surface Temperatures

    Science.gov (United States)

    1994-05-19

    water column. Diving on the reefs, they found significant tracts of bleached corals, zoanthids , gorgonians, and sea anemones (Bunckley-Williams and... zoanthids between May and July 1988 on shallow lagoonal reefs and rim margin reefs was the first indication of any sort of bleaching event at Bermuda

  3. The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus.

    Directory of Open Access Journals (Sweden)

    Nathalie Pradel

    Full Text Available Desulfovibrio piezophilus strain C1TLV30(T is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.

  4. A Taxonomic Note on the Misidentification of Anemone tschernjaewii Regel. in Kashmir Himalaya

    Directory of Open Access Journals (Sweden)

    Aijaz Hassan Ganie

    2015-03-01

    Full Text Available The correct identification of Anemone tschernjaewii Regel. previously misidentified as A. biflora DC. in the Kashmir Himalaya, India is reported. In this brief report, a detailed taxonomic description and photo-plates of its diagnostic morphological and anatomical characters are provided to validate this plant record for the region and to facilitate its easier field identification.

  5. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

    Science.gov (United States)

    Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  6. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grötzinger, Stefan W.

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  7. Short Toxin-like Proteins Abound in Cnidaria Genomes

    Directory of Open Access Journals (Sweden)

    Michal Linial

    2012-11-01

    Full Text Available Cnidaria is a rich phylum that includes thousands of marine species. In this study, we focused on Anthozoa and Hydrozoa that are represented by the Nematostella vectensis (Sea anemone and Hydra magnipapillata genomes. We present a method for ranking the toxin-like candidates from complete proteomes of Cnidaria. Toxin-like functions were revealed using ClanTox, a statistical machine-learning predictor trained on ion channel inhibitors from venomous animals. Fundamental features that were emphasized in training ClanTox include cysteines and their spacing along the sequences. Among the 83,000 proteins derived from Cnidaria representatives, we found 170 candidates that fulfill the properties of toxin-like-proteins, the vast majority of which were previously unrecognized as toxins. An additional 394 short proteins exhibit characteristics of toxin-like proteins at a moderate degree of confidence. Remarkably, only 11% of the predicted toxin-like proteins were previously classified as toxins. Based on our prediction methodology and manual annotation, we inferred functions for over 400 of these proteins. Such functions include protease inhibitors, membrane pore formation, ion channel blockers and metal binding proteins. Many of the proteins belong to small families of paralogs. We conclude that the evolutionary expansion of toxin-like proteins in Cnidaria contributes to their fitness in the complex environment of the aquatic ecosystem.

  8. Spawning of coral reef invertebrates and a second spawning season for scleractinian corals in the central Red Sea

    KAUST Repository

    Bouwmeester, Jessica; Gatins, Remy; Giles, Emily; Sinclair-Taylor, Tane; Berumen, Michael L.

    2016-01-01

    species, as well as a general lack of data for other invertebrates. Here, we document the detailed timing of spawning for 13 scleractinian coral species, one sea anemone, and six echinoderms from an inshore reef off the coast of Thuwal, Saudi Arabia

  9. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Directory of Open Access Journals (Sweden)

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  10. The draft genomes of soft–shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan

    OpenAIRE

    Wang, Zhuo; Pascual-Anaya, Juan; Zadissa, Amonida; Li, Wenqi; Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro

    2013-01-01

    The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ~267.9–248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these tu...

  11. Reproduction of Persian Gulf anemone fish (Amphiprion clarkii) in captive system

    OpenAIRE

    Javad Sahandi

    2011-01-01

    The present study was carried out to assess the reproduction of Persian Gulf anemone fish,Amphiprion clarkii (Bennett, 1830), in captive conditions with artificial features. Persian Gulf, havinggood relation with Indian Ocean, is one of the important niches of fishes and the specific position ofthis Gulf makes its fishes popular. The yellow tail clown fish which originates to this gulf has the bestsurvival rate and health than the other areas. Live food is the most important factor in product...

  12. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.

    Science.gov (United States)

    Speth, Daan R; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei-Yuan; Dutilh, Bas E; Jetten, Mike S M

    2017-07-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

  13. The Antitumor Effects of Triterpenoid Saponins from the Anemone flaccida and the Underlying Mechanism

    Directory of Open Access Journals (Sweden)

    Lin-Tao Han

    2013-01-01

    Full Text Available Anemone flaccida Fr. Schmidt, a family of ancient hopanoids, have been used as traditional Asian herbs for the treatments of inflammation and convulsant diseases. Previous study on HeLa cells suggested that triterpenoid saponins from Anemone flaccida Fr. Schmidt may have potential antitumor effect due to their apoptotic activities. Here, we confirmed the apoptotic activities of the following five triterpenoid saponins: glycoside St-I4a (1, glycoside St-J (2, anhuienoside E (3, hedera saponin B (4, and flaccidoside II (5 on human BEL-7402 and HepG2 hepatoma cell lines, as well as the model of HeLa cells treated with lipopolysaccharide (LPS. We found that COX-2/PGE2 signaling pathway, which plays key roles in the development of cancer, is involved in the antitumor activities of these saponins. These data provide the evidence that triterpenoid saponins can induce apoptosis via COX-2/PGE2 pathway, implying a preventive role of saponins from Anemone flaccida in tumor.

  14. Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

    Directory of Open Access Journals (Sweden)

    Holly L. Sewell

    2017-12-01

    Full Text Available The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4 in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2 as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA in the phylum Chloroflexi (DscP3 and Dsc4, including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187 of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of

  15. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda bears a novel gene order and unusual control region features

    Directory of Open Access Journals (Sweden)

    Podsiadlowski Lars

    2006-09-01

    Full Text Available Abstract Background Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc. comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp, and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already

  16. Characterization of glutathione peroxidase diversity in the symbiotic sea anemone Anemonia viridis

    OpenAIRE

    Pey , Alexis; Zamoum , Thamilla; Christen , Richard; Merle , Pierre-Laurent; Furla , Paola

    2016-01-01

    International audience; Cnidarians living in symbiosis with photosynthetic dinoflagellates (commonly named zooxanthellae) are exposed to high concentrations of reactive oxygen species (ROS) upon illumination. To quench ROS production, both the cnidarian host and zooxanthellae express a full suite of antioxidant enzymes. Studying antioxidative balance is therefore crucial to understanding how symbiotic cnidarians cope with ROS production. We characterized glutathione peroxidases (GPx) in the s...

  17. RGM regulates BMP-mediated secondary axis formation in the sea anemone Nematostella vectensis.

    Science.gov (United States)

    Leclère, Lucas; Rentzsch, Fabian

    2014-12-11

    Patterning of the metazoan dorsoventral axis is mediated by a complex interplay of BMP signaling regulators. Repulsive guidance molecule (RGM) is a conserved BMP coreceptor that has not been implicated in axis specification. We show that NvRGM is a key positive regulator of BMP signaling during secondary axis establishment in the cnidarian Nematostella vectensis. NvRGM regulates first the generation and later the shape of a BMP-dependent Smad1/5/8 gradient with peak activity on the side opposite the NvBMP/NvRGM/NvChordin expression domain. Full knockdown of Smad1/5/8 signaling blocks the formation of endodermal structures, the mesenteries, and the establishment of bilateral symmetry, while altering the gradient through partial NvRGM or NvBMP knockdown shifts the boundaries of asymmetric gene expression and the positioning of the mesenteries along the secondary axis. These findings provide insight into the diversification of axis specification mechanisms and identify a previously unrecognized role for RGM in BMP-mediated axial patterning. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification

    KAUST Repository

    Fan, Ming

    2012-06-28

    With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2012 Fan et al.

  19. SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification

    KAUST Repository

    Fan, Ming; Wong, Ka-Chun; Ryu, Tae Woo; Ravasi, Timothy; Gao, Xin

    2012-01-01

    With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2012 Fan et al.

  20. A deep sea community at the Kebrit brine pool in the Red Sea

    KAUST Repository

    Vestheim, Hege

    2015-02-26

    Approximately 25 deep sea brine pools occur along the mid axis of the Red Sea. These hypersaline, anoxic, and acidic environments have previously been reported to host diverse microbial communities. We visited the Kebrit brine pool in April 2013 and found macrofauna present just above the brine–seawater interface (~1465 m). In particular, inactive sulfur chimneys had associated epifauna of sea anemones, sabellid type polychaetes, and hydroids, and infauna consisting of capitellid polychaetes, gastropods of the genus Laeviphitus (fam. Elachisinidae), and top snails of the family Cocculinidae. The deep Red Sea generally is regarded as extremely poor in benthos. We hypothesize that the periphery along the Kebrit holds increased biomass and biodiversity that are sustained by prokaryotes associated with the brine pool or co-occurring seeps.

  1. The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp.

    Science.gov (United States)

    Sun, Shao'e; Hui, Ming; Wang, Minxiao; Sha, Zhongli

    2018-03-01

    Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing. The mitogenome of S. leurokolos was 15,903bp in length, containing 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of sequenced alvinocaridids. It has the longest concatenated sequences of protein-coding genes, tRNAs and shortest pooled rRNAs among the alvinocaridids. The control regions (CRs) of alvinocaridid were significantly longer (penergy metabolism to adapt to the hydrothermal environment. Phylogenetic analysis supported that the deep-sea hydrothermal vent shrimps may have originated from those living in shallow area. Positive selection analysis reveals the evidence of adaptive change in the mitogenome of Alvinocarididae. Thirty potentially important adaptive residues were identified, which were located in atp6, cox1, cox3, cytb and nad1-5. This study explores the mitochondrial genetic basis of hydrothermal vent adaptation in alvinocaridid for the first time, and provides valuable clues regarding the adaptation. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. A taxonomic review of the dry-fruited species of Anemone (Ranunculaceae in southern Africa

    Directory of Open Access Journals (Sweden)

    J. C. Manning

    2013-01-01

    Full Text Available The three dry-fruited species of Anemone sect. Pulsatilloides subsect. Alchemillifoliae (Ranunculaceae from southern Africa are reviewed, with full descriptions and nomenclature, including complete synonomy, taxonomic history with nomenclatural corrections, ecological notes, and distribution. A. tenuifolia (L.f. DC. from the Cape Floristic Region is segregated as ser. Pinnatifoliae from the two summer rainfall species, A. caffra (Eckl. & Zeyh. Harv. and A. fanninnii Harv. ex Masters, which remain in ser. Alchemillifoliae, emphasising the strong vegetative differences between the two series.

  3. Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

    OpenAIRE

    Dunlap, Paul V.; Ast, Jennifer C.

    2005-01-01

    Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (r...

  4. Draft Genome Sequence of Zobellia sp. Strain OII3, Isolated from the Coastal Zone of the Baltic Sea.

    Science.gov (United States)

    Harms, Henrik; Poehlein, Anja; Thürmer, Andrea; König, Gabriele M; Schäberle, Till F

    2017-09-07

    Zobellia sp. strain OII3 was isolated from a marine environmental sample due to its heterotrophic lifestyle, i.e., using Escherichia coli cells as prey. It shows strong agar-lytic activity. The genome was assembled into 41 contigs with a total size of 5.4 Mb, revealing the genetic basis for natural product biosynthesis. Copyright © 2017 Harms et al.

  5. Decapod crustaceans associated with the snakelock anemone Anemonia sulcata. Living there or just passing by?

    Directory of Open Access Journals (Sweden)

    Ricardo Calado

    2007-06-01

    Full Text Available The present work identifies the decapod crustaceans that associate with Anemonia sulcata on the southwestern Atlantic coast of Portugal and characterises their host use pattern. It determines whether the anemone is monopolised by any species, resulting in the exclusion of conspecifics or other decapods and, under laboratory conditions, it evaluates the degree of association between each species and A. sulcata. From all sampled anemones, 79% harboured at least 1 decapod crustacean, with the majority displaying either one or two specimens (32 and 24%, respectively. The most abundant species were the shrimp Periclimenes sagittifer and the crab Inachus phalangium (representing 36 and 31% of collected specimens, respectively, which displayed lasting associations and were commonly recorded among the tentacles of the host. The species Eualus occultus, E. complex cranchii, Clibanarius erythropus, Maja brachydactyla, Pilumnus hirtellus and Polybius (Necora puber displayed short-term associations, were mainly present on the substratum near the base, and avoided the tentacles of A. sulcata. Periclimenes sagittifer and I. phalangium were only recorded alone or in heterosexual pairs, appearing to efficiently defend their host against conspecifics. The majority of recorded species only seem to temporarily associate with A. sulcata, in order to seek protection from predators when other shelters are unavailable.

  6. The stable microbiome of inter and sub-tidal anemone species under increasing pCO2.

    Science.gov (United States)

    Muller, Erinn M; Fine, Maoz; Ritchie, Kim B

    2016-11-23

    Increasing levels of pCO 2 within the oceans will select for resistant organisms such as anemones, which may thrive under ocean acidification conditions. However, increasing pCO 2 may alter the bacterial community of marine organisms, significantly affecting the health status of the host. A pH gradient associated with a natural volcanic vent system within Levante Bay, Vulcano Island, Italy, was used to test the effects of ocean acidification on the bacterial community of two anemone species in situ, Anemonia viridis and Actinia equina using 16 S rDNA pyrosequencing. Results showed the bacterial community of the two anemone species differed significantly from each other primarily because of differences in the Gammaproteobacteria and Epsilonproteobacteria abundances. The bacterial communities did not differ within species among sites with decreasing pH except for A. viridis at the vent site (pH = 6.05). In addition to low pH, the vent site contains trace metals and sulfide that may have influenced the bacteria community of A. viridis. The stability of the bacterial community from pH 8.1 to pH 7.4, coupled with previous experiments showing the lack of, or beneficial changes within anemones living under low pH conditions indicates that A. viridis and A. equina will be winners under future ocean acidification scenarios.

  7. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grö tzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jö rg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant

  8. Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas.

    Science.gov (United States)

    Paterno, Marta; Schiavina, Marcello; Aglieri, Giorgio; Ben Souissi, Jamila; Boscari, Elisa; Casagrandi, Renato; Chassanite, Aurore; Chiantore, Mariachiara; Congiu, Leonardo; Guarnieri, Giuseppe; Kruschel, Claudia; Macic, Vesna; Marino, Ilaria A M; Papetti, Chiara; Patarnello, Tomaso; Zane, Lorenzo; Melià, Paco

    2017-04-01

    Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus , focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats.

  9. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

    Science.gov (United States)

    Wang, Zhuo; Pascual-Anaya, Juan; Zadissa, Amonida; Li, Wenqi; Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

    2013-06-01

    The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ∼267.9-248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.

  10. The draft genomes of soft–shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan

    Science.gov (United States)

    Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

    2014-01-01

    The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ~267.9–248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell. PMID:23624526

  11. Cytotoxic oleanane-type triterpenoid saponins from the Rhizomes of Anemone rivularis var. flore-minore.

    Science.gov (United States)

    Wang, Xiaoyang; Wang, Minchang; Xu, Min; Wang, Yi; Tang, Haifeng; Sun, Xiaoli

    2014-02-18

    Phytochemical investigation of the n-BuOH extract of the rhizomes of Anemone rivularis var. flore-minore led to the isolation of five new oleanane-type triterpenoid saponins 1-5, together with five known saponins 6-10. Their structures were determined by the extensive use of 1D and 2D NMR experiments, along with ESIMS analyses and acid hydrolysis. The aglycone of 4 and 5 was determined as 21α-hydroxyoleanolic acid, which was reported in this genus for the first time. The cytotoxicity of these compounds was evaluated against four human cancer cell line, including HL-60 (promyelocytic leukemia), HepG2 (hepatocellular carcinoma), A549 (lung carcinoma) and HeLa (cervical carcinoma). The monodesmosidic saponins 6-8 exhibited cytotoxic activity toward all tested cancer cell lines, with IC50 values in the 7.25-22.38 μM range.

  12. Morphological and anatomical features of achenes of Anemone L. (Ranunculaceae Juss. of the flora of Ukraine

    Directory of Open Access Journals (Sweden)

    О.М. Tsarenko

    2016-06-01

    Full Text Available Based on SEM and LM some morphological and anatomical features of achenes of Anemone L. of Ukrainian flora (A. narcissiflora, A. sylvestris, A. nemorosa, A. narcissiflora have been investigated. Сarpological features after which it is possible to diagnose species are detected: the dimensions and shape of the achenes and beaks, the peculiarities of pubescence (length and character of localization of the hairs, a presence of different appendages of pericarp (as ribs or wings which surround body of fruit, thickness of pericarp and peculiarities of the thickness of the cell walls of endocarp. Detailed descriptions of fruitlets have been represented. The key for determination of species not in a flourishing condition on the revealed signs have been composed. Data obtained are important for systematics and phylogeny of the genus and the family as a whole.

  13. Dangerous reef aquaristics: Palytoxin of a brown encrusting anemone causes toxic corneal reactions.

    Science.gov (United States)

    Ruiz, Yasmin; Fuchs, Joan; Beuschel, Ralf; Tschopp, Markus; Goldblum, David

    2015-11-01

    Although frequently observed in domestic saltwater aquariums, literature on exposure to palytoxin (PTX) of encrusting anemones (Zoanthidea) kept in aquariums is rare. Handling these animals for propagation purposes or during cleaning work can lead to dermal, ocular or respiratory contact with the PTX generated by some Zoanthids. The present study describes a case of ocular exposure to liquid from a Zoanthid, which led to corneal ulcers. The patient also suffered from systemic symptoms of dyspnea and shivering and a suspected rhabdomyolysis, which required monitoring in the Intensive Care Unit. After symptomatic treatment provided insufficient results, the corneal ulcers improved with an amniotic membrane transplantation. A review of the literature regarding ocular exposures to this diverse order of Hexacorallia reveals that severe and systemic symptoms can develop with minimal contact. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Anisakis simplex complex: ecological significance of recombinant genotypes in an allopatric area of the Adriatic Sea inferred by genome-derived simple sequence repeats.

    Science.gov (United States)

    Mladineo, Ivona; Trumbić, Željka; Radonić, Ivana; Vrbatović, Anamarija; Hrabar, Jerko; Bušelić, Ivana

    2017-03-01

    The genus Anisakis includes nine species which, due to close morphological resemblance even in the adult stage, have previously caused many issues in their correct identification. Recently observed interspecific hybridisation in sympatric areas of two closely related species, Anisakis simplex sensu stricto (s.s.) and Anisakis pegreffii, has raised concerns whether a F1 hybrid generation is capable of overriding the breeding barrier, potentially giving rise to more resistant/pathogenic strains infecting humans. To assess the ecological significance of anisakid genotypes in the Adriatic Sea, an allopatric area for the two above-mentioned species, we analysed data from PCR-RFLP genotyping of the ITS region and the sequence of the cytochrome oxidase 2 (cox2) mtDNA locus to discern the parental genotype and maternal haplotype of the individuals. Furthermore, using in silico genome-wide screening of the A. simplex database for polymorphic simple sequence repeats or microsatellites in non-coding regions, we randomly selected potentially informative loci that were tested and optimised for multiplex PCR. The first panel of microsatellites developed for Anisakis was shown to be highly polymorphic, sensitive and amplified in both A. simplex s.s. and A. pegreffii. It was used to inspect genetic differentiation of individuals showing mito-nuclear mosaicism which is characteristic for both species. The observed low level of intergroup heterozygosity suggests that existing mosaicism is likely a retention of an ancestral polymorphism rather than a recent recombination event. This is also supported by allopatry of pure A. simplex s.s. and A. pegreffii in the geographical area under study. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  15. Abundance of anemone fishes in North Bay Island and mass culture of live food organisms for their larval rearing

    Directory of Open Access Journals (Sweden)

    Rajaram Rajendran

    2014-12-01

    Full Text Available Understanding the transect survey for abundance of anemone fishes and other living organisms is important to asses reef associated fish diversity in North Bay island. The percentage distribution of 10 different substratum from the disturbed, semi-disturbed and undisturbed areas was recorded during the survey in North Bay islands during November 2009 to April 2010. The survey observations reveal that the fishes were the dominant groups followed by mollusks, lobsters and octopus. There are 5 different anemone fishes were collected during the transect survey and their distribution is more in undisturbed area. We are standardizing the different mass culture techniques for production of phytoplankton and zooplankton for the nutritional source for the anemone fish larvae. Monitoring the water quality parameters and culture the phytoplankton and zooplankton used in different culture media with 2 adjustment studies like with and without salinity adjustment. The results of this experiment indicate that zooplankton was rich in protein and fat content and it will be used as high nutritional source for feeding fish larvae.

  16. The Genome of Aiptasia and the Role of MicroRNAs in Cnidarian-Dinoflagellate Endosymbiosis

    KAUST Repository

    Baumgarten, Sebastian

    2016-02-01

    Coral reefs form marine-biodiversity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a model organism and the main aims of this dissertation were 1) to assemble and analyze its genome as a foundational resource for research in this area and 2) to investigate the role of miRNAs in modulating gene expression during the onset and maintenance of symbiosis. The genome analysis has revealed numerous features of interest in relation to the symbiotic lifestyle, including the evolution of transposable elements and taxonomically restricted genes, linkage of host and symbiont metabolism pathways, a novel family of putative pattern-recognition receptors that might function in host-microbe interactions and evidence for horizontal gene transfer within the animal-alga pair as well as with the associated prokaryotic microbiome. The new genomic resource was used to annotate the Aiptasia miRNA repertoire to illuminate the role of post-transcriptional regulatory mechanisms in regulating endosymbiosis. Aiptasia encodes a majority of species-specific miRNAs and first evidence is presented that even evolutionary conserved miRNAs are undergoing recent differentiations within the Aiptasia genome. The analysis of miRNA expression between different states of Symbiodinium infection further revealed that species-specific and conserved miRNAs are symbiotically regulated. In order to detect functional miRNA-mRNA interactions and to investigate the downstream effects of such miRNA action, a protocol for cross-linking immunoprecipitations of Argonaute, the central protein of the mi

  17. Fine-scale population structure of two anemones (Stichodactyla gigantea and Heteractis magnifica) in Kimbe Bay, Papua New Guinea

    KAUST Repository

    Gatins, Remy

    2014-12-01

    Anemonefish are one of the main groups that have been used over the last decade to empirically measure larval dispersal and connectivity in coral reef populations. A few species of anemones are integral to the life history of these fish, as well as other obligate symbionts, yet the biology and population structure of these anemones remains poorly understood. The aim of this study was to measure the genetic structure of these anemones within and between two reefs in order to assess their reproductive mode and dispersal potential. To do this, we sampled almost exhaustively two anemones species (Stichodactyla gigantea and Heteractis magnifica) at two small islands in Kimbe Bay (Papua New Guinea) separated by approximately 25 km. Both the host anemones and the anemonefish are heavily targeted for the aquarium trade, in addition to the populations being affected by bleaching pressures (Hill and Scott 2012; Hobbs et al. 2013; Saenz- Agudelo et al. 2011; Thomas et al. 2014), therefore understanding their biology is crucial for better management strategies. Panels of microsatellite markers were developed for each species using next generation sequencing tools. Clonality analyses confirm six pairs of identical genotypes for S. gigantea (n=350) and zero for H. magnifica (n=128), indicating presence/absence of asexual reproduction in this region. S. gigantea showed low structure between islands (FST= 0.003, p-value= 0.000), however, even if the majority of the individuals were unrelated (r~0), 81 families that shared 50% of their genetic material formed from two to four members were found. Out of these families, 45% were found with individuals only within Tuare Island, 11% only in Kimbe Island, and 44% were sharing individuals among islands. In comparison, H. magnifica showed no structure (FST= 0.002, p-value= 0.278), mean relatedness indicated the majority of individuals were unrelated, and 31 families were identified. Families again consisted from two to four members and

  18. Analysis of an Anemone-Type Eruption in an On-Disk Coronal Hole

    Science.gov (United States)

    Adams, Mitzi; Tennant, Allyn; Alexander, Caroline; Sterling, Alphonse; Moore, Ronald; Woolley, Robert

    2016-01-01

    We report on an eruption seen in a very small coronal hole (about 120 arcseconds across), beginning at approximately 19:00 Universal Time on March 3, 2016. The event was initially observed by an amateur astronomer (RW) in an H-alpha movie from the Global Oscillation Network Group (GONG); the eruption attracted the attention of the observer because there was no nearby active region. To examine the region in detail, we use data from the Solar Dynamics Observatory (SDO), provided by the Atmospheric Imaging Assembly (AIA) in wavelengths 193 angstroms, 304 angstroms, and 94 angstroms, and the Helioseismic and Magnetic Imager (HMI). Data analysis and calibration activities such as scaling, rotation so that north is up, and removal of solar rotation are accomplished with SunPy. The eruption in low-cadence HMI data begins with the appearance of a bipole in the location of the coronal hole, followed by (apparent) expansion outwards when the intensity of the AIA wavelengths brighten; as the event proceeds, the coronal hole disappears. From high-cadence data, we will present results on the magnetic evolution of this structure, how it is related to intensity brightenings seen in the various SDO/AIA wavelengths, and how this event compares with the standard-anemone picture.

  19. Variations in the Life Cycle of Anemone patens L. (Ranunculaceae in Wild Populations of Canada

    Directory of Open Access Journals (Sweden)

    Vladimir Kricsfalusy

    2016-06-01

    Full Text Available Based on a study of a perennial herb Anemone patens L. (Ranunculaceae in a variety of natural habitats in Saskatchewan, Canada, eight life stages (seed, seedling, juvenile, immature, vegetative, generative, subsenile, and senile are distinguished and characterized in detail. The species ontogenetic growth patterns are investigated. A. patens has a long life cycle that may last for several decades which leads to the formation of compact clumps. The distribution and age of clumps vary substantially in different environments with different levels of disturbance. The plant ontogeny includes the regular cycle with reproduction occurring through seeds. There is an optional subsenile vegetative disintegration at the end of the life span. The following variations in the life cycle of A. patens are identified: with slower development in young age, with an accelerated development, with omission of the generative stage, with retrogression to previous life stages in mature age, and with vegetative dormancy. The range of variations in the life cycle of A. patens may play an important role in maintaining population stability in different environmental conditions and management regimes.

  20. Stochastic occurrence of trimery from pentamery in floral phyllotaxis of Anemone (Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Miho S. Kitazawa

    2016-12-01

    Full Text Available Merosity, indicating the basic number of floral organs such as sepals and petals, has been constrained to specific and stable numbers during the evolution of angiosperms. The ancestral flower is considered to have a spiral arrangement of perianth organs, as in phyllotaxis, the arrangement of leaves. How has the ancestral spiral evolved into flowers with specific merosities? To address this question, we studied perianth organ arrangement in the Anemone genus of the basal eudicot family Ranunculaceae, because various merosities are found in this genus. In three species, A. flaccida, A. scabiosa, and A. nikoensis that are normally pentamerous, we found positional arrangement of the excessive sixth perianth organ indicating the possibility of a transition from pentamerous to trimerous arrangement. Arrangement was intraspecifically stochastic, but constrained to three of five types, where trimerous arrangement was the most frequent in all species except for a form of A. scabiosa. The rank of frequency of the other two types was species-dependent. We connect these observations with classical theories of spiral phyllotaxis. The phyllotaxis model for initiation of the sixth organ showed that the three arrangements occur at a divergence angle <144°, indicating the spiral nature of floral phyllotaxis rather than a perfect penta-radial symmetry of 144°. The model further showed that selective occurrence of trimerous arrangement is mainly regulated by the organ growth rate. Differential organ growth as well as divergence angle may regulate transitions between pentamerous and trimerous flowers in intraspecific variation as well as in species evolution.

  1. Triterpenoid Saponins from Anemone rivularis var. Flore-Minore and Their Anti-Proliferative Activity on HSC-T6 Cells.

    Science.gov (United States)

    Wang, Xiao-Yang; Gao, Hui; Xie, Xiao-Jie; Jurhiin, Jirimubatu; Zhang, Mu-Zi-He; Zhou, Yan-Ping; Liu, Rui; Ning, Meng; Han, Jin; Tang, Hai-Feng

    2018-02-23

    Five previously undescribed triterpenoid saponins ( 1 - 5 ), along with eight known ones ( 6 - 13 ), were isolated from the whole plants of Anemone rivularis var. flore-minore . Their structures were clarified by extensive spectroscopic data and chemical evidence. For the first time, the lupane-type saponins ( 3 and 12 ) were reported from the Anemone genus. The anti-proliferative activity of all isolated saponins was evaluated on hepatic stellate cells (HSC-T6). Saponins 12 and 13 , which possess more monosaccharides than the others, displayed potent anti-proliferative activity, with IC 50 values of 18.21 and 15.56 μM, respectively.

  2. Pharmacokinetic studies of active triterpenoid saponins and the total secondary saponin from Anemone raddeana Regel.

    Science.gov (United States)

    Zhang, Dandan; Lei, Tianli; Lv, Chongning; Zhao, Huimin; Xu, Haiyan; Lu, Jincai

    2017-02-15

    The rhizome of Anemone raddeana Regel, a Traditional Chinese Medicine (TCM) which has a robust history treating rheumatism and neuralgia. The total secondary saponin (TSS) from it has demonstrated antitumor activity. In this study, a rapid and validated LC-MS/MS method was developed to simultaneously determine the active compounds (Hederacolchiside A1 and Eleutheroside K). Analytes were separated on a reverse-phase C18 column with acetonitrile-water (5mmol/L ammonium acetate) as the mobile phase. This assay showed acceptable linearity (r>0.99) over the concentration range 5-1000 nmol/L for two analytes. The intra- and inter-day precision was within 8.06% and accuracy was ranged from -3.16% to 3.34% for two analytes. The mean extraction recoveries of analytes and IS from rat plasma were all more than 76.0%. Under the developed analytical conditions, the obtained values of main pharmacokinetic parameters (C max and AUC 0-t ) indicated that the pure compounds were more efficient than the TSS extract in Hederacolchiside A1 and Eleutheroside K absorption. In addition, pharmacokinetic studies of two individual compounds demonstrated their poor oral absorption in rat ( a F%, 0.019-1.521). In the study of absorption and transportation of Hederacolchiside A1 and Eleutheroside K in Caco-2 cell monolayer model, the uptake permeability was in 10 -6 cm/sec range suggesting poor absorption, which confirmed the previous pharmacokinetic profiles in vivo. Interestingly, the uptake ratio of them declined significantly when treated with phloridzin (SGLT1 inhibitor). It indicated that the absorption of Hederacolchiside A1 in intestine was mainly through positive transport and SGLT1 might participate in its active absorption. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Imaging intracellular pH in a reef coral and symbiotic anemone.

    Science.gov (United States)

    Venn, A A; Tambutté, E; Lotto, S; Zoccola, D; Allemand, D; Tambutté, S

    2009-09-29

    The challenges corals and symbiotic cnidarians face from global environmental change brings new urgency to understanding fundamental elements of their physiology. Intracellular pH (pHi) influences almost all aspects of cellular physiology but has never been described in anthozoans or symbiotic cnidarians, despite its pivotal role in carbon concentration for photosynthesis and calcification. Using confocal microscopy and the pH sensitive probe carboxy SNARF-1, we mapped pHi in short-term light and dark-incubated cells of the reef coral Stylophora pistillata and the symbiotic anemone Anemonia viridis. In all cells isolated from both species, pHi was markedly lower than the surrounding seawater pH of 8.1. In cells that contained symbiotic algae, mean values of pHi were significantly higher in light treated cells than dark treated cells (7.41 +/- 0.22 versus 7.13 +/- 0.24 for S. pistillata; and 7.29 +/- 0.15 versus 7.01 +/- 0.27 for A. viridis). In contrast, there was no significant difference in pHi in light and dark treated cells without algal symbionts. Close inspection of the interface between host cytoplasm and algal symbionts revealed a distinct area of lower pH adjacent to the symbionts in both light and dark treated cells, possibly associated with the symbiosome membrane complex. These findings are significant developments for the elucidation of models of inorganic carbon transport for photosynthesis and calcification and also provide a cell imaging procedure for future investigations into how pHi and other fundamental intracellular parameters in corals respond to changes in the external environment such as reductions in seawater pH.

  4. n-TiO{sub 2} and CdCl{sub 2} co-exposure to titanium dioxide nanoparticles and cadmium: Genomic, DNA and chromosomal damage evaluation in the marine fish European sea bass (Dicentrarchus labrax)

    Energy Technology Data Exchange (ETDEWEB)

    Nigro, M.; Bernardeschi, M. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Costagliola, D. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy); Della Torre, C. [Department of Physical, Earth and Environmental Sciences, University of Siena, Siena (Italy); Frenzilli, G., E-mail: giada@biomed.unipi.it [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Guidi, P.; Lucchesi, P. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Mottola, F.; Santonastaso, M. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy); Scarcelli, V. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Monaci, F.; Corsi, I. [Department of Physical, Earth and Environmental Sciences, University of Siena, Siena (Italy); Stingo, V.; Rocco, L. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy)

    2015-11-15

    Highlights: • European sea bass was exposed to CdCl{sub 2} and n-TiO{sub 2} alone and in combination. • Genotoxicity was evaluated by RAPD-assay, comet assay and cytome assay. • CdCl{sub 2} induced DNA primary damage but not chromosomal damage. • n-TiO{sub 2} induced chromosomal damage but not DNA primary damage. • Co-exposure effects depend on the biomarker used. - Abstract: Due to the large production and growing use of titanium dioxide nanoparticles (n-TiO{sub 2}), their release in the marine environment and their potential interaction with existing toxic contaminants represent a growing concern for biota. Different end-points of genotoxicity were investigated in the European sea bass Dicentrarchus labrax exposed to n-TiO{sub 2} (1 mg L{sup −1}) either alone and combined with CdCl{sub 2} (0.1 mg L{sup −1}) for 7 days. DNA primary damage (comet assay), apoptotic cells (diffusion assay), occurrence of micronuclei and nuclear abnormalities (cytome assay) were assessed in peripheral erythrocytes and genomic stability (random amplified polymorphism DNA-PCR, RAPD assay) in muscle tissue. Results showed that genome template stability was reduced after CdCl{sub 2} and n-TiO{sub 2} exposure. Exposure to n-TiO{sub 2} alone was responsible for chromosomal alteration but ineffective in terms of DNA damage; while the opposite was observed in CdCl{sub 2} exposed specimens. Co-exposure apparently prevents the chromosomal damage and leads to a partial recovery of the genome template stability.

  5. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

    Science.gov (United States)

    Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

    2015-01-01

    Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a “relay race”-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus. PMID:26634818

  6. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent

    Energy Technology Data Exchange (ETDEWEB)

    Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01

    Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge- nus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary pro- ducer in the temperature range of 45-75 C (optimum 70 C) and is incapable of growing un- der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality of the membrane at high growth temperatures. This is the second completed genome sequence of a member of the family Desulfurobacteriaceae and the first sequence from the genus Desulfu- robacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    NARCIS (Netherlands)

    Speth, Daan R.; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei Yuan; Dutilh, Bas E.|info:eu-repo/dai/nl/304546313; Jetten, Mike S M

    2017-01-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the

  8. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    NARCIS (Netherlands)

    Speth, Daan R.; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei Yuan; Dutilh, Bas E.; Jetten, M.S.M.

    2017-01-01

    Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the

  9. Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea.

    KAUST Repository

    Antunes, Andre

    2011-09-01

    We present the genome of Salinisphaera shabanensis, isolated from a brine-seawater interface and representing a new order within the Gammaproteobacteria. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.

  10. Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea.

    KAUST Repository

    Antunes, Andre; Alam, Intikhab; Bajic, Vladimir B.; Stingl, Ulrich

    2011-01-01

    We present the genome of Salinisphaera shabanensis, isolated from a brine-seawater interface and representing a new order within the Gammaproteobacteria. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.

  11. Distribution patterns of zoochlorellae and zooxanthellae hosted by two Pacific Northeast anemones, Anthopleura elegantissima and A. xanthogrammica.

    Science.gov (United States)

    Bates, Amanda E; McLean, Lily; Laing, Patrick; Raeburn, Lisa A; Hare, Crystal

    2010-06-01

    This study investigated patterns in the relative abundance of two photosynthetic algal symbionts, zoochlorellae (ZC) and zooxanthellae (ZX), hosted by two temperate anemones, Anthopleura elegantissima and A. xanthogrammica. Previous studies have documented varying proportions of each symbiont along environmental gradients, presumably determined by their respective physiological capabilities. To test for differences in the algal type between the two host species, we sampled anemone tissues (tentacle or tentacle and body column) of similarly sized polyps that were located close together in multiple habitats: tidepools, crevices, underneath rock ledges, and along natural light gradients in caves. The ZC-A. elegantissima symbiosis was rare on the west coast of Vancouver Island, British Columbia, Canada. Even in low-irradiance habitats, ZC were the dominant algae hosted by A. xanthogrammica, while nearby A. elegantissima hosted ZX or was algae-free. As a first step in determining whether symbiont growth rates differed between the two host species, we quantified mitotic index (MI), the percentage of cells with division furrows, under artificial light and in the field by simultaneously sampling tentacles from both species. MI was more stable in A. elegantissima: the MI of ZX isolated from the tentacles of A. xanthogrammica was slightly higher at a light level of 80 micromol quanta m(-2) s(-1) than it was for ZX from A. elegantissima (respectively, 7.3 vs. 6.2) and relatively lower at 40 micromol quanta m(-2) s(-1) (3.9 vs. 5.6). Our data indicate host-specific differences in symbiont distributions and MI when extrinsic physical parameters were similar.

  12. Genetic tools link long-term demographic and life-history traits of anemonefish to their anemone hosts

    KAUST Repository

    Salles, Océane C.

    2016-07-26

    The life-history traits and population dynamics of species are increasingly being attributed to the characteristics of their preferred habitats. While coral reef fish are often strongly associated with particular habitats, long-term studies establishing the demographic and life-history consequences of occupying different reef substrata are rare and no studies have monitored individuals in situ over their lifetime and determined the fate of their offspring. Here, we documented a quasi-turnover and local reproductive success for an entire population of orange clownfish (Amphiprion percula) from Kimbe Island, Papua New Guinea, by taking bi-annual samples of DNA over a 10-yr period (2003–2013). We compared demographic and life-history traits of individuals living on two host anemone species, Heteractis magnifica and Stichodactyla gigantea, including female size, adult continued presence (a proxy for relative longevity range), early post-settlement growth, the number of eggs per clutch and ‘local’ reproductive success (defined for each adult as the number of offspring returning to the natal population). Our results indicate that while the relative longevity of adults was similar on both host anemone species, females living in H. magnifica were larger than females in S. gigantea. However, despite females growing larger and producing more eggs on H. magnifica, we found that local reproductive success was significantly higher for clownfish living in S. gigantea. Life-history traits also exhibited local spatial variation, with higher local reproductive success recorded for adults living on S. gigantea on the eastern side of the island. Our findings support a ‘silver-spoon’ hypothesis that predicts individuals that are fortunate enough to recruit into good habitat and location will be rewarded with higher long-term reproductive success and will make a disproportionate contribution to population renewal. © 2016 Springer-Verlag Berlin Heidelberg

  13. Identification of a new 6-bromo-5,9-eicosadienoic acid from the anemone Condylactis gigantea and the zoanthid Palythoa caribaeorum.

    Science.gov (United States)

    Carballeira, N M; Reyes, M

    1995-11-01

    A new brominated fatty acid, 6-bromo-5,9-eicosadienoic acid [1] was identified in the phospholipids (mainly phosphatidylethanolamine) of the anemone Condylactis gigantea and the zoanthid Palythoa caribaeorum. The delta 5,9 fatty acids, 5,9-octadecadienoic acid, 5,9-eicosadienoic acid, 5,9-docosadienoic acid, and 5,9-tetracosadienoic acid, were also identified in both organisms. Structural elucidation was accomplished by spectroscopic and chemical means. Our results further corroborate that delta 5,9 phospholipid fatty acids are not unique to sponges, as recognized previously, but can be found in other marine invertebrates such as anemones and zoanthids. An improved procedure for the synthesis of picolinyl esters is also described.

  14. Genetic diversity of giant clams (Tridacna spp.) and their associated Symbiodinium in the central Red Sea

    KAUST Repository

    Pappas, Melissa

    2017-05-19

    The biodiversity of the Red Sea remains relatively understudied, particularly for invertebrate taxa. Documenting present patterns of biodiversity is essential for better understanding Red Sea reef ecosystems and how these ecosystems may be impacted by stressors (such as fishing and climate change). Several species of giant clams (genus Tridacna) are reported from the Red Sea, although the majority of research effort has occurred in the Gulf of Aqaba. We investigated the genetic diversity (16S rDNA) of the Tridacna species found in the central Saudi Arabian Red Sea. We also investigated the genetic diversity (ITS rDNA) of symbiotic dinoflagellates Symbiodinium associated with these clams. Samples were collected from nine reefs on a cross-shelf gradient near Thuwal, Saudi Arabia. Two species, T. squamosa and T. maxima, were recorded, with the latter being the most abundant. Tridacna squamosina, a species recently reported in the northern Red Sea, was not found, suggesting that this species is not present or is very rare in our study region. All tridacnids sampled were found to harbor Symbiodinium grouped in Clade A, considered an opportunistic, heat-tolerant symbiont group in anemones and corals. The consistent association with Clade A Symbiodinium in central Red Sea tridacnids may reflect the consequence of adaptation to the relatively extreme conditions of the Red Sea. This study contributes to an ever-growing catalog of Red Sea biodiversity and serves as important baseline information for a region experiencing dynamic pressures.

  15. Genetic diversity of giant clams (Tridacna spp.) and their associated Symbiodinium in the central Red Sea

    KAUST Repository

    Pappas, Melissa; He, Song; Hardenstine, Royale; Kanee, Hana; Berumen, Michael L.

    2017-01-01

    The biodiversity of the Red Sea remains relatively understudied, particularly for invertebrate taxa. Documenting present patterns of biodiversity is essential for better understanding Red Sea reef ecosystems and how these ecosystems may be impacted by stressors (such as fishing and climate change). Several species of giant clams (genus Tridacna) are reported from the Red Sea, although the majority of research effort has occurred in the Gulf of Aqaba. We investigated the genetic diversity (16S rDNA) of the Tridacna species found in the central Saudi Arabian Red Sea. We also investigated the genetic diversity (ITS rDNA) of symbiotic dinoflagellates Symbiodinium associated with these clams. Samples were collected from nine reefs on a cross-shelf gradient near Thuwal, Saudi Arabia. Two species, T. squamosa and T. maxima, were recorded, with the latter being the most abundant. Tridacna squamosina, a species recently reported in the northern Red Sea, was not found, suggesting that this species is not present or is very rare in our study region. All tridacnids sampled were found to harbor Symbiodinium grouped in Clade A, considered an opportunistic, heat-tolerant symbiont group in anemones and corals. The consistent association with Clade A Symbiodinium in central Red Sea tridacnids may reflect the consequence of adaptation to the relatively extreme conditions of the Red Sea. This study contributes to an ever-growing catalog of Red Sea biodiversity and serves as important baseline information for a region experiencing dynamic pressures.

  16. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    Science.gov (United States)

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  17. Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

    KAUST Repository

    Jimenez Infante, Francy M.

    2015-12-11

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

  18. Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

    KAUST Repository

    Jimenez Infante, Francy M.; Ngugi, David; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan; Blom, Jochen; Bajic, Vladimir B.; Stingl, Ulrich

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

  19. Saponin B, a novel cytostatic compound purified from Anemone taipaiensis, induces apoptosis in a human glioblastoma cell line.

    Science.gov (United States)

    Wang, Yuangang; Tang, Haifeng; Zhang, Yun; Li, Juan; Li, Bo; Gao, Zhenhui; Wang, Xiaoyang; Cheng, Guang; Fei, Zhou

    2013-11-01

    Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors. Saponin B, a novel compound isolated from the medicinal plant, Anemone taipaiensis, has been found to have a strong time- and dose-dependent cytostatic effect on human glioma cells and to suppress the growth of U87MG GBM cells. In this study, we investigated whether saponin B induces the apoptosis of glioblastoma cells and examined the underlying mechanism(s) of action of saponin B. Saponin B significantly suppressed U87MG cell proliferation. Flow cytometric analysis of DNA in the U87MG cells confirmed that saponin B blocked the cell cycle at the S phase. Furthermore, treatment of the U87MG cells with saponin B induced chromatin condensation and led to the formation of apoptotic bodies, as observed under a fluorescence microscope, and Annexin V/PI assay further suggested that phosphatidylserine (PS) externalization was apparent at higher drug concentrations. Treatment with saponin B activated the receptor-mediated pathway of apoptosis, as western blot analysis revealed the activation of Fas-l. Saponin B increased the Bax and caspase-3 ratio and decreased the protein expression of Bcl-2. The results from the present study demonstrate that the novel compound, saponin B, effectively induces the apoptosis of GBM cells and inhibits glioma cell growth and survival. Therefore, saponin B may be a potential candidate for the development of novel cancer therapeutics with antitumor activity against gliomas.

  20. Studies on the comparison of pollen morphology and viability of four naturally distributed and commercial varieties of anemone coronaria L

    International Nuclear Information System (INIS)

    Candan, F.

    2015-01-01

    The present study presents a comparison of the pollen morphology and viability of naturally distributed four varieties of Anemone coronaria L. These are A. coronaria var. coccinea (Jord.) Burn, A. coronaria var. rosea (Hanry) Batt, A. coronaria var. cyanea, A. coronaria var. alba Goaty and Pens) and its commercial cultivars. The four varieties were collected from areas near the road side along the Kirkagac-Soma highway in the State of Manisa. The commercial cultivars were obtained from the commercial flower growers in the Urla region of zmir. Pollen viability levels decreased in all commercial cultivars of A. coronaria. The highest reduction in pollen viability was recorded in A. coronaria pink cultivars of de Caen group. The general pollen type is prolate spheroidal in all pure forms, but there are some pollen morphological features which were not observed in the natural ones, although encountered in all commercial cultivars. On the other hand, various non-viable pollen types like wrinkled pollens, with abnormally shaped pollens or pollinia were found in the commercial cultivars. It was concluded that pesticides used to produce more flowers with rapid growth are the major cause for his reduction. Another reason could be the use of tetraploid F1 hybrids of A. coronaria cultivars of de Caen group as commercial samples. (author)

  1. Sea Dragon

    National Research Council Canada - National Science Library

    1997-01-01

    .... In preparation for these changes, the Navy is exploring new command and control relationships, and the Marine Corps established Sea Dragon to experiment with emerging technologies, operational...

  2. Changes in Alaskan soft-bottom prey communities along a gradient in sea otter predation

    Science.gov (United States)

    Kvitek, R.G.; Oliver, J.S.; DeGange, A.R.; Anderson, B.S.

    1992-01-01

    Sea Otter (Enhydra lutris), well documented as "keystone" predators in rocky marine communities, were found to exert a strong influence on infaunal prey communities in soft-sediment habitats. Direct and indirect effects of sea otter predation on subtidal soft-bottom prey communities were evaluated along a temporal gradient of sea otter occupancy around the Kodiak Archipelago. The results indicate that Kodiak otters forage primarily on bivalve prey and dramatically reduce infaunal bivalve and green sea urchin (Strongylocentrotus droebachiensis) prey populations. Bivalve prey abundance, biomass, and size were inversely related to duration of sea otter occupancy. The relative conditions of shells discarded by otters in shallow ( 20 m) water at the same sites indicate that otters first exploited Saxidomus in shallow-water feeding areas, and later switched to Macoma spp. in deeper water. Otter-cracked shells of the deep-burrowing clam Tresus capax were rarely found, even at otter foraging sites where the clam accounted for the majority of available prey biomass, suggesting that it has a partial depth refuge from otter predation. The indirect effects of otter predation included substratum disturbance and the facilitation of sea star predation on infaunal prey. Sea stars, Pycnopodia helianthoides, were attracted to experimentally dug excavations as well as natural sea otter foraging pits, where the sea stars foraged on smaller size classes of infaunal bivalves than those eaten by otters. Otters also discard clam shells on the sediment surface and expose old, buried shells during excavation. Surface shells were found to provide attachment sites for large anemones and kelp. Our study shows that sea otters can affect soft-sediment communities, not only through predation, as in rocky habitats, but also through disturbance, and thus retain a high degree of influence in two very different habitat types.

  3. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  4. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  5. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  6. Sea Legs

    Science.gov (United States)

    Macdonald, Kenneth C.

    Forty-foot, storm-swept seas, Spitzbergen polar bears roaming vast expanses of Arctic ice, furtive exchanges of forbidden manuscripts in Cold War Moscow, the New York city fashion scene, diving in mini-subs to the sea floor hot srings, life with the astronauts, romance and heartbreak, and invading the last bastions of male exclusivity: all are present in this fast-moving, non-fiction account of one woman' fascinating adventures in the world of marine geology and oceanography.

  7. Sea level trends in South East Asian Seas (SEAS)

    Science.gov (United States)

    Strassburg, M. W.; Hamlington, B. D.; Leben, R. R.; Manurung, P.; Lumban Gaol, J.; Nababan, B.; Vignudelli, S.; Kim, K.-Y.

    2014-10-01

    Southeast Asian Seas (SEAS) span the largest archipelago in the global ocean and provide a complex oceanic pathway connecting the Pacific and Indian Oceans. The SEAS regional sea level trends are some of the highest observed in the modern satellite altimeter record that now spans almost two decades. Initial comparisons of global sea level reconstructions find that 17 year sea level trends over the past 60 years exhibit good agreement in areas and at times of strong signal to noise associated decadal variability forced by low frequency variations in Pacific trade winds. The SEAS region exhibits sea level trends that vary dramatically over the studied time period. This historical variation suggests that the strong regional sea level trends observed during the modern satellite altimeter record will abate as trade winds fluctuate on decadal and longer time scales. Furthermore, after removing the contribution of the Pacific Decadal Oscillation (PDO) to sea level trends in the past twenty years, the rate of sea level rise is greatly reduced in the SEAS region. As a result of the influence of the PDO, the SEAS regional sea level trends during 2010s and 2020s are likely to be less than the global mean sea level (GMSL) trend if the observed oscillations in wind forcing and sea level persist. Nevertheless, long-term sea level trends in the SEAS will continue to be affected by GMSL rise occurring now and in the future.

  8. Sea-anemone toxin ATX-II elicits A-fiber-dependent pain and enhances resurgent and persistent sodium currents in large sensory neurons

    Directory of Open Access Journals (Sweden)

    Klinger Alexandra B

    2012-09-01

    Full Text Available Abstract Background Gain-of-function mutations of the nociceptive voltage-gated sodium channel Nav1.7 lead to inherited pain syndromes, such as paroxysmal extreme pain disorder (PEPD. One characteristic of these mutations is slowed fast-inactivation kinetics, which may give rise to resurgent sodium currents. It is long known that toxins from Anemonia sulcata, such as ATX-II, slow fast inactivation and skin contact for example during diving leads to various symptoms such as pain and itch. Here, we investigated if ATX-II induces resurgent currents in sensory neurons of the dorsal root ganglion (DRGs and how this may translate into human sensations. Results In large A-fiber related DRGs ATX-II (5 nM enhances persistent and resurgent sodium currents, but failed to do so in small C-fiber linked DRGs when investigated using the whole-cell patch-clamp technique. Resurgent currents are thought to depend on the presence of the sodium channel β4-subunit. Using RT-qPCR experiments, we show that small DRGs express significantly less β4 mRNA than large sensory neurons. With the β4-C-terminus peptide in the pipette solution, it was possible to evoke resurgent currents in small DRGs and in Nav1.7 or Nav1.6 expressing HEK293/N1E115 cells, which were enhanced by the presence of extracellular ATX-II. When injected into the skin of healthy volunteers, ATX-II induces painful and itch-like sensations which were abolished by mechanical nerve block. Increase in superficial blood flow of the skin, measured by Laser doppler imaging is limited to the injection site, so no axon reflex erythema as a correlate for C-fiber activation was detected. Conclusion ATX-II enhances persistent and resurgent sodium currents in large diameter DRGs, whereas small DRGs depend on the addition of β4-peptide to the pipette recording solution for ATX-II to affect resurgent currents. Mechanical A-fiber blockade abolishes all ATX-II effects in human skin (e.g. painful and itch-like paraesthesias, suggesting that it mediates its effects mainly via activation of A-fibers.

  9. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  10. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  11. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  12. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  13. Sea Ice

    Science.gov (United States)

    Perovich, D.; Gerland, S.; Hendricks, S.; Meier, Walter N.; Nicolaus, M.; Richter-Menge, J.; Tschudi, M.

    2013-01-01

    During 2013, Arctic sea ice extent remained well below normal, but the September 2013 minimum extent was substantially higher than the record-breaking minimum in 2012. Nonetheless, the minimum was still much lower than normal and the long-term trend Arctic September extent is -13.7 per decade relative to the 1981-2010 average. The less extreme conditions this year compared to 2012 were due to cooler temperatures and wind patterns that favored retention of ice through the summer. Sea ice thickness and volume remained near record-low levels, though indications are of slightly thicker ice compared to the record low of 2012.

  14. Sea level change

    Digital Repository Service at National Institute of Oceanography (India)

    Church, J.A.; Clark, P.U.; Cazenave, A.; Gregory, J.M.; Jevrejeva, S.; Levermann, A.; Merrifield, M.A.; Milne, G.A.; Nerem, R.S.; Nunn, P.D.; Payne, A.J.; Pfeffer, W.T.; Stammer, D.; Unnikrishnan, A.S.

    This chapter considers changes in global mean sea level, regional sea level, sea level extremes, and waves. Confidence in projections of global mean sea level rise has increased since the Fourth Assessment Report (AR4) because of the improved...

  15. Sea level trends in Southeast Asian seas

    Science.gov (United States)

    Strassburg, M. W.; Hamlington, B. D.; Leben, R. R.; Manurung, P.; Lumban Gaol, J.; Nababan, B.; Vignudelli, S.; Kim, K.-Y.

    2015-05-01

    Southeast Asian seas span the largest archipelago in the global ocean and provide a complex oceanic pathway connecting the Pacific and Indian oceans. The Southeast Asian sea regional sea level trends are some of the highest observed in the modern satellite altimeter record that now spans almost 2 decades. Initial comparisons of global sea level reconstructions find that 17-year sea level trends over the past 60 years exhibit good agreement with decadal variability associated with the Pacific Decadal Oscillation and related fluctuations of trade winds in the region. The Southeast Asian sea region exhibits sea level trends that vary dramatically over the studied time period. This historical variation suggests that the strong regional sea level trends observed during the modern satellite altimeter record will abate as trade winds fluctuate on decadal and longer timescales. Furthermore, after removing the contribution of the Pacific Decadal Oscillation (PDO) to sea level trends in the past 20 years, the rate of sea level rise is greatly reduced in the Southeast Asian sea region. As a result of the influence of the PDO, the Southeast Asian sea regional sea level trends during the 2010s and 2020s are likely to be less than the global mean sea level (GMSL) trend if the observed oscillations in wind forcing and sea level persist. Nevertheless, long-term sea level trends in the Southeast Asian seas will continue to be affected by GMSL rise occurring now and in the future.

  16. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  17. Sea salt

    OpenAIRE

    Galvis-Sánchez, Andrea C.; Lopes, João Almeida; Delgadillo, Ivone; Rangel, António O. S. S.

    2013-01-01

    The geographical indication (GI) status links a product with the territory and with the biodiversity involved. Besides, the specific knowledge and cultural practices of a human group that permit transforming a resource into a useful good is protected under a GI designation. Traditional sea salt is a hand-harvested product originating exclusively from salt marshes from specific geographical regions. Once salt is harvested, no washing, artificial drying or addition of anti-caking agents are all...

  18. A vertical wall dominated by Acesta excavata and Neopycnodonte zibrowii, part of an undersampled group of deep-sea habitats.

    Directory of Open Access Journals (Sweden)

    Mark P Johnson

    Full Text Available We describe a novel biotope at 633 to 762 m depth on a vertical wall in the Whittard Canyon, an extensive canyon system reaching from the shelf to the deep sea on Ireland's continental margin. We explored this wall with an ROV and compiled a photomosaic of the habitat. The assemblage contributing to the biotope was dominated by large limid bivalves, Acesta excavata (mean shell height 10.4 cm, and deep-sea oysters, Neopycnodonte zibrowii, at high densities, particularly at overhangs. Mean density of N. zibrowii increased with depth, with densities of the most closely packed areas of A. excavata also increasing with depth. Other taxa associated with the assemblage included the solitary coral Desmophyllum dianthus, cerianthid anemones, comatulid crinoids, the trochid gastropod Margarites sp., the portunid crab Bathynectes longispina and small fish of the family Bythitidae. The scleractinian coral Madrepora oculata, the pencil urchin Cidaris cidaris and a species of Epizoanthus were also common. Prominent but less abundant species included the flytrap anemone Actinoscyphia saginata, the carrier crab Paramola cuvieri, and the fishes Lepidion eques and Conger conger. Observations of the hydrography of the canyon system identified that the upper 500 m was dominated by Eastern North Atlantic Water, with Mediterranean Outflow Water beneath it. The permanent thermocline is found between 600 and 1000 m depth, i.e., in the depth range of the vertical wall and the dense assemblage of filter feeders. Beam attenuation indicated nepheloid layers present in the canyon system with the greatest amounts of suspended material at the ROV dive site between 500 and 750 m. A cross-canyon CTD transect indicated the presence of internal waves between these depths. We hypothesise that internal waves concentrate suspended sediment at high concentrations at the foot of the vertical wall, possibly explaining the large size and high density of filter-feeding molluscs.

  19. Community genomics among stratified microbial assemblages in the ocean's interior

    DEFF Research Database (Denmark)

    DeLong, Edward F; Preston, Christina M; Mincer, Tracy

    2006-01-01

    Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence......, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics....

  20. Insertion sequences enrichment in extreme Red sea brine pool vent

    KAUST Repository

    Elbehery, Ali H. A.

    2016-12-03

    Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world’s largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

  1. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  2. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  3. Shedding genomic light on Aristotle's lantern.

    Science.gov (United States)

    Sodergren, Erica; Shen, Yufeng; Song, Xingzhi; Zhang, Lan; Gibbs, Richard A; Weinstock, George M

    2006-12-01

    Sea urchins have proved fascinating to biologists since the time of Aristotle who compared the appearance of their bony mouth structure to a lantern in The History of Animals. Throughout modern times it has been a model system for research in developmental biology. Now, the genome of the sea urchin Strongylocentrotus purpuratus is the first echinoderm genome to be sequenced. A high quality draft sequence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with sequences from a collection of BACs selected to form a minimal tiling path along the genome. A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. This was overcome by use of the BAC tiling path backbone, in which each BAC represents a single haplotype, as well as by improvements in the Atlas software. Another innovation introduced in this project was the sequencing of pools of tiling path BACs rather than individual BAC sequencing. The Clone-Array Pooled Shotgun Strategy greatly reduced the cost and time devoted to preparing shotgun libraries from BAC clones. The genome sequence was analyzed with several gene prediction methods to produce a comprehensive gene list that was then manually refined and annotated by a volunteer team of sea urchin experts. This latter annotation community edited over 9000 gene models and uncovered many unexpected aspects of the sea urchin genetic content impacting transcriptional regulation, immunology, sensory perception, and an organism's development. Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development.

  4. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Red Sea as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-12-12

    King-Abdullah University of Science and Technology (KAUST) is located on the shores of the Red Sea in Saudi Arabia. The Red Sea is well known for its unique environment, harboring various microbes capable of surviving in salty brines. We collected sediment samples from brine pool adjacent to the Thuwal cold seeps in the Red Sea. The taxonomic analysis showed the diversity and abundance of bacterial and archaeal operational taxonomic units (OUT). Recently we established in the laboratory a microdroplet technology to encapsulate single cells. This technology enables us to analyze single-cell genomes and perform the high-throughput screening. The genomes of both cultivable and uncultivable organisms can be analyzed. We envision the collection of complimentary data, obtained by various techniques, such as single-cell genomics, metagenomics, and transcriptomics. That will enable us not only to understand the environment and microorganism communities but also will allow to discover the previously unknown genes, pathways, and whole genomes. These data will facilitate the enhancement of biological and chemical producers, and pave the way for bioprospecting.

  6. Structure revision of hupehensis saponin F and G and characterization of new trace triterpenoid saponins from Anemone hupehensis by tandem electrospray ionization mass spectrometry.

    Science.gov (United States)

    Li, Fu; Liu, Xin; Tang, Minghai; Chen, Bin; Ding, Lisheng; Chen, Lijuan; Wang, Mingkui

    2012-05-15

    Electrospray ionization ion-trap tandem mass spectrometry (ESI-MS(n)) was first employed for reinvestigating the structures of hupehensis saponin F and G previously isolated from Anemone hupehensis in our lab. Hupehensis saponin G was determined to contain one more trisaccharide unit (Rha-(1→4)-Glc-(1→6)-Glc-), not a glucose residue, than saponin F based on their molecular weights deduced from their [M+Na](+) ions in ESI-MS spectra. The (2,4)A(4α)-ion at m/z 551.3 formed by retro-Diels-Alder (RDA) rearrangement in positive mode illustrated that the C-28 sugar chains of the two saponins were composed of trisaccharide repeating moieties with (1→4) linkages rather than (1→3) linkages. The interpretation of 2D-NMR spectra of the two compounds also confirmed the results obtained by ESI-MS(n). Moreover, from the water soluble part of A. hupehensis, two novel triterpene saponins were tentatively characterized to contain 4 and 5 (1→4)-linked above trisaccharide repeating moieties at C-28 position according to their ESI-MS(n) behaviors, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  8. Diverse circovirus-like genome architectures revealed by environmental metagenomics.

    Science.gov (United States)

    Rosario, Karyna; Duffy, Siobain; Breitbart, Mya

    2009-10-01

    Single-stranded DNA (ssDNA) viruses with circular genomes are the smallest viruses known to infect eukaryotes. The present study identified 10 novel genomes similar to ssDNA circoviruses through data-mining of public viral metagenomes. The metagenomic libraries included samples from reclaimed water and three different marine environments (Chesapeake Bay, British Columbia coastal waters and Sargasso Sea). All the genomes have similarities to the replication (Rep) protein of circoviruses; however, only half have genomic features consistent with known circoviruses. Some of the genomes exhibit a mixture of genomic features associated with different families of ssDNA viruses (i.e. circoviruses, geminiviruses and parvoviruses). Unique genome architectures and phylogenetic analysis of the Rep protein suggest that these viruses belong to novel genera and/or families. Investigating the complex community of ssDNA viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA viruses.

  9. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  10. Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.

    Science.gov (United States)

    Sun, Wei; Zhang, Fengli; He, Liming; Li, Zhiyong

    2014-05-01

    Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.

  11. Taxonomic research on deep-sea macrofauna in the South China Sea using the Chinese deep-sea submersible Jiaolong.

    Science.gov (United States)

    Li, Xinzheng

    2017-07-01

    This paper reviews the taxonomic and biodiversity studies of deep-sea invertebrates in the South China Sea based on the samples collected by the Chinese manned deep-sea submersible Jiaolong. To date, 6 new species have been described, including the sponges Lophophysema eversa, Saccocalyx microhexactin and Semperella jiaolongae as well as the crustaceans Uroptychus jiaolongae, Uroptychus spinulosus and Globospongicola jiaolongi; some newly recorded species from the South China Sea have also been reported. The Bathymodiolus platifrons-Shinkaia crosnieri deep-sea cold seep community has been reported by Li (2015), as has the mitochondrial genome of the glass sponge L. eversa by Zhang et al. (2016). The population structures of two dominant species, the shrimp Shinkaia crosnieri and the mussel Bathymodiolus platifrons, from the cold seep Bathymodiolus platifrons-Shinkaia crosnieri community in the South China Sea and the hydrothermal vents in the Okinawa Trough, were compared using molecular analysis. The systematic position of the shrimp genus Globospongicola was discussed based on 16S rRNA gene sequences. © 2017 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  12. Genomics of Arctic cod

    Science.gov (United States)

    Wilson, Robert E.; Sage, George K.; Sonsthagen, Sarah A.; Gravley, Megan C.; Menning, Damian; Talbot, Sandra L.

    2017-01-01

    The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we

  13. Diversity, distribution and nature of faunal associations with deep-sea pennatulacean corals in the Northwest Atlantic.

    Directory of Open Access Journals (Sweden)

    Sandrine Baillon

    Full Text Available Anthoptilum grandiflorum and Halipteris finmarchica are two deep-sea corals (Octocorallia: Pennatulacea common on soft bottoms in the North Atlantic where they are believed to act as biogenic habitat. The former also has a worldwide distribution. To assist conservation efforts, this study examines spatial and temporal patterns in the abundance, diversity, and nature of their faunal associates. A total of 14 species were found on A. grandiflorum and 6 species on H. finmarchica during a multi-year and multi-site sampling campaign in eastern Canada. Among those, 7 and 5 species, respectively, were attached to the sea pens and categorized as close associates or symbionts. Rarefaction analyses suggest that the most common associates of both sea pens have been sampled. Biodiversity associated with each sea pen is analyzed according to season, depth and region using either close associates or the broader collection of species. Associated biodiversity generally increases from northern to southern locations and does not vary with depth (∼ 100-1400 m. Seasonal patterns in A. grandiflorum show higher biodiversity during spring/summer due to the transient presence of early life stages of fishes and shrimps whereas it peaks in fall for H. finmarchica. Two distinct endoparasitic species of highly modified copepods (families Lamippidae and Corallovexiidae commonly occur in the polyps of A. grandiflorum and H. finmarchica, and a commensal sea anemone frequently associates with H. finmarchica. Stable isotope analyses (δ(13C and δ(15N reveal potential trophic interactions between the parasites and their hosts. Overall, the diversity of obligate/permanent associates of sea pens is moderate; however the presence of mobile/transient associates highlights an ecological role that has yet to be fully elucidated and supports their key contribution to the enhancement of biodiversity in the Northwest Atlantic.

  14. The discovery of new deep-sea hydrothermal vent communities in the southern ocean and implications for biogeography.

    Directory of Open Access Journals (Sweden)

    Alex D Rogers

    2012-01-01

    Full Text Available Since the first discovery of deep-sea hydrothermal vents along the Galápagos Rift in 1977, numerous vent sites and endemic faunal assemblages have been found along mid-ocean ridges and back-arc basins at low to mid latitudes. These discoveries have suggested the existence of separate biogeographic provinces in the Atlantic and the North West Pacific, the existence of a province including the South West Pacific and Indian Ocean, and a separation of the North East Pacific, North East Pacific Rise, and South East Pacific Rise. The Southern Ocean is known to be a region of high deep-sea species diversity and centre of origin for the global deep-sea fauna. It has also been proposed as a gateway connecting hydrothermal vents in different oceans but is little explored because of extreme conditions. Since 2009 we have explored two segments of the East Scotia Ridge (ESR in the Southern Ocean using a remotely operated vehicle. In each segment we located deep-sea hydrothermal vents hosting high-temperature black smokers up to 382.8°C and diffuse venting. The chemosynthetic ecosystems hosted by these vents are dominated by a new yeti crab (Kiwa n. sp., stalked barnacles, limpets, peltospiroid gastropods, anemones, and a predatory sea star. Taxa abundant in vent ecosystems in other oceans, including polychaete worms (Siboglinidae, bathymodiolid mussels, and alvinocaridid shrimps, are absent from the ESR vents. These groups, except the Siboglinidae, possess planktotrophic larvae, rare in Antarctic marine invertebrates, suggesting that the environmental conditions of the Southern Ocean may act as a dispersal filter for vent taxa. Evidence from the distinctive fauna, the unique community structure, and multivariate analyses suggest that the Antarctic vent ecosystems represent a new vent biogeographic province. However, multivariate analyses of species present at the ESR and at other deep-sea hydrothermal vents globally indicate that vent biogeography is more

  15. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  16. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  17. Lampreys as Diverse Model Organisms in the Genomics Era.

    Science.gov (United States)

    McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

    2015-11-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

  18. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  19. Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

    KAUST Repository

    Zhang, Weipeng; Ding, Wei; Yang, Bo; Tian, Renmao; Gu, Shuo; Luo, Haiwei; Qian, Pei-Yuan

    2016-01-01

    the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota

  20. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  2. Sea Lion Diet Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — California sea lions pup and breed at four of the nine Channel Islands in southern California. Since 1981, SWFSC MMTD has been conducting a diet study of sea lions...

  3. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  4. Saponin 6 derived from Anemone taipaiensis induces U87 human malignant glioblastoma cell apoptosis via regulation of Fas and Bcl‑2 family proteins.

    Science.gov (United States)

    Ji, Chen-Chen; Tang, Hai-Feng; Hu, Yi-Yang; Zhang, Yun; Zheng, Min-Hua; Qin, Hong-Yan; Li, San-Zhong; Wang, Xiao-Yang; Fei, Zhou; Cheng, Guang

    2016-07-01

    Glioblastoma multiforme (GBM) is the most common and aggressive type of brain tumor, and is associated with a poor prognosis. Saponin 6, derived from Anemone taipaiensis, exerts potent cytotoxic effects against the human hepatocellular carcinoma HepG2 cell line and the human promyelocytic leukemia HL‑60 cell line; however, the effects of saponin 6 on glioblastoma remain unknown. The present study aimed to evaluate the effects of saponin 6 on human U87 malignant glioblastoma (U87 MG) cells. The current study revealed that saponin 6 induced U87 MG cell death in a dose‑ and time‑dependent manner, with a half maximal inhibitory concentration (IC50) value of 2.83 µM after treatment for 48 h. However, saponin 6 was needed to be used at a lesser potency in HT‑22 cells, with an IC50 value of 6.24 µM. Cell apoptosis was assessed by flow cytometry using Annexin V‑fluorescein isothiocyanate/propidium iodide double staining. DNA fragmentation and alterations in nuclear morphology were examined by terminal deoxynucleotidyl transferase‑mediated dUTP nick end labeling and transmission electron microscopy, respectively. The present study demonstrated that treatment with saponin 6 induced cell apoptosis in U87 MG cells, and resulted in DNA fragmentation and nuclear morphological alterations typical of apoptosis. In addition, flow cytometric analysis revealed that saponin 6 was able to induce cell cycle arrest. The present study also demonstrated that saponin 6‑induced apoptosis of U87 MG cells was attributed to increases in the protein expression levels of Fas, Fas ligand, and cleaved caspase‑3, ‑8 and ‑9, and decreases in the levels of B‑cell lymphoma 2. The current study indicated that saponin 6 may exhibit selective cytotoxicity toward U87 MG cells by activating apoptosis via the extrinsic and intrinsic pathways. Therefore, saponin 6 derived from A. taipaiensis may possess therapeutic potential for the treatment of GBM.

  5. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  6. Sea level report

    International Nuclear Information System (INIS)

    Schwartz, M.L.

    1979-01-01

    Study of Cenozoic Era sea levels shows a continual lowering of sea level through the Tertiary Period. This overall drop in sea level accompanied the Pleistocene Epoch glacio-eustatic fluctuations. The considerable change of Pleistocene Epoch sea level is most directly attributable to the glacio-eustatic factor, with a time span of 10 5 years and an amplitude or range of approximately 200 m. The lowering of sea level since the end of the Cretaceous Period is attributed to subsidence and mid-ocean ridges. The maximum rate for sea level change is 4 cm/y. At present, mean sea level is rising at about 3 to 4 mm/y. Glacio-eustacy and tectono-eustacy are the parameters for predicting sea level changes in the next 1 my. Glacio-eustatic sea level changes may be projected on the basis of the Milankovitch Theory. Predictions about tectono-eustatic sea level changes, however, involve predictions about future tectonic activity and are therefore somewhat difficult to make. Coastal erosion and sedimentation are affected by changes in sea level. Erosion rates for soft sediments may be as much as 50 m/y. The maximum sedimentation accumulation rate is 20 m/100 y

  7. Dicty_cDB: Contig-U02747-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 3d05.g1 Oxytricha_pSMART_OXBB Sterkiella... 50 0.098 1 ( FK749731 ) av02085g19r1.1 Symbiotic... sea anemone (Anemonia vi... 50 0.098 1 ( FK731884 ) av02115l17r1.1 Symbiotic sea anemone (Anemon

  8. Insights into bilaterian evolution from three spiralian genomes

    Energy Technology Data Exchange (ETDEWEB)

    Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin; Edsinger-Gonzales, Eric; Havlak, Paul; Hellsten, Uffe; Kuo, Dian-Han; Larsson, Tomas; Lv, Jie; Arendt, Detlev; Savage, Robert; Osoegawa, Kazutoyo; de Jong, Pieter; Grimwood, Jane; Chapman, Jarrod A.; Shapiro, Harris; Otillar, Robert P.; Terry, Astrid Y.; Boore, Jeffrey L.; Grigoriev, Igor V.; Lindberg, David R.; Seaver, Elaine C.; Weisblat, David A.; Putnam, Nicholas H.; Rokhsar, Daniel S.; Aerts, Andrea

    2012-01-07

    Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

  9. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  10. Age, Growth, Reproduction and Feeding of the Spurdog ( Squalus acanthias Linnaeus, 1758) in the South-eastern Black Sea

    Science.gov (United States)

    Avsar, D.

    2001-02-01

    Life-history parameters and diet of spurdog ( Squalus acanthias) sampled from the SE Black Sea were studied. Spurdog from age classes I to XIV were identified, with a dominance of age class VIII for both sexes. The length-weight relationship was W=0·0040*L 2·95and the mean annual growth rates in length and weight were 7·2 cm and 540·1 g, respectively. The estimated von Bertalanffy growth parameters were: W ∞=12021 (g), L ∞=157 (cm), K=0·12 (year -1) and t 0=-1·30 (year). The size at first maturity was 82 cm for males and 88 cm for females. Mean biennial fecundity was also found to be 8 pups/female. The relationships between fecundity-length, fecundity-weight and fecundity-age were found to be: F=-17·0842+0·2369*L (R=0·93), F=0·3780+0·0018*W (R=0·89) and F =-0·7859+1·1609*A (R=0·94) respectively. The spurdog can be considered an opportunistic feeder. Their natural diet was composed mainly of teleost fishes, followed by Crustaceans, Nematodes and Actinarians (=sea anemones). Whiting ( Merlangius merlangus euxinus) was the predominant prey item among their fish prey. Demersal teleosts formed the majority of the diet, and there was no difference ( P>0·05) among the food items of immature, maturing and mature individuals of both sexes.

  11. Spawning of coral reef invertebrates and a second spawning season for scleractinian corals in the central Red Sea

    KAUST Repository

    Bouwmeester, Jessica

    2016-06-22

    Recent coral spawning observations in the central Red Sea show that most scleractinian species release their gametes in the spring, with a majority of species spawning in April. There is, however, a lack of reproductive data for several other coral species, as well as a general lack of data for other invertebrates. Here, we document the detailed timing of spawning for 13 scleractinian coral species, one sea anemone, and six echinoderms from an inshore reef off the coast of Thuwal, Saudi Arabia, in the spring between April and June 2014. Furthermore, inferred from the presence of mature gametes, we report the month of spawning for three additional coral species in the spring. Seven scleractinian coral species were inferred to release their gametes in a second reproductive season, in the autumn, between September and November. This is the first report of a second spawning season in the Arabian region. Biannual spawning has so far been reported on the Great Barrier Reef, in Western Australia, in Indonesia, in Malaysia, in Palau, in Thailand, in Taiwan, and in Western Samoa. © 2016, The American Microscopical Society, Inc.

  12. Targeted mutagenesis in sea urchin embryos using TALENs.

    Science.gov (United States)

    Hosoi, Sayaka; Sakuma, Tetsushi; Sakamoto, Naoaki; Yamamoto, Takashi

    2014-01-01

    Genome editing with engineered nucleases such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) has been reported in various animals. We previously described ZFN-mediated targeted mutagenesis and insertion of reporter genes in sea urchin embryos. In this study, we demonstrate that TALENs can induce mutagenesis at specific genomic loci of sea urchin embryos. Injection of TALEN mRNAs targeting the HpEts transcription factor into fertilized eggs resulted in the impairment of skeletogenesis. Sequence analyses of the mutations showed that deletions and/or insertions occurred at the HpEts target site in the TALEN mRNAs-injected embryos. The results suggest that targeted gene disruption using TALENs is feasible in sea urchin embryos. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

  13. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  14. Salish Sea Genetics - Salish Sea genetic inventory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Salish Sea comprises most of the Puget Sound water area. Marine species are generally assemblages of discrete populations occupying various ecological niches....

  15. Mimivirus relatives in the Sargasso sea

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2005-08-01

    Full Text Available Abstract The discovery and genome analysis of Acanthamoeba polyphaga Mimivirus, the largest known DNA virus, challenged much of the accepted dogma regarding viruses. Its particle size (>400 nm, genome length (1.2 million bp and huge gene repertoire (911 protein coding genes all contribute to blur the established boundaries between viruses and the smallest parasitic cellular organisms. Phylogenetic analyses also suggested that the Mimivirus lineage could have emerged prior to the individualization of cellular organisms from the three established domains, triggering a debate that can only be resolved by generating and analyzing more data. The next step is then to seek some evidence that Mimivirus is not the only representative of its kind and determine where to look for new Mimiviridae. An exhaustive similarity search of all Mimivirus predicted proteins against all publicly available sequences identified many of their closest homologues among the Sargasso Sea environmental sequences. Subsequent phylogenetic analyses suggested that unknown large viruses evolutionarily closer to Mimivirus than to any presently characterized species exist in abundance in the Sargasso Sea. Their isolation and genome sequencing could prove invaluable in understanding the origin and diversity of large DNA viruses, and shed some light on the role they eventually played in the emergence of eukaryotes.

  16. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  17. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  18. Contemporary Arctic Sea Level

    Science.gov (United States)

    Cazenave, A. A.

    2017-12-01

    During recent decades, the Arctic region has warmed at a rate about twice the rest of the globe. Sea ice melting is increasing and the Greenland ice sheet is losing mass at an accelerated rate. Arctic warming, decrease in the sea ice cover and fresh water input to the Arctic ocean may eventually impact the Arctic sea level. In this presentation, we review our current knowledge of contemporary Arctic sea level changes. Until the beginning of the 1990s, Arctic sea level variations were essentially deduced from tide gauges located along the Russian and Norwegian coastlines. Since then, high inclination satellite altimetry missions have allowed measuring sea level over a large portion of the Arctic Ocean (up to 80 degree north). Measuring sea level in the Arctic by satellite altimetry is challenging because the presence of sea ice cover limits the full capacity of this technique. However adapted processing of raw altimetric measurements significantly increases the number of valid data, hence the data coverage, from which regional sea level variations can be extracted. Over the altimetry era, positive trend patterns are observed over the Beaufort Gyre and along the east coast of Greenland, while negative trends are reported along the Siberian shelf. On average over the Arctic region covered by satellite altimetry, the rate of sea level rise since 1992 is slightly less than the global mea sea level rate (of about 3 mm per year). On the other hand, the interannual variability is quite significant. Space gravimetry data from the GRACE mission and ocean reanalyses provide information on the mass and steric contributions to sea level, hence on the sea level budget. Budget studies show that regional sea level trends over the Beaufort Gyre and along the eastern coast of Greenland, are essentially due to salinity changes. However, in terms of regional average, the net steric component contributes little to the observed sea level trend. The sea level budget in the Arctic

  19. Arctic Sea Level Reconstruction

    DEFF Research Database (Denmark)

    Svendsen, Peter Limkilde

    Reconstruction of historical Arctic sea level is very difficult due to the limited coverage and quality of tide gauge and altimetry data in the area. This thesis addresses many of these issues, and discusses strategies to help achieve a stable and plausible reconstruction of Arctic sea level from...... 1950 to today.The primary record of historical sea level, on the order of several decades to a few centuries, is tide gauges. Tide gauge records from around the world are collected in the Permanent Service for Mean Sea Level (PSMSL) database, and includes data along the Arctic coasts. A reasonable...... amount of data is available along the Norwegian and Russian coasts since 1950, and most published research on Arctic sea level extends cautiously from these areas. Very little tide gauge data is available elsewhere in the Arctic, and records of a length of several decades,as generally recommended for sea...

  20. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  1. SEA and planning

    DEFF Research Database (Denmark)

    Stoeglehner, G.; Brown, A.L.; Kørnøv, Lone

    2009-01-01

    , and the relationship of the SEA to the planning activity itself. This paper focuses on the influence that planners have in these implementation processes, postulating the hypothesis that these are key players in achieving effectiveness in SEA. Based upon implementation theory and empirical experience, the paper......As the field of strategic environmental assessment (SEA) has matured, the focus has moved from the development of legislation, guidelines and methodologies towards improving the effectiveness of SEA. Measuring and of course achieving effectiveness is both complex and challenging. This paper...

  2. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Directory of Open Access Journals (Sweden)

    Mark Ravinet

    2018-05-01

    Full Text Available Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus and the Japan Sea stickleback (G. nipponicus, which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  3. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

    Science.gov (United States)

    Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

    2018-05-01

    Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

  4. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  5. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  6. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  7. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  8. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  9. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  10. Sea surface temperatures and salinities from platforms in the Barents Sea, Sea of Japan, North Atlantic Ocean, Philippine Sea, Red Sea, and the South China Sea (Nan Hai) from 1896-1950 (NODC Accession 0000506)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Surface temperatures and salinities were collected in the Barents Sea, Sea of Japan, North Atlantic Ocean, Philippine Sea, Red Sea, and South China Sea (Nan Hai)...

  11. Dilemmas in SEA application

    DEFF Research Database (Denmark)

    Lyhne, Ivar

    Dilemmas in SEA Application: The DK Energy SectorIvar Lyhne - lyhne@plan.aau.dk. Based on three years of collaborative research, this paper outlines dilemmas in the application of SEA in the strategic development of the Danish energy sector. The dilemmas are based on concrete examples from practice...

  12. Indicators and SEA

    DEFF Research Database (Denmark)

    Gao, Jingjing; Kørnøv, Lone; Christensen, Per

    Abstract: Indicators are widely used in SEA to measure, communicate and monitor impacts from a proposed policy, plan or programme, and can improve the effectiveness for the SEA by simplifying the complexity of both assessment and presentation. Indicators can be seen as part of the implementation...... and if the information requirement for different target groups is not addressed. Indicators are widely used in SEA to measure, communicate and monitor impacts from a proposed policy, plan or programme, and can improve the effectiveness for the SEA by simplifying the complexity of both assessment and presentation...... process helping to understand, communicate and, integrate important environmental issues in planning and decision-making. On the other hand, use of indicators can also limit SEA effectiveness, if the ones chosen are biased or limited, if the aggregation gives incorrect interpretation...

  13. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  14. Caspian sea: petroleum challenges

    International Nuclear Information System (INIS)

    2005-01-01

    The Caspian sea is one of the world areas the most promising in terms of investments and petroleum development. This study presents the petroleum challenges generated by this hydrocarbons reserve. The first part discusses the juridical status (sea or lake), the petroleum and the gas reserves, the ecosystem and the today environment (fishing and caviar), the geostrategic situation and the transport of gas and oil. It provides also a chronology from 1729 to 2005, a selection of Internet sites, books and reports on the subject and identity sheets of the countries around the Caspian sea. (A.L.B.)

  15. Radionuclides in the sea

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1971-07-01

    Water covers a little more than two-thirds of the earth's surface. What is thrown into the sea from a ship may be washed up on a shore thousands of miles away; wastes discharged into the seas or into rivers flowing into them can affect marine life and possibly also the health of man. The study, prevention and control of pollution of the seas and oceans by radionuclides introduced as by-products of man's use of nuclear energy is thus of global interest. (author)

  16. Sea Scallop Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The standardized NEFSC Sea Scallop Survey began in 1980 and has covered an area from Cape Hatteras to Georges Bank. The survey aims to determine the distribution and...

  17. Energy from sea water

    International Nuclear Information System (INIS)

    Ruberti, M.

    2000-01-01

    The devices to obtain energy from sea exploiting thermal gradient and wave motion are numerous and efficient. Costs are at present prohibitive in our country and the utilization cannot be possible [it

  18. Sea Ice Ecosystems

    Science.gov (United States)

    Arrigo, Kevin R.

    2014-01-01

    Polar sea ice is one of the largest ecosystems on Earth. The liquid brine fraction of the ice matrix is home to a diverse array of organisms, ranging from tiny archaea to larger fish and invertebrates. These organisms can tolerate high brine salinity and low temperature but do best when conditions are milder. Thriving ice algal communities, generally dominated by diatoms, live at the ice/water interface and in recently flooded surface and interior layers, especially during spring, when temperatures begin to rise. Although protists dominate the sea ice biomass, heterotrophic bacteria are also abundant. The sea ice ecosystem provides food for a host of animals, with crustaceans being the most conspicuous. Uneaten organic matter from the ice sinks through the water column and feeds benthic ecosystems. As sea ice extent declines, ice algae likely contribute a shrinking fraction of the total amount of organic matter produced in polar waters.

  19. Black Sea aerosols

    International Nuclear Information System (INIS)

    Hacisalihoglu, G.; Eliyakut, F.; Anwari, M.A.; Ataman, O.Y.; Balkas, T.I.; Tuncel, G.; Olmez, I.

    1991-01-01

    Shipboard, high volume air particulate samples were collected from the Black Sea atmosphere and analyzed by instrumental neutron activation analysis, atomic absorption spectrophotometry and ion chromatography for about 40 elements and ions. Concentrations of elements in the eastern and western parts of the Black Sea are different at the 95% confidence level, with lower concentrations in the eastern Black Sea. Back-trajectories and concentrations of elements in trajectory groups show that Europe accounts for more than 70% of the anthropogenic elements in the atmosphere. The average sulfate concentration was 7 μg/m 3 , which is comparable with rural sulfate levels in western Europe. Fluxes of elements from the atmosphere to the Black Sea are in good agreement with the results of similar flux calculations for other regions

  20. Pollution of Coastal Seas

    Indian Academy of Sciences (India)

    These are the things ideally required for locating industries also. The mega-cities .... waste water released into coastal seas raises the ambient temperature causing .... Problems of ozone holes and greenhouse gases were, perhaps, beyond ...

  1. Pollution of coastal seas

    Digital Repository Service at National Institute of Oceanography (India)

    Varkey, M.J.

    Pollution of various environments is a consequence of population growth and industrialisation. Coastal seas form part of marine environment and are very rich in minerals, crude oil fishes etc. They are also being used for disposal of wastes from...

  2. Oceanography of marginal seas

    Digital Repository Service at National Institute of Oceanography (India)

    DileepKumar, M.

    in the first two shallow seas are driven by surface densification following evaporation that in the latter is largely influenced by freshwater discharge from Irrawaddy and inflows across the Andaman Ridge from east Bay of Bengal. Biological productivity...

  3. Sea urchin vault structure, composition, and differential localization during development

    Directory of Open Access Journals (Sweden)

    Dickey-Sims Carrie

    2005-02-01

    Full Text Available Abstract Background Vaults are intriguing ribonucleoprotein assemblies with an unknown function that are conserved among higher eukaryotes. The Pacific coast sea urchin, Strongylocentrotus purpuratus, is an invertebrate model organism that is evolutionarily closer to humans than Drosophila and C. elegans, neither of which possesses vaults. Here we compare the structures of sea urchin and mammalian vaults and analyze the subcellular distribution of vaults during sea urchin embryogenesis. Results The sequence of the sea urchin major vault protein (MVP was assembled from expressed sequence tags and genome traces, and the predicted protein was found to have 64% identity and 81% similarity to rat MVP. Sea urchin MVP includes seven ~50 residue repeats in the N-terminal half of the protein and a predicted coiled coil domain in the C-terminus, as does rat MVP. A cryoelectron microscopy (cryoEM reconstruction of isolated sea urchin vaults reveals the assembly to have a barrel-shaped external structure that is nearly identical to the rat vault structure. Analysis of the molecular composition of the sea urchin vault indicates that it contains components that may be homologs of the mammalian vault RNA component (vRNA and protein components (VPARP and TEP1. The sea urchin vault appears to have additional protein components in the molecular weight range of 14–55 kDa that might correspond to molecular contents. Confocal experiments indicate a dramatic relocalization of MVP from the cytoplasm to the nucleus during sea urchin embryogenesis. Conclusions These results are suggestive of a role for the vault in delivering macromolecules to the nucleus during development.

  4. South China Sea

    Science.gov (United States)

    Morton, Brian; Blackmore, Graham

    2001-01-01

    The South China Sea is poorly understood in terms of its marine biota, ecology and the human impacts upon it. What is known is most often contained in reports and workshop and conference documents that are not available to the wider scientific community. The South China Sea has an area of some 3.3 million km2 and depths range from the shallowest coastal fringe to 5377 m in the Manila Trench. It is also studded with numerous islets, atolls and reefs many of which are just awash at low tide. It is largely confined within the Tropic of Cancer and, therefore, experiences a monsoonal climate being influenced by the Southwest Monsoon in summer and the Northeast Monsoon in winter. The South China Sea is a marginal sea and, therefore, largely surrounded by land. Countries that have a major influence on and claims to the sea include China, Malaysia, the Philippines and Vietnam, although Thailand, Indonesia and Taiwan have some too. The coastal fringes of the South China Sea are home to about 270 million people that have had some of the fastest developing and most vibrant economies on the globe. Consequently, anthropogenic impacts, such as over-exploitation of resources and pollution, are anticipated to be huge although, in reality, relatively little is known about them. The Indo-West Pacific biogeographic province, at the centre of which the South China Sea lies, is probably the world's most diverse shallow-water marine area. Of the three major nearshore habitat types, i.e., coral reefs, mangroves and seagrasses, 45 mangrove species out of a global of 51, most of the currently recognised 70 coral genera and 20 of 50 known seagrass species have been recorded from the South China Sea. The island groups of the South China Sea are all disputed and sovereignty is claimed over them by a number of countries. Conflicts have in recent decades arisen over them because of perceived national rights. It is perhaps because of this that so little research has been undertaken on the South

  5. South China Sea

    Energy Technology Data Exchange (ETDEWEB)

    Morton, Brian [Hong Kong Univ., Swire Inst. of Marine Science, Hong Kong (China); Hong Kong Univ., Dept. of Ecology and Biodiversity, Hong Kong (China); Blackmore, Graham [Hong Kong Univ. of Science and Technology, Dept. of Biology, Hong Kong (China)

    2001-07-01

    The South China Sea is poorly understood in terms of its marine biota, ecology and the human impacts upon it. What is known is most often contained in reports and workshops and conference documents that are not available to the wider scientific community. The South China Sea has an area of some 3.3 million km{sup 2} and depths range from the shallowest coastal fringe to 5377m in the Manila Trench. It is also studded with numerous islets, atolls and reefs many of which are just awash at low tide. It is largely confined within the Tropic of Cancer and, therefore, experiences a monsoonal climate being influenced by the Southwest Monsoon in summer and the Northeast Monsoon in winter. The South China Sea is a marginal sea and, therefore, largely surrounded by land. Countries that have a major influence on and claims to the sea include China, Malaysia, the Philippines and Vietnam, although Thailand, Indonesia and Taiwan have some too. The coastal fringes of the South China Sea are home to about 270 million people that have had some of the fastest developing and most vibrant economics on the globe. Consequently, anthropogenic impacts, such as over-exploitation of resources and pollution, are anticipated to be huge although, in reality, relatively little is known about them. The Indo-West Pacific biogeographic province, at the centre of which the South China Sea lies, is probably the world's most diverse shallow-water marine area. Of three major nearshore habitat types, i.e., coral reefs, mangroves and seagrasses, 45 mangrove species out of a global total of 51, most of the currently recognised 70 coral genera and 20 of 50 known seagrass species have been recorded from the South China Sea. The island groups of the South China Sea are all disputed and sovereignty is claimed over them by a number of countries. Conflicts have in recent decades arisen over them because of perceived national rights. It is perhaps because of this that so little research has been undertaken

  6. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  7. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  8. South China Sea Dispute

    OpenAIRE

    Tanderup, Kasper Buch; Grinderslev, Emil Juhler; Tønnesen-Højbjerg, Asser Laurits Svend

    2017-01-01

    China is rising rapidly in terms of economics, military spending, sphere of influence and claims to in their view former territory. This paper has aimed to discuss the latter through analysis of the present dispute concerning islands and maritime territory in the South China Sea. The Chinese have become increasingly assertive in their claims formulated through a U-shaped line entailing most of the area within the South China Sea. The claims are contested by Vietnam, the Philippines, Indonesia...

  9. Contemporary sea level rise.

    Science.gov (United States)

    Cazenave, Anny; Llovel, William

    2010-01-01

    Measuring sea level change and understanding its causes has considerably improved in the recent years, essentially because new in situ and remote sensing observations have become available. Here we report on most recent results on contemporary sea level rise. We first present sea level observations from tide gauges over the twentieth century and from satellite altimetry since the early 1990s. We next discuss the most recent progress made in quantifying the processes causing sea level change on timescales ranging from years to decades, i.e., thermal expansion of the oceans, land ice mass loss, and land water-storage change. We show that for the 1993-2007 time span, the sum of climate-related contributions (2.85 +/- 0.35 mm year(-1)) is only slightly less than altimetry-based sea level rise (3.3 +/- 0.4 mm year(-1)): approximately 30% of the observed rate of rise is due to ocean thermal expansion and approximately 55% results from land ice melt. Recent acceleration in glacier melting and ice mass loss from the ice sheets increases the latter contribution up to 80% for the past five years. We also review the main causes of regional variability in sea level trends: The dominant contribution results from nonuniform changes in ocean thermal expansion.

  10. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  11. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  12. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  13. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  14. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  15. Projecting future sea level

    Science.gov (United States)

    Cayan, Daniel R.; Bromirski, Peter; Hayhoe, Katharine; Tyree, Mary; Dettinger, Mike; Flick, Reinhard

    2006-01-01

    California’s coastal observations and global model projections indicate that California’s open coast and estuaries will experience increasing sea levels over the next century. Sea level rise has affected much of the coast of California, including the Southern California coast, the Central California open coast, and the San Francisco Bay and upper estuary. These trends, quantified from a small set of California tide gages, have ranged from 10–20 centimeters (cm) (3.9–7.9 inches) per century, quite similar to that estimated for global mean sea level. So far, there is little evidence that the rate of rise has accelerated, and the rate of rise at California tide gages has actually flattened since 1980, but projections suggest substantial sea level rise may occur over the next century. Climate change simulations project a substantial rate of global sea level rise over the next century due to thermal expansion as the oceans warm and runoff from melting land-based snow and ice accelerates. Sea level rise projected from the models increases with the amount of warming. Relative to sea levels in 2000, by the 2070–2099 period, sea level rise projections range from 11–54 cm (4.3–21 in) for simulations following the lower (B1) greenhouse gas (GHG) emissions scenario, from 14–61 cm (5.5–24 in) for the middle-upper (A2) emission scenario, and from 17–72 cm (6.7–28 in) for the highest (A1fi) scenario. In addition to relatively steady secular trends, sea levels along the California coast undergo shorter period variability above or below predicted tide levels and changes associated with long-term trends. These variations are caused by weather events and by seasonal to decadal climate fluctuations over the Pacific Ocean that in turn affect the Pacific coast. Highest coastal sea levels have occurred when winter storms and Pacific climate disturbances, such as El Niño, have coincided with high astronomical tides. This study considers a range of projected future

  16. Sustainable Seas Student Intertidal Monitoring Project, Duxbury Reef, Bolinas, CA

    Science.gov (United States)

    Soave, K.; Dean, A.; Prescutti, K.; Ball, O.; Chang, E.; Darakananda, K.; Jessup, K.; Poutian, J.; Schwalbe, H.; Storm, E.

    2008-12-01

    The Sustainable Seas Student Monitoring Project at the Branson School in Ross, CA has monitored Duxbury Reef in Bolinas, CA since 1999, in cooperation with the Farallones Marine Sanctuary Association and the Gulf of Farallones National Marine Sanctuary. Goals of the project include: 1) To monitor the rocky intertidal habitat and develop a baseline database of invertebrates and algal density and abundance; 2) To contribute to the conservation of the rocky intertidal habitat through education of students and visitors about intertidal species and requirements for maintaining a healthy, diverse intertidal ecosystem; 3) To increase stewardship in the Gulf of the Farallones National Marine Sanctuary; and 4) To contribute abundance and population data on key algae and invertebrate species to the national database, LiMPETS (Long Term Monitoring Program and Experiential Training for Students). Student volunteers complete an intensive training course on the natural history of intertidal invertebrates and algae, identification of key species, rocky intertidal ecology, interpretation and monitoring techniques, and history of the sanctuary. Students identify and count key invertebrate and algae species along two permanent transects (A and B), and using randomly determined points within a permanent 100 m2 area, three times per year (fall, winter, and late spring). Using the data collected since 2004, we will analyze the population densities of aggregating anemones, Anthopleura elegantissima, for seasonal abundance variations as well as long-term population trends. We will also follow the seasonal and long-term population fluctuations of red algal turf, Endocladia muricata and Gelidium coulteri, and black turban snails, Tegula funebralis. Comparing populations of turf algae and the herbivorous black turban snails gathered before and after the November 7, 2007 San Francisco Bay oil spill shows very little impact on the Duxbury Reef intertidal inhabitants. Future analyses will

  17. Isolation and characterization of microsatellite loci from the Australasian sea snake, Aipysurus laevis

    DEFF Research Database (Denmark)

    Lukoschek, Vimoksalehi; Waycott, Michelle; Dunshea, Glenn

    2005-01-01

    We developed 13 microsatellite loci for the olive sea snake, Aipysurus laevis, using both enriched and unenriched genomic DNA libraries. Eleven codominant loci, that reliably amplified, were used to screen 32 individuals across the geographic range of A. laevis. Four loci had four or more alleles...... (maximum 12), whereas the other seven had either two or three. All but one locus was in Hardy-Weinberg equilibrium. These loci will provide useful markers to investigate population genetic structure for the olive sea snake....

  18. The White Sea, Russia

    Science.gov (United States)

    2002-01-01

    Editor's Note: The caption below, published on May 10, 2001, is incorrect. According to Masha Vorontsova, director of the International Fund for Animal Welfare in Moscow, the situation with the seal pups in the White Sea is normal. There is no disaster and there never was. For more details, refer to the article entitled 'No Danger' on the New Scientist home page. The Earth Observatory regrets the earlier errant report. Original Caption According to the Russian Polar Research Institute for Fisheries and Oceanography, between 250,000 and 300,000 Greenland seal pups face death by starvation over the next two months due to a cruel trick by mother nature. The seals, most of them less than two months old, are trapped on ice sheets that remain locked in the White Sea, located near Archangel in Northern Russia. Typically, during the spring thaw the ice sheets break up and flow with the currents northward into the Barents Sea, the seals' spring feeding grounds. The seal pups hitch a ride on the ice floes, living on their own individual stores of fat until they arrive in the Barents Sea. Their mothers departed for the Barents Sea weeks ago. In a normal year, the seal pups' trip from the White Sea out to the Barents takes about six weeks and the seals have adapted to rely upon this mechanism of mother nature. During their yearly migration, the mother seals usually stay with their pups and feed them until their pelts turn from white to grey--a sign that the pups are mature enough to swim and feed themselves. Unfortunately, this year unusually strong northerly winds created a bottleneck of ice near the mouth of the white sea, thus blocking the flow of ice and trapping the pups. These true-color images of the White Sea were acquired by the Moderate-resolution Imaging Spectroradiometer (MODIS), flying aboard NASA's Terra spacecraft. This image, taken May 2, 2000 that there is usually much less ice in the White Sea this time of year as most of it is typically en route to the

  19. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  20. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  1. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  2. The Dead Sea

    Science.gov (United States)

    2006-01-01

    The Dead Sea is the lowest point on Earth at 418 meters below sea level, and also one of the saltiest bodies of water on Earth with a salinity of about 300 parts-per-thousand (nine times greater than ocean salinity). It is located on the border between Jordan and Israel, and is fed by the Jordan River. The Dead Sea is located in the Dead Sea Rift, formed as a result of the Arabian tectonic plate moving northward away from the African Plate. The mineral content of the Dead Sea is significantly different from that of ocean water, consisting of approximately 53% magnesium chloride, 37% potassium chloride and 8% sodium chloride. In the early part of the 20th century, the Dead Sea began to attract interest from chemists who deduced that the Sea was a natural deposit of potash and bromine. From the Dead Sea brine, Israel and Jordan produce 3.8 million tons potash, 200,000 tons elemental bromine, 45,000 tons caustic soda, 25, 000 tons magnesium metal, and sodium chloride. Both countries use extensive salt evaporation pans that have essentially diked the entire southern end of the Dead Sea. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet. ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products. The broad spectral coverage and high spectral resolution of ASTER provides scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining

  3. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  4. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  5. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  6. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  7. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  8. Sea Spray Aerosols

    DEFF Research Database (Denmark)

    Butcher, Andrew Charles

    emissions produced directly from bubble bursting as the result of air entrainment from breaking waves and particles generated from secondary emissions of volatile organic compounds. In the first paper, we study the chemical properties of particles produced from several sea water proxies with the use...... of a cloud condensation nuclei ounter. Proxy solutions with high inorganic salt concentrations and some organics produce sea spray aerosol particles with little change in cloud condensation activity relative to pure salts. Comparison is made between a frit based method for bubble production and a plunging...... a relationship between plunging jet particle ux, oceanic particle ux, and energy dissipation rate in both systems. Previous sea spray aerosol studies dissipate an order of magnitude more energy for the same particle ux production as the open ocean. A scaling factor related to the energy expended in air...

  9. Replenishment at sea

    Directory of Open Access Journals (Sweden)

    Bohdan Pac

    2012-12-01

    Full Text Available Replenishment at sea is a process which plays the key role in the contemporary naval logistics during military and crisis operations. As the last element of the supply chain, it must use specific standards within the areas of procedures, technical equipment, logistic assets and resources, as well as safety, especially in multinational operations. The methods applied enable ships to operate at sea in the long term without logistic support provided by sea ports. The paper explains all the methods of the solids and liquids replenishment, and also gives an idea how to estimate the resupply process, using the measures. The level of standardization of procedures and assets implemented by NATO, the EU and other willing states has been described.

  10. Air-Sea Interaction

    Science.gov (United States)

    Csanady, G. T.

    2001-03-01

    In recent years air-sea interaction has emerged as a subject in its own right, encompassing small-scale and large-scale processes in both air and sea. Air-Sea Interaction: Laws and Mechanisms is a comprehensive account of how the atmosphere and the ocean interact to control the global climate, what physical laws govern this interaction, and its prominent mechanisms. The topics covered range from evaporation in the oceans, to hurricanes, and on to poleward heat transport by the oceans. By developing the subject from basic physical (thermodynamic) principles, the book is accessible to graduate students and research scientists in meteorology, oceanography, and environmental engineering. It will also be of interest to the broader physics community involved in the treatment of transfer laws, and thermodynamics of the atmosphere and ocean.

  11. Caribbean Sea Level Network

    Science.gov (United States)

    von Hillebrandt-Andrade, C.; Crespo Jones, H.

    2012-12-01

    Over the past 500 years almost 100 tsunamis have been observed in the Caribbean and Western Atlantic, with at least 3510 people having lost their lives to this hazard since 1842. Furthermore, with the dramatic increase in population and infrastructure along the Caribbean coasts, today, millions of coastal residents, workers and visitors are vulnerable to tsunamis. The UNESCO IOC Intergovernmental Coordination Group for Tsunamis and other Coastal Hazards for the Caribbean and Adjacent Regions (CARIBE EWS) was established in 2005 to coordinate and advance the regional tsunami warning system. The CARIBE EWS focuses on four areas/working groups: (1) Monitoring and Warning, (2) Hazard and Risk Assessment, (3) Communication and (4) Education, Preparedness and Readiness. The sea level monitoring component is under Working Group 1. Although in the current system, it's the seismic data and information that generate the initial tsunami bulletins, it is the data from deep ocean buoys (DARTS) and the coastal sea level gauges that are critical for the actual detection and forecasting of tsunamis impact. Despite multiple efforts and investments in the installation of sea level stations in the region, in 2004 there were only a handful of sea level stations operational in the region (Puerto Rico, US Virgin Islands, Bermuda, Bahamas). Over the past 5 years there has been a steady increase in the number of stations operating in the Caribbean region. As of mid 2012 there were 7 DARTS and 37 coastal gauges with additional ones being installed or funded. In order to reach the goal of 100 operational coastal sea level stations in the Caribbean, the CARIBE EWS recognizes also the importance of maintaining the current stations. For this, a trained workforce in the region for the installation, operation and data analysis and quality control is considered to be critical. Since 2008, three training courses have been offered to the sea level station operators and data analysts. Other

  12. Baltic Sea: Radionuclides

    DEFF Research Database (Denmark)

    Nielsen, Sven Poul; Lüning, Maria; Ilus, Erkki

    2011-01-01

    The most significant source of anthropogenic radioactivity in the Baltic Sea is fallout from the accident at the Chernobyl nuclear power plant in 1986. The second most important source is global fallout from atmospheric nuclear weapons tests carried out during the late 1950s and early 1960s...... about 14%. For 90Sr in the Baltic Sea, input from atmospheric fallout from nuclear weapons tests has contributed about 81%, while the contribution from Chernobyl fallout was about 13%. Cesium-137 is the main indicator of Baltic seawater with respect to anthropogenic radioactivity. The highest...... concentrations in seawater during 1999–2006 were found in the Baltic Proper and the Bothnian Sea. The general trend is steadily decreasing. Concentrations of anthropogenic radioactivity in fish generally show decreasing trends in agreement with concentrations in seawater. Among freshwater fish, pike showed large...

  13. Baltic Sea: Radionuclides

    DEFF Research Database (Denmark)

    Nielsen, Sven Poul; Lüning, Maria; Ilus, Erkki

    2010-01-01

    The most significant source of anthropogenic radioactivity in the Baltic Sea is fallout from the accident at the Chernobyl nuclear power plant in 1986. The second most important source is global fallout from atmospheric nuclear weapons tests carried out during the late 1950s and early 1960s...... about 14%. For 90Sr in the Baltic Sea, input from atmospheric fallout from nuclear weapons tests has contributed about 81%, while the contribution from Chernobyl fallout was about 13%. Cesium-137 is the main indicator of Baltic seawater with respect to anthropogenic radioactivity. The highest...... concentrations in seawater during 1999–2006 were found in the Baltic Proper and the Bothnian Sea. The general trend is steadily decreasing. Concentrations of anthropogenic radioactivity in fish generally show decreasing trends in agreement with concentrations in seawater. Among freshwater fish, pike showed large...

  14. Mediterranean, our sea

    Science.gov (United States)

    Markaki, Foteini

    2017-04-01

    My school (1o EPAL Ymittos -Athens, Greece) is a technical school of secondary education and throughout this school year being drafted a program of environmental education. The main theme is the Mediterranean Sea, the biggest closed sea extending between three continents. Topics studied: 1. Biodiversity and the risks threat. 2. The geophysics that characterize (earthquakes, volcanoes explosions, etc). 3. The Mediterranean Sea as environment anthropogenesis, a mosaic of other cultures and even place current notions of social phenomena (refugees). Pedagogical Objectives: Cognitive/Enviromental: 1. To investigate and understand the biodiversity of the Mediterranean Sea and the risks to threaten and phenomena that characterize. 2. To understand the position of the Mediterranean Sea in the land and the role of the historical, cultural and social human environment. 3. To come in contact with texts literary, social, articles on the Mediterranean. Psychomotor: 1. To work together and collect information for the Mediterranean Sea. 2. Experiential approach to the natural environment. 3. Develop critical thinking. 4. Undertake responsibilities for the presentation of the program. Emotional: 1. To feel joy from participation in the program. 2. Being sensitized and configure attitudes and actions of respect towards the environment. Methodology implementation: Teamwork. Interdisciplinary - holistic to dissemination of program recordings to courses curriculum. Study in the field. Gathering information from newspapers, magazines, internet, maps, and photographs. Experiential method- Project. Assessment methods and self-assessment. Fields of courses: Greek language- History- Biology- Chemistry- Technology Dissemination of results: Make a page of social media (facebook), a blog, enhancing environmental awareness via video, make an electronic poster.

  15. Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang).

    Science.gov (United States)

    Luo, Yongjun; Chen, Yu; Liu, Fuyu; Jiang, Chunhua; Gao, Yuqi

    2011-02-01

    The Tibetan wild ass, or kiang (Equus kiang) is endemic to the cold and hypoxic (4000-7000 m above sea level) climates of the montane and alpine grasslands of the Tibetan Plateau. We report here the complete nucleotide sequence of the E. kiang mitochondrial genome. Our results show that E. kiang mitochondrial DNA is 16,634 bp long, and predicted to encode all the 37 genes that are typical for vertebrates.

  16. Dicty_cDB: Contig-U04457-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available tochiensis_EST Glob... 42 8.4 1 ( FK759483 ) av02078b12r1.1 Symbiotic sea anemone... (Anemonia vi... 42 8.4 1 ( FK758489 ) av01028a18r1.1 Symbiotic sea anemone (Anemonia vi... 42 8.4 1 ( FK751904 ) av02108b22r1.1 Symb...iotic sea anemone (Anemonia vi... 42 8.4 1 ( FK750287 ) av02092i15r1.1 Symbiotic se...a anemone (Anemonia vi... 42 8.4 1 ( FK745283 ) av02120i24r1.1 Symbiotic sea anemone (Anemonia vi... 42 8.4 ...1 ( FK742118 ) av01024i20r1.1 Symbiotic sea anemone (Anemonia vi... 42 8.4 1 ( FK

  17. Dicty_cDB: Contig-U03566-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available norvegicus EST, 5'-end sequence, clone etn... 44 10.0 1 ( FK755862 ) av02117h21r1.1 Symbiotic sea anemone (A...nemonia vi... 44 10.0 1 ( FK744247 ) av02071a20r1.1 Symbiotic sea anemone (Anemonia vi... 44 10.0 1 ( FK743844 ) av02079l20r1.1 Symbi...otic sea anemone (Anemonia vi... 44 10.0 1 ( FK739201 ) av02095d13r1.1 Symbiotic se...a anemone (Anemonia vi... 44 10.0 1 ( FK738983 ) av02074d14r1.1 Symbiotic sea ane...mone (Anemonia vi... 44 10.0 1 ( FK732177 ) av02130j21r1.1 Symbiotic sea anemone (Anemonia vi... 44 10.0 1 (

  18. Air-sea exchange studies at the North Sea

    NARCIS (Netherlands)

    Leeuw, G. de; Eijk, A.M.J. van; Kunz, G.J.; Veefkind, P.J.

    1996-01-01

    The North Sea can be considered as a local 'inner' sea in which many processes are quite different from these over the open ocean. The surrounding land has a major influence, being the source for man-made aerosols and gases, whereas the North Sea acts as a sink for these. At the same time the North

  19. Phosphorus dynamics in the Black Sea and Baltic Sea

    NARCIS (Netherlands)

    Dijkstra, N.|info:eu-repo/dai/nl/372617034

    2017-01-01

    The dynamics of the key nutrient phosphorus (P) in hypoxic and anoxic marine basins are still incompletely understood. This thesis focuses on the cycling of P in two of such basins: the Baltic Sea and the Black Sea. Water column particulates and sediments from the deep basin of the Black Sea were

  20. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  1. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  2. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  3. Temperature measurement in the sea

    Digital Repository Service at National Institute of Oceanography (India)

    Krishnamacharyulu, R.J.; Rao, L.V.G.

    The importance of measuring sea temperature is explained and the various methods employed for this purpose are reviewed. Instruments used for spot measurement of water temperature at the sea surface and at discrete depths (bucket thermometer...

  4. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  5. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  6. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  7. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  8. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  9. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  10. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  11. Draft genome of the lined seahorse, Hippocampus erectus.

    Science.gov (United States)

    Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa; Xu, Junming; Fu, Hongtuo; Shi, Qiong

    2017-06-01

    The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse ( H. comes ). We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. © The Authors 2017. Published by Oxford University Press.

  12. Deep-sea fungi

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, C; Damare, S.R.

    significant in terms of carbon sequestration (5, 8). In light of this, the diversity, abundance, and role of fungi in deep-sea sediments may form an important link in the global C biogeochemistry. This review focuses on issues related to collection...

  13. The Dirac Sea

    OpenAIRE

    Dimock, J.

    2010-01-01

    We give an alternate definition of the free Dirac field featuring an explicit construction of the Dirac sea. The treatment employs a semi-infinite wedge product of Hilbert spaces. We also show that the construction is equivalent to the standard Fock space construction.

  14. Farming the Sea

    Science.gov (United States)

    Morgan, William

    1971-01-01

    Florida has initiated a training program in an entirely new dimension--Sea Farming. Presented is a description of the vocational agriculture program designed to teach propagation, cultivation, harvesting, marketing, and conservation practices related to production of oysters, shrimp, scallops, crabs, and fin fishes. (Editor/GB)

  15. Pollution around Malta's sea

    OpenAIRE

    Formosa, Nicolette

    2014-01-01

    Marine littering is a global concern and every single year tons of litter end up in the ocean all around the globe. It has become such a problem that the waste has amalgamated into huge ‘islands’ floating in the world’s oceans. http://www.um.edu.mt/think/pollution-around-maltas-sea/

  16. Wadden Sea Mud

    DEFF Research Database (Denmark)

    Møller-Jensen, P.

    The present thesis deals with the transport phenomena of estuarine cohesive sediment from a laboratory and a numerical point of view. The cohesive sediment used throughout the whole process was natural mud from the Danish part of the Wadden sea, Ho Bay. In the laboratory, the work was concentrated...

  17. Sea floor magnetic observatory

    Science.gov (United States)

    Korepanov, V.; Prystai, A.; Vallianatos, F.; Makris, J.

    2003-04-01

    The electromagnetic precursors of seismic hazards are widely accepted as strong evidence of the approaching earthquake or volcano eruption. The monitoring of these precursors are of main interest in densely populated areas, what creates serious problems to extract them at the strong industrial noise background. An interesting possibility to improve signal-to-noise ratio gives the installation of the observation points in the shelf zones near the possible earthquake places, what is fairly possible in most seismically active areas in Europe, e. g. in Greece and Italy. The serious restriction for this is the cost of the underwater instrumentation. To realize such experiments it requires the unification of efforts of several countries (e. g., GEOSTAR) or of the funds of some great companies (e. g., SIO magnetotelluric instrument). The progress in electronic components development as well as the appearance of inexpensive watertight glass spheres made it possible to decrease drastically the price of recently developed sea floor magnetic stations. The autonomous vector magnetometer LEMI-301 for sea bed application is described in the report. It is produced on the base of three-component flux-gate sensor. Non-magnetic housing and minimal magnetism of electronic components enable the instrument to be implemented as a monoblock construction where the electronic unit is placed close to the sensor. Automatic circuit provides convenient compensation of the initial field offset and readings of full value (6 digits) of the measured field. Timing by internal clock provides high accuracy synchronization of data. The internal flash memory assures long-term autonomous data storage. The system also has two-axes tilt measurement system. The methodological questions of magnetometer operation at sea bed were studied in order to avoid two types of errors appearing at such experimental cases. First is sea waving influence and second one magnetometer orientation at its random positioning on

  18. Dicty_cDB: Contig-U16416-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available eg... 32 0.83 3 ( FK743489 ) av02083p10r1.1 Symbiotic sea anemone (Anemonia vi... 32 0.84 3 ( GO096539 ) CAF... regu... 32 1.1 3 ( FK745351 ) av02070p02r1.1 Symbiotic sea anemone (Anemonia vi... 32 1.2 3 ( AZ547466 ) EN....6 2 ( FK720330 ) av02061h11r1.1 Symbiotic sea anemone (Anemonia vi... 32 9.8 3 (

  19. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  20. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  1. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  2. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  3. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

  4. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  5. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  7. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  8. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  9. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  10. Decoding the human genome

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  11. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  12. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  13. Complete genome sequence of Oceanithermus profundus type strain (506T)

    Energy Technology Data Exchange (ETDEWEB)

    Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ruhl, Alina [U.S. Department of Energy, Joint Genome Institute; Mwirichia, Romano [University of Munster, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL

    2011-01-01

    Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. AID/APOBEC cytosine deaminase induces genome-wide kataegis

    Directory of Open Access Journals (Sweden)

    Lada Artem G

    2012-12-01

    Full Text Available Abstract Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm, are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC proteins. However, a direct link between APOBECs and kataegis is still lacking. We have sequenced the genomes of yeast mutants induced in diploids by expression of the gene for PmCDA1, a hypermutagenic deaminase from sea lamprey. Analysis of the distribution of 5,138 induced mutations revealed localized clusters very similar to those found in tumors. Our data provide evidence that unleashed cytosine deaminase activity is an evolutionary conserved, prominent source of genome-wide kataegis events. Reviewers This article was reviewed by: Professor Sandor Pongor, Professor Shamil R. Sunyaev, and Dr Vladimir Kuznetsov.

  15. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  16. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  17. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  18. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  19. Ultrafast comparison of personal genomes

    OpenAIRE

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  20. The radioactivity of the sea

    International Nuclear Information System (INIS)

    Walker, M.I.; Rose, K.S.B.

    1990-01-01

    The radioactivity in the world's surface sea water averages 13.6 Bq/kg of water. Over 88% of this activity arises from a single natural radionuclide, 40 K, and 7% of the remainder results from nuclear weapon test fallout. Variations in the radioactivity occur due to changes in salinity, weapon test fallout and discharges of artificial radionuclides, and are examined here on the basis of published measurements. The most radioactive sea identified by these measurements is the Dead Sea, which averages 178 Bq/kg due to its high salinity. Other enclosed, highly saline waters can be expected to have similar levels. The radioactivity in open seas varies within a much narrower range, generally within 20% of the world average. The highest averages are found in the Persian Gulf (22 Bq/kg), the Red Sea (15 Bq/kg) and the Eastern Mediterranean (14.6 Bq/kg). The Irish Sea averaged 13.7 Bq/kg in 1987, with the effect of the Sellafield discharges being partly offset by lower than average salinity. Although higher levels occurred in the Irish Sea during the 1970s when the Sellafield discharges were higher, the average level has always been much less than that in the Dead Sea, so that the Irish Sea has never been the most radioactive sea in the world. Exceptionally low levels of radioactivity (4 Bq/kg) occur in the Baltic Sea due to dilution by fresh water. (author)

  1. Invertebrate medicine

    National Research Council Canada - National Science Library

    Lewbart, G.A

    2012-01-01

    .... Coverage includes sponges, jellyfish, anemones, corals, mollusks, starfish, sea urchins, crabs, crayfish, lobsters, shrimp, hermit crabs, spiders, scorpions, and many more, with chapters organized by taxonomy...

  2. A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

    Directory of Open Access Journals (Sweden)

    Yunlan Yang

    2017-05-01

    Full Text Available The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C infecting the strain type of Dinoroseobacter shibae named DFL12T, which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages, four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host–phage interactions and the ecology of the marine Roseobacter.

  3. Genomics using the Assembly of the Mink Genome

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

  4. A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurata L.

    Directory of Open Access Journals (Sweden)

    Heiner Kuhl

    2011-01-01

    Full Text Available This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata, a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp. Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

  5. RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star.

    Directory of Open Access Journals (Sweden)

    Sabah Kadri

    Full Text Available microRNAs (miRNAs are small (20-23 nt, non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin and Patiria miniata (sea star are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc. to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads. Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common. We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html.

  6. RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star

    Science.gov (United States)

    Kadri, Sabah; Hinman, Veronica F.; Benos, Panayiotis V.

    2011-01-01

    microRNAs (miRNAs) are small (20–23 nt), non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc.) to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads). Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common). We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html. PMID:22216218

  7. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  8. Deep sea radionuclides

    International Nuclear Information System (INIS)

    Kanisch, G.; Vobach, M.

    1993-01-01

    Every year since 1979, either in sping or in summer, the fishing research vessel 'Walther Herwig' goes to the North Atlantic disposal areas of solid radioactive wastes, and, for comparative purposes, to other areas, in order to collect water samples, plankton and nekton, and, from the deep sea bed, sediment samples and benthos organisms. In addition to data on the radionuclide contents of various media, information about the plankton, nekton and benthos organisms living in those areas and about their biomasses could be gathered. The investigations are aimed at acquiring scientifically founded knowledge of the uptake of radioactive substances by microorganisms, and their migration from the sea bottom to the areas used by man. (orig.) [de

  9. Changing Sea Levels

    Science.gov (United States)

    Pugh, David

    2004-04-01

    Flooding of coastal communities is one of the major causes of environmental disasters world-wide. This textbook explains how sea levels are affected by astronomical tides, weather effects, ocean circulation and climate trends. Based on courses taught by the author in the U.K. and the U.S., it is aimed at undergraduate students at all levels, with non-basic mathematics being confined to Appendices and a website http://publishing.cambridge.org/resources/0521532183/.

  10. Sea Wind Europe

    International Nuclear Information System (INIS)

    2004-02-01

    The first and defining step towards European leadership in renewable energy must be the successful setting of an ambitious EU renewable energy target for 2020. This will set out the vision and create the framework within which our clean energy future can be delivered. Sea Wind Europe offers a clear blueprint of how to achieve its vision and outlines concrete policy measures that will give European renewables the foundation they need for success on a giant scale

  11. Black Sea challenges

    International Nuclear Information System (INIS)

    Drevet, J.F.

    2008-01-01

    In this month's European column, Jean-Francois Drevet examines the issues that arise for Europe from the Black Sea region. The Black Sea is increasingly becoming a crucial place of transit for hydrocarbon imports from the Caspian and Russia into the European Union. The considerable increase in this traffic raises both environmental problems (the risk of oil slicks) and issues of security of supply, on account of the economic and political fragility of some of the bordering or neighbouring states (Ukraine, Georgia, Armenia, Azerbaijan, Russia/Chechnya etc.). This is why, as Jean-Francois Drevet stresses, the European Union has been trying since the mid-1990's to claim a role in the management of the affairs of the region. With two bordering states (Rumania and Bulgaria) joining the EU in 2007, cooperation in the Black Sea has become a priority within the framework of the European Neighbourhood Policy, and this column delineates a number of the obstacles that still have to be surmounted. (author)

  12. Emerging Methods and Systems for Observing Life in the Sea

    Science.gov (United States)

    Chavez, F.; Pearlman, J.; Simmons, S. E.

    2016-12-01

    There is a growing need for observations of life in the sea at time and space scales consistent with those made for physical and chemical parameters. International programs such as the Global Ocean Observing System (GOOS) and Marine Biodiversity Observation Networks (MBON) are making the case for expanded biological observations and working diligently to prioritize essential variables. Here we review past, present and emerging systems and methods for observing life in the sea from the perspective of maintaining continuous observations over long time periods. Methods that rely on ships with instrumentation and over-the-side sample collections will need to be supplemented and eventually replaced with those based from autonomous platforms. Ship-based optical and acoustic instruments are being reduced in size and power for deployment on moorings and autonomous vehicles. In parallel a new generation of low power, improved resolution sensors are being developed. Animal bio-logging is evolving with new, smaller and more sophisticated tags being developed. New genomic methods, capable of assessing multiple trophic levels from a single water sample, are emerging. Autonomous devices for genomic sample collection are being miniaturized and adapted to autonomous vehicles. The required processing schemes and methods for these emerging data collections are being developed in parallel with the instrumentation. An evolving challenge will be the integration of information from these disparate methods given that each provides their own unique view of life in the sea.

  13. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  14. Experimental Induction of Genome Chaos.

    Science.gov (United States)

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  15. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  16. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  17. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  18. Arctic landfast sea ice

    Science.gov (United States)

    Konig, Christof S.

    Landfast ice is sea ice which forms and remains fixed along a coast, where it is attached either to the shore, or held between shoals or grounded icebergs. Landfast ice fundamentally modifies the momentum exchange between atmosphere and ocean, as compared to pack ice. It thus affects the heat and freshwater exchange between air and ocean and impacts on the location of ocean upwelling and downwelling zones. Further, the landfast ice edge is essential for numerous Arctic mammals and Inupiat who depend on them for their subsistence. The current generation of sea ice models is not capable of reproducing certain aspects of landfast ice formation, maintenance, and disintegration even when the spatial resolution would be sufficient to resolve such features. In my work I develop a new ice model that permits the existence of landfast sea ice even in the presence of offshore winds, as is observed in mature. Based on viscous-plastic as well as elastic-viscous-plastic ice dynamics I add tensile strength to the ice rheology and re-derive the equations as well as numerical methods to solve them. Through numerical experiments on simplified domains, the effects of those changes are demonstrated. It is found that the modifications enable landfast ice modeling, as desired. The elastic-viscous-plastic rheology leads to initial velocity fluctuations within the landfast ice that weaken the ice sheet and break it up much faster than theoretically predicted. Solving the viscous-plastic rheology using an implicit numerical method avoids those waves and comes much closer to theoretical predictions. Improvements in landfast ice modeling can only verified in comparison to observed data. I have extracted landfast sea ice data of several decades from several sources to create a landfast sea ice climatology that can be used for that purpose. Statistical analysis of the data shows several factors that significantly influence landfast ice distribution: distance from the coastline, ocean depth, as

  19. Genomics of Volvocine Algae

    Science.gov (United States)

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  20. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  1. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  2. Ebolavirus comparative genomics

    Science.gov (United States)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  3. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

  4. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  5. Observational analysis of air-sea fluxes and sea water temperature offshore South China Sea

    Science.gov (United States)

    Bi, X.; Huang, J.; Gao, Z.; Liu, Y.

    2017-12-01

    This paper investigates the air-sea fluxes (momentum flux, sensible heat flux and latent heat flux) from eddy covariance method based on data collected at an offshore observation tower in the South China Sea from January 2009 to December 2016 and sea water temperature (SWT) on six different levels based on data collected from November 2011 to June 2013. The depth of water at the tower over the sea averages about 15 m. This study presents the in-situ measurements of continuous air-sea fluxes and SWT at different depths. Seasonal and diurnal variations in air-sea fluxes and SWT on different depths are examined. Results show that air-sea fluxes and all SWT changed seasonally; sea-land breeze circulation appears all the year round. Unlike winters where SWT on different depths are fairly consistent, the difference between sea surface temperature (SST) and sea temperature at 10 m water depth fluctuates dramatically and the maximum value reaches 7 °C during summer.

  6. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  7. Waste disposal into the sea

    International Nuclear Information System (INIS)

    Ehlers, P.; Kunig, P.

    1987-01-01

    The waste disposal at sea is regulated for the most part by national administrative law, which mainly is based on international law rules supplemented by EC-law. The dumping of low-level radioactive waste into the sea is more and more called into question. The disposal of high-level radioactive waste into the subsoil of the sea does not correspond to the London Convention. (WG) [de

  8. Air sea ratio reduction initiative

    Energy Technology Data Exchange (ETDEWEB)

    Oberle, Jean

    2010-09-15

    Airfreight is the most expensive mode of transportation as well as the most impacting in terms of CO{sup 2} emissions. It is 7 times more expensive on average to ship by air than shipping by sea 1. Airfreight transportation mode emits 30 times more CO{sup 2} than sea freight mode 2. These elements provided a compelling platform to design a global logistics program to initiate a modal shift from air to sea freight without compromising service to customers.

  9. Pan genome of the phytoplankton Emiliania underpins its global distribution.

    Science.gov (United States)

    Read, Betsy A; Kegel, Jessica; Klute, Mary J; Kuo, Alan; Lefebvre, Stephane C; Maumus, Florian; Mayer, Christoph; Miller, John; Monier, Adam; Salamov, Asaf; Young, Jeremy; Aguilar, Maria; Claverie, Jean-Michel; Frickenhaus, Stephan; Gonzalez, Karina; Herman, Emily K; Lin, Yao-Cheng; Napier, Johnathan; Ogata, Hiroyuki; Sarno, Analissa F; Shmutz, Jeremy; Schroeder, Declan; de Vargas, Colomban; Verret, Frederic; von Dassow, Peter; Valentin, Klaus; Van de Peer, Yves; Wheeler, Glen; Dacks, Joel B; Delwiche, Charles F; Dyhrman, Sonya T; Glöckner, Gernot; John, Uwe; Richards, Thomas; Worden, Alexandra Z; Zhang, Xiaoyu; Grigoriev, Igor V

    2013-07-11

    Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

  10. Pan Genome of the Phytoplankton Emiliania Underpins its Global Distribution

    Energy Technology Data Exchange (ETDEWEB)

    Read, Betsy A. [California State Univ. (CalState), San Marcos, CA (United States); Kegel, Jessica [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Klute, Mary J. [Univ. of Alberta, Edmonton, AB (Canada); Kuo, Alan [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Lefebvre, Stephane C. [J. Craig Venter Inst., San Diego, CA (United States); Maumus, Florian [National Institute of Agricultural Research, Versailles (France); Mayer, Christoph [Alexander Koenig Research Museum, Bonn (Germany); Ruhr Univ., Bochum (Germany); Miller, John [Univ. of Maryland, College Park, MD (United States); Monier, Adam [Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States); Salamov, Asaf [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Young, Jeremy [Univ. College London (United Kingdom); Aguilar, Maria [Univ. of Alberta, Edmonton, AB (Canada); Claverie, Jean-Michel [Aix-Marseille Univ. (France); Frickenhaus, Stephan [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Univ. of Bremerhaven (Germany); Gonzalez, Karina [Harvard Medical School, Boston, MA (United States); Herman, Emily K. [Univ. of Alberta, Edmonton, AB (Canada); Lin, Yao-Cheng [Ghent Univ. (Belgium); Napier, Johnathan [Rothamstead Research, Harpenden (United Kingdom); Ogata, Hiroyuki [Aix-Marseille Univ. (France); Sarno, Analissa F. [California State Univ. (CalState), San Marcos, CA (United States); Schmutz, Jeremy [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Genome Sequencing Center, Huntsville, AL (United States); Schroeder, Declan [Marine Biological Association of the UK, Plymouth (United Kingdom); de Vargas, Columban [CNRS. Univ. Pierre and Marie Curie (France).; Verret, Frederic [Univ. of Essex, Colchester (United Kingdom); von Dassow, Peter [Pontifical Catholic University of Chile, Santiago (Chile); Valentin, Klaus [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Van de Peer, Yves [Ghent Univ. (Belgium); Wheeler, Glen [Marine Biological Association of the UK, Plymouth (United Kingdom); Plymouth Marine Lab. (United Kingdom); Annotation Consortium, Emiliania huxleyi; Dacks, Joel B. [Univ. of Alberta, Edmonton, AB (Canada); Delwiche, Charles F. [Univ. of Maryland, College Park, MD (United States); Dyhrman, Sonya T. [Woods Hole Oceanographic Inst., MA (United States); Columbia Univ., Palisades, NY (United States); Glockner, Gernot [Univ. of Cologne (Germany); John, Uwe [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Richards, Thomas [National History Museum, London (United Kingdom); Worden, Alexandra Z. [Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States); Zhang, Xiaoyu [California State Univ. (CalState), San Marcos, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Inst., Walnut Creek, CA (United States)

    2012-06-18

    Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering themvisible fromspace3.Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate thatE. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

  11. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  12. Differential DNA Methylation Analysis without a Reference Genome

    Directory of Open Access Journals (Sweden)

    Johanna Klughammer

    2015-12-01

    Full Text Available Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS, which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish. Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org. The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

  13. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Science.gov (United States)

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. The USGS Salton Sea Science Office

    Science.gov (United States)

    Case, Harvey Lee; Barnum, Douglas A.

    2007-01-01

    The U.S. Geological Survey's (USGS) Salton Sea Science Office (SSSO) provides scientific information and evaluations to decisionmakers who are engaged in restoration planning and actions associated with the Salton Sea. The primary focus is the natural resources of the Salton Sea, including the sea?s ability to sustain biological resources and associated social and economic values.

  15. Japan nuclear ship sea trial

    International Nuclear Information System (INIS)

    Yamazaki, Hiroshi; Kitamura, Toshikatus; Mizushima, Toshihiko

    1992-01-01

    The sea trial of the first Japan nuclear Ship 'MUTSU' was conducted from the end of October to December in 1990. The purpose of the sea trial was to verify the nuclear propulsive performances and maneuverabilities. The present report describes the results of the sea trial. These results are classified into four items: 1. Speed test and engineering performance tests 2. Maneuvering performance tests 3. Vibration tests 4. Other tests. Acceptable performances were demonstrated, as expected in the original design. The experience of the use of the Global Positioning System (GPS), which were newly adopted for the sea trial, is also reported. (author)

  16. Low-pass sequencing for microbial comparative genomics

    Directory of Open Access Journals (Sweden)

    Kennedy Sean

    2004-01-01

    Full Text Available Abstract Background We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1 the metabolically versatile Haloarcula marismortui; (2 the non-pigmented Natrialba asiatica; (3 the psychrophile Halorubrum lacusprofundi and (4 the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. Results As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI for their predicted proteins. Multiple insertion sequence (IS elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP and transcription factor IIB (TFB homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. Conclusion Despite the diverse habitats of these species, all five halophiles share (1 high GC content and (2 low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the

  17. Sea Urchin Morphogenesis.

    Science.gov (United States)

    McClay, David R

    2016-01-01

    In the sea urchin morphogenesis follows extensive molecular specification. The specification controls the many morphogenetic events and these, in turn, precede patterning steps that establish the larval body plan. To understand how the embryo is built it was necessary to understand those series of molecular steps. Here an example of the historical sequence of those discoveries is presented as it unfolded over the last 50 years, the years during which major progress in understanding development of many animals and plants was documented by CTDB. In sea urchin development a rich series of experimental studies first established many of the phenomenological components of skeletal morphogenesis and patterning without knowledge of the molecular components. The many discoveries of transcription factors, signals, and structural proteins that contribute to the shape of the endoskeleton of the sea urchin larva then followed as molecular tools became available. A number of transcription factors and signals were discovered that were necessary for specification, morphogenesis, and patterning. Perturbation of the transcription factors and signals provided the means for assembling models of the gene regulatory networks used for specification and controlled the subsequent morphogenetic events. The earlier experimental information informed perturbation experiments that asked how patterning worked. As a consequence it was learned that ectoderm provides a series of patterning signals to the skeletogenic cells and as a consequence the skeletogenic cells secrete a highly patterned skeleton based on their ability to genotypically decode the localized reception of several signals. We still do not understand the complexity of the signals received by the skeletogenic cells, nor do we understand in detail how the genotypic information shapes the secreted skeletal biomineral, but the current knowledge at least outlines the sequence of events and provides a useful template for future

  18. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  19. National Human Genome Research Institute

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  20. Sea Fighter Analysis

    Science.gov (United States)

    2007-02-01

    which is used by the model to drive the normal activities of the crew (Figure C.1-2). These routines consist of a sequential list of high- level...separately. Figure C.1-3: Resources & Logic Sheet C.1.1.4 Scenario The scenario that is performed during a model run is a sequential list of all...were marked with a white fore and aft lineup stripe on both landing spots. Current Sea Fighter design does not provide a hangar; however, there