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  • Springer  (453,137)
  • Public Library of Science  (118,079)
  • American Institute of Physics (AIP)  (61,555)
  • 2010-2014  (632,771)
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  • 1
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    Marine viruses: the beneficial side of a threat (2014)
    Springer
    In:  EPIC3Applied Biochemistry and Biotechnology, Springer, ISSN: 0273-2289
    Details
    Publication Date: 2014-09-30
    Description: Marine viruses are ubiquitous, extremely diverse, and outnumber any form of life in the sea. Despite their ecological importance, viruses in marine environments have been largely ignored by the academic community, and only those that have caused substantial economic losses have received more attention. Fortunately, our current understanding on marine viruses has advanced considerably during the last decades. These advances have opened new and exciting research opportunities as several unique structural and genetic characteristics of marine viruses have shown to possess an immense potential for various biotechnological applications. Here, a condensed overview of the possibilities of using the enormous potential offered by marine viruses to develop innovative products in industries as pharmaceuticals, environmental remediation, cosmetics, material sciences, and several others, is presented. The importance of marine viruses to biotechnology should not be underestimated.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    Ocean Acidification and Oceanic Carbon Cycling (2014)
    Springer
    In:  EPIC3Global Environmental Change, (Handbook of Global Environmental Pollution ;1), Dordrecht ; London, Springer, 973 p., pp. 103-110, ISBN: 978-94-007-5783-7
    Details
    Publication Date: 2014-10-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 3
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    Monitoring glacier changes on the Antarctic Peninsula (2014)
    Springer
    In:  EPIC3Global Land Ice Measurements from Space, Berlin Heidelberg, Springer, pp. 717-741, ISBN: 978-3-540-79817-0
    Details
    Publication Date: 2016-11-15
    Description: The Antarctic Peninsula has exhibited some of the most spectacular changes observed in glacial systems in recent decades. The events include disintegration of ice shelves, acceleration and thinning of glaciers, variations in the limits between glacier facies, and retreat of glacier fronts. However, due to the lack of both consistent systematic observations of the glacial systems and information on their boundary conditions, it is difficult to accurately predict the contribution of Antarctic Peninsula glaciers to sea level rise and further responses of these ice masses to climatic and oceanographic changes. In this context, the activities of the GLIMS Regional Center for the Antarctic Peninsula and its network of international collaborators are based on the use of various types of Earth observation imagery, mainly optical and radar data. Although a complete glacier inventory is still lacking, we present the results of changes in glacier frontal positions and boundaries of glacier facies as well as links to dynamical adjustments for various locations in the Antarctic Peninsula’s ice masses. Evaluation of Advanced Spaceborne Thermal Emission and reflection Radiometer (ASTER) digital elevation models generated for the Antarctic Peninsula is also discussed.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Subfossil cladoceran from sediment in thermokarst lakes in northeastern Siberia, Russia and their relationship to limnological and climatic variables (2014)
    Springer
    In:  EPIC3Journal of Paleolimnology, Springer, 52(1), pp. 107-119
    Details
    Publication Date: 2016-10-22
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Escape performance of temperate king scallop, Pecten maximus under ocean warming and acidification (2014)
    Springer
    In:  EPIC3Marine Biology, Springer, 161(12), pp. 2819-2829, ISSN: 0025-3162
    Details
    Publication Date: 2015-01-16
    Description: Among bivalves, scallops are exceptional due to their capacity to escape from predators by swimming which is provided by rapid and strong claps that are produced by the phasic muscle interspersed with tonic muscle contractions. Based on the concept of oxygen and capacity-limited thermal tolerance, the following hypothesis was tested: ocean warming and acidification (OWA) would induce disturbances in aerobic metabolic scope and extracellular acid-case status and impair swimming performance in temperate scallops. Following longterm incubation under near-future OWA scenarios [20 vs. 10 °C (control) and 0.112 kPa CO2 (hypercapnia) vs. 0.040 kPa CO2 (normocapnic control)], the clapping performance and metabolic rates (MR) were measured in resting (RMR) and fatigued (maximum MR) king scallops, Pecten maximus, from Roscoff, France. Exposure to OA, either alone or combined with warming, left MR and swimming parameters such as the total number of claps and clapping forces virtually unchanged. Only the duration of the escape response was affected by OA which caused earlier exhaustion in hyper- than in normocapnic scallops at 10 °C. While maximum MR was unaffected, warm exposure increased RMR in both normocapnic and hypercapnic P. maximus resulting in similar Q10 values of ~2.2. The increased costs of maintenance and the observation of strongly reduced haemolymph PO2 levels indicate that at 20 °C scallops have reached the upper thermal pejus range with unbalanced capacities for aerobic energy metabolism. As a consequence, warming to 20 °C decreased mean phasic force during escape performance until fatigue. The observed prolonged recovery time in warm incubated scallops might be a consequence of elevated metabolic costs at reduced oxygen availability in the warmth.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Ocean-Bottom Seismometer (2014)
    Springer
    In:  EPIC3Encyclopedia of Earthquake Engineering, Encyclopedia of Earthquake Engineering, Berlin, Heidelberg, Springer, pp. 1-16, ISBN: 978-3-642-36197-5
    Details
    Publication Date: 2014-12-16
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    Analysis of Lava Flow Effusion Rate Using High Spatial Resolution Infrared Data (2014)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Remote sensing thermal data of active lava flows allow for the evaluation of instantaneous effusion rates. This is made possible by simple formulae relating the lava effusion rate to the power energy radiated per unit time from the surface to the flow. Such formulae are based on a specific flow model and, consequently, their validity is subject to the model assumptions. The most questionable assumption is probably the constancy of the surface temperature. Herein, we use high spatial resolution infrared data to demonstrate the existence of an underlying relationship between the surface temperature and the lava flow thickness, using the 2001 Mt. Etna flow as a case study. According to this relationship, observed changes in surface temperature does not represent a weakness of the model but is the expected consequence of actual variations in the topographic down flow profile.
    Description: Published
    Description: 391-408
    Description: 3V. Dinamiche e scenari eruttivi
    Description: restricted
    Keywords: Remote sensing, effusion rate, heat flux, Etna, MIVIS ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 8
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    Long-time variation of soil CO2 fluxes at the summit crater of Vulcano (Italy) (2014)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Here, we report the first continuous data of geochemical parameters acquired directly from the active summit crater of Vulcano. This approach provides a means to better investigate deep geochemical processes associated with the degassing system of Vulcano Island. In particular, we report on soil CO2 fluxes from the upper part of Vulcano, a closed-conduit volcano, from September 2007 to October 2010. Large variations in the soil CO2 and plume SO2 fluxes (order of magnitude), coinciding with other discontinuous geochemical parameters (CO2 concentrations in fumarole gas) and physical parameters (increase of shallow seismic activity and fumarole temperatures) have been recorded. The results from this work suggest new prospects for strengthening geochemical monitoring of volcanic activity and for improving the constraints in the construction of a “geochemical model”, this being a necessary condition to better understand the functioning of volcanic systems.
    Description: Published
    Description: 1859-1863
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: 1R. Reti di monitoraggio e Osservazioni
    Description: JCR Journal
    Description: restricted
    Keywords: Vulcano Island ; Geochemical monitoring ; CO2 flux ; CO2 fumaroles ; SO2 flux ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Effects of Flow Volume and Grain Size on Mobility of Granular Flows of Angular Rock Fragments (2014)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Laboratory experiments have shown that the finer the grain size of granular flows of angular rock fragments (all the other features the same), the more mobile their centre of mass. This is due to the fact that the finer the grain size, the larger the number of particles in the flow so that their agitation due to the interaction with the subsurface asperities has a smaller penetration within the flow. The smaller the agitation of the particles per unit of flow mass, the smaller the energy dissipated per unit of travel distance. Also, the larger the flow volume, the smaller the mobility of its centre of mass. This is due to the fact that a deposit accretes backward during its deposition on a slope change. However, the frontal end of a larger-volume deposit is more distal than that of a smaller-volume deposit because the larger the volume, the larger its longitudinal spreading.
    Description: Published
    Description: 1621-1624
    Description: 3V. Dinamiche e scenari eruttivi
    Description: restricted
    Keywords: Pyroclastic Flows ; Mobility ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 10
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    Multiple Sclerosis in the Mount Etna Region: Possible Role of Volcanogenic Trace Elements (2014)
    Public Library of Science
    Details
    Publication Date: 2017-04-04
    Description: Background: Trace elements have been hypothesised to be involved in the pathogenesis of Multiple Sclerosis and volcanic degassing is the major natural sources of trace elements. Both incidence of Multiple Sclerosis in Catania and volcanic activity of Mount Etna have been significantly increased during the last 30 years. Due to prevailing trade winds direction, volcanic gases from Etna summit craters are mostly blown towards the eastern and southern sectors of the volcano. Objective: To evaluate the possible association between Multiple Sclerosis and exposure to volcanogenic trace elements. Methods: We evaluated prevalence and incidence of Multiple Sclerosis in four communities (47,234 inhabitants) located in the eastern flank and in two communities (52,210 inhabitants) located in the western flank of Mount Etna, respectively the most and least exposed area to crater gas emissions. Results: A higher prevalence was found in the population of the eastern flank compared to the population of the western one (137.6/100,000 versus 94.3/100,000; p-value 0.04). We found a borderline significantly higher incidence risk during the incidence study period (1980–2009) in the population of the eastern flank 4.6/100,000 (95% CI 3.1–5.9), compared with the western population 3.2/100,000 (95% CI 2.4–4.2) with a RR of 1.41 (95% CI 0.97–2.05; p-value 0.06). Incidence risks have increased over the time in both populations reaching a peak of 6.4/100,000 in the eastern flank and of 4.4/100.000 in the western flank during 2000–2009. Conclusion: We found a higher prevalence and incidence of Multiple Sclerosis among populations living in the eastern flank of Mount Etna. According to our data a possible role of TE cannot be ruled out as possible co-factor in the MS pathogenesis. However larger epidemiological study are needed to confirm this hypothesis.
    Description: Published
    Description: e74259
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: JCR Journal
    Description: open
    Keywords: Mt. Etna volcano ; Multiple Sclerosis ; trace elements ; volcanic activity ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Geosphere-biosphere interacions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica). (2014)
    Public Library of Science
    Details
    Publication Date: 2020-02-24
    Description: Hule and Rı´o Cuarto are maar lakes located 11 and 18 km N of Poa´s volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Rı´o Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).
    Description: Published
    Description: e102456
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: open
    Keywords: bio activity, volcanic lakes, costa rica ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Simulation and evaluation of 2-m temperature over Antarctica in polar regional climate model (2014)
    Springer
    In:  EPIC3Science China Earth Sciences, Springer, 57(4), pp. 703-709, ISSN: 1674-7313
    Details
    Publication Date: 2015-01-14
    Description: The European Centre for Medium-Range Weather Forecasts Reanalysis ERA40, National Centers for Environmental Prediction (NCEP) 20th-century reanalysis, and three station observations along an Antarctic traverse from Zhongshan to Dome-A stations are used to assess 2-m temperature simulation skill of a regional climate model. This model (HIRHAM) is from the Alfred Wegener Institute for Polar and Marine Research in Germany. Results show: (1) The simulated multiyear averaged 2-m temperature field pattern is close to that of ERA40 and NCEP; (2) the cold bias relative to ERA40 over all of Antarctic regions is 1.8°C, and that to NCEP reaches 5.1°C; (3) bias of HIRHAM relative to ERA40 has seasonal variation, with a cold bias mainly in the summer, as much as 3.4°C. There is a small inland warm bias in autumn of 0.3°C. Further analysis reveals that the reason for the cold bias of 2-m temperature is that physical conditions of the near-surface boundary layer simulated by HIRHAM are different from observations: (1) During the summer, observations show that near-surface atmospheric stability conditions have both inversions and non-inversions, which is due to the existence of both positive and negative sensible heat fluxes, but HIRHAM almost always simulates a situation of inversion and negative sensible heat flux; (2) during autumn and winter, observed near-surface stability is almost always that of inversions, consistent with HIRHAM simulations. This partially explains the small bias during autumn and winter.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Abrupt Climate Change Modeling (2014)
    Springer
    In:  EPIC3Encyclopedia of Complexity and Systems Science, Encyclopedia of Complexity and Systems Science, Springer, pp. 1-30
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    Publication Date: 2015-03-10
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    The seaward limit of wave effects on coastal macrobenthos (2014)
    Springer
    In:  EPIC3Helgoland Marine Research, Springer, 68(1), pp. 1-16, ISSN: 1438-387X
    Details
    Publication Date: 2016-07-19
    Description: Exposed sandy coasts are predominantly physically controlled environments where benthic communities are structured by the independent response of species to the physical environment, with minimal biological interactions (swash exclusion hypothesis). This prevalence of physical control may be regarded as a typical property of exposed coastal areas. In an offshore direction, the importance of wave effects on the benthos will diminish until a depth is reached where they are no longer significant [wave exclusion hypothesis (WEH)]. This loss of a coastal property may be used to define an offshore depth limit of the coastal zone. We used a large set of benthos data from the SE North Sea to test whether an offshore limit of the coast can be clearly recognised despite strong small-scale variability and how this limit would vary seasonally and from year to year. In accordance with WEH, both species density and total abundance of macrobenthos were low in the surf zone, strongly increased with depth, and averaged over all sampling dates became relatively constant below 30 m depth. Seasonally, these gradients were weaker during summer recruitment than during autumn. Species richness, by contrast, showed no significant difference with depth. In single years, the depth of the turning point from increasing abundances to constant abundances varied between 20 and 31 m (equivalent to 40–80 km off the coastline) depending on wave height. We conclude that this zone can be derived from benthic community gradients.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Cephalopods in neuroscience: regulations, research and the 3Rs (2014)
    Springer
    In:  EPIC3Invertebrate Neuroscience, Springer, ISSN: 1354-2516
    Details
    Publication Date: 2019-07-17
    Description: Cephalopods have been utilised in neurosci- ence research for more than 100 years particularly because of their phenotypic plasticity, complex and centralised nervous system, tractability for studies of learning and cellular mechanisms of memory (e.g. long-term potentia- tion) and anatomical features facilitating physiological studies (e.g. squid giant axon and synapse). On 1 January 2013, research using any of the about 700 extant species of ‘‘live cephalopods’’ became regulated within the European Union by Directive 2010/63/EU on the ‘‘Protection of Animals used for Scientific Purposes’’, giving cephalopods the same EU legal protection as previously afforded only to vertebrates. The Directive has a number of implications, particularly for neuroscience research. These include: (1) projects will need justification, authorisation from local competent authorities, and be subject to review including a harm-benefit assessment and adherence to the 3Rs princi- ples (Replacement, Refinement and Reduction). (2) To support project evaluation and compliance with the new EU law, guidelines specific to cephalopods will need to be developed, covering capture, transport, handling, housing, care, maintenance, health monitoring, humane anaesthesia, analgesia and euthanasia. (3) Objective criteria need to be developed to identify signs of pain, suffering, distress and lasting harm particularly in the context of their induction by an experimental procedure. Despite diversity of views existing on some of these topics, this paper reviews the above topics and describes the approaches being taken by the cephalopod research community (represented by the authorship) to produce ‘‘guidelines’’ and the potential contribution of neuroscience research to cephalopod welfare.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    The influence of intrinsic and extrinsic factors on developmental parameters and their relationships in the marine isopod Idotea linearis (Crustacea) (2014)
    Springer
    In:  EPIC3Hydrobiologia, Springer, 732, pp. 197-212, ISSN: 0018-8158
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    Publication Date: 2014-05-06
    Description: Developmental and reproductive parameters and their relationships were studied in the marine isopod Idotea linearis. We hypothesized that (1) the temporal patterns of molting and growth undergo complex and sex-specific changes with age as well as with the onset of sexual maturation, and that (2) sexual maturation (and dependent parameters) is controlled by the photoperiod. Both males and females were singly cultured in the laboratory at two alternative photoperiods (constant long and short days, respectively) from hatching until death. Males molted and grew throughout their life, showing a steady increase in stage duration and body size with each molt. Females, in contrast, showed much more complex modifications in molt chronology due to reproductive demands. There was some variability in the stage number, when females reached maturity. Reaching maturity early in the succession of molts was associated with smaller body size at maturity, smaller size of broods, but higher average number of broods per lifetime. Post-puberty molts in females occurred without further growth, and successive broods did not differ in size. The photoperiod strongly affected sexual maturation (and thus in turn molting and growth patterns) in females, while males remained completely unaffected by the photo regime.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Mass, Volume and Velocity of the Antarctic Ice Sheet: Present-Day Changes and Error Effects (2014)
    Springer
    In:  EPIC3Surveys in Geophysics, Springer, pp. 1-25, ISSN: 0169-3298
    Details
    Publication Date: 2019-07-17
    Description: This study examines present-day changes of the Antarctic ice sheet (AIS) by means of different data sets. We make use of monthly gravity field solutions acquired by the Gravity Recovery and Climate Experiment (GRACE) to study mass changes of the AIS for a 10-year period. In addition to "standard" solutions of release 05, solutions based on radial base functions were used. Both solutions reveal an increased mass loss in recent years. For a 6-year period surface-height changes were inferred from laser altimetry data provided by the Ice, Cloud, and land Elevation Satellite (ICESat). The basin-scale volume trends were converted into mass changes and were compared with the GRACE estimates for the same period. Focussing on the Thwaites Glacier, Landsat optical imagery was utilised to determine ice-flow velocities for a period of more than two decades. This data set was extended by means of high-resolution synthetic aperture radar (SAR) data from the TerraSAR-X mission, revealing an accelerated ice flow of all parts of the glacier. ICESat data over the Thwaites Glacier were complemented by digital elevation models inferred from TanDEM-X data. This extended data set exhibits an increased surface lowering in recent times. Passive microwave remote sensing data prove the long-term stability of the accumulation rates in a low accumulation zone in East Antarctica over several decades. Finally, we discuss the main error sources of present-day mass-balance estimates: the glacial isostatic adjustment effect for GRACE as well as the biases between laser operational periods and the volume-mass conversion for ICESat.
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  • 18
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    The scientific challenge of bridging the gap from the local to the earth system level: lessons from the study of mangroves and people in North Brazil (2014)
    Springer
    In:  EPIC3Regional Environmental Change, Springer, ISSN: 1436-3798
    Details
    Publication Date: 2016-10-07
    Description: This article aims to address the challenges of sustainable earth system governance from a multi-scale level perspective. The local to regional system level reviews findings from a social-ecological system (SES) approach of a mangrove ecosystem in North Brazil. Seven challenges (Glaser et al. 2010) that could provide relevant knowledge to society were identified. Their respective justification and recommendations are presented here. Further, these “challenges from the field” are linked and discussed with those challenges on earth system level elaborated by the International Council for Science in 2010. There it was stressed that sustainability problems are increasingly caused by drivers from multiple spatial and institutional levels in a single global human-nature system. The comparison between the global and local to regional challenges shows that most of these are reappearing disregarding the level of analysis, indicating that there is a universal core of global change problems. However, there are gaps are visible which hamper the effective connections across the different spatial levels. These gaps pertain to i.e. the subjects of knowledge generation and stakeholder inclusion. The final section elaborates on these recognized gaps and their science-policy dimensions. The article closes with the identification of a number of factors which currently impede global sustainability efforts: shortcomings in inter- and transdisciplinary research practice, lack of consistent structures for earth system governance and shortcomings in dealing with up-scaling challenges whilst remaining locally relevant. A blueprint for a globally focused but regionally informed social-ecological analysis framework remains to be worked out.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    Isolation, characterization and cross amplification of eleven novel microsatellite loci for the hydrozoan coral Millepora (2014)
    Springer
    In:  EPIC3Conservation Genetics Resources, Springer, ISSN: 1877-7252
    Details
    Publication Date: 2019-07-16
    Description: Milleporidae are of high ecological and economic importance, as, together with the scleractinian corals, they belong to the main reef builders of tropical coral reefs. Coral reefs face severe threats mainly due to anthropogenic disturbance. Understanding their population structure and dynamics is crucial for any conservation effort. Here we report the first microsatellite loci for the Milleporidae. Eleven polymorphic markers were developed for the hydrozoan corals Millepora dichotoma from the Great Barrier Reef (Australia) and tested for amplification in M. dichotoma from the Red Sea (Egypt), as well as for Millepora platyphylla from the Pacific Ocean (Moorea, French Polynesia). All loci were variable with 4–15 alleles per locus. Nine loci were transferable between geographic regions and species. These are the first microsatellites for hydrozoan corals. They will provide valuable tools for characterizing the population structure and genetic diversity of the group thereby benefitting coral reef conservation.
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  • 20
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    Uptake of Fluorescent Iron Oxide Nanoparticles by Oligodendroglial OLN-93 Cells (2014)
    Springer
    In:  EPIC3Neurochemical Research, Springer, 39(2), pp. 372-383, ISSN: 0364-3190
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    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    Biosignatures in chimney structures and sediment from the Loki’s Castle low-temperature hydrothermal vent field at the Arctic Mid-Ocean Ridge (2014)
    Springer
    In:  EPIC3Extremophiles, Springer, 18(3), pp. 545-560, ISSN: 1431-0651
    Details
    Publication Date: 2014-05-12
    Description: We investigated microbial life preserved in a hydrothermally inactive silica–barite chimney in comparison with an active barite chimney and sediment from the Loki’s Castle low-temperature venting area at the Arctic Mid-Ocean Ridge (AMOR) using lipid biomarkers. Carbon and sulfur isotopes were used to constrain possible metabolic pathways. Multiple sulfur (δ34S, ∆33S) isotopes on barite over a cross section of the extinct chimney range between 21.1 and 22.5 ‰ in δ34S, and between 0.020 and 0.034 ‰ in Δ33S, indicating direct precipitation from seawater. Biomarker distributions within two discrete zones of this silica–barite chimney indicate a considerable difference in abundance and diversity of microorganisms from the chimney exterior to the interior. Lipids in the active and inactive chimney barite and sediment were dominated by a range of 13C-depleted unsaturated and branched fatty acids with δ13C values between −39.7 and −26.7 ‰, indicating the presence of sulfur-oxidizing and sulfate-reducing bacteria. The majority of lipids (99.5 %) in the extinct chimney interior that experienced high temperatures were of archaeal origin. Unusual glycerol monoalkyl glycerol tetraethers (GMGT) with 0–4 rings were the dominant compounds suggesting the presence of mainly (hyper-) thermophilic archaea. Isoprenoid hydrocarbons with δ13C values as low as −46 ‰ also indicated the presence of methanogens and possibly methanotrophs.
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    Isolation and characterization of 11 microsatellite markers from the squat lobster Munida gregaria (Decapoda: Galatheidae) around the Falkland Islands/Islas Malvinas (2014)
    Springer
    In:  EPIC3Conservation Genetics Resources, Springer, ISSN: 1877-7252
    Details
    Publication Date: 2014-09-04
    Description: Understanding phylogenetic relationship and patterns of contemporary population genetic structure is a prerequisite for conservation and management of potential fishery resources. In this study we report the isolation and characterization of 11 polymorphic microsatellite loci for the squat lobster Munida gregaria from around the Falkland Islands/Islas Malvinas. The number of alleles ranged from 3 to 31, observed heterozygosity varied from 0.130 to 0.870. Cross-amplification was 100 % successfully in the species/morph M. subrugosa and 36.4 % in another congeneric species M. gracilis. This set of microsatellites is useful for studies focused on taxonomy, genetic diversity and genetic connectivity further may provide stock assessment information for monitoring this important fishery resource.
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    Distribution and characteristics of marine habitats in a subpolar bay based on hydroacoustics and bed shear stress estimates - Potter Cove, King George Island, Antarctica (2014)
    Springer
    In:  EPIC3Geo-Marine Letters, Springer, 34(5), pp. 435-446, ISSN: 0276-0460
    Details
    Publication Date: 2018-08-10
    Description: Marine habitats worldwide are increasingly pressurized by climate change, especially along the Antarctic Peninsula. Well-studied areas in front of rapidly retreating tidewater glaciers like Potter Cove are representative for similar coastal environments and, therefore, shed light on habitat formation and development on not only a local but also regional scale. The objective of this study was to provide insights into habitat distribution in Potter Cove, King George Island, Antarctica, and to evaluate the associated environmental processes. Furthermore, an assessment concerning the future development of the habitats is provided. To describe the seafloor habitats in Potter Cove, an acoustic seabed discrimination system (RoxAnn) was used in combination with underwater video images and sediment samples. Due to the absence of wave and current measurements in the study area, bed shear stress estimates served to delineate zones prone to sediment erosion. On the basis of the investigations, two habitat classes were identified in Potter Cove, namely soft-sediment and stone habitats that, besides influences from sediment supply and coastal morphology, are controlled by sediment erosion. A future expansion of the stone habitat is predicted if recent environmental change trends continue. Possible implications for the Potter Cove environment, and other coastal ecosystems under similar pressure, include changes in biomass and species composition.
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    Characterization of Ice-Binding Proteins from Sea Ice Algae (2014)
    Springer
    In:  EPIC3Plant Cold Acclimation: Methods and Protocols, (Methods in Molecular Biology ; 1166), New York, Springer, 282 p., pp. 241-253, ISBN: 978-1-4939-0843-1
    Details
    Publication Date: 2014-09-24
    Description: ICE BINDING PROTEINS FROM SEA ICE ALGAE Sea ice is mainly a two-phase system, and its porous structure is largely determinant for biological activity within ice. During ice formation, solutes in the seawater are excluded from the ice matrix and segregate into brine droplets or brine channels, generally defined as brine inclusions inside sea ice. Outflow of high salinity brine and inflow of seawater of lower salinity, as well as further cooling, cause brine inclusions to narrow and eventually separate into individual pockets divided by ice bridges. Despite the harsh conditions that govern within sea ice, where temperatures range from about -1.8°C on the bottom to -20°C or less on the top, and brine salinities can be as high as 200 on the Practical Salinity Scale, brine inclusions offer a habitat for a variety of microalgae. These algae play a crucial role for the ecology of the Polar Oceans, since they represent a concentrated food source in the low-productivity ice-covered sea, and in the months of melting they initiate blooms by seeding the water column. Algae have been found distributed within brine inclusions throughout the entire thickness of the ice column. The strategies adopted by ice microorganisms to cope with conditions in sea ice remain to be unraveled. Recent studies showed that several organisms that populate sea ice, spreading from bacteria to diatoms and a crustacean species, have ice binding proteins (IBPs). These proteins are common in polar species, but lack in temperate organisms, suggesting that IBPs play a key role in adaptation to subzero conditions. The nomenclature of these proteins varies, depending on authors, from ice binding to antifreeze or ice structuring. In the generally accepted adsorption–inhibition model describing the mechanism of action of IBPs, proteins bind to the ice lattice and locally inhibit ice growth by the Gibbs-Thomson effect. Recent publications showed that some IBPs organize water molecules into an ice-like structure that matches defined planes of the ice crystal and is then gradually frozen to the ice lattice. One of the most prominent and best described effects of IBPs is thermal hysteresis, which describes the lowering of the freezing point of a solution below the melting point. Another effect which defines IBPs is inhibition of recrystallization, which is the grain boundary migration resulting in a growth of larger crystals at the expenses of small grains. The biological role of IBPs from sea ice microalgae remains an open question. The importance of some IBP families, as observed in fishes or insects, lies in lowering the freezing point below environmental temperature, in order to avoid ice formation in cells or organs. Other IBPs have the function to inhibit recrystallization, as it has been suggested for plant IBPs. In the context of sea ice, it seems unlikely that the biological role of IBPs may be thermal hysteresis (measured in the order of 1°C) or recrystallization inhibition. Most of the IBPs from sea ice algae are active extracellularly. It has been suggested that they are trapped and accumulate within a layer of extracellular polysaccharide substances (EPS) secreted by several sea ice organisms. Microalgal IBPs produced recombinantly or collected from spent growth medium affect the structure of ice surface, causing pitting and characteristic microstructural features. This suggests that the proteins shape their frozen environment in order to increase their habitable space within sea ice. However, the characterization of IBPs is of relevance not only to understand their functional role in sea ice, but also in the frame of possible applications of IBPs in the medical field, in the food industry and in other fields related to a control of ice crystals. In the following we present some standard techniques to determine the protein activity in terms of thermal hysteresis (TH) and recrystallization inhibition (RI), which define the proteins as ice binding. Also, we present further methods (ice pitting assay, determination of the nucleating temperature) to characterize the activity of IBPs.
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    Cyclones and their possible changes in the Arctic by the end of the twenty first century from regional climate model Simulations (2014)
    Springer
    In:  EPIC3Theoretical and Applied Climatology, Springer, ISSN: 0177-798X
    Details
    Publication Date: 2019-10-23
    Description: Characteristics of cyclones (frequency, intensity and size) and their changes in the Arctic region in a warmer climate have been analyzed with the use of the HIRHAM regional climate model simulations with SRES-A1B anthropogenic scenario for the twenty first century. The focus was on cyclones for the warm (April–September) and cold (October–March) seasons. The present-day cyclonic characteristics from HIRHAM simulations are in general agreement with those from ERA–40 reanalysis data. Differences noted for the frequency of cyclones are related with different spatial resolution in the model simulations and reanalysis data. Potential future changes in cyclone characteristics at the end of the twenty first century have been analyzed. According to the model simulations, the frequency of cyclones is increasing in warm seasons and decreasing in cold seasons for a warmer climate in the twenty first century, but these changes are statistically insignificant. Noticeable changes were detected for the intensity and size of cyclones for the both seasons. Significant increase was found for the frequency of weak cyclones during cold season. Further, a general increase in the frequency of small cyclones was calculated in cold seasons, while its frequency decreases in warm seasons.
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    Predation of calanoid copepods on their own and other copepods’ offspring (2014)
    Springer
    In:  EPIC3Marine Biology, Springer, ISSN: 0025-3162
    Details
    Publication Date: 2019-07-17
    Description: Predation of eggs and nauplii by adult copepods is often used to explain unexpected death rates in population dynamics studies, but the phenomenon has been rarely investigated or quantified. Therefore, we studied the predatory feeding of adult females (Acartia clausi, Centropages hamatus, Centropages typicus, and Temora longicornis) on their own and other species’ eggs and young nauplii with different densities of single animal-prey, mixtures of animal-prey and in the presence of diatoms. All species preyed on eggs and nauplii of their own and all other species. Maximal egg predation varied between 7 and 64 eggs fem−1 day−1. Ingestion of Centropages spp. eggs was lowest, potentially due to the spiny egg surface. Maximal feeding rates on nauplii ranged from 5 to 45 nauplii fem−1 day−1. T. longicornis preferred eggs, when eggs and nauplii were offered together at the same densities, and the other predators selected for nauplii. At a diatom concentration of 60 μg C l−1 predation on eggs by C. typicus was higher than without algae, whereas A. clausi and T. longicornis did not change their uptake of eggs. Feeding on nauplii in the presence of diatoms was again enhanced in C. typicus, and unaffected in A. clausi and C. hamatus. T. longicornis reduced its feeding on nauplii in the presence of diatoms. Calculated predation rates, using field abundances of predators and prey, suggest that predation of copepods on their own young stages may account for ca. 30 % of total mortality of young stages in North Sea copepod populations.
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    The reaction of European lobster larvae (Homarus gammarus) to different quality food: effects of ontogenetic shifts and pre-feeding history (2014)
    Springer
    In:  EPIC3Oecologia, Springer, 174(2), pp. 581-594, ISSN: 0029-8549
    Details
    Publication Date: 2019-07-17
    Description: Young larval stages of many organisms represent bottlenecks in the life-history of many species. The high mortality commonly observed in, for example, decapod larvae has often been linked to poor nutrition, with most studies focussing on food quantity. Here, we focus instead on the effects of quality and have investigated its effects on the nutritional condition of lobster larvae. We established a tri-trophic food chain consisting of the cryptophyte Rhodomonas salina, the calanoid copepod Acartia tonsa and larvae of the European lobster Homarus gammarus. In a set of experiments, we manipulated the C:N:P stoichiometry of the primary producers, and accordingly those of the primary consumer. In a first experiment, R. salina was grown under N- and P-limitation and the nutrient content of the algae was manipulated by addition of the limiting nutrient to create a food quality gradient. In a second experiment, the effect on lobster larvae of long- and short-term exposure to food of varying quality during ontogenetic development was investigated. The condition of the lobster larvae was negatively affected even by subtle N- and P-nutrient limitations of the algae. Furthermore, younger lobster larvae were more vulnerable to nutrient limitation than older ones, suggesting an ontogenetic shift in the capacity of lobster larvae to cope with low quality food. The results presented here might have substantial consequences for the survival of lobster larvae in the field, as, in the light of future climate change and re-oligotrophication of the North Sea, lobster larvae might face marked changes in temperature and nutrient conditions, thus significantly altering their condition and growth.
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    Digestive enzymes of two brachyuran and two anomuran land crabs from Christmas Island, Indian Ocean (2014)
    Springer
    In:  EPIC3Journal of Comparative Physiology B-Biochemical Systemic and Environmentalphysiol, Springer, ISSN: 0174-1578
    Details
    Publication Date: 2019-07-16
    Description: The digestive ability of four sympatric land crabs species (the gecarcinids, Gecarcoidea natalis and Discoplax celeste and the anomurans, Birgus latro and Coenobita perlatus) was examined by determining the activity of their digestive enzymes. The gecarcinids are detritivores that consume mainly leaf litter; the robber crab, B. latro, is an omnivore that preferentially consumes items high in lipid, carbohydrate and/or protein; C. perlatus is also an omnivore/detritivore. All species possess protease, lipase and amylase activity for hydrolysing ubiquitous protein, lipid and storage polysaccharides (glycogen and starch). Similarly all species possess enzymes such as N-acetyl-β-d-glucosaminidase, the cellulases, endo-β-1,4-glucanase and β-glucohydrolase and hemicellulases, lichenase and laminarinase for the respective hydrolysis of structural substrates chitin, cellulose and hemicelluloses, lichenan and laminarin. Except for the enzyme activities of C. perlatus, enzyme activity could not be correlated to dietary preference. Perhaps others factors such as olfactory and locomotor ability and metabolic status may determine the observed dietary preferences. The digestive fluid of C. perlatus possessed higher endo-β-1,4-glucanase, lichenase and laminarinase activities compared to that of the other species. Thus, C. perlatus may be efficient at digestion of cellulose and hemicellulose within plant material. Zymography indicated that the majority of protease, lipase, phosphatase, amylase, endo-β-1,4-glucanase, β-glucohydrolase and N-acetyl-β-d-glucosaminidase isozymes were common to all species, and hence were inherited from a common aquatic ancestor. Differences were observed for the phosphatase, lipase and endo-β-1,4-glucanase isozymes. These differences are discussed in relation to phylogeny and possible evolution to cope with the adoption of a terrestrial diet.
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    Animating the Carbon Cycle (2014)
    Springer
    In:  EPIC3Ecosystems, Springer, 17(2), pp. 344-359, ISSN: 1432-9840
    Details
    Publication Date: 2019-07-17
    Description: Understanding the biogeochemical processes reg- ulating carbon cycling is central to mitigating atmospheric CO2 emissions. The role of living organisms has been accounted for, but the focus has traditionally been on contributions of plants and microbes. We develop the case that fully ‘‘animating’’ the carbon cycle requires broader consideration of the functional role of animals in mediating biogeochemical processes and quanti- fication of their effects on carbon storage and exchange among terrestrial and aquatic reservoirs and the atmosphere. To encourage more hypothesis-driven experimental research that quantifies animal effects we discuss the mecha- nisms by which animals may affect carbon ex- changes and storage within and among ecosystems and the atmosphere. We illustrate how those mechanisms lead to multiplier effects whose magnitudes may rival those of more tra- ditional carbon storage and exchange rate esti- mates currently used in the carbon budget. Many animal species are already directly managed. Thus improved quantitative understanding of their influence on carbon budgets may create oppor- tunity for management and policy to identify and implement new options for mitigating CO2 re- lease at regional scales.
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    Chapter 5: Perspectives and Integration in SOLAS Science. (2014)
    Springer
    In:  EPIC3Ocean-Atmosphere Interactions of Gases and Particles, Springer Earth System Sciences., Heidelberg, Springer, 147 p., pp. 247-306, ISBN: 978-3-642-25642-4
    Details
    Publication Date: 2014-04-15
    Description: Why a chapter on Perspectives and Integration in SOLAS Science in this book? SOLAS science by its nature deals with interactions that occur: across a wide spectrum of time and space scales, involve gases and particles, between the ocean and the atmosphere, across many disciplines including chemistry, biology, optics, physics, mathematics, computing, socio-economics and consequently interactions between many different scientists and across scientific generations. This chapter provides a guide through the remarkable diversity of cross-cutting approaches and tools in the gigantic puzzle of the SOLAS realm. Here we overview the existing prime components of atmospheric and oceanic observing systems, with the acquisition of ocean–atmosphere observables either from in situ or from satellites, the rich hierarchy of models to test our knowledge of Earth System functioning, and the tremendous efforts accomplished over the last decade within the COST Action 735 and SOLAS Integration project frameworks to understand, as best we can, the current physical and biogeochemical state of the atmosphere and ocean commons. A few SOLAS integrative studies illustrate the full meaning of interactions, paving the way for even tighter connections between thematic fields. Ultimately, SOLAS research will also develop with an enhanced consideration of societal demand while preserving fundamental research coherency. The exchange of energy, gases and particles across the air-sea interface is controlled by a variety of biological, chemical and physical processes that operate across broad spatial and temporal scales. These processes influence the composition, biogeochemical and chemical properties of both the oceanic and atmospheric boundary layers and ultimately shape the Earth system response to climate and environmental change, as detailed in the previous four chapters. In this cross-cutting chapter we present some of the SOLAS achievements over the last decade in terms of integration, upscaling observational information from process-oriented studies and expeditionary research with key tools such as remote sensing and modelling. Here we do not pretend to encompass the entire legacy of SOLAS efforts but rather offer a selective view of some of the major integrative SOLAS studies that combined available pieces of the immense jigsaw puzzle. These include, for instance, COST efforts to build up global climatologies of SOLAS relevant parameters such as dimethyl sulphide, interconnection between volcanic ash and ecosystem response in the eastern subarctic North Pacific, optimal strategy to derive basin-scale CO2 uptake with good precision, or significant reduction of the uncertainties in sea-salt aerosol source functions. Predicting the future trajectory of Earth’s climate and habitability is the main task ahead. Some possible routes for the SOLAS scientific community to reach this overarching goal conclude the chapter.
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    Advances in Predicting the Impacts of Global Warming on the Mussels Mytilus galloprovincialis in the Mediterranean Sea (2014)
    Springer
    In:  EPIC3The Mediterranean Sea: Its history and present challenges, The Mediterranean Sea: Its history and present challenges, Springer, pp. 319-339, ISBN: 978-94-007-6704-1
    Details
    Publication Date: 2014-04-15
    Description: Mussels Mytilus galloprovincialis have been used as model bivalves to study the impacts of global warming on their physiological performance in Themaikos Gulf, North Greece. The studies have been conducted under laboratory and field conditions for more than 6 years and focused on the biochemical, metabolic, physiological and energetic responses of M. galloprovincialis to increases in the ambient temperature. Here we summarize the findings concerning the responses of mussels to environmental temperature, present an integrated model of their physiological performance during thermal stress and discuss these findings in the light of the predicted temperature changes in the Thermaikos Gulf from the regional climate trends and the mean global temperature projections for the period 1990–2100 based on IS92 emission scenarios of the Intergovernmental Panel for Climate Change (IPCC). Our findings indicate that mussels in Themaikos Gulf currently face the temperatures close to their upper thermal limits, especially during the summer, and thus are likely vulnerably to any further increase in the temperature such as expected during the global warming
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    New insights into the genetic diversity of zooxanthellae in Mediterranean anthozoans (2014)
    Springer
    In:  EPIC3Symbiosis, Springer, 63(1), pp. 41-46, ISSN: 0334-5114
    Details
    Publication Date: 2015-01-05
    Description: Symbiotic dinoflagellates of the genus Symbiodinium, also called zooxanthellae, are found in association with a wide diversity of shallow-water anthozoans. The Symbiodinium genus includes numerous lineages, also referred to as clades or phylotypes, as well as a wide diversity of genetic sub-clades and sub-phylotypes. There are few studies characterizing the genetic diversity of zooxanthellae in Mediterranean anthozoans. In this study, we included anthozoans from the Western Mediterranean Sea and by means of internal transcriber (ITS) and large sub-unit (LSU) rRNA markers we corroborate what has been previously identified, demonstrating that phylotype “Temperate A” is very common among host Cnidaria in this basin. Our finding of fixed differences in ITS and LSU markers that correspond to different host taxa, indicate that this clade may comprise several closely-related species. Previous studies have reported the occurrence of Symbiodinium psygmophilum (formerly subclade B2) associated with Oculina patagonica and Cladocora caespitosa in the Eastern Mediterranean. Here, we identify this association in O. patagonica from the Western Mediterranean but not in C. caespitosa, suggesting some differences in symbiotic combinations between the Western and Eastern Mediterranean Basins.
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    Compositional discrimination of decompression and decomposition gas bubbles in bycaught seals and dolphins (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 8 (2013): e83994, doi:10.1371/journal.pone.0083994.
    Description: Gas bubbles in marine mammals entangled and drowned in gillnets have been previously described by computed tomography, gross examination and histopathology. The absence of bacteria or autolytic changes in the tissues of those animals suggested that the gas was produced peri- or post-mortem by a fast decompression, probably by quickly hauling animals entangled in the net at depth to the surface. Gas composition analysis and gas scoring are two new diagnostic tools available to distinguish gas embolisms from putrefaction gases. With this goal, these methods have been successfully applied to pathological studies of marine mammals. In this study, we characterized the flux and composition of the gas bubbles from bycaught marine mammals in anchored sink gillnets and bottom otter trawls. We compared these data with marine mammals stranded on Cape Cod, MA, USA. Fresh animals or with moderate decomposition (decomposition scores of 2 and 3) were prioritized. Results showed that bycaught animals presented with significantly higher gas scores than stranded animals. Gas composition analyses indicate that gas was formed by decompression, confirming the decompression hypothesis.
    Description: This study was funded by the Woods Hole Oceanographic Institution Marine Mammal Center, and Wick and Sloan Simmons.
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    Decadal changes in zooplankton of the Northeast U.S. continental shelf (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e87720, doi:10.1371/journal.pone.0087720.
    Description: The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf (NEUS) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine (GOM), Georges Bank (GB), Southern New England (SNE), and Mid-Atlantic Bight (MAB). Results suggested that there was significant difference in long term variation between northern region (GOM and GB), and the MAB for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the MAB. The long term abundance of C. finmarchicus showed more fluctuation in the MAB than the GOM and GB, whereas the long term abundance of Cen. typicus was more variable in the GB than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index (GSNWI) in the GOM and GB, but the GSNWI only explained 12–15% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the GSNWI, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.
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    The challenge to detect and attribute effects of climate change on human and natural systems (2014)
    Springer
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Climatic Change 121 (2013): 381-395, doi:10.1007/s10584-013-0873-6.
    Description: Anthropogenic climate change has triggered impacts on natural and human systems world-wide, yet the formal scientific method of detection and attribution has been only insufficiently described. Detection and attribution of impacts of climate change is a fundamentally cross-disciplinary issue, involving concepts, terms, and standards spanning the varied requirements of the various disciplines. Key problems for current assessments include the limited availability of long-term observations, the limited knowledge on processes and mechanisms involved in changing environmental systems, and the widely different concepts applied in the scientific literature. In order to facilitate current and future assessments, this paper describes the current conceptual framework of the field and outlines a number of conceptual challenges. Based on this, it proposes workable cross-disciplinary definitions, concepts, and standards. The paper is specifically intended to serve as a baseline for continued development of a consistent cross-disciplinary framework that will facilitate integrated assessment of the detection and attribution of climate change impacts.
    Description: Modeling Program of the Office of Biological and Environmental Research in the Department of Energy Office of Science under contract number DE-AC02-05CH11231. GH was supported by a grant from the German Ministry for Education and Research.
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    A quantitative assessment of the role of the parasite Amoebophrya in the termination of Alexandrium fundyense blooms within a small coastal embayment (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e81150, doi:10.1371/journal.pone.0081150.
    Description: Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). High prevalence of Amoebophrya spp. has been linked to the decline of some HABs in marine systems. The objective of this study was to evaluate the impact of Amoebophrya spp. on the dynamics of dinoflagellate blooms in Salt Pond (MA, USA), particularly the harmful species Alexandrium fundyense. The abundance of Amoebophrya life stages was estimated 3–7 days per week through the full duration of an annual A. fundyense bloom using fluorescence in situ hybridization coupled with tyramide signal amplification (FISH- TSA). More than 20 potential hosts were recorded including Dinophysis spp., Protoperidinium spp. and Gonyaulax spp., but the only dinoflagellate cells infected by Amoebophrya spp. during the sampling period were A. fundyense. Maximum A. fundyense concentration co-occurred with an increase of infected hosts, followed by a massive release of Amoebophrya dinospores in the water column. On average, Amoebophrya spp. infected and killed ~30% of the A. fundyense population per day in the end phase of the bloom. The decline of the host A. fundyense population coincided with a dramatic life-cycle transition from vegetative division to sexual fusion. This transition occurred after maximum infected host concentrations and before peak infection percentages were observed, suggesting that most A. fundyense escaped parasite infection through sexual fusion. The results of this work highlight the importance of high frequency sampling of both parasite and host populations to accurately assess the impact of parasites on natural plankton assemblages.
    Description: L. Velo-Sua´rez was supported by a Marie Curie International Outgoing Fellowship (IOF; grant agreement: MOHAB PIOF-GA-252260). This work was supported in part by NSF grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences grants 1P50-ES01274201 and 1P01ES021923-01 to D.M. Anderson and D.J. McGillicuddy through the Woods Hole Center for Oceans and Human Health, National Park Service Cooperative Agreement H238015504 to D.M. Anderson.
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    Diving behavior of the reef manta ray links coral reefs with adjacent deep pelagic habitats (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88170, doi:10.1371/journal.pone.0088170.
    Description: Recent successful efforts to increase protection for manta rays has highlighted the lack of basic ecological information, including vertical and horizontal movement patterns, available for these species. We deployed pop-up satellite archival transmitting tags on nine reef manta rays, Manta alfredi, to determine diving behaviors and vertical habitat use. Transmitted and archived data were obtained from seven tagged mantas over deployment periods of 102–188 days, including three recovered tags containing 2.6 million depth, temperature, and light level data points collected every 10 or 15 seconds. Mantas frequented the upper 10 m during daylight hours and tended to occupy deeper water throughout the night. Six of the seven individuals performed a cumulative 76 deep dives (〉150 m) with one individual reaching 432 m, extending the known depth range of this coastal, reef-oriented species and confirming its role as an ecological link between epipelagic and mesopelagic habitats. Mean vertical velocities calculated from high-resolution dive data (62 dives 〉150 m) from three individuals suggested that mantas may use gliding behavior during travel and that this behavior may prove more efficient than continuous horizontal swimming. The behaviors in this study indicate manta rays provide a previously unknown link between the epi- and mesopelagic layers of an extremely oligotrophic marine environment and provide evidence of a third marine species that utilizes gliding to maximize movement efficiency.
    Description: inancial support was provided in part by KAUST baseline research funds (to MLB), KAUST award numbers USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).
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    Identification of cinnabarinic acid as novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e87877, doi:10.1371/journal.pone.0087877.
    Description: The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.
    Description: This work was supported in part by National Institutes of Health (NIH) grants OD000329 and R01AI40312 (to JMM), R01ES006272 (to MEH), P42ES007381 (Superfund Research Program at Boston University to JS, DHS and MEH), R21CA134882 (to JS), NIH Training Grant T32 GM007175 (MML), and the Harvey V. Berneking Living Trust. BK is supported by Career Development Awards from the NIH/National Institute of Diabetes and Digestive and Kidney Diseases (DK083334) and the NASPGHAN Foundation. JEM is a recipient of the Human Frontiers Science Program Long-Term Fellowship (LT000231/2011-L). JMM is a recipient of the NIH Director's Pioneer Award Program, part of the NIH Roadmap for Medical Research, through grant DPI OD00329.
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  • 39
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    Shifts in the microbial community composition of Gulf Coast beaches following beach oiling (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e74265, doi:10.1371/journal.pone.0074265.
    Description: Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.
    Description: Financial support for this work was provided by the University of Wisconsin-Milwaukee National Institute of Environmental Health Sciences program, grant ES-004184 to SLM and the Alfred P. Sloan Foundation's grant for the Rare Biosphere in the Built Environment MLS.
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  • 40
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    Vertebral bomb radiocarbon suggests extreme longevity in white sharks (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed free of all copyright. The definitive version was published in PLoS One 9 (2014): e84006, doi:10.1371/journal.pone.0084006.
    Description: Conservation and management efforts for white sharks (Carcharodon carcharias) remain hampered by a lack of basic demographic information including age and growth rates. Sharks are typically aged by counting growth bands sequentially deposited in their vertebrae, but the assumption of annual deposition of these band pairs requires testing. We compared radiocarbon (Δ14C) values in vertebrae from four female and four male white sharks from the northwestern Atlantic Ocean (NWA) with reference chronologies documenting the marine uptake of 14C produced by atmospheric testing of thermonuclear devices to generate the first radiocarbon age estimates for adult white sharks. Age estimates were up to 40 years old for the largest female (fork length [FL]: 526 cm) and 73 years old for the largest male (FL: 493 cm). Our results dramatically extend the maximum age and longevity of white sharks compared to earlier studies, hint at possible sexual dimorphism in growth rates, and raise concerns that white shark populations are considerably more sensitive to human-induced mortality than previously thought.
    Description: This study was funded by the National Science Foundation (OCE 0825148 was awarded to SRT) and LLH was supported by the National Science Foundation Graduate Research Fellowship Program.
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  • 41
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    Strong depth-related zonation of megabenthos on a rocky continental margin (∼700–4000 m) off southern Tasmania, Australia (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e85872, doi:10.1371/journal.pone.0085872.
    Description: Assemblages of megabenthos are structured in seven depth-related zones between ~700 and 4000 m on the rocky and topographically complex continental margin south of Tasmania, southeastern Australia. These patterns emerge from analysis of imagery and specimen collections taken from a suite of surveys using photographic and in situ sampling by epibenthic sleds, towed video cameras, an autonomous underwater vehicle and a remotely operated vehicle (ROV). Seamount peaks in shallow zones had relatively low biomass and low diversity assemblages, which may be in part natural and in part due to effects of bottom trawl fishing. Species richness was highest at intermediate depths (1000–1300 m) as a result of an extensive coral reef community based on the bioherm-forming scleractinian Solenosmilia variabilis. However, megabenthos abundance peaked in a deeper, low diversity assemblage at 2000–2500 m. The S. variabilis reef and the deep biomass zone were separated by an extensive dead, sub-fossil S. variabilis reef and a relatively low biomass stratum on volcanic rock roughly coincident with the oxygen minimum layer. Below 2400 m, megabenthos was increasingly sparse, though punctuated by occasional small pockets of relatively high diversity and biomass. Nonetheless, megabenthic organisms were observed in the vast majority of photographs on all seabed habitats and to the maximum depths observed - a sandy plain below 3950 m. Taxonomic studies in progress suggest that the observed depth zonation is based in part on changing species mixes with depth, but also an underlying commonality to much of the seamount and rocky substrate biota across all depths. Although the mechanisms supporting the extraordinarily high biomass in 2000–2500 m depths remains obscure, plausible explanations include equatorwards lateral transport of polar production and/or a response to depth-stratified oxygen availability.
    Description: Components of this work were supported by the National Science Foundation, the Australian Department of Environment, Water, Heritage, and the Arts, the Australian Commonwealth Environmental Research Fund, a grant of ship time by the Australian National Research Facility, and the CSIRO Wealth from Oceans and Climate Adaptation Flagships.
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    Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88618, doi:10.1371/journal.pone.0088618.
    Description: The taxon Syndermata comprises the biologically interesting wheel animals (“Rotifera”: Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.
    Description: The work was funded by the Deutsche Forschungsgemeinschaft (DFG grant Ha2103/4-3, Priority Project "Deep Metazoan Phylogeny", SPP1174; www. dfg.de). Additional financial support came from the Center for Computational Sciences (SRFN) of Johannes Gutenberg University Mainz (http://www.csm.unimainz. de).
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    Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e97338, doi:10.1371/journal.pone.0097338.
    Description: Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
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    Capture of lipopolysaccharide (endotoxin) by the blood clot : a comparative study (2014)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e80192, doi:10.1371/journal.pone.0080192.
    Description: In vertebrates and arthropods, blood clotting involves the establishment of a plug of aggregated thrombocytes (the cellular clot) and an extracellular fibrillar clot formed by the polymerization of the structural protein of the clot, which is fibrin in mammals, plasma lipoprotein in crustaceans, and coagulin in the horseshoe crab, Limulus polyphemus. Both elements of the clot function to staunch bleeding. Additionally, the extracellular clot functions as an agent of the innate immune system by providing a passive anti-microbial barrier and microbial entrapment device, which functions directly at the site of wounds to the integument. Here we show that, in addition to these passive functions in immunity, the plasma lipoprotein clot of lobster, the coagulin clot of Limulus, and both the platelet thrombus and the fibrin clot of mammals (human, mouse) operate to capture lipopolysaccharide (LPS, endotoxin). The lipid A core of LPS is the principal agent of gram-negative septicemia, which is responsible for more than 100,000 human deaths annually in the United States and is similarly toxic to arthropods. Quantification using the Limulus Amebocyte Lysate (LAL) test shows that clots capture significant quantities of LPS and fluorescent-labeled LPS can be seen by microscopy to decorate the clot fibrils. Thrombi generated in the living mouse accumulate LPS in vivo. It is suggested that capture of LPS released from gram-negative bacteria entrapped by the blood clot operates to protect against the disease that might be caused by its systemic dispersal.
    Description: Grant # 0344360 from the National Science Foundation (PBA).
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    Climate Sensitivity During and Between Interglacials (2014)
    Springer
    In:  EPIC3Integrated Analysis of Interglacial Climate Dynamics (INTERDYNAMIC), Integrated Analysis of Interglacial Climate Dynamics (INTERDYNAMIC), Heidelberg, Springer, pp. 19-23, ISBN: 978-3-319-00693-2, ISSN: 2191-589X
    Details
    Publication Date: 2015-06-05
    Description: Studying the climate dynamics of past interglacials (IGs) may help to better assess the anthropogenically influenced dynamics of the current IG, the Holocene. We select IG sections from the longest ice core archive, EPICA Dome C (EDC), which covers the past 800 thousand years, and study as well several long, high-resolution marine sediment records. We analyze records of Antarctic temperature, radiative forcing (greenhouse gases and other factors), and sea-surface temperature (SST). Change-point regressions inform about longer-term climate changes and trends within IGs. Comparing trends in temperature with trends in forcing allows inference of longer-term IG climate sensitivities. Results from many records indicate deviations from a “Holocene climate optimum”. IG sensitivities are found to be comparable to estimates for the instrumental period; warming or cooling phases during Marine Isotope Stage (MIS) 5 or 11 do not show significant differences in climate sensitivity.
    Repository Name: EPIC Alfred Wegener Institut
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    Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.
    Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
    Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.
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    Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e103536, doi:10.1371/journal.pone.0103536.
    Description: Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the United States National Science Foundation (OCE 0825148 to SRT and GBS).
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  • 48
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    Aggregation and Sedimentation of Thalassiosira weissflogii (diatom) in a Warmer and More Acidified Future Ocean (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112379, doi:10.1575/1912/6845.
    Description: Increasing Transparent Exopolymer Particle (TEP) formation during diatom blooms as a result of elevated temperature and pCO2 have been suggested to result in enhanced aggregation and carbon flux, therewith potentially increasing the sequestration of carbon by the ocean. We present experimental results on TEP and aggregate formation by Thalassiosira weissflogii (diatom) in the presence or absence of bacteria under two temperature and three pCO2 scenarios. During the aggregation phase of the experiment TEP formation was elevated at the higher temperature (20°C vs. 15°C), as predicted. However, in contrast to expectations based on the established relationship between TEP and aggregation, aggregation rates and sinking velocity of aggregates were depressed in warmer treatments, especially under ocean acidification conditions. If our experimental findings can be extrapolated to natural conditions, they would imply a reduction in carbon flux and potentially reduced carbon sequestration after diatom blooms in the future ocean.
    Description: This work was supported by National Science Foundation grants OCE-0926711 & OCE-1041038 to UP and Helmholtz Graduate School for Polar and Marine Research and Jacobs University Bremen to SS.
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    Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e92277, doi:10.1371/journal.pone.0092277.
    Description: Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were 〈5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.
    Description: This research was primarily funded by Fundação para a Ciência e a Tecnologia (FCT), Fundo Regional da Ciência, Tecnologia (FRCT), through research projects TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER], the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, and Proconvergencia Açores/EU Program]. We acknowledge funds provided by FCT to LARSyS Associated Laboratory and IMAR-University of the Azores/the Thematic Area D & E of the Strategic Project PEst-OE/EEI/LA0009/2011–1012 and 2013–2014 (OE & Compete) and by the FRCT - Government of the Azores pluriannual funding. MAS was supported by an FCT postdoctoral grant (SFRH/BPD/29841/2006) and is currently supported by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education through an FCT Investigator grant. RP was supported by an FCT doctoral grant (SFRH/BD/41192/2007) and by the research grant from the Azores Regional Fund for Science and Technology (M3.1.5/F/115/2012). IJ was supported by the Natural Sciences and Engineering Research Council (NSERC) and the Canada Foundation for Innovation (CFI) through their support of the Ocean Tracking Network. DJFR is funded by the United Kingdom Department of Energy and Climate Change as part of their Offshore Energy Strategic Environmental Assessment program. DT is funded by Natural Environment Research Council and Marine Scotland.
    Repository Name: Woods Hole Open Access Server
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    Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e94249, doi:10.1371/journal.pone.0094249.
    Description: The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
    Description: This work was partially funded by an Emerging Frontiers in Research and Innovation – Multicellular and Inter-kingdom Signaling (EFRI-MIKS) grant awarded by the US National Science Foundation to Joerg Graf and NIH RO1 GM095390 to JG and HGM.
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    Validated age and growth estimates for Carcharhinus obscurus in the northwestern Atlantic Ocean, with pre- and post management growth comparisons (2014)
    Springer
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Environmental Biology of Fishes 97 (2014): 881-896, doi:10.1007/s10641-013-0189-4.
    Description: Age and growth estimates for the dusky shark, Carcharhinus obscurus, were derived from vertebral centra collected in the northwestern Atlantic Ocean. Sample collection spanned the years prior to and following the implementation of management measures (1963–2010). Growth was compared pre- and post- population depletion and pre- and post- management to investigate the possibility of density-mediated shifts in age and growth parameters over time. There was no evidence of difference between periods for either sex. Additionally, bomb radiocarbon dating was used to determine the periodicity of band pair formation. Results support the traditional interpretation of annual band pairs up to approximately 11 years of age. After this time, vertebral counts considerably underestimate true age. Maximum validated ages were estimated to be between 38 and 42 years of age (an increase of 15 to 19 years over the band count estimates), confirming longevity to at least 42 years of age. Growth curves estimated using only validated data were compared to those generated using band pair counts. Logistic growth parameters derived from validated vertebral length-at-age data were L ∞  = 261.5 cm FL, L o  = 85.5 cm, t o  = 4.89 year and g = 0.15 year−1 for the sexes combined. Revised estimates of age at maturity were 17.4 years for males and 17.6 years for females.
    Keywords: Dusky shark ; Age and growth ; Elasmobranch ; Vertebrae ; Bomb radiocarbon ; Validation
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    First autonomous bio-optical profiling float in the Gulf of Mexico reveals dynamic biogeochemistry in deep waters (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e101658, doi:10.1371/journal.pone.0101658.
    Description: Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (bbp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R2 = 0.62). Particulate backscattering, bbp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between bbp and chlorophyll (R2 = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R2 = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.
    Description: This project was funded by Bureau of Ocean Energy Management (BOEM) Contract M10PC00112 to Leidos, Inc. with subcontract to ASB (www.boem.gov).
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    Swimming speed of larval snail does not correlate with size and ciliary beat frequency (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e82764, doi:10.1371/journal.pone.0082764.
    Description: Many marine invertebrates have planktonic larvae with cilia used for both propulsion and capturing of food particles. Hence, changes in ciliary activity have implications for larval nutrition and ability to navigate the water column, which in turn affect survival and dispersal. Using high-speed high-resolution microvideography, we examined the relationship between swimming speed, velar arrangements, and ciliary beat frequency of freely swimming veliger larvae of the gastropod Crepidula fornicata over the course of larval development. Average swimming speed was greatest 6 days post hatching, suggesting a reduction in swimming speed towards settlement. At a given age, veliger larvae have highly variable speeds (0.8–4 body lengths s−1) that are independent of shell size. Contrary to the hypothesis that an increase in ciliary beat frequency increases work done, and therefore speed, there was no significant correlation between swimming speed and ciliary beat frequency. Instead, there are significant correlations between swimming speed and visible area of the velar lobe, and distance between centroids of velum and larval shell. These observations suggest an alternative hypothesis that, instead of modifying ciliary beat frequency, larval C. fornicata modify swimming through adjustment of velum extension or orientation. The ability to adjust velum position could influence particle capture efficiency and fluid disturbance and help promote survival in the plankton.
    Description: K.Y.K. Chan was supported by the Postdoctoral Scholar 1 Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. H. Jiang was supported by National Science Foundation grant NSF OCE-1129496 and an award from WHOI's Ocean Life Institute, and D.K. Padilla was supported by NSF IOS-0920032.
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    Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e93296, doi:10.1371/journal.pone.0093296.
    Description: Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.
    Description: This research was made possible by a grant from the National Science Foundation Biological Oceanography Program and the Brown University Undergraduate Teaching and Research Award Program.
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    Humpback whale populations share a core skin bacterial community : towards a health index for marine mammals? (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90785, doi:10.1371/journal.pone.0090785.
    Description: Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.
    Description: A.A. was funded by a WHOI Ocean Life Institute post-doctoral scholar award, and this research was supported by a grant to A.A. and T.J.M. from Woods Hole Oceanographic Institution's (WHOI) Marine Mammal Center.
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    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380.
    Description: Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
    Description: This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The contributions of S.K. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security (DHS) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.
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    Inner-shelf circulation and sediment dynamics on a series of shoreface-connected ridges offshore of Fire Island, NY (2014)
    Springer
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ocean Dynamics 64 (2014): 1767-1781, doi:10.1007/s10236-014-0781-y.
    Description: Locations along the inner-continental shelf offshore of Fire Island, NY, are characterized by a series of shoreface-connected ridges (SFCRs). These sand ridges have approximate dimensions of 10 km in length, 3 km spacing, and up to ∼8 m ridge to trough relief and are oriented obliquely at approximately 30° clockwise from the coastline. Stability analysis from previous studies explains how sand ridges such as these could be formed and maintained by storm-driven flows directed alongshore with a key maintenance mechanism of offshore deflected flows over ridge crests and onshore in the troughs. We examine these processes both with a limited set of idealized numerical simulations and analysis of observational data. Model results confirm that alongshore flows over the SFCRs exhibit offshore veering of currents over the ridge crests and onshore-directed flows in the troughs, and demonstrate the opposite circulation pattern for a reverse wind. To further investigate these maintenance processes, oceanographic instruments were deployed at seven sites on the SFCRs offshore of Fire Island to measure water levels, ocean currents, waves, suspended sediment concentrations, and bottom stresses from January to April 2012. Data analysis reveals that during storms with winds from the northeast, the processes of offshore deflection of currents over ridge crests and onshore in the troughs were observed, and during storm events with winds from the southwest, a reverse flow pattern over the ridges occurred. Computations of suspended sediment fluxes identify periods that are consistent with SFCR maintenance mechanisms. Alongshore winds from the northeast drove fluxes offshore on the ridge crest and onshore in the trough that would tend to promote ridge maintenance. However, alongshore winds from the southwest drove opposite circulations. The wind fields are related to different storm types that occur in the region (low-pressure systems, cold fronts, and warm fronts). From the limited data set, we identify that low-pressure systems drive sediment fluxes that tend to promote stability and maintain the SFCRs while cold front type storms appear to drive circulations that are in the opposite sense and may not be a supporting mechanism for ridge maintenance.
    Description: This research was funded by the U.S. Geological Survey, Coastal and Marine Geology Program, and conducted by the Coastal Change Processes Project.
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
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    Assessing the health of the U.S. west coast with a regional-scale application of the Ocean Health Index (2014)
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e98995, doi:10.1371/journal.pone.0098995.
    Description: Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions scoring from 65 (Washington) to 74 (Oregon). Highest scoring goals included tourism and recreation (99) and clean waters (87), while the lowest scoring goals were sense of place (48) and artisanal fishing opportunities (57). Surprisingly, even in this well-studied area data limitations precluded robust assessments of past trends in overall ocean health. Nonetheless, retrospective calculation of current status showed that many goals have declined, by up to 20%. In contrast, near-term future scores were on average 6% greater than current status across all goals and sub-regions. Application of hypothetical but realistic management scenarios illustrate how the Index can be used to predict and understand the tradeoffs among goals and consequences for overall ocean health. We illustrate and discuss how this index can be used to vet underlying assumptions and decisions with local stakeholders and decision-makers so that scores reflect regional knowledge, priorities and values. We also highlight the importance of ongoing and future monitoring that will provide robust data relevant to ocean health assessment.
    Description: Beau and Heather Wrigley generously provided the founding grant. Additional financial and in-kind support was provided by the Pacific Life Foundation, Thomas W. Haas Fund of the New Hampshire Charitable Foundation, the Oak Foundation, Akiko Shiraki Dynner Fund for Ocean Exploration and Conservation, Darden Restaurants Inc. Foundation, Conservation International, New England Aquarium, National Geographic, and the University of California Santa Barbara's National Center for Ecological Analysis and Synthesis, which supported the Ecosystem Health Working Group as part of the Science of Ecosystem-Based Management project funded by the David and Lucile Packard Foundation. Individual authors also acknowledge support from the U.S. National Science Foundation.
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    A framework for the probabilistic analysis of meteotsunamis (2014)
    Springer
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    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Natural Hazards 74 (2014): 123-142, doi:10.1007/s11069-014-1294-1.
    Description: A probabilistic technique is developed to assess the hazard from meteotsunamis. Meteotsunamis are unusual sea-level events, generated when the speed of an atmospheric pressure or wind disturbance is comparable to the phase speed of long waves in the ocean. A general aggregation equation is proposed for the probabilistic analysis, based on previous frameworks established for both tsunamis and storm surges, incorporating different sources and source parameters of meteotsunamis. Parameterization of atmospheric disturbances and numerical modeling is performed for the computation of maximum meteotsunami wave amplitudes near the coast. A historical record of pressure disturbances is used to establish a continuous analytic distribution of each parameter as well as the overall Poisson rate of occurrence. A demonstration study is presented for the northeast U.S. in which only isolated atmospheric pressure disturbances from squall lines and derechos are considered. For this study, Automated Surface Observing System stations are used to determine the historical parameters of squall lines from 2000 to 2013. The probabilistic equations are implemented using a Monte Carlo scheme, where a synthetic catalog of squall lines is compiled by sampling the parameter distributions. For each entry in the catalog, ocean wave amplitudes are computed using a numerical hydrodynamic model. Aggregation of the results from the Monte Carlo scheme results in a meteotsunami hazard curve that plots the annualized rate of exceedance with respect to maximum event amplitude for a particular location along the coast. Results from using multiple synthetic catalogs, resampled from the parent parameter distributions, yield mean and quantile hazard curves. Further refinements and improvements for probabilistic analysis of meteotsunamis are discussed.
    Keywords: Meteotsunami ; Probabilistic analysis ; Squall line ; Derecho ; Shallow-water wave ; Linear long wave
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    Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.
    Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
    Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.
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    Volatile (F and Cl) concentrations in Iwate olivine-hosted melt inclusions indicating low-temperature subduction (2014)
    Springer
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Earth, Planets and Space 66 (2014): 81, doi:10.1186/1880-5981-66-81.
    Description: Investigation of olivine-hosted melt inclusions provides information about the abundance of volatile elements that are often lost during subaerial eruptions of lavas. We have measured the abundances of H2O, CO2, F, Cl, and S as well as Pb isotopes in 29 melt inclusions in the scoria of the 1686 eruption of the Iwate volcano, a frontal-arc volcano in the northeast Japan arc. Pb Isotope compositions identify that Iwate magma is derived from a mixture of depleted mantle, subducted basalt, and sediment. Systematics of F in comparison to MORB and other arc magma indicates that (1) the slab surface temperature must be among the lowest on Earth and (2) hydrous minerals, such as amphibole, humites, and/or mica, must be present as residual phases during the dehydration of the slab.
    Description: The authors acknowledge financial support from the French Agence Nationale de la Recherche (projects: SlabFlux grant no. ANR 2009 Blanc 0338 and DegazMag, grant no. ANR 2011 Blanc SIMI 5-6 003). This research was financed by the French Government Laboratory of Excellence initiative no. ANR-10-LABX-0006, the Région Auvergne, and the European Regional Development Fund.
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    The transcriptional response to oxidative stress during vertebrate development : effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e113158, doi:10.1371/journal.pone.0113158.
    Description: Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
    Description: This research was supported in part by National Institutes of Health grants R01ES016366 (MEH), R01ES006272 (MEH), R01ES015912 (JJS), and F32ES017585 (ART-L), the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a WHOI (Woods Hole Oceanographic Institution) Postdoctoral Scholar award, and the Walter A. and Hope Noyes Smith endowed chair (MEH). AGM and MJC were supported in part by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.
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