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  • Oxford University Press  (12,384)
  • Nature Publishing Group
  • Wiley-Blackwell
  • 2015-2019  (12,429)
  • 1955-1959
  • 2017  (12,429)
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  • 2015-2019  (12,429)
  • 1955-1959
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  • 1
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    Strong geologic methane emissions from discontinuous terrestrial permafrost in the Mackenzie Delta, Canada (2017)
    Nature Publishing Group
    In:  EPIC3Scientific Reports, Nature Publishing Group, 7(5828)
    Details
    Publication Date: 2017-10-10
    Description: Arctic permafrost caps vast amounts of old, geologic methane (CH4) in subsurface reservoirs. Thawing permafrost opens pathways for this CH4 to migrate to the surface. However, the occurrence of geologic emissions and their contribution to the CH4 budget in addition to recent, biogenic CH4 is uncertain. Here we present a high-resolution (100 m × 100 m) regional (10,000 km²) CH4 flux map of the Mackenzie Delta, Canada, based on airborne CH4 flux data from July 2012 and 2013. We identify strong, likely geologic emissions solely where the permafrost is discontinuous. These peaks are 13 times larger than typical biogenic emissions. Whereas microbial CH4 production largely depends on recent air and soil temperature, geologic CH4 was produced over millions of years and can be released year-round provided open pathways exist. Therefore, even though they only occur on about 1% of the area, geologic hotspots contribute 17% to the annual CH4 emission estimate of our study area. We suggest that this share may increase if ongoing permafrost thaw opens new pathways. We conclude that, due to permafrost thaw, hydrocarbon-rich areas, prevalent in the Arctic, may see increased emission of geologic CH4 in the future, in addition to enhanced microbial CH4 production.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks (2017)
    Nature Publishing Group
    In:  EPIC3Scientific Reports, Nature Publishing Group, 7(2542), ISSN: 2045-2322
    Details
    Publication Date: 2019-03-07
    Description: Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
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  • 3
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    The Mozambique Ridge: a document of massive multi-stage magmatism (2017)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 208(1), pp. 449-467, ISSN: 1365-246X
    Details
    Publication Date: 2016-12-03
    Description: The Mozambique Ridge, a prominent basement high in the southwestern Indian Ocean, consists of four major geomorphological segments associated with numerous phases of volcanic activity in the Lower Cretaceous. The nature and origin of the Mozambique Ridge have been intensely debated with one hypothesis suggesting a Large Igneous Province origin. High-resolution seismic reflection data reveal a large number of extrusion centres with a random distribution throughout the southern Mozambique Ridge and the nearby Transkei Rise. Intra-basement reflections emerge from the extrusion centres and are interpreted to represent massive lava flow sequences. Such lava flow sequences are characteristic of eruptions leading to the formation of continental and oceanic flood basalt provinces, hence supporting a Large Igneous Province origin of the Mozambique Ridge. We observe evidence for widespread post-sedimentary magmatic activity that we correlate with a southward propagation of the East African Rift System. Based on our volumetric analysis of the southern Mozambique Ridge we infer a rapid sequential emplacement between ~131 Ma and ~125 Ma, which is similar to the short formation periods of other Large Igneous Provinces like the Agulhas Plateau.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Impacts of Climate Change on the Southern Ocean (2017)
    Wiley-Blackwell
    In:  EPIC3Climate Change Impacts on Fisheries and Aquaculture: A Global Analysis, Climate Change Impacts on Fisheries and Aquaculture: A Global Analysis, Wiley-Blackwell, pp. 663-701, ISBN: 978-1-119-15404-4
    Details
    Publication Date: 2017-10-09
    Description: Exploitation of Southern Ocean marine resources began more than 200 years ago with the massive hunt for seals and whales. In the 1960s/70s, fisheries for finfish and krill entered Southern Ocean waters. Within a few years many fish populations were heavily overfished and dramatically depleted, and some of these stocks still did not recover. Today, fish stocks and fisheries activities are managed and monitored by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) which was established in 1982 to ensure sustainable exploitation and protection of the delicate marine ecosystem. Current target species include Mackerel icefish (Champsocephalus gunnari), Patagonian as well as Antarctic toothfish (Dissostichus eleginoides and D. mawsoni) and Antarctic krill (Euphausia superba). Most of these species are vulnerable to overfishing due to slow growth, late age at maturity, and rather low fecundity. This vulnerability might increase, as Southern Ocean living communities are currently also faced with alterations of their environment due to climate change, such as increasing water temperatures and decreasing sea ice. Species, including the ones targetted by fisheries, are well-adapted to their particular environmental conditions and are believed to be highly sensitive to changes because of their cold-adapted physiology, their life history traits, and their direct or indirect dependence on sea ice. The species will be exposed to several stressors at the same time, and fishing pressure, direct abiotic forcing and changes mediated via the food web might act synergistically and result in significant population declines. In particular the strongly sea ice-dependent Antarctic krill, a key species in the food web, might be adversely affected. Fish species seems to have low tolerance towards higher water temperatures and may thus, in the long run, be replaced by lower latitude species.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus (2017)
    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 541, pp. 536-540, ISSN: 0028-0836
    Details
    Publication Date: 2019-03-08
    Description: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent from those of temperate diatoms (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Taxonomy of planktonic microbial eukaryotes (2017)
    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
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    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    Sampling, preservation, and counting of samples i) Phytoplankton (2017)
    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
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    Publication Date: 2017-04-28
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Diatoms (2017)
    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
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    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    New insights on the provenance of obsidian fragments of Ustica Island (Palermo, Sicily). (2017)
    Wiley-Blackwell
    Details
    Publication Date: 2017-12-11
    Description: In this study we applied a multidisciplinary approach, coupling geophysical and geochemical measurements, to unveil the provenance of 170 obsidian flakes, collected on the volcanic island of Ustica (Sicily). On this island there are some prehistoric settlements dated from the Neolithic to the Middle Bronze Age. Despite not having geological outcrops of obsidian rocks, the countryside of Ustica is rich in fragments of this volcanic glass, imported from other source areas. The study of obsidian findings was carried out first through visual observations and density measurements. At least two different obsidian families have been distinguished, probably imported from Lipari and Pantelleria islands. Analysing the magnetic properties of the samples, these two main sources were confirmed, but the possibility of other provenances was inferred. Finally, we characterized the geochemical signature of the Ustica obsidians by performing microchemical analyses through electron microprobe (EMPA) and laser ablation (LA–ICP–MS). The results were compared with literature data, confirming the presence of the Lipari and Pantelleria sources (Sicily) and indicating for the first time in this part of Italy a third provenance from Palmarola island (Latium). Our results shed new light on the commercial exchanges in the peri-Tyrrhenian area during the prehistoric age.
    Description: Published
    Description: 435–454
    Description: 1SR. TERREMOTI - Servizi e ricerca per la Società
    Description: 2SR. VULCANI - Servizi e ricerca per la Società
    Description: 3SR. AMBIENTE - Servizi e ricerca per la Società
    Description: JCR Journal
    Description: restricted
    Keywords: obsdian provenance ; LA-ICPMS ; 05. General::05.04. Instrumentation and techniques of general interest::05.04.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    A global multiproxy database for temperature reconstructions of the Common Era (2017)
    Nature Publishing Group
    In:  EPIC3Scientific Data, Nature Publishing Group, 4(170088), pp. 1-33, ISSN: 2052-4463
    Details
    Publication Date: 2017-07-21
    Description: Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850–2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Paleochannel and beach-bar palimpsest topography as initial substrate for coralligenous buildups offshore Venice, Italy (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1321, doi:10.1038/s41598-017-01483-z.
    Description: We provide a model for the genesis of Holocene coralligenous buildups occurring in the northwestern Adriatic Sea offshore Venice at 17–24 m depth. High-resolution geophysical surveys and underwater SCUBA diving reconnaissance revealed meandering shaped morphologies underneath bio-concretionned rocky buildups. These morphologies are inferred to have been inherited from Pleistocene fluvial systems reactivated as tidal channels during the post- Last Glacial Maximum transgression, when the study area was a lagoon protected by a sandy barrier. The lithification of the sandy fossil channel-levee systems is estimated to have occurred at ca. 7 cal. ka BP, likely due to the interaction between marine and less saline fluids related to onshore freshwater discharge at sea through a sealed water-table. The carbonate-cemented sandy layers served as nucleus for subsequent coralligenous buildups growth.
    Description: Funded by the Italian Ministry of Education, University and Research within the National Research Program 2011–2013.
    Repository Name: Woods Hole Open Access Server
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  • 12
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    El Niño increases the risk of lower Mississippi River flooding (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1772, doi:10.1038/s41598-017-01919-6.
    Description: Mississippi River floods rank among the costliest climate-related disasters in the world. Improving flood predictability, preparedness, and response at seasonal to decadal time-scales requires an understanding of the climatic controls that govern flood occurrence. Linking flood occurrence to persistent modes of climate variability like the El Niño-Southern Oscillation (ENSO) has proven challenging, due in part to the limited number of high-magnitude floods available for study in the instrumental record. To augment the relatively short instrumental record, we use output from the Community Earth System Model (CESM) Last Millennium Ensemble (LME) to investigate the dynamical controls on discharge extremes of the lower Mississippi River. We show that through its regional influence on surface water storage, the warm phase of ENSO preconditions the lower Mississippi River to be vulnerable to flooding. In the 6–12 months preceding a flood, El Niño generates a positive precipitation anomaly over the lower Mississippi basin that gradually builds up soil moisture and reduces the basin’s infiltration capacity, thereby elevating the risk of a major flood during subsequent rainstorms. Our study demonstrates how natural climate variability mediates the formation of extreme floods on one of the world’s principal commercial waterways, adding significant predictive ability to near- and long-term forecasts of flood risk.
    Description: This work was funded through the Postdoctoral Scholar Program of the Woods Hole Oceanographic Institution and the Voss Environmental Postdoctoral Fellows Program at Brown University.
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  • 13
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    Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 15595, doi:10.1038/ncomms15595.
    Description: Although increasing atmospheric nitrous oxide (N2O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N2O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N2O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N2O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N2O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N2O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N2O fluxes, especially in redox-dynamic sediments of coastal ecosystems.
    Description: D.D.B. acknowledges support from the Max Planck Institute for Marine Microbiology. This work was supported by the National Science Foundation grants to W.Z. and S.D.W. (OCE-1260373) and to S.D.W. (EAR-1252161).
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  • 14
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    Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 11 (2017): 186–200, doi:10.1038/ismej.2016.95.
    Description: Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.
    Description: This research was supported by a KAUST-WHOI Post-doctoral Partnership Award to MN and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to CRV and AA. Research in this study was further supported by baseline research funds to CRV by KAUST and NSF award OCE-1233612 to AA. RR was supported by the ct-PIRE Project, Robert Lemelson Fellowship, Graduate Research Award (UCLA), Women Divers Hall of Fame—Sister Fund Conservation Award and a Betty and E. P. Franklin Grant in Tropical Biology and Conservation.
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  • 15
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    Assessing the dynamics of organic aerosols over the North Atlantic Ocean (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 45476, doi:10.1038/srep45476.
    Description: The influence of aerosols on climate is highly dependent on the particle size distribution, concentration, and composition. In particular, the latter influences their ability to act as cloud condensation nuclei, whereby they impact cloud coverage and precipitation. Here, we simultaneously measured the concentration of aerosols from sea spray over the North Atlantic on board the exhaust-free solar-powered vessel “PlanetSolar”, and the sea surface physico-chemical parameters. We identified organic-bearing particles based on individual particle fluorescence spectra. Organic-bearing aerosols display specific spatio-temporal distributions as compared to total aerosols. We propose an empirical parameterization of the organic-bearing particle concentration, with a dependence on water salinity and sea-surface temperature only. We also show that a very rich mixture of organic aerosols is emitted from the sea surface. Such data will certainly contribute to providing further insight into the influence of aerosols on cloud formation, and be used as input for the improved modeling of aerosols and their role in global climate processes.
    Description: We gratefully acknowledge the financial support by the H. Dudley Wright and the Henri Moser Foundations, the Rector’s Office and the Institute for Environmental Sciences at the University of Geneva, as well as a generous anonymous donator.
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  • 16
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    Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 772, doi:10.1038/s41467-017-00759-2.
    Description: In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO2. This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.
    Description: Funding for this work was provided by NSF grants OPP 1023270, 1022876, CAREER 1351745, DEB 1147378, 1347042, 0639790, 1147336, 1026843, PLR 1504006, DOE-JGI-CSP 1782, and the Camille and Henry Dreyfus Foundation Postdoctoral Program in Environmental Chemistry.
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  • 17
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    Defining a critical period for inhibitory circuits within the somatosensory cortex (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 7271, doi:10.1038/s41598-017-07400-8.
    Description: Although experience-dependent changes in brain inhibitory circuits are thought to play a key role during the “critical period” of brain development, the nature and timing of these changes are poorly understood. We examined the role of sensory experience in sculpting an inhibitory circuit in the primary somatosensory cortex (S1) of mice by using optogenetics to map the connections between parvalbumin (PV) expressing interneurons and layer 2/3 pyramidal cells. Unilateral whisker deprivation decreased the strength and spatial range of inhibitory input provided to pyramidal neurons by PV interneurons in layers 2/3, 4 and 5. By varying the time when sensory input was removed, we determined that the critical period closes around postnatal day 14. This yields the first precise time course of critical period plasticity for an inhibitory circuit.
    Description: This work was supported by a fellowship from NUS to SQL, A*STAR intramural funding for the Integrative Neuroscience Programme, Singapore Institute for Clinical Sciences for JCGS, and a Competitive Research Programme (CRP) grant from the National Research Foundation of Singapore (NRF Grant Number 2008 NRF-CRP 002-082).
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  • 18
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    Climate oscillations reflected within the microbiome of Arabian Sea sediments (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 6040, doi:10.1038/s41598-017-05590-9.
    Description: Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
    Description: his work was primarily supported by NSF MGG Grant #1357017 to MJLC, VG, and LG, and the KAUST-WHOI Special Academic Partnership Program OCRF-SP-WHOI-2013 (grants 7000000463 to XI and 7000000464 to MJLC). Additional financial support was provided via a C-DEBI grant #OCE-0939564 to WDO.
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  • 19
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    Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 832, doi:10.1038/s41467-017-00890-0.
    Description: Colonially-breeding seabirds have long served as indicator species for the health of the oceans on which they depend. Abundance and breeding data are repeatedly collected at fixed study sites in the hopes that changes in abundance and productivity may be useful for adaptive management of marine resources, but their suitability for this purpose is often unknown. To address this, we fit a Bayesian population dynamics model that includes process and observation error to all known Adélie penguin abundance data (1982–2015) in the Antarctic, covering 〉95% of their population globally. We find that process error exceeds observation error in this system, and that continent-wide “year effects” strongly influence population growth rates. Our findings have important implications for the use of Adélie penguins in Southern Ocean feedback management, and suggest that aggregating abundance across space provides the fastest reliable signal of true population change for species whose dynamics are driven by stochastic processes.
    Description: H.J.L., C.C.-C., G.H., C.Y., and K.T.S. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AC32G and U.S. National Science Foundation Office of Polar Programs Award No. NSF/OPP-1255058. S.J., L.L., M.M.H., Y.L., and R.J. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AH74G. H.J.L., C.Y., S.J., Y.L., and R.J. gratefully acknowledge funding provided by U.S. National Science Foundation Office of Polar Programs Award No. NSF/PLR-1341548. S.J. gratefully acknowledges support from the Dalio Explore Fund.
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  • 20
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    Long-term passive acoustic recordings track the changing distribution of North Atlantic right whales (Eubalaena glacialis) from 2004 to 2014 (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 13460, doi:10.1038/s41598-017-13359-3.
    Description: Given new distribution patterns of the endangered North Atlantic right whale (NARW; Eubalaena glacialis) population in recent years, an improved understanding of spatio-temporal movements are imperative for the conservation of this species. While so far visual data have provided most information on NARW movements, passive acoustic monitoring (PAM) was used in this study in order to better capture year-round NARW presence. This project used PAM data from 2004 to 2014 collected by 19 organizations throughout the western North Atlantic Ocean. Overall, data from 324 recorders (35,600 days) were processed and analyzed using a classification and detection system. Results highlight almost year-round habitat use of the western North Atlantic Ocean, with a decrease in detections in waters off Cape Hatteras, North Carolina in summer and fall. Data collected post 2010 showed an increased NARW presence in the mid-Atlantic region and a simultaneous decrease in the northern Gulf of Maine. In addition, NARWs were widely distributed across most regions throughout winter months. This study demonstrates that a large-scale analysis of PAM data provides significant value to understanding and tracking shifts in large whale movements over long time scales.
    Description: This research was funded and supported by many organizations, specified by projects as follows: Data recordings from region 1 were provided by K. Stafford and this research effort was funded by the National Science Foundation #NSF-ARC 0532611. Region 2 data were provided by D. K. Mellinger and S. Nieukirk, funded by National Oceanic and Atmospheric Agency (NOAA) and the Office of Naval Research (ONR) #N00014–03–1–0099, NOAA #NA06OAR4600100, US Navy #N00244-08-1-0029, N00244-09-1-0079, and N00244-10-1-0047.
    Repository Name: Woods Hole Open Access Server
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    Seasonal variations of leaf and canopy properties tracked by ground-based NDVI imagery in a temperate forest (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1267, doi:10.1038/s41598-017-01260-y.
    Description: Changes in plant phenology affect the carbon flux of terrestrial forest ecosystems due to the link between the growing season length and vegetation productivity. Digital camera imagery, which can be acquired frequently, has been used to monitor seasonal and annual changes in forest canopy phenology and track critical phenological events. However, quantitative assessment of the structural and biochemical controls of the phenological patterns in camera images has rarely been done. In this study, we used an NDVI (Normalized Difference Vegetation Index) camera to monitor daily variations of vegetation reflectance at visible and near-infrared (NIR) bands with high spatial and temporal resolutions, and found that the infrared camera based NDVI (camera-NDVI) agreed well with the leaf expansion process that was measured by independent manual observations at Harvard Forest, Massachusetts, USA. We also measured the seasonality of canopy structural (leaf area index, LAI) and biochemical properties (leaf chlorophyll and nitrogen content). We found significant linear relationships between camera-NDVI and leaf chlorophyll concentration, and between camera-NDVI and leaf nitrogen content, though weaker relationships between camera-NDVI and LAI. Therefore, we recommend ground-based camera-NDVI as a powerful tool for long-term, near surface observations to monitor canopy development and to estimate leaf chlorophyll, nitrogen status, and LAI.
    Description: This research was supported by US Department of Energy Office of Biological and Environmental Research Grant DE-SC0006951, National Science Foundation Grants DBI-959333 and AGS-1005663, and the University of Chicago and the MBL Lillie Research Innovation Award to J.T. and China Scholarship Council (CSC) to H.Y.
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    A-to-I RNA editing in the earliest-diverging Eumetazoan phyla (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.
    Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
    Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).
    Keywords: RNA editing ; ADAR ; Evolution ; Coral
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    Spiraling pathways of global deep waters to the surface of the Southern Ocean (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 172, doi:10.1038/s41467-017-00197-0.
    Description: Upwelling of global deep waters to the sea surface in the Southern Ocean closes the global overturning circulation and is fundamentally important for oceanic uptake of carbon and heat, nutrient resupply for sustaining oceanic biological production, and the melt rate of ice shelves. However, the exact pathways and role of topography in Southern Ocean upwelling remain largely unknown. Here we show detailed upwelling pathways in three dimensions, using hydrographic observations and particle tracking in high-resolution models. The analysis reveals that the northern-sourced deep waters enter the Antarctic Circumpolar Current via southward flow along the boundaries of the three ocean basins, before spiraling southeastward and upward through the Antarctic Circumpolar Current. Upwelling is greatly enhanced at five major topographic features, associated with vigorous mesoscale eddy activity. Deep water reaches the upper ocean predominantly south of the Antarctic Circumpolar Current, with a spatially nonuniform distribution. The timescale for half of the deep water to upwell from 30° S to the mixed layer is ~60–90 years.
    Description: V.T., L.D.T., and M.R.M. were supported by NSF OCE-1357072. A.K.M., H.F.D., and W.W. were supported by the RGCM program of the US Department of Energy under Contract DE-SC0012457. J.L.S. acknowledges NSF’s Southern Ocean Carbon and Climate Observations and Modeling project under NSF PLR-1425989, which partially supported L.D.T. and M.R.M. as well. C.O.D was supported by the National Aeronautics and Space Administration (NASA) under Award NNX14AL40G and by the Princeton Environmental Institute Grand Challenge initiative. A.R.G. was supported by a Climate and Global Change Postdoctoral Fellowship from the National Oceanic and Atmospheric Administration (NOAA). S.M.G. acknowledges the ongoing support of NOAA/GFDL for high-end ocean and climate-modeling activities. J.W. acknowledges support from NSF OCE-1234473.
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    On the physics of frequency-domain controlled source electromagnetics in shallow water. 1: isotropic conductivity (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 208 (2017): 1026-1042, doi:10.1093/gji/ggw435.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the subseafloor conductivity that is assumed to be isotropic. The deep water (ocean layer electrically much thicker than the overburden) seafloor EM response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a half-space, or a stronger and faster response. For an ocean whose electrical thickness is comparable to or much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. These transitions can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire subseafloor resistivity structure with the sea surface. A stronger and faster response occurs when guided energy flow is dominant, while a weaker and slower response occurs when the air interaction is dominant. However, at intermediate offsets for some models, the air interaction can partially or fully reverse the direction of energy flux in the reservoir layer toward rather than away from the source, resulting in a stronger and slower response. The Fréchet derivatives are dominated by preferential sensitivity to the reservoir layer conductivity for all water depths except at high frequencies, but also display a shift with offset from the galvanic to the inductive mode in the underburden and overburden due to the interplay of guided energy flow and the air interaction. This means that the sensitivity to the horizontal conductivity is almost as strong as to the vertical component in the shallow parts of the subsurface, and in fact is stronger than the vertical sensitivity deeper down. However, the sensitivity to horizontal conductivity is still weak compared to the vertical component within thin resistive regions. The horizontal sensitivity is gradually decreased when the water becomes deep. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Keywords: Electrical properties ; Marine electromagnetics
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    Created mangrove wetlands store belowground carbon and surface elevation change enables them to adjust to sea-level rise (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1030, doi:10.1038/s41598-017-01224-2.
    Description: Mangrove wetlands provide ecosystem services for millions of people, most prominently by providing storm protection, food and fodder. Mangrove wetlands are also valuable ecosystems for promoting carbon (C) sequestration and storage. However, loss of mangrove wetlands and these ecosystem services are a global concern, prompting the restoration and creation of mangrove wetlands as a potential solution. Here, we investigate soil surface elevation change, and its components, in created mangrove wetlands over a 25 year developmental gradient. All created mangrove wetlands were exceeding current relative sea-level rise rates (2.6 mm yr−1), with surface elevation change of 4.2–11.0 mm yr−1 compared with 1.5–7.2 mm yr−1 for nearby reference mangroves. While mangrove wetlands store C persistently in roots/soils, storage capacity is most valuable if maintained with future sea-level rise. Through empirical modeling, we discovered that properly designed creation projects may not only yield enhanced C storage, but also can facilitate wetland persistence perennially under current rates of sea-level rise and, for most sites, for over a century with projected medium accelerations in sea-level rise (IPCC RCP 6.0). Only the fastest projected accelerations in sea-level rise (IPCC RCP 8.5) led to widespread submergence and potential loss of stored C for created mangrove wetlands before 2100.
    Description: Funding for this research was provided by the U.S. Environmental Protection Agency, Gulf Ecology Division; U.S. Geological Survey, Climate and Land Use Change R&D Program; and U.S. Geological Survey, Environments Program.
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    Google haul out : Earth observation imagery and digital aerial surveys in coastal wildlife management and abundance estimation (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioscience 67 (2017): 760–768, doi:10.1093/biosci/bix059.
    Description: As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances.
    Description: We would like to thank generous support from International Fund for Animal Welfare, the Bureau of Ocean Energy, and the Oak Foundation for funding support for the telemetry devices.
    Keywords: Abundance estimation ; Gray seals (Halichoerus grypus) ; Cape Cod ; Remote sensing ; Earth observation
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    Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 11 (2017): 2090–2101, doi:10.1038/ismej.2017.74.
    Description: Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting ‘new’ nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont. Here we demonstrate the presence of a core Trichodesmium microbiome that is modulated to suit different ocean regions, and contributes over 10 times the metabolic potential of Trichodesmium to the holobiont. Given the ubiquitous nature of epibionts on colonies, the substantial functional diversity within the microbiome is likely an integral facet of Trichodesmium physiological ecology across the oligotrophic oceans where this biogeochemically significant diazotroph thrives.
    Description: This research was funded by grants from the National Science Foundation to STD (OCE-1332912) and BASVM (OCE-1332898).
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    Tracing the Vedic Saraswati River in the Great Rann of Kachchh (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 5476, doi:10.1038/s41598-017-05745-8.
    Description: The lost Saraswati River mentioned in the ancient Indian tradition is postulated to have flown independently of the Indus River into the Arabian Sea, perhaps along courses of now defunct rivers such as Ghaggar, Hakra and Nara. The persistence of such a river during the Harappan Bronze Age and the Iron Age Vedic period is strongly debated. We drilled in the Great Rann of Kachchh (Kutch), an infilled gulf of the Arabian Sea, which must have received input from the Saraswati, if active. Nd and Sr isotopic measurements suggest that a distinct source may have been present before 10 ka. Later in Holocene, under a drying climate, sediments from the Thar Desert probably choked the signature of an independent Saraswati-like river. Alternatively, without excluding a Saraswati-like secondary source, the Indus and the Thar were the dominant sources throughout the post-glacial history of the GRK. Indus-derived sediment accelerated the infilling of GRK after ~6 ka when the Indus delta started to grow. Until its complete infilling few centuries ago, freshwater input from the Indus, and perhaps from the Ghaggar-Hakra-Nara, probably sustained a productive marine environment as well as navigability toward old coastal Harappan and historic towns in the region.
    Description: The drilling effort and subsequent study of the cores was funded by Department of Science and Technology (DST), Government of India sponsored research project to DMM (Project No. SR/S4/ES-21/Kachchh Window/P1) under the science of Shallow Subsurface Programme (SSS). N. Khonde gratefully acknowledges Indo-US Post-doctoral Fellowship sponsored by SERB-IUSSTF for research work at Woods Hole Oceanographic Institution.
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    Cenozoic global cooling and increased seawater Mg/Ca via reduced reverse weathering (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 844, doi:10.1038/s41467-017-00853-5.
    Description: Authigenic clay minerals formed on or in the seafloor occur in every type of marine sediment. They are recognized to be a major sink of many elements in the ocean but are difficult to study directly due to dilution by detrital clay minerals. The extremely low dust fluxes and marine sedimentation rates in the South Pacific Gyre (SPG) provide a unique opportunity to examine relatively undiluted authigenic clay. Here, using Mg isotopes and element concentrations combined with multivariate statistical modeling, we fingerprint and quantify the abundance of authigenic clay within SPG sediment. Key reactants include volcanic ash (source of reactive aluminium) and reactive biogenic silica on or shallowly buried within the seafloor. Our results, together with previous studies, suggest that global reorganizations of biogenic silica burial over the Cenozoic reduced marine authigenic clay formation, contributing to the rise in seawater Mg/Ca and decline in atmospheric CO2 over the past 50 million years.
    Description: Funding for this research was provided by the U.S. National Science Foundation to R.W.M. (OCE1130531) and to J.A.H. (OCE1654571).
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    Aerial photography based census of Adélie Penguin and its application in CH4 and N2O budget estimation in Victoria Land, Antarctic (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 12942, doi:10.1038/s41598-017-13380-6.
    Description: Penguin guano provides favorable conditions for production and emission of greenhouse gases (GHGs). Many studies have been conducted to determine the GHG fluxes from penguin colonies, however, at regional scale, there is still no accurate estimation of total GHG emissions. We used object-based image analysis (OBIA) method to estimate the Adélie penguin (Pygoscelis adeliae) population based on aerial photography data. A model was developed to estimate total GHG emission potential from Adélie penguin colonies during breeding seasons in 1983 and 2012, respectively. Results indicated that OBIA method was effective for extracting penguin information from aerial photographs. There were 17,120 and 21,183 Adélie penguin breeding pairs on Inexpressible Island in 1983 and 2012, respectively, with overall accuracy of the estimation of 76.8%. The main reasons for the increase in Adélie penguin populations were attributed to increase in temperature, sea ice and phytoplankton. The average estimated CH4 and N2O emissions tended to be increasing during the period from 1983 to 2012 and CH4 was the main GHG emitted from penguin colonies. Total global warming potential (GWP) of CH4 and N2O emissions was 5303 kg CO2-eq in 1983 and 6561 kg CO2-eq in 2012, respectively.
    Description: This work was supported by the Fundamental Research Funds for the Central Universities (Grant No. 312231103), the Chinese Arctic and Antarctic Administration, National Natural Science Foundation of China (Grant Nos 41676176 and 41676182), the Chinese Polar Environment Comprehensive Investigation, Assessment Program.
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    Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1114, doi:10.1038/s41467-017-01228-6.
    Description: Little is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.
    Description: R.E.A. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute. This work was supported by a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-327 09AB75G and a grant from Deep Carbon Observatory's Deep Life Initiative to J.A.H. and J.S.S., and the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI). Ship and vehicle time in 2012 was supported by the NSF-OCE grant OCE-1061863 to J.S.S.
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    Effect of water activity on rates of serpentinization of olivine (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 16107, doi:10.1038/ncomms16107.
    Description: The hydrothermal alteration of mantle rocks (referred to as serpentinization) occurs in submarine environments extending from mid-ocean ridges to subduction zones. Serpentinization affects the physical and chemical properties of oceanic lithosphere, represents one of the major mechanisms driving mass exchange between the mantle and the Earth’s surface, and is central to current origin of life hypotheses as well as the search for microbial life on the icy moons of Jupiter and Saturn. In spite of increasing interest in the serpentinization process by researchers in diverse fields, the rates of serpentinization and the controlling factors are poorly understood. Here we use a novel in situ experimental method involving olivine micro-reactors and show that the rate of serpentinization is strongly controlled by the salinity (water activity) of the reacting fluid and demonstrate that the rate of serpentinization of olivine slows down as salinity increases and H2O activity decreases.
    Description: This material is based upon work supported by the National Science Foundation under Grant OCE-1459433 to R.J.B. and E.M.S. Consejo Nacional de Ciencia y Tecnología (CONACyT), the Virginia Tech Department of Geosciences and Virginia Tech Graduate School provided partial funding to HML during this study. F.K. was supported by The Andrew W. Mellon Foundation Endowed Fund for Innovative Research.
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    Seal whiskers vibrate over broad frequencies during hydrodynamic tracking (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 8350, doi:10.1038/s41598-017-07676-w.
    Description: Although it is known that seals can use their whiskers (vibrissae) to extract relevant information from complex underwater flow fields, the underlying functioning of the system and the signals received by the sensors are poorly understood. Here we show that the vibrations of seal whiskers may provide information about hydrodynamic events and enable the sophisticated wake-tracking abilities of these animals. We developed a miniature accelerometer tag to study seal whisker movement in situ. We tested the ability of the tag to measure vibration in excised whiskers in a flume in response to laminar flow and disturbed flow. We then trained a seal to wear the tag and follow an underwater hydrodynamic trail to measure the whisker signals available to the seal. The results showed that whiskers vibrated at frequencies of 100–300 Hz, with a dynamic response. These measurements are the first to capture the incoming signals received by the vibrissae of a live seal and show that there are prominent signals at frequencies where the seal tactogram shows good sensitivity. Tapping into the mechanoreceptive interface between the animal and the environment may help to decipher the functional basis of this extraordinary hydrodynamic detection ability.
    Description: Funding was provided by the NSF GRFP and NISE section 219 to C. Murphy and by the Office of Naval Research (N000141910468) to B. Calhoun.
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    On the physics of frequency domain controlled source electromagnetics in shallow water, 2: transverse anisotropy (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 211 (2017): 1046–1061, doi:10.1093/gji/ggx360.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically-polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the sub-seafloor conductivity that is assumed to be transversely anisotropic, with a vertical-to-horizontal resistivity ratio of 3:1. For an ocean whose electrical thickness is comparable to that of the overburden, the seafloor electromagnetic response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a halfspace, or a stronger and faster response, and displays little to no evidence for the air interaction. For an ocean whose electrical thickness is much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets, and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. By comparison to the isotropic case with the same horizontal conductivity, transverse anisotropy stretches the Poynting vector and the electric field response from a thin resistive layer to much longer offsets. These phenomena can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire sub-seafloor resistivity structure with the sea surface. The Fréchet derivatives are dominated by preferential sensitivity to the vertical conductivity in the reservoir layer and overburden at short offsets. The horizontal conductivity Fréchet derivatives are weaker than to comparable to the vertical derivatives at long offsets in the substrate. This means that the sensitivity to the horizontal conductivity is present in the shallow parts of the subsurface. In the presence of transverse anisotropy, it is necessary to go to higher frequencies to sense the horizontal conductivity in the overburden as compared to an isotropic model with the same horizontal conductivity. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Description: This work was supported at WHOI by an Independent Research and Development award, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
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    Joint inversion estimate of regional glacial isostatic adjustment in Antarctica considering a lateral varying Earth structure (ESA STSE Project REGINA) (2017)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 211(3), pp. 1534-1553
    Details
    Publication Date: 2022-06-20
    Description: A major uncertainty in determining the mass balance of the Antarctic ice sheet from measurements of satellite gravimetry, and to a lesser extent satellite altimetry, is the poorly known correction for the ongoing deformation of the solid Earth caused by glacial isostatic adjustment (GIA). Although much progress has been made in consistently modeling the ice-sheet evolution throughout the last glacial cycle, as well as the induced bedrock deformation caused by these load changes, forward models of GIA remain ambiguous due to the lack of observational constraints on the ice sheet's past extent and thickness and mantle rheology beneath the continent. As an alternative to forward-modeling GIA, we estimate GIA from multiple space-geodetic observations: Gravity Recovery and Climate Experiment (GRACE), Envisat/ICESat and Global Positioning System (GPS). Making use of the different sensitivities of the respective satellite observations to current and past surface-mass (ice mass) change and solid Earth processes, we estimate GIA based on viscoelastic response functions to disc load forcing. We calculate and distribute the viscoelastic response functions according to estimates of the variability of lithosphere thickness and mantle viscosity in Antarctica. We compare our GIA estimate with published GIA corrections and evaluate its impact in determining the ice-mass balance in Antarctica from GRACE and satellite altimetry. Particular focus is applied to the Amundsen Sea Sector in West Antarctica, where uplift rates of several centimetres per year have been measured by GPS. We show that most of this uplift is caused by the rapid viscoelastic response to recent ice-load changes, enabled by the presence of a low-viscosity upper mantle in West Antarctica. This paper presents the second and final contributions summarizing the work carried out within a European Space Agency funded study, REGINA (www.regina-science.eu).
    Repository Name: EPIC Alfred Wegener Institut
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    Evidence of a shallow magma intrusion beneath the NE Rift system of Mt. Etna during 2013 (2017)
    Wiley-Blackwell
    Details
    Publication Date: 2022-05-24
    Description: Continuous GPS (CGPS) data, collected at Mt. Etna between April 2012 and October 2013, clearly define inflation/deflation processes typically observed before/after an eruption onset. During the inflationary process from May to October 2013, a particular deformation pattern localised in the upper North Eastern sector of the volcano suggests that a magma intrusion had occurred a few km away from the axis of the summit craters, beneath the NE Rift system. This is the first time that this pattern has been recorded by CGPS data at Mt. Etna. We believe that this inflation process might have taken place periodically at Mt. Etna and might be associated with the intrusion of batches of magma that are separate from the main feeding system. We provide a model to explain this unusual behaviour and the eruptive regime of this rift zone, which is characterised by long periods of quiescence followed by often dangerous eruptions in which vents can open at low elevation and thus threaten the villages in this sector of the volcano.
    Description: Published
    Description: 356-363
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Shallow intrusion beneath NE Rift system ; Mt. Etna volcano ; CGPS data ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Seismic hazards implications of uplifted Pleistocene coral terraces in the Gulf of Aqaba (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 38, doi:10.1038/s41598-017-00074-2.
    Description: The Gulf of Aqaba transform plate boundary is a source of destructive teleseismic earthquakes. Seismicity is concentrated in the central sub-basin and decreases to both the north and south. Although principally a strike-slip plate boundary, the faulted margins of the Gulf display largely dip-slip extensional movement and accompanying footwall uplift. We have constrained rates of this uplift by measurements of elevated Pleistocene coral terraces. In particular the terrace that formed during the last interglacial (~125 ka) is found discontinuously along the length of the Gulf at elevations of 3 to 26 m. Global sea level was ~7 m higher than today at 125 ka indicating net maximum tectonic uplift of ~19 m with an average rate of ~0.015 cm/yr. Uplift has been greatest adjacent to the central sub-basin and like the seismicity decreases to the north and south. We suggest that the present pattern of a seismically active central region linked to more aseismic areas in the north and south has therefore persisted for at least the past 125 kyr. Consequently the potential for future destructive earthquakes in the central Gulf is greater than in the sub-basins to the north and south.
    Repository Name: Woods Hole Open Access Server
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    Mutations underlying Episodic Ataxia type-1 antagonize Kv1.1 RNA editing (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 41095, doi:10.1038/srep41095.
    Description: Adenosine-to-inosine RNA editing in transcripts encoding the voltage-gated potassium channel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from inactivation. Numerous Kv1.1 mutations have been associated with the human disorder Episodic Ataxia Type-1 (EA1), characterized by stress-induced ataxia, myokymia, and increased prevalence of seizures. Three EA1 mutations, V404I, I407M, and V408A, are located within the RNA duplex structure required for RNA editing. Each mutation decreased RNA editing both in vitro and using an in vivo mouse model bearing the V408A allele. Editing of transcripts encoding mutant channels affects numerous biophysical properties including channel opening, closing, and inactivation. Thus EA1 symptoms could be influenced not only by the direct effects of the mutations on channel properties, but also by their influence on RNA editing. These studies provide the first evidence that mutations associated with human genetic disorders can affect cis-regulatory elements to alter RNA editing.
    Description: This work was supported by the Vanderbilt Molecular Endocrinology Training Program (T32DK007563; E.A.F.K.), a Ruth L. Kirschstein National Research Service Award (F31NS087911; E.A.F.K), a Vanderbilt Dissertation Enhancement Grant (E.A.F.K.), and the Vanderbilt Joel G. Hardman Chair in Pharmacology (R.B.E). Additional support for J.J.C.R. included NINDS (R0111223855, R01NS64259) and the Cystic Fibrosis Foundation Therapeutics (Rosent14XXO). Infrastructural support for J.J.C.R. was provided by NIGMS (P20GM103642), NIMH (G12-MD007600), and NSF (DBI 0115825, DBI 1337284).
    Repository Name: Woods Hole Open Access Server
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    Topographic enhancement of vertical turbulent mixing in the Southern Ocean (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 14197, doi:10.1038/ncomms14197.
    Description: It is an open question whether turbulent mixing across density surfaces is sufficiently large to play a dominant role in closing the deep branch of the ocean meridional overturning circulation. The diapycnal and isopycnal mixing experiment in the Southern Ocean found the turbulent diffusivity inferred from the vertical spreading of a tracer to be an order of magnitude larger than that inferred from the microstructure profiles at the mean tracer depth of 1,500 m in the Drake Passage. Using a high-resolution ocean model, it is shown that the fast vertical spreading of tracer occurs when it comes in contact with mixing hotspots over rough topography. The sparsity of such hotspots is made up for by enhanced tracer residence time in their vicinity due to diffusion toward weak bottom flows. The increased tracer residence time may explain the large vertical fluxes of heat and salt required to close the abyssal circulation.
    Description: Financial support for A.M. and R.F. under the US National Science Foundation grant OCE-1233832 is gratefully acknowledged. A.M. also acknowledges support from an NSERC PDF award.
    Repository Name: Woods Hole Open Access Server
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    The landscape of extreme genomic variation in the highly adaptable Atlantic killifish (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.
    Description: Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.
    Description: This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.).
    Keywords: Population genomics ; Genome sequence ; Comparative genomics ; Adaptation ; Genetic diversity
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    Organic carbon budget for the eastern boundary of the North Atlantic subtropical gyre : major role of DOC in mesopelagic respiration (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 10129, doi:10.1038/s41598-017-10974-y.
    Description: Transports of suspended particulate (POCsusp) and dissolved (DOC) organic carbon are inferred from a box-model covering the eastern boundary of the North Atlantic subtropical gyre. Corresponding net respiration rates (R) are obtained from a net organic carbon budget that is based on the transport estimates, and includes both vertical and lateral fluxes. The overall R in the mesopelagic layer (100–1500 m) is 1.6 ± 0.4 mmol C m−2 d−1. DOC accounts for up to 53% of R as a result of drawdown of organic carbon within Eastern North Atlantic Central Water (ENACW) that is entrained into sinking Mediterranean Overflow Water (MOW) that leads to formation of Mediterranean water (MW) at intermediate depths (~900 m). DOC represents 90% of the respired non-sinking organic carbon. When converted into oxygen units, the computed net respiration rate represents less than half the oxygen utilization rates (OUR) reported for the mesopelagic waters of the subtropical North Atlantic. Mesoscale processes in the area, not quantified with our approach, could account in part for the OUR differences observed between our carbon budget and other published studies from the North Atlantic, although seasonal or interannual variability could also be responsible for the difference in the estimates.
    Description: This research was supported by projects ORCA (CTM2005-04701-CO2-01), Malaspina (CSD2008-00077), HOTMIX (CTM2011-30010-C02) and FLUXES (CTM2015-69392-C3), financed by the Spanish “Plan Nacional de I + D”. YSF was supported by a Spanish fellowship from the Agencia Canaria de Investigación, Innovación y Sociedad de la Información (ACIISI). EM has been partially supported by the Copernicus Marine Environment Monitoring Service (CMEMS) MedSUB project, and a post-doctoral grant from the Conselleria d’Educació, Cultura i Universitats del Govern de les Illes Balears (Mallorca, Spain) and the European Social Fund.
    Repository Name: Woods Hole Open Access Server
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    Restoring tides to reduce methane emissions in impounded wetlands : a new and potent Blue Carbon climate change intervention (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 11914, doi::10.1038/s41598-017-12138-4.
    Description: Coastal wetlands are sites of rapid carbon (C) sequestration and contain large soil C stocks. Thus, there is increasing interest in those ecosystems as sites for anthropogenic greenhouse gas emission offset projects (sometimes referred to as “Blue Carbon”), through preservation of existing C stocks or creation of new wetlands to increase future sequestration. Here we show that in the globallywidespread occurrence of diked, impounded, drained and tidally-restricted salt marshes, substantial methane (CH4) and CO2 emission reductions can be achieved through restoration of disconnected saline tidal flows. Modeled climatic forcing indicates that tidal restoration to reduce emissions has a much greater impact per unit area than wetland creation or conservation to enhance sequestration. Given that GHG emissions in tidally-restricted, degraded wetlands are caused by human activity, they are anthropogenic emissions, and reducing them will have an effect on climate that is equivalent to reduced emission of an equal quantity of fossil fuel GHG. Thus, as a landuse-based climate change intervention, reducing CH4 emissions is an entirely distinct concept from biological C sequestration projects to enhance C storage in forest or wetland biomass or soil, and will not suffer from the non-permanence risk that stored C will be returned to the atmosphere.
    Description: Research supported by the USGS Coastal & Marine Geology Program, USGS Land Carbon Program, and NOAA Science Collaborative grant #NA09NOS4190153.
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    Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1452, doi:10.1038/s41467-017-01250-8.
    Description: Light-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, and gentle imaging of live specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of four complementary views in 250 ms, doubling speed and improving information content relative to symmetric dual-view LSFM. We also report a modified deconvolution algorithm that removes associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to 〈300 nm in all three dimensions) by applying our method to single-view LSFM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture. We demonstrate the broad applicability of our method in a variety of samples, studying mitochondrial, membrane, Golgi, and microtubule dynamics in cells and calcium activity in nematode embryos.
    Description: This work was supported by the Intramural Research Program of the National Institute of Biomedical Imaging and Bioengineering at the National Institutes of Health. P.L. and H.S. acknowledge summer support from the Marine Biological Laboratory at Woods Hole, through the Whitman- and Fellows- program. P.L. acknowledges support from NIH National Institute of Biomedical Imaging and Bioengineering (NIBIB) of the National Institutes of Health (NIH) under grant number R01EB017293. C.S. acknowledges funding from the National Institute of General Medical Sciences of NIH under Award Number R25GM109439 (Project Title: University of Chicago Initiative for Maximizing Student Development [IMSD]) and NIBIB under grant number T32 EB002103. Partial funding for the computation in this work was provided by NIH grant numbers S10 RRO21039 and P30 CA14599. A.U. and I.R.-S. were supported by the NSF grant number 1607645.
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    Multiple steroid and thyroid hormones detected in baleen from eight whale species (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 5 (2017): cox061, doi:10.1093/conphys/cox061.
    Description: Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.
    Description: This work was supported by (1) the Center for Bioengineering Innovation at Northern Arizona University and (2) the New England Aquarium.
    Keywords: Baleen ; Cetaceans ; Hormones ; Marine mammals ; Reproduction ; Stress
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    Rapid global ocean-atmosphere response to Southern Ocean freshening during the last glacial (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 520, doi:10.1038/s41467-017-00577-6.
    Description: Contrasting Greenland and Antarctic temperatures during the last glacial period (115,000 to 11,650 years ago) are thought to have been driven by imbalances in the rates of formation of North Atlantic and Antarctic Deep Water (the ‘bipolar seesaw’). Here we exploit a bidecadally resolved 14C data set obtained from New Zealand kauri (Agathis australis) to undertake high-precision alignment of key climate data sets spanning iceberg-rafted debris event Heinrich 3 and Greenland Interstadial (GI) 5.1 in the North Atlantic (~30,400 to 28,400 years ago). We observe no divergence between the kauri and Atlantic marine sediment 14C data sets, implying limited changes in deep water formation. However, a Southern Ocean (Atlantic-sector) iceberg rafted debris event appears to have occurred synchronously with GI-5.1 warming and decreased precipitation over the western equatorial Pacific and Atlantic. An ensemble of transient meltwater simulations shows that Antarctic-sourced salinity anomalies can generate climate changes that are propagated globally via an atmospheric Rossby wave train.
    Description: This work was funded by the Australian Research Council (FL100100195, DP170104665 and SR140300001) and the Natural Environment Research Council (NE/H009922/1 and NE/H007865/1).
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    Bisphenol A in eggs causes development-specific liver molecular reprogramming in two generations of rainbow trout (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 14131, doi:10.1038/s41598-017-13301-7.
    Description: Bisphenol A (BPA) is widely used in the manufacture of plastics and epoxy resins and is prevalent in the aquatic environment. BPA disrupts endocrine pathways in fish, but the long-term developmental implications are unknown. We demonstrate that BPA deposition in the eggs of rainbow trout (Oncorhynchus mykiss), an ecologically and economically important species of fish, reprograms liver metabolism in the offspring and alters the developmental growth trajectory in two generations. Specifically, BPA reduces growth during early development, followed by a catch-up growth post-juveniles. More importantly, we observed a developmental shift in the liver transcriptome, including an increased propensity for protein breakdown during early life stages to lipid and cholesterol synthesis post- juveniles. The liver molecular responses corresponded with the transient growth phenotypes observed in the F1 generation, and this was also evident in the F2 generation. Altogether, maternal and/or ancestral embryonic exposure to BPA affects liver metabolism leading to development-distinct effects on growth, underscoring the need for novel risk assessment strategies for this chemical in the aquatic environment. This is particularly applicable to migratory species, such as salmon, where distinct temporal changes in growth and physiology during development are critical for their spawning success.
    Description: This study was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and Strategic Project Grants to MMV. Drs. Neel Aluru and Oana Birceanu received a NSERC post-doctoral fellowship and Canada Graduate Scholarship.
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    Pelagic barite precipitation at micromolar ambient sulfate (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1342, doi:10.1038/s41467-017-01229-5.
    Description: Geochemical analyses of sedimentary barites (barium sulfates) in the geological record have yielded fundamental insights into the chemistry of the Archean environment and evolutionary origin of microbial metabolisms. However, the question of how barites were able to precipitate from a contemporary ocean that contained only trace amounts of sulfate remains controversial. Here we report dissolved and particulate multi-element and barium-isotopic data from Lake Superior that evidence pelagic barite precipitation at micromolar ambient sulfate. These pelagic barites likely precipitate within particle-associated microenvironments supplied with additional barium and sulfate ions derived from heterotrophic remineralization of organic matter. If active during the Archean, pelagic precipitation and subsequent sedimentation may account for the genesis of enigmatic barite deposits. Indeed, barium-isotopic analyses of barites from the Paleoarchean Dresser Formation are consistent with a pelagic mechanism of precipitation, which altogether offers a new paradigm for interpreting the temporal occurrence of barites in the geological record.
    Description: This research was made possible with support from the National Science Foundation Division of Ocean Sciences (OCE-PRF 1421196, OCE-1430015, and OCE-1443577), The Andrew W. Mellon Foundation Endowed Fund for Innovative Research, and the Agouron Institute Geobiology Postdoctoral Fellowship Program.
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    Methane- and dissolved organic carbon-fueled microbial loop supports a tropical subterranean estuary ecosystem (2017)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1835, doi:10.1038/s41467-017-01776-x.
    Description: Subterranean estuaries extend inland into density-stratified coastal carbonate aquifers containing a surprising diversity of endemic animals (mostly crustaceans) within a highly oligotrophic habitat. How complex ecosystems (termed anchialine) thrive in this globally distributed, cryptic environment is poorly understood. Here, we demonstrate that a microbial loop shuttles methane and dissolved organic carbon (DOC) to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy, and chemoautotrophy, based on characterization by 16S rRNA gene amplicon sequencing and respiratory quinone composition. Fatty acid and bulk stable carbon isotope values of cave-adapted shrimp suggest that carbon from methanotrophic bacteria comprises 21% of their diet, on average. These findings reveal a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.
    Description: Funding for T.M.I. and D.B. was provided by TAMU-CONACYT (project no: 2015-049). D.B. was supported by Research-in-Residence program (NSF award #1137336, Inter-University Training in Continental-scale Ecology), Cave Research Foundation Graduate Student Grant, Cave Conservancy Foundation PhD Fellowship, Ralph W. Stone Fellowship (National Speleological Society), Grants-in-Aid of Graduate Student Research Award (Texas Sea Grant College Program), and Boost Fellowship (Texas A&M University at Galveston). Additional financial support was provided by NSF DEB-1257424 (M.B.L. and M.C.L.), the Postdoctoral Program at Woods Hole Oceanographic Institution and U.S. Geological Survey (K.W.B.).
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    Mass coral mortality under local amplification of 2°C ocean warming (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 44586, doi:10.1038/srep44586.
    Description: A 2°C increase in global temperature above pre-industrial levels is considered a reasonable target for avoiding the most devastating impacts of anthropogenic climate change. In June 2015, sea surface temperature (SST) of the South China Sea (SCS) increased by 2 °C in response to the developing Pacific El Niño. On its own, this moderate, short-lived warming was unlikely to cause widespread damage to coral reefs in the region, and the coral reef “Bleaching Alert” alarm was not raised. However, on Dongsha Atoll, in the northern SCS, unusually weak winds created low-flow conditions that amplified the 2°C basin-scale anomaly. Water temperatures on the reef flat, normally indistinguishable from open-ocean SST, exceeded 6°C above normal summertime levels. Mass coral bleaching quickly ensued, killing 40% of the resident coral community in an event unprecedented in at least the past 40 years. Our findings highlight the risks of 2°C ocean warming to coral reef ecosystems when global and local processes align to drive intense heating, with devastating consequences.
    Description: This research was funded by the National Science Foundation (OCE-1031971 and OCE-1605365 to A.L.C), the Sustainability Science Research Program of the Academia Sinica (G.T.F.W. and A.L.C), a Woods Hole Oceanographic Institution Coastal Ocean Institute award to T.M.D., and a National Science Foundation Graduate Research Fellowship awarded to T.M.D.
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    Multi-scale magnetic mapping of serpentinite carbonation (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1870, doi:10.1038/s41467-017-01610-4.
    Description: Peridotite carbonation represents a critical step within the long-term carbon cycle by sequestering volatile CO2 in solid carbonate. This has been proposed as one potential pathway to mitigate the effects of greenhouse gas release. Most of our current understanding of reaction mechanisms is based on hand specimen and laboratory-scale analyses. Linking laboratory-scale observations to field scale processes remains challenging. Here we present the first geophysical characterization of serpentinite carbonation across scales ranging from km to sub-mm by combining aeromagnetic observations, outcrop- and thin section-scale magnetic mapping. At all scales, magnetic anomalies coherently change across reaction fronts separating assemblages indicative of incipient, intermittent, and final reaction progress. The abundance of magnetic minerals correlates with reaction progress, causing amplitude and wavelength variations in associated magnetic anomalies. This correlation represents a foundation for characterizing the extent and degree of in situ ultramafic rock carbonation in space and time.
    Description: This project was supported by the Woods Hole Oceanographic Institution Independent Study Award (Tivey and Tominaga) and by NASA Astrobiology Institute NNA15BB02A (Tominaga). M.T. and A.B. are grateful to B. Jamtveit and H. Austrheim (University of Oslo) for their support during the 2011 and 2013 field campaigns. B.W. and E.A.L. thank the National Science Foundation grant DMS-1521765 and Thomas F. Peterson, Jr for generous support.
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    Implications of improved representations of plant respiration in a changing climate (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1602, doi:10.1038/s41467-017-01774-z.
    Description: Land-atmosphere exchanges influence atmospheric CO2. Emphasis has been on describing photosynthetic CO2 uptake, but less on respiration losses. New global datasets describe upper canopy dark respiration (Rd) and temperature dependencies. This allows characterisation of baseline Rd, instantaneous temperature responses and longer-term thermal acclimation effects. Here we show the global implications of these parameterisations with a global gridded land model. This model aggregates Rd to whole-plant respiration Rp, driven with meteorological forcings spanning uncertainty across climate change models. For pre-industrial estimates, new baseline Rd increases Rp and especially in the tropics. Compared to new baseline, revised instantaneous response decreases Rp for mid-latitudes, while acclimation lowers this for the tropics with increases elsewhere. Under global warming, new Rd estimates amplify modelled respiration increases, although partially lowered by acclimation. Future measurements will refine how Rd aggregates to whole-plant respiration. Our analysis suggests Rp could be around 30% higher than existing estimates.
    Description: C.H. acknowledges the NERC CEH National Capability fund. The support of the Australian Research Council to O.K.A. and P.M. (DP130101252, CE140100008, FT0991448, FT110100457) is acknowledged, as are awards DE-FG02-07ER64456 from the US Department of Energy, Office of Science, Office of Biological and Environmental Research and DEB-1234162 from the U.S. National Science Foundation (NSF) Long-Term Ecological Research Program (to P.B.R.); and National Science Foundation International Polar Year Grant (to K.L.G.). L.M.M. acknowledges the support of the Natural Environment Research Council (NERC) South American Biomass Burning Analysis (SAMBBA) project grant code NE/J010057/1.
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    Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration (2017)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 2047, doi:10.1038/s41467-017-01848-y.
    Description: Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.
    Description: Supported by the Lillie Research award from Marine Biological Laboratory and the University of Chicago (C.M.W., T.A.S., S.M., T.T.), NIH 5R13GM085967 grant to the Physiology Course at Marine Biological Laboratory, HHMI Summer Institute at Marine Biological Laboratory (S.M.), NIH CA31798 (T.A.S., P.N., T.I.M.), NIH GM100160 (T.T., S.M.), NIH GM092802 (D.B., N.K.), NIH GM114274 (R.O., S.M.) National Center for Biological Sciences-Tata Institute of Fundamental Research (S.M., J.M.K.), J.C. Bose Fellowship and HFSP Grant RGP0027/2012 (S.M.), NHLBI Division of Intramural Research (C.M.W., V.S.), Swedish Research Council VR 524-2011-891 Fellowship (P.N.), Swedish Society for Medical Research SSMF Fellowship (P.N.), Crafoord Foundation (P.N.).
    Keywords: Actin ; Integrin signalling ; Integrins ; Molecular imaging ; Polarization microscopy
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    Exact free oscillation spectra, splitting functions and the resolvability of Earth's density structure (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉Seismic free oscillations, or normal modes, provide a convenient tool to calculate low-frequency seismograms in heterogeneous Earth models. A procedure called ‘full mode coupling’ allows the seismic response of the Earth to be computed. However, in order to be theoretically exact, such calculations must involve an infinite set of modes. In practice, only a finite subset of modes can be used, introducing an error into the seismograms. By systematically increasing the number of modes beyond the highest frequency of interest in the seismograms, we investigate the convergence of full-coupling calculations. As a rule-of-thumb, it is necessary to couple modes 1–2 mHz above the highest frequency of interest, although results depend upon the details of the Earth model. This is significantly higher than has previously been assumed. Observations of free oscillations also provide important constraints on the heterogeneous structure of the Earth. Historically, this inference problem has been addressed by the measurement and interpretation of splitting functions. These can be seen as secondary data extracted from low frequency seismograms. The measurement step necessitates the calculation of synthetic seismograms, but current implementations rely on approximations referred to as self- or group-coupling and do not use fully accurate seismograms. We therefore also investigate whether a systematic error might be present in currently published splitting functions. We find no evidence for any systematic bias, but published uncertainties must be doubled to properly account for the errors due to theoretical omissions and regularization in the measurement process. Correspondingly, uncertainties in results derived from splitting functions must also be increased. As is well known, density has only a weak signal in low-frequency seismograms. Our results suggest this signal is of similar scale to the true uncertainties associated with currently published splitting functions. Thus, it seems that great care must be taken in any attempt to robustly infer details of Earth's density structure using current splitting functions.〈/span〉
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    Wavelet-based 3-D inversion for frequency-domain airborne EM data (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉In this paper, we propose a new wavelet-based 3-D inversion method for frequency-domain airborne electromagnetic (FDAEM) data. Instead of inverting the model in the space domain using a smoothing constraint, this new method recovers the model in the wavelet domain based on a sparsity constraint. In the wavelet domain, the model is represented by two types of coefficients, which contain both large- and fine-scale informations of the model, meaning the wavelet-domain inversion has inherent multiresolution. In order to accomplish a sparsity constraint, we minimize an L〈sub〉1〈/sub〉-norm measure in the wavelet domain that mostly gives a sparse solution. The final inversion system is solved by an iteratively reweighted least-squares method. We investigate different orders of Daubechies wavelets to accomplish our inversion algorithm, and test them on synthetic frequency-domain AEM data set. The results show that higher order wavelets having larger vanishing moments and regularity can deliver a more stable inversion process and give better local resolution, while the lower order wavelets are simpler and less smooth, and thus capable of recovering sharp discontinuities if the model is simple. At last, we test this new inversion algorithm on a frequency-domain helicopter EM (HEM) field data set acquired in Byneset, Norway. Wavelet-based 3-D inversion of HEM data is compared to L〈sub〉2〈/sub〉-norm-based 3-D inversion's result to further investigate the features of the new method.〈/span〉
    Print ISSN: 2051-1965
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    Monitoring of the spatio-temporal change in the interplate coupling at northeastern Japan subduction zone based on the spatial gradients of surface velocity field (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉A monitoring method to grasp the spatio-temporal change in the interplate coupling in a subduction zone based on the spatial gradients of surface displacement rate fields is proposed. I estimated the spatio-temporal change in the interplate coupling along the plate boundary in northeastern (NE) Japan by applying the proposed method to the surface displacement rates based on global positioning system observations. The gradient of the surface velocities is calculated in each swath configured along the direction normal to the Japan Trench for time windows such as 0.5, 1, 2, 3 and 5 yr being shifted by one week during the period of 1997–2016. The gradient of the horizontal velocities is negative and has a large magnitude when the interplate coupling at the shallow part (less than approximately 50 km in depth) beneath the profile is strong, and the sign of the gradient of the vertical velocity is sensitive to the existence of the coupling at the deep part (greater than approximately 50 km in depth). The trench-parallel variation of the spatial gradients of a displacement rate field clearly corresponds to the trench-parallel variation of the amplitude of the interplate coupling on the plate interface, as well as the rupture areas of previous interplate earthquakes. Temporal changes in the trench-parallel variation of the spatial gradient of the displacement rate correspond to the strengthening or weakening of the interplate coupling. We can monitor the temporal change in the interplate coupling state by calculating the spatial gradients of the surface displacement rate field to some extent without performing inversion analyses with applying certain constraint conditions that sometimes cause over- and/or underestimation at areas of limited spatial resolution far from the observation network. The results of the calculation confirm known interplate events in the NE Japan subduction zone, such as the post-seismic slip of the 2003 M8.0 Tokachi-oki and 2005 M7.2 Miyagi-oki earthquakes and the recovery of the interplate coupling around the rupture area of the 1994 M7.6 Sanriku-Haruka-oki earthquake. The results also indicate the semi-periodic occurrence of slow slip events and the expansion of the area of slow slip events before the 2011 Tohoku-oki earthquake (M9.0) approaching the hypocentre of the Tohoku-oki earthquake.〈/span〉
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    Internal structure of the San Jacinto fault zone in the trifurcation area southeast of Anza, California, from data of dense seismic arrays (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉We image the internal structure of the San Jacinto fault zone (SJFZ) in the trifurcation area southeast of Anza, California, with seismic records from dense linear and rectangular arrays. The examined data include recordings from more than 20 000 local earthquakes and nine teleseismic events. Automatic detection algorithms and visual inspection are used to identify 〈span〉P〈/span〉 and 〈span〉S〈/span〉 body waves, along with 〈span〉P〈/span〉- and 〈span〉S〈/span〉-types fault zone trapped waves (FZTW). The location at depth of the main branch of the SJFZ, the Clark fault, is identified from systematic waveform changes across lines of sensors within the dense rectangular array. Delay times of 〈span〉P〈/span〉 arrivals from teleseismic and local events indicate damage asymmetry across the fault, with higher damage to the NE, producing a local reversal of the velocity contrast in the shallow crust with respect to the large-scale structure. A portion of the damage zone between the main fault and a second mapped surface trace to the NE generates 〈span〉P〈/span〉- and 〈span〉S〈/span〉-types FZTW. Inversions of high-quality 〈span〉S〈/span〉-type FZTW indicate that the most likely parameters of the trapping structure are width of ∼70 m, 〈span〉S〈/span〉-wave velocity reduction of 60 per cent, 〈span〉Q〈/span〉 value of 60 and depth of ∼2 km. The local reversal of the shallow velocity contrast across the fault with respect to large-scale structure is consistent with preferred propagation of earthquake ruptures in the area to the NW.〈/span〉
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    Efficient anisotropic quasi-P wavefield extrapolation using an isotropic low-rank approximation (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉The computational cost of quasi-〈span〉P〈/span〉 wave extrapolation depends on the complexity of the medium, and specifically the anisotropy. Our effective-model method splits the anisotropic dispersion relation into an isotropic background and a correction factor to handle this dependency. The correction term depends on the slope (measured using the gradient) of current wavefields and the anisotropy. As a result, the computational cost is independent of the nature of anisotropy, which makes the extrapolation efficient. A dynamic implementation of this approach decomposes the original pseudo-differential operator into a Laplacian, handled using the low-rank approximation of the spectral operator, plus an angular dependent correction factor applied in the space domain to correct for anisotropy. We analyse the role played by the correction factor and propose a new spherical decomposition of the dispersion relation. The proposed method provides accurate wavefields in phase and more balanced amplitudes than a previous spherical decomposition. Also, it is free of 〈span〉SV〈/span〉-wave artefacts. Applications to a simple homogeneous transverse isotropic medium with a vertical symmetry axis (VTI) and a modified Hess VTI model demonstrate the effectiveness of the approach. The Reverse Time Migration applied to a modified BP VTI model reveals that the anisotropic migration using the proposed modelling engine performs better than an isotropic migration.〈/span〉
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    Tectonic predictions with mantle convection models (2017)
    Oxford University Press
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    Publication Date: 2017
    Description: 〈span〉〈div〉Summary〈/div〉Over the past 15 yr, numerical models of convection in Earth’s mantle have made a leap forward: they can now produce self-consistent plate-like behaviour at the surface together with deep mantle circulation. These digital tools provide a new window into the intimate connections between plate tectonics and mantle dynamics, and can therefore be used for tectonic predictions, in principle. This contribution explores this assumption. First, initial conditions at 30, 20, 10 and 0 Ma are generated by driving a convective flow with imposed plate velocities at the surface. We then compute instantaneous mantle flows in response to the guessed temperature fields without imposing any boundary conditions. Plate boundaries self-consistently emerge at correct locations with respect to reconstructions, except for small plates close to subduction zones. As already observed for other types of instantaneous flow calculations, the structure of the top boundary layer and upper-mantle slab is the dominant character that leads to accurate predictions of surface velocities. Perturbations of the rheological parameters have little impact on the resulting surface velocities. We then compute fully dynamic model evolution from 30 and 10 to 0 Ma, without imposing plate boundaries or plate velocities. Contrary to instantaneous calculations, errors in kinematic predictions are substantial, although the plate layout and kinematics in several areas remain consistent with the expectations for the Earth. For these calculations, varying the rheological parameters makes a difference for plate boundary evolution. Also, identified errors in initial conditions contribute to first-order kinematic errors. This experiment shows that the tectonic predictions of dynamic models over 10 My are highly sensitive to uncertainties of rheological parameters and initial temperature field in comparison to instantaneous flow calculations. Indeed, the initial conditions and the rheological parameters can be good enough for an accurate prediction of instantaneous flow, but not for a prediction after 10 My of evolution. Therefore, inverse methods (sequential or data assimilation methods) using short-term fully dynamic evolution that predict surface kinematics are promising tools for a better understanding of the state of the Earth’s mantle.〈/span〉
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    22Ne and 23Na ejecta from intermediate-mass stars: the impact of the new LUNA rate for 22Ne(p, {gamma})23Na (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We investigate the impact of the new LUNA rate for the nuclear reaction 22 Ne( p , ) 23 Na on the chemical ejecta of intermediate-mass stars, with particular focus on the thermally pulsing asymptotic giant branch (TP-AGB) stars that experience hot-bottom burning. To this aim, we use the PARSEC and COLIBRI codes to compute the complete evolution, from the pre-main sequence up to the termination of the TP-AGB phase, of a set of stellar models with initial masses in the range 3.0–6.0 M and metallicities Z i = 0.0005, 0.006 and 0.014. We find that the new LUNA measures have much reduced the nuclear uncertainties of the 22 Ne and 23 Na AGB ejecta that drop from factors of ~=10 to only a factor of few for the lowest metallicity models. Relying on the most recent estimations for the destruction rate of 23 Na, the uncertainties that still affect the 22 Ne and 23 Na AGB ejecta are mainly dominated by the evolutionary aspects (efficiency of mass-loss, third dredge-up, convection). Finally, we discuss how the LUNA results impact on the hypothesis that invokes massive AGB stars as the main agents of the observed O–Na anticorrelation in Galactic globular clusters. We derive quantitative indications on the efficiencies of key physical processes (mass-loss, third dredge-up, sodium destruction) in order to simultaneously reproduce both the Na-rich, O-poor extreme of the anticorrelation and the observational constraints on the CNO abundance. Results for the corresponding chemical ejecta are made publicly available.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Relation between spectral changes and the presence of the lower kHz QPO in the neutron star low-mass X-ray binary 4U 1636-53 (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We fitted the 3–180 keV spectrum of all the observations of the neutron star low-mass X-ray binary 4U 1636–53 taken with the Rossi X-ray Timing Explorer using a model that includes a thermal Comptonization component. We found that in the low hard state the power-law index of this component, , gradually increases as the source moves in the colour–colour diagram. When the source undergoes a transition from the hard to the soft state drops abruptly; once the source is in the soft state increases again and then decreases gradually as the source spectrum softens further. The changes in , together with changes of the electron temperature, reflect changes of the optical depth in the corona. The lower kilohertz quasi-periodic oscillation (kHz QPO) in this source appears only in observations during the transition from the hard to the soft state, when the optical depth of the corona is high and changes depends strongly upon the position of the source in the colour–colour diagram. Our results are consistent with a scenario in which the lower kHz QPO reflects a global mode in the system that results from the resonance between the disc and/or the neutron star surface, and the Comptonizing corona.
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    Do stellar winds prevent the formation of supermassive stars by accretion? (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: Supermassive stars (SMSs; ~10 5 M ) formed from metal-free gas in the early Universe attract attention as progenitors of supermassive black holes observed at high redshifts. To form SMSs by accretion, central protostars must accrete at as high rates as ~0.1–1 M yr –1 . Such protostars have very extended structures with bloated envelopes, like supergiant stars, and are called supergiant protostars (SGPSs). Under the assumption of hydrostatic equilibrium, SGPSs have density-inverted layers, where the luminosity becomes locally super-Eddington, near the surface. If the envelope matter is allowed to flow out, however, a stellar wind could be launched and hinder the accretion growth of SGPSs before reaching the supermassive regime. We examine whether radiation-driven winds are launched from SGPSs by constructing steady and spherically symmetric wind solutions. We find that the wind velocity does not reach the escape velocity in any case considered. This is because once the temperature falls below ~10 4 K, the opacity plummet drastically owing to the recombination of hydrogen and the acceleration ceases suddenly. This indicates that, in realistic non-steady cases, even if outflows are launched from the surface of SGPSs, they would fall back again. Such a ‘wind’ does not result in net mass-loss and does not prevent the growth of SGPSs. In conclusion, SGPSs will grow to SMSs and eventually collapse to massive black holes of ~10 5 M , as long as the rapid accretion is maintained.
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    On the complexity and the information content of cosmic structures (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.
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    Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa) (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp . japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard ( Gallotia galloti ) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from 〉20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti . However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.
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    Comparative Genome Analysis of the Daptomycin-Resistant Streptococcus anginosus Strain J4206 Associated with Breakthrough Bacteremia (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Streptococcus anginosus is a member of the normal oral flora that can become a pathogen causing pyogenic infections in humans. The genome of daptomycin-resistant strain J4206, originally isolated from a patient suffering from breakthrough bacteremia and septic shock at the University of Texas Health Science Center at San Antonio, was determined. The circular genome is 2,001,352 bp long with a GC content of 38.62% and contains multiple mobile genetic elements, including the phage-like chromosomal island SanCI that mediates a mutator phenotype, transposons, and integrative conjugative elements. Daptomycin resistance involves multiple alterations in the cell membrane and cell wall, and unique features were identified in J4206 that may contribute to resistance. A cluster of capsular polysaccharide (CPS) genes for choline metabolism and transport are present that may help neutralize cell surface charges, destabilizing daptomycin binding. Further, unique J4206 genes encoding sortases and LPXTG-target proteins that are involved in cell wall modification were present. The J4206 genome is phylogenetically closely related to the recently reported vancomycin-resistant SA1 strain; however, these genomes differ with SNPs in cardiolipin synthetase, histidine kinase yycG , teichoic acid modification genes, and other genes involved in cell surface modification. Transmission electron microscopy showed that the cell walls of both strains J4206 and SA1 were significantly thicker and more electron dense than daptomycin- and vancomycin-sensitive strain J4211. This comparative genomic study has identified unique genes as well as allelic variants in the J4206 genome that are involved in cell surface modification and thus might contribute to the acquisition of daptomycin resistance.
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    The Evolution of Haploid Chromosome Numbers in the Sunflower Family (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events; however, it did not find evidence for a paleopolyploidization at the base of this family, which has previously been hypothesized on the basis of sequence data from a limited number of species. The obtained results and potential causes of these discrepancies are discussed.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Least-squares reverse time migration in elastic media (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Elastic reverse time migration (RTM) can yield accurate subsurface information (e.g. PP and PS reflectivity) by imaging the multicomponent seismic data. However, the existing RTM methods are still insufficient to provide satisfactory results because of the finite recording aperture, limited bandwidth and imperfect illumination. Besides, the P - and S -wave separation and the polarity reversal correction are indispensable in conventional elastic RTM. Here, we propose an iterative elastic least-squares RTM (LSRTM) method, in which the imaging accuracy is improved gradually with iteration. We first use the Born approximation to formulate the elastic de-migration operator, and employ the Lagrange multiplier method to derive the adjoint equations and gradients with respect to reflectivity. Then, an efficient inversion workflow (only four forward computations needed in each iteration) is introduced to update the reflectivity. Synthetic and field data examples reveal that the proposed LSRTM method can obtain higher-quality images than the conventional elastic RTM. We also analyse the influence of model parametrizations and misfit functions in elastic LSRTM. We observe that Lamé parameters, velocity and impedance parametrizations have similar and plausible migration results when the structures of different models are correlated. For an uncorrelated subsurface model, velocity and impedance parametrizations produce fewer artefacts caused by parameter crosstalk than the Lamé coefficient parametrization. Correlation- and convolution-type misfit functions are effective when amplitude errors are involved and the source wavelet is unknown, respectively. Finally, we discuss the dependence of elastic LSRTM on migration velocities and its antinoise ability. Imaging results determine that the new elastic LSRTM method performs well as long as the low-frequency components of migration velocities are correct. The quality of images of elastic LSRTM degrades with increasing noise.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Ribosomal RNAs (rRNAs) account for 〉60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Sensitivity of 2-D complex resistivity measurements to subsurface anisotropy (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: In general, the complex electrical resistivity in the subsurface is anisotropic. Despite this, algorithms for the tomographic inversion of complex resistivity data commonly assume isotropy, mainly due to the lack of anisotropic modelling and inversion schemes, potentially leading to artefacts in the inversion results in the presence of anisotropy. The development of an effective anisotropic complex resistivity inversion algorithm which utilizes the gradient information of some cost function benefits from understanding the characteristics of the problem's sensitivities, that is, the partial derivative of the impedance forward response with respect to the complex conductivities in the different spatial directions, as well as with respect to the different ratios of complex conductivities, that is, the different anisotropy ratios. We here derive expressions for these sensitivities and, based on a 2.5-D finite-element modelling algorithm, we compute and discuss sensitivity distributions as well as measurement response curves of typical surface and cross-borehole measurement configurations for 2-D subsurface anisotropic complex resistivity distributions. Depending on the electrode layout and measurement configuration, the sensitivity with respect to the conductivity in a particular direction shows a unique pattern, while for other directions sensitivity patterns are qualitatively similar. These sensitivity characteristics translate into important equivalences between impedance responses of local anisotropic and isotropic anomalies, for both magnitude and phase. Accordingly, with collinear surface arrays only the complex conductivity in the direction of the electrode layout can be unambiguously resolved, and with cross-borehole arrays only the conductivity in the vertical direction, provided an in-hole current injection is used. Nevertheless, anisotropy ratios involving these resolvable conductivity components are likewise detectable. The distinct shape of the measurement response curves, reflecting the distinct spatial patterns of the corresponding sensitivity distributions, suggest that optimized measurement configurations can be inferred for specific exploration questions involving electrical anisotropy and given electrode layouts. The gained insight into the characteristics of the sensitivity distributions of complex resistivity measurements in case of subsurface anisotropy should guide the implementation of effective anisotropic complex resistivity inversion schemes and lead to a routine use of such schemes in any resistivity and induced polarization surveys whenever subsurface electrical anisotropy could be encountered.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Two-phase Lattice Boltzmann modelling of streaming potentials: influence of the air-water interface on the electrokinetic coupling (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: The streaming potential phenomenon is an electrokinetic effect that occurs in porous media. It is characterized by an electrokinetic (EK) coefficient. The aim of this paper is to simulate the EK coefficient in unsaturated conditions using the Lattice Boltzmann method in a 2-D capillary channel. The multiphase flow is simulated with the model of Shan & Chen. The Poisson–Boltzmann equation is solved by implementing the model of Chai & Shi. The streaming potential response shows a non-monotonous behaviour due to the combination of the increase of charge density and decrease of flow velocity with decreasing water saturation. Using a potential of –20 mV at the air–water interface, an enhancement of a factor 5–30 of the EK coefficient, compared to the saturated state, can be observed due to the positive charge excess at this interface which is magnified by the fluid velocity away from the rock surface. This enhancement is correlated to the fractioning of the bubbles, and to the dynamic state of these bubbles, moving or entrapped in the crevices of the channel.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    The role of disc self-gravity in circumbinary planet systems - I. Disc structure and evolution (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We present the results of two-dimensional hydrodynamic simulations of self-gravitating circumbinary discs around binaries whose parameters match those of the circumbinary planet-hosting systems Kepler-16, Kepler-34 and Kepler-35. Previous work has shown that non-self-gravitating discs in these systems form an eccentric precessing inner cavity due to tidal truncation by the binary, and planets which form at large radii migrate until stalling at this cavity. Whilst this scenario appears to provide a natural explanation for the observed orbital locations of the circumbinary planets, previous simulations have failed to match the observed planet orbital parameters. The aim of this work is to examine the role of self-gravity in modifying circumbinary disc structure as a function of disc mass, prior to considering the evolution of embedded circumbinary planets. In agreement with previous work, we find that for disc masses between one and five times the minimum mass solar nebula (MMSN), disc self-gravity affects modest changes in the structure and evolution of circumbinary discs. Increasing the disc mass to 10 or 20 MMSN leads to two dramatic changes in disc structure. First, the scale of the inner cavity shrinks substantially, bringing its outer edge closer to the binary. Secondly, in addition to the eccentric inner cavity, additional precessing eccentric ring-like features develop in the outer regions of the discs. If planet formation starts early in the disc lifetime, these changes will have a significant impact on the formation and evolution of planets and precursor material.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Radio and infrared study of the star-forming region IRAS 20286+4105 (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: In this paper, we present a multiwavelength investigation of the star-forming complex IRAS 20286+4105, located in the Cygnus X region. Near-infrared K -band data are used to revisit the cluster/stellar group identified in previous studies. Radio continuum observations at 610 and 1280 MHz show the presence of a H ii region possibly powered by a star of spectral type B0–B0.5. The cometary morphology of the ionized region is explained by invoking the bow-shock model, where the likely association with a nearby supernova remnant is also explored. A compact radio knot with a non-thermal spectral index is detected towards the centre of the cloud. Mid-infrared data from the Spitzer Legacy Survey of the Cygnus X region show the presence of six Class I young stellar objects inside the cloud. Thermal dust emission in this complex is modelled using Herschel far-infrared data to generate dust temperature and column density maps. Herschel images also show the presence of two clumps in this region, the masses of which are estimated to be ~175 and 30 M . The mass–radius relation and the surface density of the clumps mean that they do not qualify as massive star-forming sites. An overall picture of a runaway star ionizing the cloud and a triggered population of intermediate-mass, Class I sources located towards the cloud centre emerges from this multiwavelength study. Variation in the dust emissivity spectral index is shown to exist in this region and is seen to have an inverse relation with the dust temperature.
    Print ISSN: 0035-8711
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    Reconstructing the velocity dispersion profiles from the line-of-sight kinematic data in disc galaxies (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We present a modification of the method for reconstructing the stellar velocity ellipsoid (SVE) in disc galaxies. Our version does not need any parametrization of the velocity dispersion profiles and uses only one assumption that the ratio z / R remains constant along the profile or along several pieces of the profile. The method was tested on two galaxies from the sample of other authors and for the first time applied to three lenticular galaxies NGC 1167, NGC 3245 and NGC 4150, as well as to one Sab galaxy NGC 338. We found that for galaxies with a high inclination ( $i 〉 55^\circ \text{--}60^\circ$ ) it is difficult or rather impossible to extract the information about SVE, while for galaxies at an intermediate inclination the procedure of extracting is successful. For NGC 1167 we managed to reconstruct SVE, provided that the value of z / R is piecewise constant. We found z / R = 0.7 for the inner parts of the disc and z / R = 0.3 for the outskirts. We also obtained a rigid constraint on the value of the radial velocity dispersion R for highly inclined galaxies, and tested the result using the asymmetric-drift equation, provided that the gas rotation curve is available.
    Print ISSN: 0035-8711
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    The extremely metal-poor galaxy DDO 68: the luminous blue variable, H{alpha} shells and the most luminous stars (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: This paper presents new results from the ongoing study of the unusual Lynx–Cancer void galaxy DDO 68, which has star-forming regions of record low metallicity [12+log (O/H) ~7.14]. The results include the following. (i) A new spectrum and photometry have been obtained with the 6-m SAO RAS telescope (BTA) for the luminous blue variable (LBV = DDO68-V1). Photometric data sets were complemented with others based on the Sloan Digital Sky Survey (SDSS) and the Hubble Space Telescope ( HST ) archive images. (ii) We performed an analysis of the DDO 68 supergiant shell (SGS) and the prominent smaller Hα arcs/shells visible in the HST image coupled with kinematic maps in Hα obtained with the Fabry–Perot interferometer (FPI) at the BTA. (iii) We compiled a list of about 50 of the most luminous stars (–9.1 mag 〈 M V 〈 –6.0 mag) identified from the HST images associated with the star-forming regions with known extremely low O/H. This is intended to pave the path for the current science to be investigated with the next generation of giant telescopes. We have confirmed earlier hints of significant variation of the LBV optical light, deriving its amplitude as V 3.7 mag for the first time. New data suggest that in 2008–2010 the LBV reached M V = –10.5 mag and probably underwent a giant eruption. We argue that the structure of star-forming complexes along the SGS (‘Northern Ring’) perimeter provides evidence for sequential induced star-formation episodes caused by the shell gas instabilities and gravitational collapse. The variability of some luminous extremely metal-poor stars in DDO 68 can currently be monitored with medium-size telescopes at sites with superb seeing.
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    Characterizing dw1335-29, a recently discovered dwarf satellite of M83 (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: The number, distribution and properties of dwarf satellites are crucial probes of the physics of galaxy formation at low masses and the response of satellite galaxies to the tidal and gas dynamical effects of their more massive parent. To make progress, it is necessary to augment and solidify the census of dwarf satellites of galaxies outside the Local Group. Müller et al. presented 16 dwarf galaxy candidates near M83, but lacking reliable distances, it is unclear which candidates are M83 satellites. Using red-giant-branch stars from the HST /GHOSTS survey in conjunction with ground-based images from VLT/VIMOS, we confirm that one of the candidates, dw1335-29 – with a projected distance of 26 kpc from M83 and a distance modulus of $(m-M)_0 = 28.5^{+0.3}_{-0.1}$ – is a satellite of M83. We estimate an absolute magnitude M V  = –10.1 ± 0.4, an ellipticity of $0.40^{+0.14}_{-0.22}$ , a half-light radius of $656^{+121}_{-170}$  pc and [Fe/H] = $-1.3^{+0.3}_{-0.4}$ . Owing to dw1335-29's somewhat irregular shape and possible young stars, we classify this galaxy as a dwarf irregular or transition dwarf. This is curious, as with a projected distance of 26 kpc from M83, dw1335-29 is expected to lack recent star formation. Further study of M83's dwarf population will reveal if star formation in its satellites is commonplace (suggesting a lack of a hot gas envelope for M83 that would quench star formation) or rare (suggesting that dw1335-29 has a larger M83-centric distance, and is fortuitously projected to small radii).
    Print ISSN: 0035-8711
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    GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias.
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    Successive Losses of Central Immune Genes Characterize the Gadiformes Alternate Immunity (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene ( Mx ) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus , thus predating the loss of Major Histocompatibility Complex class II ( MHCII ) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time.
    Electronic ISSN: 1759-6653
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    Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
    Electronic ISSN: 1759-6653
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    Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus . Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
    Electronic ISSN: 1759-6653
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    Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India.
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    Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the 〉10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.
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    Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae , the cause of mango malformation, and two isolates of F. proliferatum , one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression ( in vitro and in planta ) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum , the pathogenic versus endophytic life style.
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    The dynamic response of prone-to-fall columns to ambient vibrations: comparison between measurements and numerical modelling (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Seismic noise measurements (ambient vibrations) have been increasingly used in rock slope stability assessment for both investigation and monitoring purposes. Recent studies made on gravitational hazard revealed significant spectral amplification at given frequencies and polarization of the wave-field in the direction of maximum rock slope displacement. Different properties (resonance frequencies, polarization and spectral ratio amplitudes) can be derived from the spectral analysis of the seismic noise to characterize unstable rock masses. The objective here is to identify the dynamic parameters that could be used to gain information on prone-to-fall rock columns’ geometry. To do so, the dynamic response of prone-to-fall columns to seismic noise has been studied on two different sites exhibiting cliff-like geometry. Dynamic parameters (main resonance frequency and spectral ratio amplitudes) that could characterize the column decoupling were extracted from seismic noise and their variations were studied taking into account the external environmental parameter fluctuations. Based on this analysis, a two-dimensional numerical model has been set up to assess the influence of the rear vertical fractures identified on both sites on the rock column motion response. Although a simple relation was found between spectral ratio amplitudes and the rock column slenderness, it turned out that the resonance frequency is more stable than the spectral ratio amplitudes to characterize this column decoupling, provided that the elastic properties of the column can be estimated. The study also revealed the effect of additional remote fractures on the dynamic parameters, which in turn could be used for detecting the presence of such discontinuities.
    Keywords: Seismology
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    Present-day velocity field and block kinematics of Tibetan Plateau from GPS measurements (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: In this study, we present a new synthesis of GPS velocities for tectonic deformation within the Tibetan Plateau and its surrounding areas, a combined data set of ~1854 GPS-derived horizontal velocity vectors. Assuming that crustal deformation is localized along major faults, a block modelling approach is employed to interpret the GPS velocity field. We construct a 30-element block model to describe present-day deformation in western China, with half of them located within the Tibetan Plateau, and the remainder located in its surrounding areas. We model the GPS velocities simultaneously for the effects of block rotations and elastic strain induced by the bounding faults. Our model yields a good fit to the GPS data with a mean residual of 1.08 mm a –1 compared to the mean uncertainty of 1.36 mm a –1 for each velocity component, indicating a good agreement between the predicted and observed velocities. The major strike-slip faults such as the Altyn Tagh, Xianshuihe, Kunlun and Haiyuan faults have relatively uniform slip rates in a range of 5–12 mm a –1 along most of their segments, and the estimated fault slip rates agree well with previous geologic and geodetic results. Blocks having significant residuals are located at the southern and southeastern Tibetan Plateau, suggesting complex tectonic settings and further refinement of accurate definition of block geometry in these regions.
    Keywords: Geodynamics and Tectonics
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    Imaging of first-order surface-related multiples by reverse-time migration (2017)
    Oxford University Press
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    Publication Date: 2017-01-01
    Description: Surface-related multiples have been utilized in the reverse-time migration (RTM) procedures, and additional illumination for subsurface can be provided. Meanwhile, many cross-talks are generated from undesired interactions between forward- and backward-propagated seismic waves. In this paper, subsequent to analysing and categorizing these cross-talks, we propose RTM of first-order multiples to avoid most undesired interactions in RTM of all-order multiples, where only primaries are forward-propagated and crosscorrelated with the backward-propagated first-order multiples. With primaries and multiples separated during regular seismic data processing as the input data, first-order multiples can be obtained by a two-step scheme: (1) the dual-prediction of higher-order multiples; and (2) the adaptive subtraction of predicted higher-order multiples from all-order multiples within local offset-time windows. In numerical experiments, two synthetic and a marine field data sets are used, where different cross-talks generated by RTM of all-order multiples can be identified and the proposed RTM of first-order multiples can provide a very interpretable image with a few cross-talks.
    Keywords: Seismology
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    A candidate dual AGN in a double-peaked emission-line galaxy with precessing radio jets (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We present high-resolution radio continuum observations with the Karl G. Jansky very large array at 6, 8.5, 11.5 and 15 GHz of the double-peaked emission-line galaxy 2MASXJ12032061+1319316. The radio emission has a prominent S-shaped morphology with highly symmetric radio jets that extend over a distance of ~1.5 arcsec (1.74 kpc) on either side of the core of size ~0.1 arcsec (116 pc). The radio jets have a helical structure resembling the precessing jets in the galaxy NGC 326 which has confirmed dual active galactic nuclei (AGN). The nuclear bulge velocity dispersion gives an upper limit of (1.56 ± 0.26) x 10 8 M for the total mass of nuclear black hole(s). We present a simple model of precessing jets in 2MASXJ1203 and find that the precession time-scale is around 10 5 yr: this matches the source lifetime estimate via spectral ageing. We find that the expected supermassive black hole (SMBH) separation corresponding to this time-scale is 0.02 pc. We used the double-peaked emission lines in 2MASXJ1203 to determine an orbital speed for a dual AGN system and the associated jet precession time-scale, which turns out to be more than the Hubble time, making it unfeasible. We conclude that the S-shaped radio jets are due to jet precession caused either by a binary/dual SMBH system, a single SMBH with a tilted accretion disc or a dual AGN system where a close pass of the secondary SMBH in the past has given rise to jet precession.
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    Estimating the distribution of rest-frame time-scales for blazar jets: a statistical approach (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: In any flux-density limited sample of blazars, the distribution of the time-scale modulation factor t '/ t , which quantifies the change in observed time-scales compared to the rest-frame ones due to redshift and relativistic compression follows an exponential distribution with a mean depending on the flux limit of the sample. In this work, we produce the mathematical formalism that allows us to use this information in order to uncover the underlining rest-frame probability density function of measurable time-scales of blazar jets. We extensively test our proposed methodology using a simulated Flat Spectrum Radio Quasar population with a 1.5 Jy flux-density limit in the simple case (where all blazars share the same intrinsic time-scale), in order to identify limits of applicability and potential biases due to observational systematics and sample selection. We find that for monitoring with time intervals between observations longer than ~30 per cent of the intrinsic time-scale under investigation the method loses its ability to produce robust results. For time intervals of ~3 per cent of the intrinsic time-scale, the error of the method is as low as 1 per cent in recovering the intrinsic rest-frame time-scale. We applied our method to rotations of the optical polarization angle of blazars observed by RoboPol. We found that the intrinsic time-scales of the longest duration rotation event in each blazar follows a narrow distribution, well described by a normal distribution with mean 87 d and standard deviation 5 d. We discuss possible interpretations of this result.
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    Turbulence and particle acceleration in giant radio haloes: the origin of seed electrons (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: About one-third of X-ray-luminous clusters show smooth, Mpc-scale radio emission, known as giant radio haloes. One promising model for radio haloes is Fermi-II acceleration of seed relativistic electrons by compressible turbulence. The origin of these seed electrons has never been fully explored. Here, we integrate the Fokker–Planck equation of the cosmic ray (CR) electron and proton distributions when post-processing cosmological simulations of cluster formation and confront them with radio surface brightness and spectral data of Coma. For standard assumptions, structure formation shocks lead to a seed electron population that produces too centrally concentrated radio emission. Matching observations requires modifying properties of the CR population (rapid streaming; enhanced CR electron acceleration at shocks) or turbulence (increasing turbulent-to-thermal energy density with radius), but at the expense of fine-tuning. In a parameter study, we find that radio properties are exponentially sensitive to the amplitude of turbulence, which is inconsistent with small scatter in scaling relations. This sensitivity is removed if we relate the acceleration time to the turbulent dissipation time. In this case, turbulence above a threshold value provides a fixed amount of amplification; observations could thus potentially constrain the unknown CR seed population. To obtain sufficient acceleration, the turbulent magneto-hydrodynamics cascade has to terminate by transit time damping on CRs, i.e. thermal particles must be scattered by plasma instabilities. Understanding the small scatter in radio halo scaling relations may provide a rich source of insight on plasma processes in clusters.
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    Testing gravity on large scales by combining weak lensing with galaxy clustering using CFHTLenS and BOSS CMASS (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We measure a combination of gravitational lensing, galaxy clustering and redshift-space distortions (RSDs) called E G . The quantity E G probes both parts of metric potential and is insensitive to galaxy bias and 8 . These properties make it an attractive statistic to test lambda cold dark matter, general relativity and its alternate theories. We have combined CMASS Data Release 11 with CFHTLenS and recent measurements of β from RSD analysis, and find E G ( z  = 0.57) = 0.42 ± 0.056, a 13 per cent measurement in agreement with the prediction of general relativity E G ( z  = 0.57) = 0.396 ± 0.011 using the Planck 2015 cosmological parameters. We have corrected our measurement for various observational and theoretical systematics. Our measurement is consistent with the first measurement of E G using cosmic microwave background lensing in place of galaxy lensing at small scales, but shows 2.8 tension when compared with their final results including large scales. This analysis with future surveys will provide improved statistical error and better control over systematics to test general relativity and its alternate theories.
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    The global history of reionization (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: Using a Bayesian framework, we quantify what current observations imply about the history of the epoch of reionization (EoR). We use a popular, three-parameter EoR model, flexible enough to accommodate a wide range of physically plausible reionization histories. We study the impact of various EoR observations: (i) the optical depth to the CMB measured by Planck 2016; (ii) the dark fraction in the Lyman α and β forests; (iii) the redshift evolution of galactic Lyα emission (so-called ‘Lyα fraction’); (iv) the clustering of Lyα emitters; (v) the IGM damping wing imprint in the spectrum of QSO ULASJ1120+0641; (vi) and the patchy kinetic Sunyaev–Zel'dovich signal. Combined, (i) and (ii) already place interesting constraints on the reionization history, with the epochs corresponding to an average neutral fraction of (75, 50, 25) per cent, constrained at 1 to $z= (9.21^{+1.22 }_{ -1.15}, 8.14^{+1.08 }_{ -1.00}, 7.26^{+1.13 }_{ -0.96})$ . Folding-in more model-dependent EoR observations [(iii)–(vi)], strengthens these constraints by tens of per cent, at the cost of a decrease in the likelihood of the best-fitting model, driven mostly by (iii). The tightest constraints come from (v). Unfortunately, no current observational set is sufficient to break degeneracies and constrain the astrophysical EoR parameters. However, model-dependent priors on the EoR parameters themselves can be used to set tight limits by excluding regions of parameter space with strong degeneracies. Motivated by recent observations of z ~ 7 faint, lensed galaxies, we show how a conservative upper limit on the virial temperature of haloes which host reionizing galaxies can constrain the escape fraction of ionizing photons to $f_{\rm esc} = 0.14^{+0.26 }_{ -0.09}$ .
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    Hunting for eclipses: high-speed observations of cataclysmic variables (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We present new time-resolved photometry of 74 cataclysmic variables (CVs), 47 of which are eclipsing. Thirteen of these eclipsing systems are newly discovered. For all 47 eclipsing systems, we show high cadence (1–20 s) light curves obtained with the high-speed cameras ULTRACAM and ULTRASPEC. We provide new or refined ephemerides, and supply mid-eclipse times for all observed eclipses. We assess the potential for light-curve modelling of all 47 eclipsing systems to determine their system parameters, finding 20 systems that appear to be suitable for future study. Systems of particular interest include V713 Cep, in which we observed a temporary switching-off of accretion; and ASASSN-14mv and CSS111019:233313–155744, which both have orbital periods well below the CV period minimum. The short orbital periods and light-curve shapes suggest that they may be double degenerate (AM CVn) systems or CVs with evolved donor stars.
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    Giant Metrewave Radio Telescope detection of associated H I 21-cm absorption at z = 1.2230 towards TXS 1954+513 (2017)
    Oxford University Press
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    Publication Date: 2017-01-02
    Description: We have used the 610-MHz receivers of the Giant Metrewave Radio Telescope (GMRT) to detect associated H i 21-cm absorption from the z  = 1.2230 blazar TXS 1954+513. The GMRT H i 21-cm absorption is likely to arise against either the milliarcsecond-scale core or the one-sided milliarcsecond-scale radio jet, and is blueshifted by 328 km s –1 from the blazar redshift. This is consistent with a scenario in which the H i cloud giving rise to the absorption is being driven outwards by the radio jet. The integrated H i 21-cm optical depth is (0.716 ± 0.037) km s –1 , implying a high H i column density, $N_{\rm H\small {I}} = (1.305 \pm 0.067) \times ({ T_{\rm s}/100\,{\rm K}}) \times 10^{20}$  cm –2 , for an assumed H i spin temperature of 100 K. We use Nickel Telescope photometry of TXS 1954+513 to infer a high rest-frame 1216 Å luminosity of (4.1 ± 1.2)  x  10 23 W Hz –1 . The z  = 1.2230 absorber towards TXS 1954+513 is only the fifth case of a detection of associated H i 21-cm absorption at z  〉 1, and is also the first case of such a detection towards an active galactic nucleus (AGN) with a rest-frame ultraviolet (UV) luminosity 〉〉10 23 W Hz –1 , demonstrating that neutral hydrogen can survive in AGN environments in the presence of high UV luminosities.
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    Parsimonious refraction interferometry and tomography (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉We present the theory of parsimonious refraction interferometry and tomography where a densely populated refraction data set can be obtained from two reciprocal and several infill shot gathers. The assumptions are that the refraction arrivals are head waves, and a pair of reciprocal shot gathers and several infill shot gathers are recorded over the line of interest. Refraction traveltimes from these shot gathers are picked and spawned into 〈span style="font-style:italic;"〉O〈/span〉(〈span style="font-style:italic;"〉N〈/span〉〈sup〉2〈/sup〉) virtual refraction traveltimes generated by 〈span style="font-style:italic;"〉N〈/span〉 virtual sources, where 〈span style="font-style:italic;"〉N〈/span〉 is the number of geophones in the 2-D survey. The virtual traveltimes can be inverted to give the velocity tomogram. This enormous increase in the number of traveltime picks and associated rays, compared to the many fewer traveltimes from the reciprocal and infill shot gathers, allows for increased model resolution and a better condition number with the system of normal equations. A significant benefit is that the parsimonious survey and the associated traveltime picking can be an order-of-magnitude less time consuming than that for a standard refraction survey with a dense distribution of sources.〈/span〉
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    A ground motion simulation coupled with an eikonal solver and its application with a decomposed isochrones formula (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉We describe three achievements for a ground motion simulation. First, we propose a kinematic modelling in which rupture delay time is governed by an eikonal equation on a Riemannian manifold and develop a coupling method between the ground motion simulation and the eikonal solver. In general the rupture velocity distribution is not spatially uniform and the rupture propagation depends on a fault shape. So we derive the eikonal equation by considering the Riemannian metric of the fault surface and give a detailed discretization of its difference scheme to deal with a curved surface fault. Next, in order to explain the effect of spatially discontinuous non-uniformity of rupture velocity, we introduce an isochrones jumping intensity and obtain a new decomposed isochrones formula in general settings. It is known that the representation theorem with the Green's function can be rewritten into an expression with a contour integral by the isochrones theory. The new formula says that the known isochrones formula for ground velocity can be decomposed into a trend component and a disturbance component. The disturbance component consists of the isochrones jumping intensity. Finally, by applying our ground motion simulation coupled with the eikonal solver and the decomposed isochrones formula, we investigate some relations between the non-uniformity of the rupture velocity and pulse-like disturbance of the ground motion velocity. Our simulations show that the disturbance of velocity waveform corresponds with that of rate of change of isochrones band area. It turns out that the pulse-like disturbance of velocity waveform occurs when isochrones move across the region where rupture velocity varies discontinuously. Thus we can explain that the pulse-like disturbance of the ground motion velocity occurs when the isochrones jumping intensity has nonzero value. Moreover, as another example of application of our simulation and formula, we show a distinctive dependence of peak ground velocity upon parameters such as the rupture velocity and the distance between a fault and an observer.〈/span〉
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    Steel-cased wells in 3-D controlled source EM modelling (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉Over the last decades, electromagnetic methods have become an accepted tool for a wide range of geophysical exploration purposes and nowadays even for monitoring. Application to hydrocarbon monitoring, for example for enhanced oil recovery, is hampered by steel-cased wells, which typically exist in large numbers in producing oil fields and which distort electromagnetic fields in the subsurface. Steel casings have complex geometries as they are very thin but vertically extended; moreover, the conductivity contrast of steel to natural materials is in the range of six orders of magnitude. It is therefore computationally prohibitively costly to include such structures directly into the modelling grid, even for finite element methods. To tackle the problem we developed a method to describe steel-cased wells as series of substitute dipole sources, which effectively interact with the primary field. The new approach cannot only handle a single steel-cased well, but also an arbitrary number, and their interaction with each other. We illustrate the metal casing effect with synthetic 3-D modelling of land-based controlled source electromagnetic data. Steel casings distort electromagnetic fields even for large borehole-transmitter distances above 2 km. The effect depends not only on the distance between casing and transmitter, but also on the orientation of the transmitter to the borehole. Finally, we demonstrate how the presence of steel-cased wells can be exploited to increase the sensitivity and enhance resolution in the target region. Our results show that it is at least advisable to consider the distribution of steel-cased wells already at the planning phase of a controlled source electromagnetic field campaign.〈/span〉
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    CO 2 -crystal wettability in potassic magmas: implications for eruptive dynamics in light of experimental evidence for heterogeneous nucleation (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉The volatile content in magmas is fundamental for the triggering and style of volcanic eruptions. Carbon dioxide, the second most abundant volatile component in magmas after H〈sub〉2〈/sub〉O, is the first to reach saturation upon ascent and depressurization. We investigate experimentally CO〈sub〉2〈/sub〉-bubble nucleation in trachybasalt and trachyte melts at high temperature and high pressure (〈span style="font-style:italic;"〉HT〈/span〉 and 〈span style="font-style:italic;"〉HP〈/span〉) through wetting-angle measurements on different (sialic, mafic or oxide) phenocryst phases. The presence of crystals lowers the supersaturation required for CO〈sub〉2〈/sub〉-bubble nucleation up to 37 per cent (heterogeneous nucleation, 〈span style="font-style:italic;"〉HeN〈/span〉), with a minor role of mineral chemistry. Different from H〈sub〉2〈/sub〉O-rich systems, feldspar crystals are effective in reducing required supersaturation for bubble nucleation. Our data suggest that leucite, the dominant 〈span style="font-style:italic;"〉liquidus〈/span〉 phase in ultrapotassic systems at shallow depth (i.e. 〈100 MPa), facilitates late-stage, extensive magma vesiculation through CO〈sub〉2〈/sub〉〈span style="font-style:italic;"〉HeN〈/span〉, which may explain the shifting of CO〈sub〉2〈/sub〉-rich eruptive systems towards an apparently anomalous explosive behaviour.〈/span〉
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    Contribution of the GOCE gradiometer components to regional gravity solutions (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉The contribution of the GOCE gravity gradients to regional gravity field solutions is investigated in this study. We employ radial basis functions to recover the gravity field on regional scales over Amazon and Himalayas as our test regions. In the first step, four individual solutions based on the more accurate gravity gradient components 〈span style="font-style:italic;"〉Txx〈/span〉, 〈span style="font-style:italic;"〉Tyy〈/span〉, 〈span style="font-style:italic;"〉Tzz〈/span〉 and 〈span style="font-style:italic;"〉Txz〈/span〉 are derived. The 〈span style="font-style:italic;"〉Tzz〈/span〉 component gives better solution than the other single-component solutions despite the less accuracy of 〈span style="font-style:italic;"〉Tzz〈/span〉 compared to 〈span style="font-style:italic;"〉Txx〈/span〉 and 〈span style="font-style:italic;"〉Tyy〈/span〉. Furthermore, we determine five more solutions based on several selected combinations of the gravity gradient components including a combined solution using the four gradient components. The 〈span style="font-style:italic;"〉Tzz〈/span〉 and 〈span style="font-style:italic;"〉Tyy〈/span〉 components are shown to be the main contributors in all combined solutions whereas the 〈span style="font-style:italic;"〉Txz〈/span〉 adds the least value to the regional gravity solutions. We also investigate the contribution of the regularization term. We show that the contribution of the regularization significantly decreases as more gravity gradients are included. For the solution using all gravity gradients, regularization term contributes to about 5 per cent of the total solution. Finally, we demonstrate that in our test areas, regional gravity modelling based on GOCE data provide more reliable gravity signal in medium wavelengths as compared to pre-GOCE global gravity field models such as the EGM2008.〈/span〉
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    Was the Devonian geomagnetic field dipolar or multipolar? Palaeointensity studies of Devonian igneous rocks from the Minusa Basin (Siberia) and the Kola Peninsula dykes, Russia (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Defining variations in the behaviour of the geomagnetic field through geological time is critical to understanding the dynamics of Earth's core and its response to mantle convection and planetary evolution. Furthermore, the question of whether the axial dipole dominance of the recent palaeomagnetic field persists through the whole of Earth's history is fundamental to determining the reliability of palaeogeographic reconstructions and the efficacy of the magnetosphere in shielding Earth from solar wind radiation. Previous palaeomagnetic directional studies have suggested that the palaeofield had a complex configuration in the Devonian period (419–359 Ma). Here we present new high-quality palaeointensity determinations from rocks aged between 408 and 375 Ma from the Minusa Basin (southern Siberia), and the Kola Peninsula that enable the first reliable investigation of the strength of the field during this enigmatic period. Palaeointensity experiments were performed using the thermal Thellier, microwave Thellier and Wilson methods on 165 specimens from 25 sites. Six out of eight successful sites from the Minusa Basin and all four successful sites from the Kola Peninsula produced extremely low palaeointensities (〈10 μT). These findings challenge the uniformitarian view of the palaeomagnetic field: field intensities of nearly an order of magnitude lower than Neogene values (except during relatively rare geomagnetic excursions and reversals) together with the widespread appearance of strange directions found in the Devonian suggest that the Earth's field during this time may have had a dominantly multipolar geometry. A persistent, low intensity multipolar magnetic field and associated diminished magnetosphere would increase the impact of solar particles on the Earth's magnetosphere, ionosphere and atmosphere with potential major implications for Earth's climate and biosphere.〈/span〉
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    Inverting Glacial Isostatic Adjustment signal using Bayesian framework and two linearly relaxing rheologies (2017)
    Oxford University Press
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    Publication Date: 2017-04-19
    Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Glacial Isostatic Adjustment (GIA) models commonly assume a mantle with a viscoelastic Maxwell rheology and a fixed ice history model. Here, we use a Bayesian Monte Carlo approach with a Markov chain formalism to invert the global GIA signal simultaneously for the mechanical properties of the mantle and the volumes of the ice sheets, using as starting ice models two previously published ice histories. Two stress relaxing rheologies are considered: Burgers and Maxwell linear viscoelasticities. A total of 5720 global palaeo sea level records are used, covering the last 35 kyr. Our goal is not only to seek the model best fitting this data set, but also to determine and display the range of possible solutions with their respective probability of explaining the data. In all cases, our 〈span style="font-style:italic;"〉a posteriori〈/span〉 probability maps exhibit the classic character of solutions for GIA-determined mantle viscosity with two distinct peaks. What is new in our treatment is the presence of the bi-viscous Burgers rheology and the fact that we invert rheology jointly with ice history, in combination with the greatly expanded palaeo sea level records. The solutions tend to be characterized by an upper-mantle viscosity of around 5 × 10〈sup〉20〈/sup〉 Pa s with one preferred lower-mantle viscosities at 3 × 10〈sup〉21〈/sup〉 Pa s and the other more than 2 × 10〈sup〉22〈/sup〉 Pa s, a rather classical pairing. Best-fitting models depend upon the starting ice history and the stress relaxing law. A first peak (P1) has the highest probability only in the case with a Maxwell rheology and ice history based on ICE-5G, while the second peak (P2) is favoured for ANU-based ice history or Burgers stress relaxation. The latter solution also may satisfy lower-mantle viscosity inferences from long-term geodynamics and gravity gradient anomalies over Laurentia. P2 is also consistent with large Laurentian and Fennoscandian ice-sheet volumes at the Last Glacial Maximum (LGM) and smaller LGM Antarctic ice volume than in either ICE-5G or ANU. Exploration of a bi-viscous linear relaxing rheology in GIA now seems logical due to a new set of requirements to satisfy observations of transient post-seismic flow seen so ubiquitously in space gravimetry and other global geodetic data.〈/span〉
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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