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  • Institute of Physics  (65,595)
  • American Physical Society  (40,867)
  • Copernicus  (22,259)
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  • BioMed Central  (16,585)
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  • 2010-2014  (160,590)
  • 1995-1999
  • 1955-1959  (10,426)
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  • 1935-1939  (6,207)
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  • 1
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    Monitoring of gas and seismic energy release by multiparametric benthic observatory along the North Anatolian Fault in the Sea of Marmara (NW Turkey) (2014)
    Wiley-Blackwell
    Details
    Publication Date: 2024-05-09
    Description: Episodic gas seepage occurs at the seafloor in the Gulf of Izmit (Sea of Marmara, NW Turkey) along the submerged segment of the North Anatolian Fault (NAF), which ruptured during the 1999 Mw7.4 Izmit earthquake, and caused tectonic loading of the fault segment in front of the Istanbul metropolitan area. In order to study gas seepage and seismic energy release along the NAF, a multiparametric benthic observatory (SN-4) was deployed in the gulf at the western end of the 1999 Izmit earthquake rupture, and operated for about 1 yr at 166 m water depth. The SN-4 payload included a three-component broad-band seismometer, as well as gas and oceanographic sensors. We analysed data collected continuously for 161 d in the first part of the experiment, from 2009 October to 2010 March. The main objective of our work was to verify whether tectonic deformation along the NAF could trigger methane seepage. For this reason, we considered only local seismicity, that is, within 100 km from the station. No significant (ML ≥ 3.6) local earthquakes occurred during this period; on the other hand, the seismometer recorded high-frequency SDEs (short duration events), which are not related to seismicity but to abrupt increases of dissolved methane concentration in the sea water that we called MPEs (methane peak events). Acquisition of current velocity, dissolved oxygen, turbidity, temperature and salinity, allowed us to analyse the local oceanographic setting during each event, and correlate SDEs to episodic gas discharges from the seabed. We noted that MPEs are the result of such gas releases, but are detected only under favourable oceanographic conditions. This stresses the importance of collecting long-term multiparametric time-series to address complex phenomena such as gas and seismic energy release at the seafloor. Results from the SN-4 experiment in the Sea of Marmara suggest that neither low-magnitude local seismicity, nor regional events affect intensity and frequency of gas flows from the seafloor.
    Description: Published
    Description: 850-866
    Description: 1T. Geodinamica e interno della Terra
    Description: 3A. Ambiente Marino
    Description: 7A. Geofisica di esplorazione
    Description: JCR Journal
    Description: restricted
    Keywords: Time-series analysis ; Seismicity and tectonics ; Broad-band seismometers ; multiparametric seafloor observatory ; Izmit Gulf ; Sea of Marmara ; gas seepage ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 04. Solid Earth::04.04. Geology::04.04.04. Marine geology ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    Geochemistry of volcanic rocks from the Woodlark Basin (2011)
    Copernicus
    Details
    Publication Date: 2023-11-08
    Description: EGU2011-12864 The Woodlark Basin east of Papua New Guinea represents one of the few places on Earth where a spreading axis propagates into continental crust. This special tectonic setting allows insights into the evolution of magma composition as continental extension and break-up changes to the formation of ocean crust. We report here geochemical results on samples collected in 2009 from the four segments closest to the continental breakup, from segment 1 which abuts the detachment fault responsible for continental extension on Moresby Seamount in the West, to segment 4, representing mature oceanic crust in the East. A total of 208 glass samples have been analyzed for their major (EMPA) and trace element (LA-ICPMS) compositions. The data show strong E-W variations. Samples ranging from tholeiitic basalt and basaltic andesite to andesite and rhyolite are found on Segment 1. They have generally high alkali values and a wide range of trace element contents and ratios. Segments 2 to 4 magmas in contrast only comprise tholeiitic basalt with lower alkali contents and a more restricted range of trace element chemistry. The geochemical differences between the segments cannot be attributed to differentiation processes alone, and different sources are required. High Ba/La, (La/Sm)N, Rb/Sr, and Th/La on Segment 1 suggest a derivation from an enriched mantle source, while low Nd/Pb and Nb/U suggest that some of the enrichment may also reflect the influence of continental crust during magma genesis. Whether this continental signature is present in the form of recycled material in the mantle or as rafted continental blocks in the axial region is at present unclear. In contrast to rocks from segment 1, trace element compositions of volcanic glasses from segments 2 to 4 show a stronger MORB signature, presumably reflecting more mature spreading in this part of the basin. The influence of continental material appears to be minimal, suggesting that uncontaminated asthenosphere quickly flows into the rift and/or that continental blocks are not retained in the axial region for long time periods following the rifting-spreading transition.
    Type: Conference or Workshop Item , NonPeerReviewed
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  • 3
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    Interannual atmospheric variability forced by the deep equatorial Atlantic Ocean (2011)
    Nature Publishing Group
    Details
    Publication Date: 2023-11-08
    Description: Climate variability in the tropical Atlantic Ocean is determined by large-scale ocean–atmosphere interactions, which particularly affect deep atmospheric convection over the ocean and surrounding continents1. Apart from influences from the Pacific El Niño/Southern Oscillation2 and the North Atlantic Oscillation3, the tropical Atlantic variability is thought to be dominated by two distinct ocean–atmosphere coupled modes of variability that are characterized by meridional4, 5 and zonal6, 7 sea-surface-temperature gradients and are mainly active on decadal and interannual timescales, respectively8, 9. Here we report evidence that the intrinsic ocean dynamics of the deep equatorial Atlantic can also affect sea surface temperature, wind and rainfall in the tropical Atlantic region and constitutes a 4.5-yr climate cycle. Specifically, vertically alternating deep zonal jets of short vertical wavelength with a period of about 4.5 yr and amplitudes of more than 10 cm s−1 are observed, in the deep Atlantic, to propagate their energy upwards, towards the surface10, 11. They are linked, at the sea surface, to equatorial zonal current anomalies and eastern Atlantic temperature anomalies that have amplitudes of about 6 cm s−1 and 0.4 °C, respectively, and are associated with distinct wind and rainfall patterns. Although deep jets are also observed in the Pacific12 and Indian13 oceans, only the Atlantic deep jets seem to oscillate on interannual timescales. Our knowledge of the persistence and regularity of these jets is limited by the availability of high-quality data. Despite this caveat, the oscillatory behaviour can still be used to improve predictions of sea surface temperature in the tropical Atlantic. Deep-jet generation and upward energy transmission through the Equatorial Undercurrent warrant further theoretical study.
    Type: Article , PeerReviewed
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  • 4
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    Transgenerational plasticity in marine sticklebacks: maternal effects mediate impacts of a warming ocean (2014)
    Wiley-Blackwell
    In:  EPIC3Functional Ecology, Wiley-Blackwell, 28, pp. 1482-1493, ISSN: 0269-8463
    Details
    Publication Date: 2023-09-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 5
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    An environmental bacterial taxon with a large and distinct metabolic repertoire (2014)
    Nature Publishing Group
    Details
    Publication Date: 2023-02-14
    Description: Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.
    Type: Article , PeerReviewed
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  • 6
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    Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 643, doi:10.1186/1471-2164-11-643.
    Description: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.
    Description: This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil.
    Repository Name: Woods Hole Open Access Server
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  • 7
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    VAMPS : a website for visualization and analysis of microbial population structures (2014)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.
    Description: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
    Description: Funding provided by the National Science Foundation [grant NSF/BDI 0960626 to SMH] and the Sloan Foundation through a collaborative project with the Microbiology of the Built Environment program.
    Keywords: Microbiome ; Microbial ecology ; Microbial diversity ; Data visualization ; Website ; Bacteria ; SSU rRNA ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis (2014)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4342, doi:10.1038/ncomms5342.
    Description: Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.
    Description: This work was mainly supported by Howard Hughes Medical Institute. H.P. is currently supported by the Allen Institute for Brain Science. R.W.T. and A.M. were supported by a grant MH071739 (MERIT).
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Scientific names of organisms : attribution, rights, and licensing (2014)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.
    Description: As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.
    Keywords: Scientific names ; Taxonomy ; Copyright ; Intellectual property rights ; Name-based infrastructure ; Big data
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Eruption of a deep-sea mud volcano triggers rapid sediment movement (2014)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 5385, doi:10.1038/ncomms6385.
    Description: Submarine mud volcanoes are important sources of methane to the water column. However, the temporal variability of their mud and methane emissions is unknown. Methane emissions were previously proposed to result from a dynamic equilibrium between upward migration and consumption at the seabed by methane-consuming microbes. Here we show non-steady-state situations of vigorous mud movement that are revealed through variations in fluid flow, seabed temperature and seafloor bathymetry. Time series data for pressure, temperature, pH and seafloor photography were collected over 431 days using a benthic observatory at the active Håkon Mosby Mud Volcano. We documented 25 pulses of hot subsurface fluids, accompanied by eruptions that changed the landscape of the mud volcano. Four major events triggered rapid sediment uplift of more than a metre in height, substantial lateral flow of muds at average velocities of 0.4 m per day, and significant emissions of methane and CO2 from the seafloor.
    Description: Participation of the Sentry AUV and TETHYS team from WHOI was funded by the Arctic Research Initiative of WHOI’s Ocean and Climate Change Institute and the NASA ASTEP grant NNX09AB76G. Additional funds were made available by the AWI, the Max Planck Society and the DFG METEOR/MERIAN programme, as well as the Leibniz programme to A.B.
    Repository Name: Woods Hole Open Access Server
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