ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Oxford University Press  (78,429)
  • Copernicus  (48,969)
  • Institute of Electrical and Electronics Engineers (IEEE)
  • 2020-2023  (50)
  • 2010-2014  (152,765)
Collection
Keywords
Publisher
Years
Year
  • 1
    facet.materialart.
    Unknown
    Magma andVolatile Supply to Post-collapse Volcanism and Block Resurgence in Siwi Caldera (Tanna Island,Vanuatu Arc) (2011)
    Oxford University Press
    Details
    Publication Date: 2020-11-20
    Description: Siwi caldera, in the Vanuatu arc (Tanna island), is a rare volcanic complex where both persistent eruptive activity (Yasur volcano)and rapid block resurgence (Yenkahe horst) can be investigated simultaneously during a post-caldera stage. Here we provide new constraints on the feeding system of this volcanic complex, based on a detailed study of the petrology, geochemistry and volatile content of Yasur^Siwi bulk-rocks and melt inclusions, combined with measurements of the chemical composition and mass fluxes of Yasur volcanic gases. Major and trace element analyses of Yasur^ Siwi volcanic rocks, together with literature data for other volcanic centers, point to a single magmatic series and possibly long-lived feeding of Tanna volcanism by a homogeneous arc basalt. Olivine-hosted melt inclusions show that the parental basaltic magma, which produces basaltic-trachyandesites to trachyandesites by 50^70% crystal fractionation, is moderately enriched in volatiles ( 1wt % H2O, 0·1wt % S and 0·055 wt % Cl). The basaltic-trachyandesite magma, emplaced at between 4^5 km depth and the surface, preserves a high temperature (1107 158C) and constant H2O content ( 1wt %) until very shallow depths, where it degasses extensively and crystallizes. These conditions, maintained over the past 1400 years of Yasur activity, require early water loss during basalt differentiation, prevalent open-system degassing, and a relatively high heat flow ( 109W). Yasur volcano releases on average 13·4 103 tons d 1 of H2O and 680 tons d 1 of SO2, but moderate amounts of CO2 (840 tons d 1), HCl (165 tons d 1), and HF (23 tons d 1). Combined with melt inclusion data, these gas outputs constrain a bulk magma degassing rate of 5 107 m3 a 1, about a half of which is due to degassing of the basaltic-trachyandesite. We compute that 25 km3 of this magma have degassed without erupting and have accumulated beneath Siwi caldera over the past 1000 years, which is one order of magnitude larger than the accumulated volume uplift of the Yenkahe resurgent block. Hence, basalt supply and gradual storage of unerupted degassed basaltictrachyandesite could easily account for (or contribute to) the Yenkahe block resurgence.
    Description: Published
    Description: 1077-1105
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Vanuatu arc ; Yasur ; gas fluxes ; volatiles ; melt inclusions ; resurgent block ; volcano thermal budget ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 2
    facet.materialart.
    Unknown
    Impact of appendicularians on detritus and export fluxes: a model approach at Dyfamed site (2012)
    Oxford University Press
    Details
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    Using empirical orthogonal functions derived from remote sensing reflectance for the prediction of concentrations of phytoplankton pigments. (2014)
    Copernicus
    In:  EPIC3Ocean Science Discussions, Copernicus, 11(5), pp. 2073-2117, ISSN: 1812-0822
    Details
    Publication Date: 2014-10-14
    Description: The composition and abundance of algal pigments provide information on characteristics of a phytoplankton community in respect to its photoacclimation, overall biomass, and taxonomic composition. Particularly, these pigments play a major role in photoprotection and in the light-driven part of photosynthesis. Most phytoplankton pigments can be measured by High Performance Liquid Chromatography (HPLC) techniques to filtered water samples. This method, like others when water samples have to be analysed in the laboratory, is time consuming and therefore only a limited number of data points can be obtained. In order to receive information on phytoplankton pigment composition with a higher temporal and spatial resolution, we have developed a method to assess pigment concentrations from continuous optical measurements. The method applies an Empirical Orthogonal Function (EOF) analysis to remote sensing reflectance data derived from ship-based hyper-spectral underwater radiometric and from multispectral satellite data (using the MERIS Polymer product developed by Steinmetz et al., 2011) measured in the Eastern Tropical Atlantic. Subsequently we developed statistically linear models with measured (collocated) pigment concentrations as the response variable and EOF loadings as predictor variables. The model results, show that surface concentrations of a suite of pigments and pigment groups can be well predicted from the ship-based reflectance measurements, even when only a multi-spectral resolution is chosen (i.e. eight bands similar to those used by MERIS). Based on the MERIS reflectance data, concentrations of total and monovinyl chlorophyll a and the groups of photoprotective and photosynthetic carotenoids can be predicted with high quality. The fitted statistical model constructed on the satellite reflectance data as input was applied to one month of MERIS Polymer data to predict the concentration of those pigment groups for the whole Eastern Tropical Atlantic area. Bootstrapping explorations of cross-validation error indicate that the method can produce reliable predictions with relatively small data sets (e.g., 〈 50 collocated values of reflectance and pigment concentration). The method allows for the derivation of time series from continuous reflectance data of various pigment groups at various regions, which can be used to study variability and change of phytoplankton composition and photo-physiology.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    Ocean acidification alleviates low-temperature effects on growth and photosynthesis of the red alga Neosiphonia harveyi (Rhodophyta) (2013)
    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Details
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    Static chamber methane flux measurements in volcanic/geothermal areas: preliminary data from Sousaki and Nisyros (Greece) (2010)
    Copernicus
    Details
    Publication Date: 2017-04-04
    Description: Methane plays an important role in the Earth’s atmospheric chemistry and radiative balance being the second most important greenhouse gas after carbon dioxide. Methane is released to the atmosphere by a wide number of sources, both natural and anthropogenic, with the latter being twice as large as the former (IPCC, 2007). It has recently been established that significant amounts of geological methane, produced within the Earth’s crust, are currently released naturally into the atmosphere (Etiope, 2004). Active or recent volcanic/geothermal areas represent one of these sources of geological methane. But due to the fact that methane flux measurements are laboratory intensive, very few data have been collected until now and the contribution of this source has been generally indirectly estimated (Etiope et al., 2007). The Greek territory is geodynamically very active and has many volcanic and geothermal areas. Here we report on methane flux measurements made at two volcanic/geothermal systems along the South Aegean volcanic arc: Sousaki and Nisyros. The former is an extinct volcanic area of Plio-Pleistocene age hosting nowadays a low enthalpy geothermal field. The latter is a currently quiescent active volcanic system with strong fumarolic activity due to the presence of a high enthalpy geothermal system. Both systems have gas manifestations that emit significant amounts of hydrothermal methane and display important diffuse carbon dioxide emissions from the soils. New data on methane isotopic composition and higher hydrocarbon contents point to an abiogenic origin of the hydrothermal methane in the studied systems. Measured methane flux values range from –48 to 29,000 (38 sites) and from –20 to 1100 mg/mˆ2/d (35 sites) at Sousaki and Nisyros respectively. At Sousaki measurement sites covered almost all the degassing area and the diffuse methane output can be estimated in about 20 t/a from a surface of about 10,000 mˆ2. At Nisyros measurements covered the Stephanos and Kaminakia areas, which represent only a part of the entire degassing area. The two areas show very different methane degassing pattern with latter showing much higher flux values. Methane output can be estimated in about 0.25 t/a from an area of about 30,000 mˆ2 at Stephanos and about 1 t/a from an area of about 20,000 mˆ2 at Kaminakia. The total output from the entire geothermal system of Nisyros probably should not exceed 2 t/a.
    Description: Published
    Description: Vienna, Austria
    Description: 4.5. Studi sul degassamento naturale e sui gas petroliferi
    Description: open
    Keywords: methane output ; diffuse degassing ; volcanic/hydrothermal systems ; Greece ; 01. Atmosphere::01.01. Atmosphere::01.01.03. Pollution ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Poster session
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    Environmental impact of Mt. Etna’s degassing: volcanogenic trace elements bioaccumulation in two endemic plant species (Senecio aethnensis and Rumex aethnensis) (2010)
    Copernicus
    Details
    Publication Date: 2017-04-04
    Description: A biomonitoring survey, above tree line level, using two endemic species (Senecio aethnensis and Rumex aethnensis) was performed on Mt. Etna, in order to evaluate the dispersion and the impact of volcanic atmospheric emissions. Samples of leaves were collected in summer 2008 from 30 sites in the upper part of the volcano (1500- 3000 m a.s.l). Acid digestion of samples was carried out with a microwave oven, and 44 elements were analyzed by using plasma spectrometry (ICP-MS and ICP-OES). The highest concentrations of all investigated elements were found in the samples collected closest to the degassing craters, and in the downwind sector, confirming that the eastern flank of Mt. Etna is the most impacted by volcanic emissions. Leaves collected along two radial transects from the active vents on the eastern flank, highlight that the levels of metals decrease one or two orders of magnitude with increasing distance from the source. This variability is higher for volatile elements (As, Bi, Cd, Cs, Pb, Sb, Tl) than for more refractory elements (Al, Ba, Sc, Si, Sr, Th, U). The two different species of plants do not show significant differences in the bioaccumulation of most of the analyzed elements, except for lanthanides, which are systematically enriched in Rumex leaves. The high concentrations of many toxic elements in the leaves allow us to consider these plants as highly tolerant species to the volcanic emissions, and suitable for biomonitoring researches in the Mt. Etna area.
    Description: Published
    Description: Vienna, Austria
    Description: 4.4. Scenari e mitigazione del rischio ambientale
    Description: open
    Keywords: Mt. Etna ; biomonitoring ; Trace elements ; 01. Atmosphere::01.01. Atmosphere::01.01.03. Pollution ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Poster session
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    Estimation of the magmatic gas and heat flux through the Etnean volcanic aquifer (2010)
    Copernicus
    Details
    Publication Date: 2017-04-04
    Description: Etna volcano, Italy, hosts one of the major groundwater systems of the island of Sicily. Waters circulate within highly permeable fractured, mainly hawaiitic, volcanic rocks. Aquifers are limited downwards by the underlying impermeable sedimentary terrains. Thickness of the volcanic rocks generally does not exceed some 300 m, preventing the waters to reach great depths. This is faced by short travel times (years to tens of years) and low thermalisation of the Etnean groundwaters. Measured temperatures are, in fact, generally lower than 25 °C. But the huge annual meteoric recharge (about 0.97 kmˆ3) with a high actual infiltration coefficient (0.75) implies a great underground circulation. During their travel from the summit area to the periphery of the volcano, waters acquire magmatic heat together with volcanic gases and solutes through water-rock interaction processes. In the last 20 years the Etnean aquifers has been extensively studied. Their waters were analysed for dissolved major, minor and trace element, O, H, C, S, B, Sr and He isotopes, and dissolved gas composition. These data have been published in several articles. Here, after a summary of the obtained results, the estimation of the magmatic heat flux through the aquifer will be discussed. To calculate heat uptake during subsurface circulation, for each sampling point (spring, well or drainage gallery) the following data have been considered: flow rate, water temperature, and oxygen isotopic composition. The latter was used to calculate the mean recharge altitude through the measured local isotopic lapse rate. Mean recharge temperatures, weighted for rain amount throughout the year, were obtained from the local weather station network. Calculations were made for a representative number of sampling points (216) including all major issues and corresponding to a total water flow of about 0.315 kmˆ3/a, which is 40% of the effective meteoric recharge. Results gave a total energy output of about 140 MW/a the half of which is ascribable to only 13 sampling points. These correspond to the highest flow drainage galleries with fluxes ranging from 50 to 1000 l/s and wells with pumping rates from 70 to 250 l/s. Geographical distribution indicates that, like magmatic gas leakage, heat flow is influenced by structural features of the volcanic edifice. The major heat discharge through groundwater are all tightly connected either to the major regional tectonic systems or to the major volcanic rift zones along which the most important flank eruptions take place. But rift zones are much more important for heat upraise due to the frequent dikes injection than for gas escape because generally when dikes have been emplaced the structure is no more permeable to gases because it becomes sealed by the cooling magma.
    Description: Published
    Description: Vienna, Austria
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: open
    Keywords: groundwaters ; volcanic surveillance ; water chemistry ; dissolved gases ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Oral presentation
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    Magma chambers emplaced in carbonate substrate: petrogenesis of skarn and cumulate rocks and implication on CO2-degassing in volcanic areas (2012)
    Oxford University Press
    Details
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Geomagnetic field observations at a new Antarctic site, within the AIMNet project (2011)
    Copernicus
    Details
    Publication Date: 2017-04-04
    Description: During the 2007-2008 antarctic campaign, the Italian PNRA installed a Low Power Magnetometer within the framework of the AIMNet (Antarctic International Magnetometer Network) project, proposed and coordinated by BAS. The magnetometer is situated at Talos Dome, around 300 km geographically North-West from Mario Zucchelli Station (MZS), and approximately at the same geomagnetic latitude as MZS. In this work we present a preliminary analysis of the geomagnetic field 1-min data, and a comparison with simultaneous data from different Antarctic stations.
    Description: Published
    Description: Vienna, Austria
    Description: 1.6. Osservazioni di geomagnetismo
    Description: open
    Keywords: daily variation ; AIMNet project ; Antarctica ; 04. Solid Earth::04.05. Geomagnetism::04.05.02. Geomagnetic field variations and reversals
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Poster session
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 10
    facet.materialart.
    Unknown
    Remote sensing of coccolithophore blooms in selected oceanic regions using the PhytoDOAS method applied to hyper-spectral satellite data. (2011)
    Copernicus
    In:  EPIC3Biogeosciences Discussion, Copernicus, 8, pp. 11725-11765, ISSN: 1810-6285
    Details
    Publication Date: 2019-07-17
    Description: In this study temporal variations of coccolithophore blooms are investigated using satellite data. Eight years, from 2003 to 2010, of data of SCIAMACHY, a hyper-spectral satellite sensor on-board ENVISAT, were processed by the PhytoDOAS method to 5 monitor the biomass of coccolithophores in three selected regions. These regions are characterized by frequent occurrence of large coccolithophore blooms. The retrieval results, shown as monthly mean time-series, were compared to related satellite products, including the total surface phytoplankton, i.e., total chlorophyll-a (from GlobColour merged data) and the particulate inorganic carbon (from MODIS-Aqua). The 10 inter-annual variations of the phytoplankton bloom cycles and their maximum monthly mean values have been compared in the three selected regions to the variations of the geophysical parameters: sea-surface temperature (SST), mixed-layer depth (MLD) and surface wind speed, which are known to affect phytoplankton dynamics. For each region the anomalies and linear trends of the monitored parameters over the period of this 15 study have been computed. The patterns of total phytoplankton biomass and specific dynamics of coccolithophores chlorophyll-a in the selected regions are discussed in relation to other studies. The PhytoDOAS results are consistent with the two other ocean color products and support the reported dependencies of coccolithophore biomass’ dynamics to the compared geophysical variables. This suggests, that PhytoDOAS 20 is a valid method for retrieving coccolithophore biomass and for monitoring its bloom developments in the global oceans. Future applications of time-series studies using the PhytoDOAS data set are proposed, also using the new upcoming generations of hyper-spectral satellite sensors with improved spatial resolution.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 11
    facet.materialart.
    Unknown
    Reconstruction of a continuous high-resolution CO2 record over the past 20 Million years (2011)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 7, pp. 1459-1469
    Details
    Publication Date: 2019-07-17
    Description: The gradual cooling of the climate during the Cenozoic has generally been attributed to a decrease in CO2 concentration in the atmosphere. The lack of transient climate models and in particular the lack of high-resolution proxy records of CO2, beyond the ice-core record prohibit however a full understanding of for example the inception of the Northern Hemisphere glaciation and mid-Pleistocene transition. Here we elaborate on an inverse modelling technique to reconstruct a continuous CO2 series over the past 20 million year (Myr), by decomposing the global deep-sea benthic d18O record into a mutually consistent temperature and sea level record, using a set of 1-D models of the major Northern and Southern Hemisphere ice sheets. We subsequently compared the modelled temperature record with ice core and proxy-derived CO2 data to create a continuous CO2 reconstruction over the past 20 Myr. Results show a gradual decline from 450 ppmv around 15 Myr ago to 225 ppmv for mean conditions of the glacial-interglacial cycles of the last 1 Myr, coinciding with a gradual cooling of the global surface temperature of 10 K. Between 13 to 3 Myr ago there is no long-term sea level variation caused by ice-volume changes. We find no evidence for a change in the long-term relation between temperature change and CO2, other than the effect following from the saturation of the absorption bands for CO2. The reconstructed CO2 record shows that the Northern Hemisphere glaciation starts once the long-term average CO2 concentration drops below 265 ppmv after a period of strong decrease in CO2. Finally, only a small long-term decline of 23 ppmv is found during the mid-Pleistocene transition, constraining theories on this major transition in the climate system. The approach is not accurate enough to revise current ideas about climate sensitivity.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 12
    facet.materialart.
    Unknown
    Conditions of Magma Storage, Degassing and Ascent at Stromboli: New Insights into the Volcano Plumbing System with Inferences on the Eruptive Dynamics (2011)
    Oxford University Press
    Details
    Publication Date: 2017-04-04
    Description: Stromboli is known for its persistent degassing and rhythmic strombolian activity occasionally punctuated by paroxysmal eruptions. The basaltic pumice and scoria emitted during paroxysms and strombolian activity, respectively, differ in their textures, crystal contents and glass matrix compositions, which testify to distinct conditions of crystallization, degassing and magma ascent. We present here an extensive dataset on major elements and volatiles (CO2, H2O, S and Cl) in olivine-hosted melt inclusions and embayments from pyroclasts emplaced during explosive eruptions of variable magnitude. Magma saturation pressures were assessed from the dissolved amounts of H2O and CO2 taking into account the melt composition evolution. Both pressures and melt inclusion compositions indicate that (1) Ca-basaltic melts entrapped in high-Mg olivines (Fo89–90) generate Stromboli basalts through crystal fractionation, and (2) the Stromboli plumbing system can be imaged as a succession of magma ponding zones connected by dikes. The 7–10 km interval, where magmas are stored and differentiate, is periodically recharged by new magma batches, possibly ranging from Ca-basalts to basalts, with a CO2-rich gas phase. These deep recharges promote the formation of bubbly basalt blobs, which are able to intrude the shallow plumbing system (2–4 km), where CO2 gas fluxing enhances H2O loss, crystallization and generation of crystal-rich, dense, degassed magma. Chlorine partitioning into the H2O–CO2-bearing gas phase accounts for its efficient degassing (≥69%) under the open-system conditions of strombolian activity. Paroxysms, however, are generated through predominantly closed-system ascent of basaltic magma batches from the deep storage zone. In this situation crystallization is negligible and sulfur exsolution starts at ≤170 MPa. Chlorine remains dissolved in the melt until lower pressures, only 16% being lost upon eruption. Finally, we propose a continuum in explosive eruption energy, from strombolian activity to large paroxysmal events, ultimately controlled by variable pressurization of the deep feeding system associated with magma and gas recharges.
    Description: Published
    Description: 603-626
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; melt inclusions ; magmatic volatiles ; CO2 fluxing ; magma degassing ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 13
    facet.materialart.
    Unknown
    Evaluation of the criticality of cracks in ice shelves using finite element simulations (2012)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 6(5), pp. 973-984, ISSN: 1994-0416
    Details
    Publication Date: 2019-07-17
    Description: The ongoing disintegration of large ice shelf parts in Antarctica raise the need for a better understanding of the physical processes that trigger critical crack growth in ice shelves. Finite elements in combination with configurational forces facilitate the analysis of single surface fractures in ice under various boundary conditions and material parameters. The principles of linear elastic fracture mechanics are applied to show the strong influence of different depth dependent functions for the density and the Young’s modulus on the stress intensity factor KI at the crack tip. Ice, for this purpose, is treated as an elastically compressible solid and the conse- quences of this choice in comparison to the predominant in- compressible approaches are discussed. The computed stress intensity factors KI for dry and water filled cracks are com- pared to critical values KIc from measurements that can be found in literature.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 14
    facet.materialart.
    Unknown
    Ocean acidification: knowns, unknowns, and perspectives (2011)
    Oxford University Press
    In:  EPIC3Ocean Acidification, Oxford, Oxford University Press, pp. 291-311, ISBN: 978-0-19-959109-1
    Details
    Publication Date: 2014-04-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 15
    facet.materialart.
    Unknown
    A reconstruction of atmospheric carbon dioxide and its stable carbon isotopic composition from the penultimate glacial maximum to the last glacial inception (2013)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 9(6), pp. 2507-2523, ISSN: 1814-9332
    Details
    Publication Date: 2014-11-28
    Description: The reconstruction of the stable carbon isotope evolution in atmospheric CO2 (δ13Catm), as archived in Antarctic ice cores, bears the potential to disentangle the contributions of the different carbon cycle fluxes causing past CO2 variations. Here we present a new record of δ13Catm before, during and after the Marine Isotope Stage 5.5 (155 000 to 105 000 yr BP). The dataset is archived on the data repository PANGEA® (www.pangea.de) under 10.1594/PANGAEA.817041. The record was derived with a well established sublimation method using ice from the EPICA Dome C (EDC) and the Talos Dome ice cores in East Antarctica. We find a 0.4‰ shift to heavier values between the mean δ13Catm level in the Penultimate (~ 140 000 yr BP) and Last Glacial Maximum (~ 22 000 yr BP), which can be explained by either (i) changes in the isotopic composition or (ii) intensity of the carbon input fluxes to the combined ocean/atmosphere carbon reservoir or (iii) by long-term peat buildup. Our isotopic data suggest that the carbon cycle evolution along Termination II and the subsequent interglacial was controlled by essentially the same processes as during the last 24 000 yr, but with different phasing and magnitudes. Furthermore, a 5000 yr lag in the CO2 decline relative to EDC temperatures is confirmed during the glacial inception at the end of MIS5.5 (120 000 yr BP). Based on our isotopic data this lag can be explained by terrestrial carbon release and carbonate compensation.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 16
    facet.materialart.
    Unknown
    On the interference of Kr during carbon isotope analysis of methane using continuous-flow combustion–isotope ratio mass spectrometry (2013)
    Copernicus
    In:  EPIC3Atmospheric Measurement Techniques, Copernicus, 6(5), pp. 1425-1445, ISSN: 1867-8548
    Details
    Publication Date: 2019-07-17
    Description: Stable carbon isotope analysis of methane (δ13C of CH4) on atmospheric samples is one key method to constrain the current and past atmospheric CH4 budget. A frequently applied measurement technique is gas chromatography (GC) isotope ratio mass spectrometry (IRMS) coupled to a combustion-preconcentration unit. This report shows that the atmospheric trace gas krypton (Kr) can severely interfere during the mass spectrometric measurement, leading to significant biases in δ13C of CH4, if krypton is not sufficiently separated during the analysis. According to our experiments, the krypton interference is likely composed of two individual effects, with the lateral tailing of the doubly charged 86Kr peak affecting the neighbouring m/z 44 and partially the m/z 45 Faraday cups. Additionally, a broad signal affecting m/z 45 and especially m/z 46 is assumed to result from scattered ions of singly charged krypton. The introduced bias in the measured isotope ratios is dependent on the chromatographic separation, the krypton-to-CH4 mixing ratio in the sample, the focusing of the mass spectrometer as well as the detector configuration and can amount to up to several per mil in δ13C. Apart from technical solutions to avoid this interference, we present correction routines to a posteriori remove the bias.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 17
    facet.materialart.
    Unknown
    Using ground data from the Global Terrestrial Network of Permafrost (GTN-P) for the evaluation of ESA Data User Element (DUE) Permafrost remote sensing derived products. (2012)
    Copernicus
    In:  EPIC3EGU 2012 General Assembly, Vienna, Austria, 2012-04-22-2012-04-27Vienna, Austria, Copernicus
    Details
    Publication Date: 2019-07-16
    Description: Permafrost is one of the essential climate variables addressed by the Global Terrestrial Observing System (GCOS). Remote sensing data provide area-wide monitoring of e.g. surface temperatures or soil surface status (frozen or thawed state) in the Arctic and Subarctic, where ground data collection is difficult and restricted to local measurements at few monitoring sites. The task of the ESA Data User Element (DUE) Permafrost project is to build-up an Earth observation service for northern high-latitudinal permafrost applications with extensive involvement of the international permafrost research community (www.ipf.tuwien.ac.at/permafrost). The satellite-derived DUE Permafrost products are Land Surface Temperature, Surface Soil Moisture, Surface Frozen and Thawed State, Digital Elevation Model (locally as remote sensing product and circumpolar as non-remote sensing product) and Subsidence, and Land Cover. Land Surface Temperature, Surface Soil Moisture, and Surface Frozen and Thawed State will be provided for the circumpolar permafrost area north of 55° N with 25 km spatial resolution. In addition, regional products with higher spatial resolution were developed for five case study regions in different permafrost zones of the tundra and taiga (Laptev Sea [RU], Central Yakutia [RU], Western Siberia [RU], Alaska N-S transect, [US] Mackenzie River and Valley [CA]). This study shows the evaluation of two DUE Permafrost regional products, Land Surface Temperature and Surface Frozen and Thawed State, using freely available ground truth data from the Global Terrestrial Network of Permafrost (GTN-P) and monitoring data from the Russian-German Samoylov research station in the Lena River Delta (Central Siberia, RU). The GTN-P permafrost monitoring sites with their position in different permafrost zones are highly qualified for the validation of DUE Permafrost remote sensing products. Air and surface temperatures with high-temporal resolution from eleven GTN-P sites in Alaska and four sites in Siberia were used to match up LST products. Daily average GTN-P borehole- and air temperature data for three Alaskan and six Western Siberian sites were used to evaluate surface frozen and thawed. First results are promising and demonstrate the great benefit of freely available ground truth databases for remote sensing products.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 18
    facet.materialart.
    Unknown
    Direct linking of Greenland and Antarctic ice cores at the Toba eruption (74 ka BP) (2013)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 9(2), pp. 749-766, ISSN: 1814-9324
    Details
    Publication Date: 2019-07-17
    Description: The Toba eruption that occurred some 74 ka ago in Sumatra, Indonesia, is among the largest volcanic events on Earth over the last 2 million years. Tephra from this eruption has been spread over vast areas in Asia, where it constitutes a major time marker close to the Marine Isotope Stage 4/5 boundary. As yet, no tephra associated with Toba has been identified in Greenland or Antarctic ice cores. Based on new accurate dating of Toba tephra and on accurately dated European stalagmites, the Toba event is known to occur between the onsets of Greenland interstadials (GI) 19 and 20. Furthermore, the existing linking of Greenland and Antarctic ice cores by gas records and by the bipolar seesaw hypothesis suggests that the Antarctic counterpart is situated between Antarctic Isotope Maxima (AIM) 19 and 20. In this work we suggest a direct synchronization of Greenland (NGRIP) and Antarctic (EDML) ice cores at the Toba eruption based on matching of a pattern of bipolar volcanic spikes. Annual layer counting between volcanic spikes in both cores allows for a unique match. We first demonstrate this bipolar matching technique at the already synchronized Laschamp geomagnetic excursion (41 ka BP) before we apply it to the suggested Toba interval. The Toba synchronization pattern covers some 2000 yr in GI-20 and AIM-19/20 and includes nine acidity peaks that are recognized in both ice cores. The suggested bipolar Toba synchronization has decadal precision. It thus allows a determination of the exact phasing of inter-hemispheric climate in a time interval of poorly constrained ice core records, and it allows for a discussion of the climatic impact of the Toba eruption in a global perspective. The bipolar linking gives no support for a long-term global cooling caused by the Toba eruption as Antarctica experiences a major warming shortly after the event. Furthermore, our bipolar match provides a way to place palaeo-environmental records other than ice cores into a precise climatic context.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 19
    facet.materialart.
    Unknown
    Sulphur compounds, methane, and phytoplankton: interactions along a north-south transit in the western Pacific Ocean (2012)
    Copernicus
    In:  EPIC3Biogeosciences Discussion, Copernicus, 9, pp. 15011-15049, ISSN: 1810-6285
    Details
    Publication Date: 2019-07-17
    Description: Here we present results of the first comprehensive study of sulphur compounds and methane in the oligotrophic tropical West Pacific Ocean. The concentrations of dimethylsuphide (DMS), dimethylsulphoniopropionate (DMSP), dimethylsulphoxide (DMSO), and methane (CH4), as well as various phytoplankton marker pigments in the surface ocean were measured along a north-south transit from Japan to Australia in October 2009. DMS (0.9 nmol l−1), dissolved DMSP (DMSPd, 1.6 nmol l−1) and particulate DMSP (DMSPp, 2 nmol l−1) concentrations were generally low, while dissolved DMSO (DMSOd, 4.4 nmol l−1) and particulate DMSO (DMSOp, 11.5 nmol l−1) concentrations were comparably enhanced. Positive correlations were found between DMSO and DMSP as well as DMSP and DMSO with chlorophyll a, which suggests a similar source for both compounds. Similar phytoplankton groups were identified as being important for the DMSO and DMSP pool, thus, the same algae taxa might produce both DMSP and DMSO. In contrast, phytoplankton seemed to play only a minor role for the DMS distribution in the western Pacific Ocean. The observed DMSPp : DMSOp ratios were very low and seem to be characteristic of oligotrophic tropical waters representing the extreme endpoint of the global DMSPp : DMSOp ratio vs. SST relationship. It is most likely that nutrient limitation and oxidative stress in the tropical West Pacific Ocean triggered enhanced DMSO production leading to an accumulation of DMSO in the sea surface. Positive correlations between DMSPd and CH4, as well as between DMSO (particulate and total) and CH4, were found along the transit. We conclude that both DMSP and DMSO serve as substrates for methanogenic bacteria in the western Pacific Ocean.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 20
    facet.materialart.
    Unknown
    Phytoplankton community structure in the Lena Delta (Siberia, Russia) in relation to hydrography (2013)
    Copernicus
    In:  EPIC3Biogeosciences, Copernicus, 10(11), pp. 7263-7277, ISSN: 1726-4170
    Details
    Publication Date: 2018-02-16
    Description: The Lena Delta in Northern Siberia is one of the largest river deltas in the world. During peak discharge, after the ice melt in spring, it delivers between 60–8000 m3 s−1 of water and sediment into the Arctic Ocean. The Lena Delta and the Laptev Sea coast also constitute a continuous permafrost region. Ongoing climate change, which is particularly pronounced in the Arctic, is leading to increased rates of permafrost thaw. This has already profoundly altered the discharge rates of the Lena River. But the chemistry of the river waters which are discharged into the coastal Laptev Sea have also been hypothesized to undergo considerable compositional changes, e.g. by increasing concentrations of inorganic nutrients such as dissolved organic carbon (DOC) and methane. These physical and chemical changes will also affect the composition of the phytoplankton communities. However, before potential consequences of climate change for coastal arctic phytoplankton communities can be judged, the inherent status of the diversity and food web interactions within the delta have to be established. In 2010, as part of the AWI Lena Delta programme, the phyto- and microzooplankton community in three river channels of the delta (Trofimov, Bykov and Olenek) as well as four coastal transects were investigated to capture the typical river phytoplankton communities and the transitional zone of brackish/marine conditions. Most CTD profiles from 23 coastal stations showed very strong stratification. The only exception to this was a small, shallow and mixed area running from the outflow of Bykov channel in a northerly direction parallel to the shore. Of the five stations in this area, three had a salinity of close to zero. Two further stations had salinities of around 2 and 5 throughout the water column. In the remaining transects, on the other hand, salinities varied between 5 and 30 with depth. Phytoplankton counts from the outflow from the Lena were dominated by diatoms (Aulacoseira species) cyanobacteria (Aphanizomenon, Pseudanabaena) and chlorophytes. In contrast, in the stratified stations the plankton was mostly dominated by dinoflagellates, ciliates and nanoflagellates, with only an insignificant diatom component from the genera Chaetoceros and Thalassiosira (brackish as opposed to freshwater species). Ciliate abundance was significantly coupled with the abundance of total flagellates. A pronounced partitioning in the phytoplankton community was also discernible with depth, with a different community composition and abundance above and below the thermocline in the stratified sites. This work is a first analysis of the phytoplankton community structure in the region where Lena River discharge enters the Laptev Sea.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 21
    facet.materialart.
    Unknown
    On the low frequency component of the ENSO–Indian Monsoon relationship; a paired proxy perspective (2013)
    Copernicus
    In:  EPIC3Climate of the Past Discussions, Copernicus, 9, pp. 3103-3123, ISSN: 1814-9324
    Details
    Publication Date: 2019-07-17
    Description: There are a number of clear examples in the instrumental period where positive El Niño events were coincident with a severely weakened summer monsoon over India (ISM). ENSO's influence on the Indian Monsoon has therefore remained the centerpiece of various predictive schemes of ISM rainfall for over a century. The teleconnection between the monsoon and ENSO has undergone a protracted weakening since the late 1980's suggesting the strength of ENSO's influence on the monsoon may vary considerably on multidecadal timescales. The recent weakening has specifically prompted questions as to whether this shift represents a natural mode of climate variability or a fundamental change in ENSO and/or ISM dynamics due to anthropogenic warming. The brevity of empirical observations and large systematic errors in the representation of these two systems in state-of-the-art general circulation models hamper efforts to reliably assess the low frequency nature of this dynamical coupling under varying climate forcings. Here we place the 20th century ENSO-Monsoon relationship in a millennial context by assessing the phase angle between the two systems across the time spectrum using a continuous tree-ring ENSO reconstruction from North America and a speleothem oxygen isotope (δ18O) based reconstruction of the ISM. The results suggest that in the high-frequency domain (≤ 15 yr), El Niño (La Niña) events persistently lead to a weakened (strengthened) monsoon consistent with the observed relationship between the two systems during the instrumental period. However, in the low frequency domain (≥ 60 yr), periods of strong monsoon are, in general, coincident with periods of enhanced ENSO variance. This relationship is opposite to which would be predicted dynamically and leads us to conclude that ENSO is not pacing the prominent multidecadal variability that has characterized the ISM over the last millennium.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 22
    facet.materialart.
    Unknown
    Empirical sea ice thickness retrieval during the freeze up period from SMOS high incident angle observations (2014)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 8(2), pp. 439-451, ISSN: 1994-0416
    Details
    Publication Date: 2019-07-17
    Description: Sea ice thickness information is important for sea ice modelling and ship operations. Here a method to detect the thickness of sea ice up to 50 cm during the freeze-up season based on high incidence angle observations of the Soil Moisture and Ocean Salinity (SMOS) satellite working at 1.4 GHz is suggested. By comparison of thermodynamic ice growth data with SMOS brightness temperatures, a high correlation to intensity and an anticorrelation to the difference between vertically and horizontally polarised brightness temperatures at incidence angles between 40 and 50° are found and used to develop an empirical retrieval algorithm sensitive to thin sea ice up to 50 cm thickness. The algorithm shows high correlation with ice thickness data from airborne measurements and reasonable ice thickness patterns for the Arctic freeze-up period.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 23
    facet.materialart.
    Unknown
    SMOS derived sea ice thickness: algorithm baseline, product specifications and initial verification (2014)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 8(3), pp. 997-1018, ISSN: 1994-0416
    Details
    Publication Date: 2014-06-02
    Description: Following the launch of ESA's Soil Moisture and Ocean Salinity (SMOS) mission, it has been shown that brightness temperatures at a low microwave frequency of 1.4 GHz (L-band) are sensitive to sea ice properties. In the first demonstration study, sea ice thickness up to 50 cm has been derived using a semi-empirical algorithm with constant tie-points. Here, we introduce a novel iterative retrieval algorithm that is based on a thermodynamic sea ice model and a three-layer radiative transfer model, which explicitly takes variations of ice temperature and ice salinity into account. In addition, ice thickness variations within the SMOS spatial resolution are considered through a statistical thickness distribution function derived from high-resolution ice thickness measurements from NASA's Operation IceBridge campaign. This new algorithm has been used for the continuous operational production of a SMOS-based sea ice thickness data set from 2010 on. The data set is compared to and validated with estimates from assimilation systems, remote sensing data, and airborne electromagnetic sounding data. The comparisons show that the new retrieval algorithm has a considerably better agreement with the validation data and delivers a more realistic Arctic-wide ice thickness distribution than the algorithm used in the previous study (Kaleschke et al., 2012).
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 24
    facet.materialart.
    Unknown
    A data-constrained model for compatibility check of remotely sensed basal melting with the hydrography in front of Antarctic ice shelves (2014)
    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus, 8(1), pp. 919-951, ISSN: 1994-0440
    Details
    Publication Date: 2019-07-16
    Description: The ice shelf caverns around Antarctica are sources of cold and fresh water which contributes to the formation of Antarctic bottom water and thus to the ventilation of the deep basins of the World Ocean. While a realistic simulation of the cavern circulation requires high resolution, because of the complicated bottom topography and ice shelf morphology, the physics of melting and freezing at the ice shelf base is relatively simple. We have developed an analytically solvable box model of the cavern thermohaline state, using the formulation of melting and freezing as in Olbers and Hellmer (2010). There is high resolution along the cavern's path of the overturning circulation whereas the cross-path resolution is fairly coarse. The circulation in the cavern is prescribed and used as a tuning parameter to constrain the solution by attempting to match observed ranges for outflow temperature and salinity at the ice shelf front as well as of the mean basal melt rate. The method, tested for six Antarctic ice shelves, can be used for a quick estimate of melt/freeze rates and the overturning rate in particular caverns, given the temperature and salinity of the inflow and the above mentioned constrains for outflow and melting. In turn, the model can also be used for testing the compatibility of remotely sensed basal mass loss with observed cavern inflow characteristics.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 25
    facet.materialart.
    Unknown
    Brazil-Malvinas confluence: effects of environmental variability on phytoplankton community structure (2012)
    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Details
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 26
    facet.materialart.
    Unknown
    Contribution to a bio-optical model for remote sensing of Lena River water (2013)
    Copernicus
    In:  EPIC3Biogeosciences, Copernicus, 10(11), pp. 7081-7094, ISSN: 1726-4189
    Details
    Publication Date: 2018-02-16
    Description: Bio-optical measurements and sampling were carried out in the delta of the Lena River (northern Siberia, Russia) between 26 June and 4 July 2011. The aim of this study was to determine the inherent optical properties of the Lena water, i.e., absorption, attenuation, and scattering coefficients, during the period of maximum runoff. This aimed to contribute to the development of a bio-optical model for use as the basis for optical remote sensing of coastal water of the Arctic. In this context the absorption by CDOM (colored dissolved organic matter) and particles, and the concentrations of total suspended matter, phytoplankton-pigments, and carbon were measured. CDOM was found to be the most dominant parameter affecting the optical properties of the river, with an absorption coefficient of 4.5–5 m−1 at 442 nm, which was almost four times higher than total particle absorption values at visible wavelength range. The wavelenght-dependence of absorption of the different water constituents was chracterized by determining the semi logarithmic spectral slope. Mean CDOM, and detritus slopes were 0.0149 nm−1(standard deviation (stdev) = 0.0003, n = 18), and 0.0057 nm−1 (stdev = 0.0017, n = 19), respectively, values which are typical for water bodies with high concentrations of dissolved and particulate carbon. Mean chlorophyll a and total suspended matter were 1.8 mg m−3 (stdev = 0.734 n = 18) and 31.9 g m−3 (stdev = 19.94, n = 27), respectively. DOC (dissolved organic carbon) was in the range 8–10 g m−3 and the total particulate carbon (PC) in the range 0.25–1.5 g m−3. The light penetration depth (Secchi disc depth) was in the range 30–90 cm and was highly correlated with the suspended matter concentration. The period of maximum river runoff in June was chosen to obtain bio-optical data when maximum water constituents are transported into the Laptev Sea. However, we are aware that more data from other seasons and other years need to be collected to establish a general bio-optical model of the Lena water and conclusively characterize the light climate with respect to primary production.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 27
    facet.materialart.
    Unknown
    An update to the Surface Ocean CO2 Atlas (SOCAT version 2) (2014)
    Copernicus
    In:  EPIC3Earth System Science Data, Copernicus, 6(1), pp. 69-90, ISSN: 1866-3516
    Details
    Publication Date: 2015-03-19
    Description: The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 28
    facet.materialart.
    Unknown
    Corrigendum to "Solar-forced shifts of the Southern Hemisphere Westerlies during the Holocene" published in Clim. Past, 7, 339–347, 2011 (2011)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 7(3), pp. 985-985, ISSN: 1814-9332
    Details
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 29
    facet.materialart.
    Unknown
    Can sparse proxy data constrain the strength of the Atlantic meridional overturning circulation? (2014)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(1), pp. 419-432, ISSN: 1991-9603
    Details
    Publication Date: 2019-07-17
    Description: In a feasibility study, the potential of proxy data for the temperature and salinity during the Last Glacial Maximum (LGM, about 19 000 to 23 000 years before present) in constraining the strength of the Atlantic meridional overturning circulation (AMOC) with a general ocean circulation model was explored. The proxy data were simulated by drawing data from four different model simulations at the ocean sediment core locations of the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface (MARGO) project, and perturbing these data with realistic noise estimates. The results suggest that our method has the potential to provide estimates of the past strength of the AMOC even from sparse data, but in general, paleo-sea-surface temperature data without additional prior knowledge about the ocean state during the LGM is not adequate to constrain the model. On the one hand, additional data in the deep-ocean and salinity data are shown to be highly important in estimating the LGM circulation. On the other hand, increasing the amount of surface data alone does not appear to be enough for better estimates. Finally, better initial guesses to start the state estimation procedure would greatly improve the performance of the method. Indeed, with a sufficiently good first guess, just the sea-surface temperature data from the MARGO project promise to be sufficient for reliable estimates of the strength of the AMOC.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 30
    facet.materialart.
    Unknown
    3D tracer advection in polar ice sheets: modeling stratigraphy and isotope distributions in Greenland & Antarctica (2013)
    Copernicus
    In:  EPIC3EGU General Assembly 2013, Vienna, 2013-04Geophysical Research Abstracts, Copernicus
    Details
    Publication Date: 2015-07-22
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 31
    facet.materialart.
    Unknown
    Tracing isotopes through ice: Integration of passive tracers in a three-dimensional ice sheet model (2012)
    Copernicus
    In:  EPIC3EGU General Assembly 2012, Vienna, 2012-04Geophysical Research Abstracts, Copernicus
    Details
    Publication Date: 2015-07-22
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 32
    facet.materialart.
    Unknown
    The genesis of Yedoma Ice Complex permafrost – grain-size endmember modeling analysis from Siberia and Alaska (2020)
    Copernicus
    In:  EPIC3E&G Quaternary Sci. J., Copernicus, 69, pp. 33-53, ISSN: 0424-7116
    Details
    Publication Date: 2022-04-19
    Description: The late Pleistocene Yedoma Ice Complex is an ice-rich and organic-bearing type of permafrost deposit widely distributed across Beringia and is assumed to be especially prone to deep degradation with warming temperature, which is a potential tipping point of the climate system. To better understand Yedoma formation, its local characteristics, and its regional sedimentological composition, we compiled the grain-size distributions (GSDs) of 771 samples from 23 Yedoma locations across the Arctic; samples from sites located close together were pooled to form 17 study sites. In addition, we studied 160 samples from three non-Yedoma ice-wedge polygon and floodplain sites for the comparison of Yedoma samples with Holocene depositional environments. The multimodal GSDs indicate that a variety of sediment production, transport, and depositional processes were involved in Yedoma formation. To disentangle these processes, a robust endmember modeling analysis (rEMMA) was performed. Nine robust grain-size endmembers (rEMs) characterize Yedoma deposits across Beringia. The study sites of Yedoma deposits were finally classified using cluster analysis. The resulting four clusters consisted of two to five sites that are distributed randomly across northeastern Siberia and Alaska, suggesting that the differences are associated with rather local conditions. In contrast to prior studies suggesting a largely aeolian contribution to Yedoma sedimentation, the wide range of rEMs indicates that aeolian sedimentation processes cannot explain the entire variability found in GSDs of Yedoma deposits. Instead, Yedoma sedimentation is controlled by local conditions such as source rocks and weathering processes, nearby paleotopography, and diverse sediment transport processes. Our findings support the hypothesis of a polygenetic Yedoma origin involving alluvial, fluvial, and niveo-aeolian transport; accumulation in ponding waters; and in situ frost weathering as well as postdepositional processes of solifluction, cryoturbation, and pedogenesis. The characteristic rEM composition of the Yedoma clusters will help to improve how grain-size-dependent parameters in permafrost models and soil carbon budgets are considered. Our results show the characteristic properties of ice-rich Yedoma deposits in the terrestrial Arctic. Characterizing and quantifying site-specific past depositional processes is crucial for elucidating and understanding the trajectories of this unique kind of ice-rich permafrost in a warmer future.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 33
    facet.materialart.
    Unknown
    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-02
    Description: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Description: Published
    Description: 452–464
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 34
    facet.materialart.
    Unknown
    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publication Date: 2022-03-07
    Description: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Description: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Description: Published
    Description: 536–547
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 35
    facet.materialart.
    Unknown
    Overcoming the challenges of studying conservation physiology in large whales : a review of available methods (2013)
    Oxford University Press
    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 Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 36
    facet.materialart.
    Unknown
    New broadband methods for resonance classification and high-resolution imagery of fish with swimbladders using a modified commercial broadband echosounder (2010)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 365-378, doi:10.1093/icesjms/fsp262.
    Description: A commercial acoustic system, originally designed for seafloor applications, has been adapted for studying fish with swimbladders. The towed system contains broadband acoustic channels collectively spanning the frequency range 1.7–100 kHz, with some gaps. Using a pulse-compression technique, the range resolution of the echoes is ~20 and 3 cm in the lower and upper ranges of the frequencies, respectively, allowing high-resolution imaging of patches and resolving fish near the seafloor. Measuring the swimbladder resonance at the lower frequencies eliminates major ambiguities normally associated with the interpretation of fish echo data: (i) the resonance frequency can be used to estimate the volume of the swimbladder (inferring the size of fish), and (ii) signals at the lower frequencies do not depend strongly on the orientation of the fish. At-sea studies of Atlantic herring demonstrate the potential for routine measurements of fish size and density, with significant improvements in accuracy over traditional high-frequency narrowband echosounders. The system also detected patches of scatterers, presumably zooplankton, at the higher frequencies. New techniques for quantitative use of broadband systems are presented, including broadband calibration and relating target strength and volume-scattering strength to quantities associated with broadband signal processing.
    Description: The research was supported by the US Office of Naval Research, grants number N00014-04-1-0440 and N00014-04-1-0475, NOAA/CICOR cooperative agreement NA17RJ1223, NOAA/ National Marine Fisheries Service, and the J. Seward Johnson Chair of the WHOI Academic Programs Office.
    Keywords: Acoustic scattering ; Broadband ; Echosounder ; Fish ; Resonance
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 37
    facet.materialart.
    Unknown
    TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage (2013)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 38
    facet.materialart.
    Unknown
    DRISEE overestimates errors in metagenomic sequencing data (2013)
    Oxford University Press
    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 Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/msword
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 39
    facet.materialart.
    Unknown
    Marine plankton phenology and life history in a changing climate : current research and future directions (2010)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in Journal of Plankton Research 32 (2010): 1355-1368, doi:10.1093/plankt/fbq062.
    Description: Increasing availability and extent of biological ocean time series (from both in situ and satellite data) have helped reveal significant phenological variability of marine plankton. The extent to which the range of this variability is modified as a result of climate change is of obvious importance. Here we summarize recent research results on phenology of both phytoplankton and zooplankton. We suggest directions to better quantify and monitor future plankton phenology shifts, including (i) examining the main mode of expected future changes (ecological shifts in timing and spatial distribution to accommodate fixed environmental niches vs. evolutionary adaptation of timing controls to maintain fixed biogeography and seasonality), (ii) broader understanding of phenology at the species and community level (e.g. for zooplankton beyond Calanus and for phytoplankton beyond chlorophyll), (iii) improving and diversifying statistical metrics for indexing timing and trophic synchrony and (iv) improved consideration of spatio-temporal scales and the Lagrangian nature of plankton assemblages to separate time from space changes.
    Description: This study was supported by NSF grants to R.J.: OCE-0727033, 0815838 and 0732152. NSF grants to A.C.T.: OCE-0535386, 0815051 and 0814413. NSF grant to J.A.R.: OCE 0815336.
    Keywords: Plankton ; Phenology ; Life history ; Climate change
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 40
    facet.materialart.
    Unknown
    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Description: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Description: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Keywords: population structure ; connectivity ; migration ; gene flow
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 41
    facet.materialart.
    Unknown
    The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism (2010)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial 2.5 License. The definitive version was published in Genome Biology and Evolution 2 (2010): 304, doi:10.1093/gbe/evq022.
    Description: Reduction of various biological processes is a hallmark of the parasitic lifestyle. Generally, the more intimate the association between parasites and hosts the stronger the parasite relies on its host's physiology for survival and reproduction. However, some systems have been held to be indispensable, for example, the core pathways of carbon metabolism that produce energy from sugars. Even the most hardened anaerobes that lack oxidative phosphorylation and the tricarboxylic acid cycle have retained glycolysis and some downstream means to generate ATP. Here we describe the deep-coverage genome resequencing of the pathogenic microsporidiian, Enterocytozoon bieneusi, which shows that this parasite has crossed this line and abandoned complete pathways for the most basic carbon metabolism. Comparing two genome sequence surveys of E. bieneusi to genomic data from four other microsporidia reveals a normal complement of 353 genes representing 30 functional pathways in E. bieneusi, except that only 2 out of 21 genes collectively involved in glycolysis, pentose phosphate, and trehalose metabolism are present. Similarly, no genes encoding proteins involved in the processing of spliceosomal introns were found. Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host.
    Description: This work was supported by grants from the Canadian Institutes for Health Research (MOP-84265), the National Institutes of Health (NIH AI31788, R21 AI52792, and R21 AI064118), and the National Science Foundation (MCB- 0135272). N.C. is a Scholar of the Canadian Institute for Advanced Research and is supported by a fellowship from the Swiss National Science Foundation (NSF) (PA00P3- 124166). D.E. is supported by the Swiss NSF. P.J.K. is a Fellow of the Canadian Institute for Advanced Research and a Senior Scholar of the Michael Smith Foundation for Health Research.
    Keywords: Microsporidia ; Parasite ; Glycolysis ; Carbon metabolism ; Reduction ; Evolution
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/vnd.ms-excel
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 42
    facet.materialart.
    Unknown
    Post-seismic viscoelastic deformation and stress transfer after the 1960 M9.5 Valdivia, Chile earthquake : effects on the 2010 M8.8 Maule, Chile earthquake (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 43
    facet.materialart.
    Unknown
    Persistence of ozone anomalies in the Arctic stratospheric vortex in autumn (2012)
    Copernicus
    In:  EPIC3Atmospheric Chemistry and Physics, Copernicus, 12(11), pp. 4817-4823
    Details
    Publication Date: 2019-07-16
    Description: Dynamical processes during the formation phase of the Arctic stratospheric vortex in autumn (from September to December) can introduce considerable interannual variability in the amount of ozone that is incorporated into the vortex. Chemistry in autumn tends to remove part of this variability because ozone relaxes towards equilibrium. As a quantitative measure of how important dynamical variability during vortex formation is for the winter ozone abundances above the Arctic we analyze which fraction of an ozone anomaly induced during vortex formation persists until early winter (3 January). The work is based on the Lagrangian Chemistry Transport Model ATLAS. In a case study, model runs for the winter 1999–2000 are used to assess the fate of an ozone anomaly artificially introduced during the vortex formation phase on 16 September. The runs provide information about the persistence of the induced ozone anomaly as a function of time, potential temperature and latitude. The induced ozone anomaly survives longer inside the polar vortex compared to outside the vortex. Half of the initial perturbation survives until 3 January at 540 K inside the polar vortex, with a rapid fall off towards higher levels, mainly due to NOx induced chemistry. Above 750 K the signal falls to values below 0.5%. Hence, dynamically induced ozone variability from the early vortex formation phase cannot significantly contribute to early winter variability above 750 K. At lower levels increasingly larger fractions of the initial perturbation survive, reaching 90% at 450 K. In this vertical range dynamical processes during the vortex formation phase are crucial for the ozone abundance in early winter.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 44
    facet.materialart.
    Unknown
    Ice sheet dynamics within an earth system model: downscaling, coupling and first results (2014)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(5), pp. 2003-2013, ISSN: 1991-9603
    Details
    Publication Date: 2016-12-09
    Description: We present first results from a coupled model setup, consisting of the state-of-the-art ice sheet model RIMBAY (Revised Ice Model Based on frAnk pattYn), and the community earth system model COSMOS. We show that special care has to be provided in order to ensure physical distributions of the forcings as well as numeric stability of the involved models. We demonstrate that a suitable statistical downscaling is crucial for ice sheet stability, especially for southern Greenland where surface temperatures are close to the melting point. The downscaling of net snow accumulation is based on an empirical relationship between surface slope and rainfall. The simulated ice sheet does not show dramatic loss of ice volume for pre-industrial conditions and is comparable with present-day ice orography. A sensitivity study with high CO2 level is used to demonstrate the effects of dynamic ice sheets onto climate compared to the standard setup with prescribed ice sheets.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 45
    facet.materialart.
    Unknown
    Crustal structures of the Boreas Basin and the Knipovich Ridge, North Atlantic (2013)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Details
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 46
    facet.materialart.
    Unknown
    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Description: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Description: Published
    Description: 704–718
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 47
    facet.materialart.
    Unknown
    Reduced El Niño variability in the mid-Pliocene according to the PlioMIP2 ensemble (2021)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 17(6), pp. 2427-2450, ISSN: 1814-9332
    Details
    Publication Date: 2022-01-10
    Description: The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 48
    facet.materialart.
    Unknown
    Evaluating the large-scale hydrological cycle response within the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) ensemble (2021)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 17(6), pp. 2537-2558, ISSN: 1814-9332
    Details
    Publication Date: 2022-01-10
    Description: The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 49
    facet.materialart.
    Unknown
    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-24
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Description: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Description: Published
    Description: 151–170
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 50
    facet.materialart.
    Unknown
    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-15
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Description: Published
    Description: 1465–1477
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 51
    facet.materialart.
    Unknown
    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-22
    Description: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Description: Published
    Description: egab062
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 52
    facet.materialart.
    Unknown
    INSTANCE – the Italian seismic dataset for machine learning (2021)
    Copernicus
    Details
    Publication Date: 2021-12-14
    Description: The Italian earthquake waveform data are collected here in a dataset suited for machine learning analysis (ML) applications. The dataset consists of nearly 1.2 million three-component (3C) waveform traces from about 50 000 earthquakes and more than 130 000 noise 3C waveform traces, for a total of about 43 000 h of data and an average of 21 3C traces provided per event. The earthquake list is based on the Italian Seismic Bulletin (http://terremoti.ingv.it/bsi, last access: 15 February 2020​​​​​​​) of the Istituto Nazionale di Geofisica e Vulcanologia between January 2005 and January 2020, and it includes events in the magnitude range between 0.0 and 6.5. The waveform data have been recorded primarily by the Italian National Seismic Network (network code IV) and include both weak- (HH, EH channels) and strong-motion (HN channels) recordings. All the waveform traces have a length of 120 s, are sampled at 100 Hz, and are provided both in counts and ground motion physical units after deconvolution of the instrument transfer functions. The waveform dataset is accompanied by metadata consisting of more than 100 parameters providing comprehensive information on the earthquake source, the recording stations, the trace features, and other derived quantities. This rich set of metadata allows the users to target the data selection for their own purposes. Much of these metadata can be used as labels in ML analysis or for other studies. The dataset, assembled in HDF5 format, is available at http://doi.org/10.13127/instance (Michelini et al., 2021).
    Description: Published
    Description: 5509–5544
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 53
    facet.materialart.
    Unknown
    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-24
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Description: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Description: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 54
    facet.materialart.
    Unknown
    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Description: Published
    Description: 29–49
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 55
    facet.materialart.
    Unknown
    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Description: Published
    Description: 1394–1418
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 56
    facet.materialart.
    Unknown
    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
    Details
    Publication Date: 2022-09-01
    Description: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Description: Published
    Description: 1404–1420
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 57
    facet.materialart.
    Unknown
    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publication Date: 2022-09-16
    Description: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 58
    facet.materialart.
    Unknown
    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Description: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Description: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Keywords: Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 59
    facet.materialart.
    Unknown
    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 60
    facet.materialart.
    Unknown
    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Description: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Description: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 61
    facet.materialart.
    Unknown
    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 62
    facet.materialart.
    Unknown
    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 63
    facet.materialart.
    Unknown
    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 64
    facet.materialart.
    Unknown
    Community comment on "Predicting trends in atmospheric CO2 across the Mid-Pleistocene Transition using existing climate archives" by Jordan R. W. Martin et al (2022)
    Copernicus
    In:  EPIC3Comment on egusphere-2022-574, EGUsphere, Copernicus
    Details
    Publication Date: 2022-10-24
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 65
    facet.materialart.
    Unknown
    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Description: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Description: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Description: 2023-07-04
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 66
    facet.materialart.
    Unknown
    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Description: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Keywords: Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 67
    facet.materialart.
    Unknown
    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Description: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Description: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 68
    facet.materialart.
    Unknown
    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-26
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Description: Published
    Description: 1283–1297
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 69
    facet.materialart.
    Unknown
    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Description: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 70
    facet.materialart.
    Unknown
    AWI-CM3 coupled climate model: Description and evaluation experiments for a prototype post-CMIP6 model (2022)
    Copernicus
    In:  EPIC3EGUsphere, Copernicus
    Details
    Publication Date: 2022-06-29
    Description: We developed a new version of the Alfred Wegener Institute Climate Model (AWI-CM3), which has higher skills in representing the observed climatology and better computational efficiency than its predecessors. Its ocean component FESOM2 has the multi-resolution functionality typical for unstructured-mesh models while still featuring a scalability and efficiency similar to regular-grid models. The atmospheric component OpenIFS (CY43R3) enables the use of latest developments in the numerical weather prediction community in climate sciences. In this paper we describe the coupling of the model components and evaluate the model performance on a variable resolution (25–125 km) ocean mesh and a 61 km atmosphere grid, which serves as a reference and starting point for other on-going research activities with AWI-CM3. This includes the exploration of high and variable resolution, the development of a full Earth System Model as well as the creation of a new sea ice prediction system. At this early development stage and with the given coarse to medium resolutions, the model already features above CMIP6-average skills in representing the climatology and competitive model throughput. Finally we identify remaining biases and suggest further improvements to be made to the model.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 71
    facet.materialart.
    Unknown
    The influence of tides on the marine carbonate chemistry of a coastal polynya in the south-eastern Weddell Sea (2022)
    Copernicus
    In:  EPIC3Ocean Science, Copernicus, 18(5), pp. 1293-1320, ISSN: 1812-0792
    Details
    Publication Date: 2022-09-23
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 72
    facet.materialart.
    Unknown
    Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates (2014)
    Oxford University Press
    Details
    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 Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 73
    facet.materialart.
    Unknown
    Magnetotelluric data, stable distributions and impropriety: an existential combination (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 74
    facet.materialart.
    Unknown
    Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/msword
    Format: image/jpeg
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 75
    facet.materialart.
    Unknown
    The evolution of the four subunits of voltage-gated calcium channels : ancient roots, increasing complexity, and multiple losses (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 76
    facet.materialart.
    Unknown
    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
    Details
    Publication Date: 2022-06-07
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Description: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Description: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Description: 2022-06-07
    Keywords: domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 77
    facet.materialart.
    Unknown
    On the true and the perceived minor interactions of dissolved phosphate and dissolved sulphate and some other constituents with the Alkalinity of oceanic seawater (2022)
    Copernicus
    In:  EPIC3On the true and the perceived minor interactions of dissolved phosphate and dissolved sulphate and some other constituents with the Alkalinity of oceanic seawater, EGUsphere [preprint], Copernicus
    Details
    Publication Date: 2022-08-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 78
    facet.materialart.
    Unknown
    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Description: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio-Environmental Synthesis Center under the US National Science Foundation Grant DBI-1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1-1).
    Keywords: Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 79
    facet.materialart.
    Unknown
    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 80
    facet.materialart.
    Unknown
    Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis (2012)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 81
    facet.materialart.
    Unknown
    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 82
    facet.materialart.
    Unknown
    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Description: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 83
    facet.materialart.
    Unknown
    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Description: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Description: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 84
    facet.materialart.
    Unknown
    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2020. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Description: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Description: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Description: 2021-10-16
    Keywords: dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 85
    facet.materialart.
    Unknown
    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 86
    facet.materialart.
    Unknown
    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Description: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Description: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 87
    facet.materialart.
    Unknown
    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Description: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Description: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Keywords: porpoise's physical model ; metamaterials ; biosonar ; directional emission
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 88
    facet.materialart.
    Unknown
    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Description: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Description: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 89
    facet.materialart.
    Unknown
    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Description: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Description: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 90
    facet.materialart.
    Unknown
    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Description: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Description: This work was supported by the National Science Foundation [OCE-1356192].
    Keywords: Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 91
    facet.materialart.
    Unknown
    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 92
    facet.materialart.
    Unknown
    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Description: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Description: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Keywords: Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 93
    facet.materialart.
    Unknown
    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 94
    facet.materialart.
    Unknown
    Variations in export production, lithogenic sediment transport and iron fertilization in the Pacific sector of the Drake Passage over the past 400 kyr (2022)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 18, pp. 147-166, ISSN: 1814-9324
    Details
    Publication Date: 2022-11-14
    Description: Changes in Southern Ocean export production have broad biogeochemical and climatic implications. Specifically, iron fertilization likely increased subantarctic nutrient utilization and enhanced the efficiency of the biological pump during glacials. However, past export production in the subantarctic Southeast Pacific is poorly documented, and its connection to Fe fertilization, potentially related to Patagonian Ice Sheet dynamics is unknown. We report on biological productivity changes over the past 400 ka, based on a combination of 230Thxs-normalized and stratigraphy-based mass accumulation rates of biogenic barium, organic carbon, biogenic opal, and calcium carbonate as indicators of paleo-export production in a sediment core upstream of the Drake Passage. In addition, we use fluxes of iron and lithogenic material as proxies for terrigenous matter, and thus potential micronutrient supply. Stratigraphy-based mass accumulation rates are strongly influenced by bottom-current dynamics, which result in variable sediment focussing or winnowing at our site. Carbonate is virtually absent in the core, except during peak interglacial intervals of the Holocene, and Marine Isotope Stages (MIS) 5 and 11, likely caused by transient decreases in carbonate dissolution. All other proxies suggest that export production increased during most glacial periods, coinciding with high iron fluxes. Such augmented glacial iron fluxes at the core site were most likely derived from glaciogenic input from the Patagonian Ice Sheet promoting the growth of phytoplankton. Additionally, glacial export production peaks are also consistent with northward shifts of the Subantarctic and Polar Fronts, which positioned our site south of the Subantarctic Front and closer to silicic acid-rich waters of the Polar Frontal Zone, as well as a with a decrease in the diatom utilization of Si relative to nitrate under Fe-replete conditions. However, glacial export production near the Drake Passage was lower than in the Atlantic and Indian sectors of the Southern Ocean, which may relate to complete consumption of silicic acid in the study area. Our results underline the importance of micro-nutrient fertilization through lateral terrigenous input from South America rather than aeolian transport, and exemplify the role of frontal shifts and nutrient limitation for past productivity changes in the Pacific entrance to the Drake Passage.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 95
    facet.materialart.
    Unknown
    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 96
    facet.materialart.
    Unknown
    River flooding as a driver of polygon dynamics: modern vegetation data and a millennial peat record from the Anabar River lowlands (Arctic Siberia) (2013)
    Copernicus
    In:  EPIC3Biogeosciences, Copernicus, 10(3), pp. 5703-5728, ISSN: 1726-4189
    Details
    Publication Date: 2024-04-23
    Description: 〈jats:p〉Abstract. The spatial and temporal variability of a low-centred polygon on the eastern floodplain area of the lower Anabar River (72.070° N, 113.921° E, northern Yakutia, Siberia) has been investigated using a multi-method approach. The present-day vegetation in each square metre was analysed revealing a community of Larix shrubby Betula and Salix on the polygon rim, a dominance of Carex and Andromeda polifolia in the rim-to-pond transition zone, and a predominantly monospecific Scorpidium scorpioides coverage within the pond. The TOC content, TOC/TN ratio, grain-size, vascular plant macrofossils, moss remains, diatoms, and pollen were analysed for two vertical sections and a sediment core from a transect across the polygon. Radiocarbon dating indicates that the formation of the polygon started at least 1500 yr ago; the general positions of the pond and rim have not changed since that time. Two types of pond vegetation were identified, indicating two contrasting development stages of the polygon. The first was a well-established moss association dominated by submerged or floating Scorpidium scorpioides and/or Drepanocladus spp. and overgrown by epiphytic diatoms such as Tabellaria flocculosa and Eunotia taxa. This stage coincides temporally with a period in which the polygon was only drained by lateral subsurface water flow, as indicated by mixed grain sizes. A different moss association occurred during times of repeated river flooding (indicated by homogeneous medium-grained sand that probably accumulated during the annual spring snow melt), characterized by an abundance of Meesia triquetra and a dominance of benthic diatoms (e.g. Navicula vulpina), indicative of a relatively high pH and a high tolerance of disturbance. A comparison of the local polygon vegetation (inferred from moss and macrofossil spectra) with the regional vegetation (inferred from pollen spectra) indicated that the moss association with Scorpidium scorpioides became established during relatively favourable climatic conditions while the association dominated by Meesia triquetra occurred during periods of harsh climatic conditions. Our study revealed a strong riverine influence (in addition to climatic influences) on polygon development and the type of peat accumulated. 〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 97
    facet.materialart.
    Unknown
    Fertilization success of an arctic sea urchin species, Strongylocentrotus droebachiensis (O. F. Mueller, 1776) under CO2-induced ocean acidification (2013)
    Copernicus
    In:  EPIC3Biogeosciences Discuss, Copernicus, 10, pp. 8027-8064
    Details
    Publication Date: 2024-04-11
    Description: Sea urchins as broadcasting spawners, release their gametes into open water for fertilization, thus being particularly vulnerable to ocean acidification. In this study, we assessed the effects of different pH scenarios on fertilization success of Strongylocen- 5 trotus droebachiensis, collected at Spitsbergen, Arctic. We achieved acidification by bubbling CO2 into filtered seawater using partial pressures (pCO2) of 180, 380, 980, 1400 and 3000 μatm. Untreated filtered seawater was used as control. We recorded fertilization rates and diagnosed morphological aberrations after post-fertilization periods of 1 h and 3 h under different exposure conditions in experiments with and without 10 pre-incubation of the eggs prior to fertilization. In parallel, we conducted measurements of intracellular pH changes using BCECF/AM in unfertilized eggs exposed to a range of acidified seawater. We observed increasing rates of polyspermy in relation to higher seawater pCO2, which might be due to failures in the formation of the fertilization envelope. In addition, our experiments showed anomalies in fertilized eggs: incomplete 15 lifting-off of the fertilization envelope and blebs of the hyaline layer. Other drastic malformations consisted of constriction, extrusion, vacuolization or degeneration (observed as a gradient from the cortex to the central region of the cell) of the egg cytoplasm, and irregular cell divisions until 2- to 4-cell stages. The intracellular pH (pHi) decreased significantly from 1400 μatm on. All results indicate a decreasing fertilization success 20 at CO2 concentrations from 1400 μatm upwards. Exposure time to low pH might be a threatening factor for the cellular buffer capacity, viability, and development after fertilization.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 98
    facet.materialart.
    Unknown
    Population Size Dependence of Fitness Effect Distribution and Substitution Rate Probed by Biophysical Model of Protein Thermostability (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-07
    Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 99
    facet.materialart.
    Unknown
    Regional and local patterns in depth to water table, hydrochemistry and peat properties of bogs and their laggs in coastal British Columbia (2013)
    Copernicus
    Details
    Publication Date: 2013-09-06
    Description: Regional and local patterns in depth to water table, hydrochemistry and peat properties of bogs and their laggs in coastal British Columbia Hydrology and Earth System Sciences, 17, 3421-3435, 2013 Author(s): S. A. Howie and H. J. van Meerveld In restoration planning for damaged raised bogs, the lagg at the bog margin is often not given considerable weight and is sometimes disregarded entirely. However, the lagg is critical for the proper functioning of the bog, as it supports the water mound in the bog. In order to include the lagg in a restoration plan for a raised bog, it is necessary to understand the hydrological characteristics and functions of this rarely studied transition zone. We studied 13 coastal British Columbia (BC) bogs and identified two different gradients in depth to water table, hydrochemistry and peat properties: (1) a local bog expanse–bog margin gradient, and (2) a regional gradient related to climate and proximity to the ocean. Depth to water table generally increased across the transition from bog expanse to bog margin. In the bog expanse, pH was above 4.2 in the Pacific Oceanic wetland region (cooler and wetter climate) and below 4.3 in the Pacific Temperate wetland region (warmer and drier climate). Both pH and pH-corrected electrical conductivity increased significantly across the transition from bog expanse to bog margin, though not in all cases. Na + and Mg 2+ concentrations were generally highest in exposed, oceanic bogs and lower in inland bogs. Ash content in peat samples increased across the bog expanse–bog margin transition, and appears to be a useful abiotic indicator of the location of the bog margin. The observed variation in the hydrological and hydrochemical gradients across the bog expanse–bog margin transition highlights both local and regional diversity of bogs and their associated laggs.
    Print ISSN: 1027-5606
    Electronic ISSN: 1607-7938
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 100
    facet.materialart.
    Unknown
    Imperfect scaling in distributions of radar-derived rainfall fields (2013)
    Copernicus
    Details
    Publication Date: 2013-09-06
    Description: Imperfect scaling in distributions of radar-derived rainfall fields Hydrology and Earth System Sciences Discussions, 10, 11385-11422, 2013 Author(s): M. J. van den Berg, L. Delobbe, and N. E. C. Verhoest Fine scale rainfall observations for modeling exercises are often not available, but rather coarser data derived from a variety of sources are used. Effectively using these data sources in models often requires the probability distribution of the data at the applicable scale. Although numerous models for scaling distributions exist, these are often based on theoretical developments, rather than on data. In this study, we develop a model based on the α-stable distribution of rainfall fields, and tested on 5 min radar data from a Belgian weather radar. We use these data to estimate functions that describe parameters of the distribution over various scales. Moreover, we study how the mean of the distribution and the intermittency change with scale, and validate and design functions to describe the shape parameter of the distribution. This information was combined into an effective model of the distribution. Finally, the model was fitted to data from numerous storms, and the resulting parameters were compared to investigate the change in scaling behavior through time.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...