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  • 1
    Publication Date: 2021-06-08
    Description: The Aegean water masses and circulation structure are studied via two large-scale surveys performed during the late winters of 1988 and 1990 by the R/V Yakov Gakkel of the former Soviet Union. The analysis of these data sheds light on the mechanisms of water mass formation in the Aegean Sea that triggered the outflow of Cretan Deep Water (CDW) from the Cretan Sea into the abyssal basins of the eastern Mediterranean Sea (the so-called Eastern Mediterranean Transient). It is found that the central Aegean Basin is the site of the formation of Aegean Intermediate Water, which slides southward and, depending on their density, renews either the intermediate or the deep water of the Cretan Sea. During the winter of 1988, the Cretan Sea waters were renewed mainly at intermediate levels, while during the winter of 1990 it was mainly the volume of CDW that increased. This Aegean water mass redistribution and formation process in 1990 differed from that in 1988 in two major aspects: (i) during the winter of 1990 the position of the front between the Black Sea Water and the Levantine Surface Water was displaced farther north than during the winter of 1988 and (ii) heavier waters were formed in 1990 as a result of enhanced lateral advection of salty Levantine Surface Water that enriched the intermediate waters with salt. In 1990 the 29.2 isopycnal rose to the surface of the central basin and a large volume of CDW filled the Cretan Basin. It is found that, already in 1988, the 29.2 isopycnal surface, which we assume is the lowest density of the CDW, was shallower than the Kassos Strait sill and thus CDW egressed into the Eastern Mediterranean.
    Description: Published
    Description: 1841-1859
    Description: JCR Journal
    Description: reserved
    Keywords: Aegean Sea ; Water Masses ; 03. Hydrosphere::03.03. Physical::03.03.03. Interannual-to-decadal ocean variability
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-06-01
    Description: Five non-eddy-resolving oceanic general circulation models driven by atmospheric fluxes derived from the NCEP reanalysis are used to investigate the link between the Gulf Stream (GS) variability, the atmospheric circulation, and the Atlantic meridional overturning circulation (AMOC). Despite the limited model resolution, the temperature at the 200-m depth along the mean GS axis behaves similarly in most models to that observed, and it is also well correlated with the North Atlantic Oscillation (NAO), indicating that a northward (southward) GS shift lags a positive (negative) NAO phase by 0–2 yr. The northward shift is accompanied by an increase in the GS transport, and conversely the southward shift with a decrease in the GS transport. Two dominant time scales appear in the response of the GS transport to the NAO forcing: a fast time scale (less than 1 month) for the barotropic component, and a slower one (about 2 yr) for the baroclinic component. In addition, the two components are weakly coupled. The GS response seems broadly consistent with a linear adjustment to the changes in the wind stress curl, and evidence for baroclinic Rossby wave propagation is found in the southern part of the subtropical gyre. However, the GS shifts are also affected by basin-scale changes in the oceanic conditions, and they are well correlated in most models with the changes in the AMOC. A larger AMOC is found when the GS is stronger and displaced northward, and a higher correlation is found when the observed changes of the GS position are used in the comparison. The relation between the GS and the AMOC could be explained by the inherent coupling between the thermohaline and the wind-driven circulation, or by the NAO variability driving them on similar time scales in the models.
    Description: This research was supported by the PREDICATE project of the European Community, and for M. Bentsen by the Research Council of Norway through RegClim, NOClim, and the Programme of Supercomputing.
    Description: Published
    Description: 2119–2135
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: ocean modelling ; gulf stream variability ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2020-11-19
    Description: A land surface model (LSM) has been included in the ECMWF Hamburg version 4 (ECHAM4) atmospheric general circulation model (AGCM). The LSM is an early version of the Organizing Carbon and Hydrology in Dynamic Ecosystems (ORCHIDEE) and it replaces the simple land surface scheme previously included in ECHAM4. The purpose of this paper is to document how a more exhaustive consideration of the land surface–vegetation processes affects the simulated boreal summer surface climate. To investigate the impacts on the simulated climate, different sets of Atmospheric Model Intercomparison Project (AMIP)-type simulations have been performed with ECHAM4 alone and with the AGCM coupled with ORCHIDEE. Furthermore, to assess the effects of the increase in horizontal resolution the coupling of ECHAM4 with the LSM has been implemented at different horizontal resolutions. The analysis reveals that the LSM has large effects on the simulated boreal summer surface climate of the atmospheric model. Considerable impacts are found in the surface energy balance due to changes in the surface latent heat fluxes over tropical and midlatitude areas covered with vegetation. Rainfall and atmospheric circulation are substantially affected by these changes. In particular, increased precipitation is found over evergreen and summergreen vegetated areas. Because of the socioeconomical relevance, particular attention has been devoted to the Indian summer monsoon (ISM) region. The results of this study indicate that precipitation over the Indian subcontinent is better simulated with the coupled ECHAM4–ORCHIDEE model compared to the atmospheric model alone.
    Description: Published
    Description: 255–278
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: partially_open
    Keywords: Land Atmosphere interactions ; Global climate models ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2017-04-04
    Description: In this paper results from the application of an ocean data assimilation (ODA) system, combining a multivariate reduced-order optimal interpolator (OI) scheme with a global ocean general circulation model (OGCM), are described. The present ODA system, designed to assimilate in situ temperature and salinity observations, has been used to produce ocean reanalyses for the 1962–2001 period. The impact of assimilating observed hydrographic data on the ocean mean state and temporal variability is evaluated. A special focus of this work is on the ODA system skill in reproducing a realistic ocean salinity state. Results from a hierarchy of different salinity reanalyses, using varying combinations of assimilated data and background error covariance structures, are described. The impact of the space and time resolution of the background error covariance parameterization on salinity is addressed.
    Description: This work has been funded by the ENACT Project (Contract EVK2-CT2001-00117) for A. Bellucci and P. Di Pietro, and partially by the ENSEMBLES Project (Contract GOCE-CT-2003-505539) for A. Bellucci.
    Description: Published
    Description: 3785-3807
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: ocean modelling ; data assimilation ; reanalysis ; upper ocean variability ; temperature ; Salinity ; 03. Hydrosphere::03.01. General::03.01.04. Ocean data assimilation and reanalysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: Red Pompeian paintings, very famous for their deep intensity, are currently suffering from darkening. The origins of this darkening degradation are not clearly identified yet and remain a major issue for curators. In the specific case of cinnabar (HgS)-based red pigment, a photoinduced conversion into black metacinnabar is usually suspected. This work is focused on the blackening of red cinnabar paintings coated on a sparry calcite mortar. Different samples exhibiting different levels of degradation were selected upon visual observations and analyzed by synchrotron-based microanalytical techniques. Atomic and molecular compositions of the different debased regions revealed two possible degradation mechanisms. On one hand, micro X-ray fluorescence elemental maps show peculiar distributions of chlorine and sulfur. On the other hand, X-ray absorption spectroscopy performed at both Cl and S K-edges confirms the presence of characteristic degradation products: (i) Hg- Cl compounds (e.g., corderoite, calomel, and terlinguaite), which may result from the reaction with exogenous NaCl, in gray areas; (ii) gypsum, produced by the calcite sulfation, in black coatings. Metacinnabar is never detected. Finally, a cross section was analyzed to map the in-depth alteration gradient. Reduced and oxidized sulfur distributions reveal that the sulfated black coating consists of a 5-ím-thick layer covering intact cinnabar.
    Description: Published
    Description: 7484-7492
    Description: reserved
    Keywords: Microspectroscopy Analysis ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2017-04-04
    Description: The effect of horizontal resolution on tropical variability is investigated within the modified SINTEX model, SINTEX-F, developed jointly at INGV, IPSL and at the Frontier Research System. The horizontal resolutions T30 and T106 are investigated in terms of the coupling characteristics, frequency and variability of the tropical ocean-atmosphere interactions. It appears that the T106 resolution is generally beneficial even if it does not eliminate all the major systematic errors of the coupled model. There is an excessive shift west of the cold tongue and ENSO variability, and high resolution has also a somewhat negative impact to the variability in the East Indian Ocean. A dominant two-year peak for the NINO3 variabilty in the T30 model is moderated in the T106 as it shifts to longer time scale. At high resolution new processes come into play, as the coupling of tropical instability waves, the resolution of coastal flows at the Pacific Mexican coasts and improved coastal forcing along the coast of South America. The delayed oscillator seems the main mechanism that generates the interannual variability in both models, but the models realize it in different ways. In the T30 model it is confined close to the equator, involving relatively fast equatorial and near-equatorial modes, in the high resolution, it involves a wider latitudinal region and slower waves. It is speculated that the extent of the region that is involved in the interannual variability may be linked to the time scale of the variability itself.
    Description: This research was partially supported by the Italy–USA Cooperation Program of the Italian Ministry of Environment and by the EU projects ENSEMBLES and DYNAMITE.
    Description: Published
    Description: 730-750
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: coupled models ; tropical variability ; ENSO system ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2017-04-04
    Description: The Indian Summer Monsoon (ISM) is one of the main components of the Asian summer monsoon. It is well known that one of the starting mechanisms of a summer monsoon is the thermal contrast between land and ocean and that sea surface temperature (SST) and moisture are crucial factors for its evolution and intensity. The Indian Ocean, therefore, may play a very important role in the generation and evolution of the ISM itself. A coupled general circulation model, implemented with a high resolution atmospheric component, appears to be able to simulate the Indian summer monsoon in a realistic way. In particular, the features of the simulated ISM variability are similar to the observations. In this study, the relationships between ISM and Tropical Indian Ocean (TIO) SST anomalies are investigated, as well as the ability of the coupled model to capture those connections. The recent discovery of the Indian Ocean Dipole Mode (IODM) may suggest new perspectives in the relationship between ISM and TIO SST. A new statistical technique, the Coupled Manifold, is used to investigate the TIO SST variability and its relation with the Tropical Pacific Ocean (TPO). The analysis shows that the SST variability in the TIO contains a significant portion that is independent from the TPO variability. The same technique is used to estimate the amount of Indian rainfall variability that can be explained by the Tropical Indian Ocean SST. Indian Ocean SST anomalies are separated in a part remotely forced from the Tropical Pacific Ocean variability and a part independent from that. The relationships between the two SSTA components and the Indian monsoon variability are then investigated in detail.
    Description: Published
    Description: 3083-3105
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: Indian Ocean ; monsoon ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2017-04-04
    Description: An assessment of the present European operational marine monitoring and forecasting systems shows how observations, atmospheric forcing fields and ocean models combine to make useful oceanographic products possible.
    Description: Published
    Description: 1081-1090
    Description: open
    Keywords: MARINE ENVIRONMENT ; 03. Hydrosphere::03.01. General::03.01.05. Operational oceanography
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: Ensemble experiments are performed with five coupled atmosphere–ocean models to investigate the potential for initial-value climate forecasts on interannual to decadal time scales. Experiments are started from similar model-generated initial states, and common diagnostics of predictability are used. We find that variations in the ocean meridional overturning circulation (MOC) are potentially predictable on interannual to decadal time scales, a more consistent picture of the surface temperature impact of decadal variations in the MOC is now apparent, and variations of surface air temperatures in the North Atlantic Ocean are also potentially predictable on interannual to decadal time scales, albeit with potential skill levels that are less than those seen for MOC variations. This intercomparison represents a step forward in assessing the robustness of model estimates of potential skill and is a prerequisite for the development of any operational forecasting system.
    Description: Published
    Description: 1195-1203
    Description: JCR Journal
    Description: reserved
    Keywords: Decadal Climate ; North Atlantic ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models ; 03. Hydrosphere::03.02. Hydrology::03.02.05. Models and Forecasts ; 03. Hydrosphere::03.03. Physical::03.03.03. Interannual-to-decadal ocean variability
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    American Meteorological Society
    In:  EPIC3Journal of Atmospheric and Oceanic Technology, American Meteorological Society, 25(2), pp. 149-166, ISSN: 0739-0572
    Publication Date: 2019-07-17
    Description: The accuracy of all types of Vaisala radiosondes and two types of Snow White chilled-mirror hygrosondes was assessed in an intensive in situ comparison with reference hygrometers. Fourteen nighttime reference comparisons were performed to determine a working reference for the radiosonde comparisons. These showed that the night version of the Snow White agreed best with the references [i.e., the NOAA frost-point hygrometer (FPH) and University of Colorado cryogenic frost-point hygrometer (CFH)], but that the daytime version had severe problems with contamination in the humid upper troposphere. Since the RS92 performance was superior to the other radiosondes and to the day version of the Snow White, it was selected to be the working reference. According to the reference comparison, the RS92 has no bias in the mid- and lower troposphere, with deviations 〈±5% in relative humidity (RH). In the upper troposphere, the RS92 has a 5% RH wet bias, which is partly due to the RS92 time lag error and the termination of the heating cycle. It was shown that the time lag effects relating to Vaisala radiosondes can be corrected. Because these were nighttime comparisons, they can be considered to be free from solar radiation effects. Neither the radiosondes nor the Snow White succeeded in reproducing reference class hygrometer profiles in the stratosphere. According to the 29 radiosonde intercomparisons, the RS92 and the modified RS90 (FN) had the best mutual agreement and no bias. The disagreement is largest (〈±10% RH) at low temperatures (T ≪ −30°C), where the FN underestimated (overestimated) in high (low) ambient RH. In comparison with the RS92, the RS90 had a semilinearly increasing wet bias with decreasing temperature, where the bias was 10% RH at −60°C. The RS80-A suffers from a large temperature-dependent dry bias in high RH conditions, being over 30% RH at −60°C and 5% RH near 0°C. The RS80-A dry bias can be almost totally removed with the correction algorithm by Leiterer et al., which was chosen as the best available. The other approach tested tends to overcorrect in high RH conditions when T 〈 −50°C. For T 〉 −30°C it is ineffective and does not correct the RS80-A dry bias in high ambient RH.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 11
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    American Meteorological Society
    Publication Date: 2021-05-19
    Description: In this study we show a teleconnection pattern relating Outgoing Longwave Radiation (OLR) anomalies over the western Pacific Ocean and sea surface temperature anomalies (SSTA) over the western Indian Ocean over two seasons (Sept-Oct-Nov and Dec-Jan-Feb) at zero lag from observations and atmospheric general circulation model (AGCM) integrations. This teleconnection pattern suggests that a positive SSTA in Sept-Oct-Nov (SON) and Dec-Jan-Feb (DJF) seasons over the western Indian Ocean increases the contemporaneous positive OLR anomalies over the western Pacific Ocean. This teleconnection pattern is also simulated by the Center for Ocean-Land- Atmosphere studies (COLA) AGCM forced with observed SST’s. From the experimental COLA AGCM runs (wherein the Pacific Ocean SST variability is suppressed except for the climatological annual cycle) it is diagnosed that the interannual variability of OLR over the western Pacific Ocean persists because of this teleconnection. In relation to this teleconnection pattern it is shown that there is a significant linear response of the SON and DJF equatorial zonal wind anomaly over the Pacific Ocean to contemporaneous SSTA over the western Indian Ocean which is comparable to that of the eastern and western Pacific Oceans. The experimental AGCM runs clearly show that this response of the equatorial zonal wind anomaly to the western Indian Ocean forcing shifts westward towards the Indian Ocean in the absence of Pacific SST variability.
    Description: Published
    Keywords: Sea surface temperature ; Atmospheric conditions ; Teleconnections
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed , Article
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  • 12
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    American Meteorological Society
    Publication Date: 2021-05-19
    Description: Skill in ensemble-mean dynamical seasonal climate hindcasts with a coupled land-atmosphere model and specified observed sea surface temperature is compared to that for long multi-decade integrations of the same model where the initial conditions are far removed from the seasons of validation. The evaluations are performed for surface temperature and compared among all seasons. Skill is found to be higher in the seasonal simulations than the multi-decadal integrations except during boreal winter. The higher skill is prominent even beyond the first month when the direct influence of the atmospheric initial state elevates model skill. Skill is generally found to be lowest during the winter season for the dynamical seasonal forecasts, equal to that of the long integrations, which show some of the highest skill during winter. The reason for the differences in skill during the non-winter months is attributed to the severe climate drift in the long simulations, manifest through errors in downward fluxes of water and energy over land and evident in soil wetness. The drift presses the land surface to extreme dry or wet states over much of the globe, into a range where there is little sensitivity of evaporation to fluctuations in soil moisture. Thus, the land-atmosphere feedback is suppressed, which appears to lessen the model’s ability to respond correctly over land to remote ocean temperature anomalies.
    Description: Center for Ocean-Land-Atmosphere Studies
    Description: Published
    Keywords: Atmosphere-ocean system
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed , Article
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  • 13
    Publication Date: 2021-05-19
    Description: In this paper, the circulations driven by deep heating and shallow heating are investigated through analytically solving a set of linear equations and examining circulations simulated by a dry primitive equation model. Special emphasis is placed on the low-level mass (moisture) convergence associated with the forced circulation and the maintenance of the shallow and deep heat sources. It is found that the forced circulation driven by shallow heating is more likely to be trapped horizontally near the heating area but relatively extended in the vertical. As a consequence, diabatic heating can not balance adiabatic cooling due to upward motion. At the levels slightly above the top of the heating, a negative vertical gradient of temperature perturbation appears. For the atmosphere driven by deep heating, however, the temperature perturbation cannot accumulate because the heating signals propagate away very fast, allowing an approximate equilibrium between the convective diabatic heating and adiabatic cooling due to upward motion. The converged moisture associated with circulation driven by shallow heating exceeds the amount needed to maintain the heat source. However, the circulation driven by deep heating does not feed back effectively to the moisture convergence, and thus can not be self-sustaining.
    Description: Center for Ocean-Land-Atmosphere Studies - Calverton
    Description: Published
    Keywords: Atmospheric circulation
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed , Article
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  • 14
    Publication Date: 2022-05-25
    Description: © 2008 Hutt et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Developmental Biology 8 (2008): 1, doi:10.1186/1471-213X-8-1.
    Description: Environmental toxicants, whose actions are often mediated through the aryl hydrocarbon receptor (AhR) pathway, pose risks to the health and well-being of exposed species, including humans. Of particular concern are exposures during the earliest stages of development that while failing to abrogate embryogenesis, may have long term effects on newborns or adults. The purpose of this study was to evaluate the effect of maternal exposure to the AhR-specific ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the development of rat pre-implantation embryos with respect to nuclear and cytoskeletal architecture and cell lineage allocation. We performed a systematic 3 dimensional (3D) confocal microscopy analysis of rat pre-implantation embryos following maternal exposure to environmentally relevant doses of TCDD. Both chronic (50 ng/kg/wk for 3 months) and acute (50 ng/kg and 1 μg/kg at proestrus) maternal TCDD exposure disrupted morphogenesis at the compaction stage (8–16 cell), with defects including monopolar spindle formation, f-actin capping and fragmentation due to aberrant cytokinesis. Additionally, the size, shape and position of nuclei were modified in compaction stage pre-implantation embryos collected from treated animals. Notably, maternal TCDD exposure did not compromise survival to blastocyst, which with the exception of nuclear shape, were morphologically similar to control blastocysts. We have identified the compaction stage of pre-implantation embryogenesis as critically sensitive to the effects of TCDD, while survival to the blastocyst stage is not compromised. To the best of our knowledge this is the first in vivo study to demonstrate a critical window of pre-implantation mammalian development that is vulnerable to disruption by an AhR ligand at environmentally relevant doses.
    Description: This research was supported by NIH/NIEHS-012916 (BKP), ESHE Fund (DFA), Hall Family Foundation (DFA and KJH) and Biomedical Research Training Grant KUMC (KJH).
    Repository Name: Woods Hole Open Access Server
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  • 15
    Publication Date: 2022-05-25
    Description: © 2007 Ioannidis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 8 (2007): 182, doi:10.1186/1471-2164-8-182.
    Description: Background: The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria. Results: Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein). Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites. Conclusion: The sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.
    Description: PI, PS, SS, GT and KB acknowledge support of their work from intramural funding from the University of Ioannina. SB, JDH, LB and JW acknowledge support of their work from the U.S. National Science Foundation grant EF-0328363. SB also acknowledges the support from the NASA Astrobiology Institute (NNA04CC04A)
    Repository Name: Woods Hole Open Access Server
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  • 16
    Publication Date: 2022-05-25
    Description: © 2007 Huse et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R143, doi:10.1186/gb-2007-8-7-r143.
    Description: Additional data file 1 is a fasta file of the 43 known sequences used. Additional data file 2 is a gzip-compressed fasta file of the sequences output by the GS20. These sequences correspond to those included in Additional data files 3, 4, 5 but include only the final sequence information. Additional data files 3, 4, 5 are three compressed text files representing the text translations of the original GS20 binary output (sff) files for all of the sequencing used in the analysis, including sequence, flowgram and other run information. GS20 data are reported by region of the PicoTiterPlate™; we sequenced three plate regions.
    Description: Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls. We performed an empirical study of the per-base error rate for the Roche GS20 system using sequences of the V6 hypervariable region from cloned microbial ribosomal DNA (tag sequencing). We calculated a 99.5% accuracy rate in unassembled sequences, and identified several factors that can be used to remove a small percentage of low-quality reads, improving the accuracy to 99.75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.
    Description: This work was supported by National Aeronautics and Space Administration Astrobiology Institute Cooperative Agreement NNA04CC04A (to MLS), subcontracts from the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J Stegeman PI to HGM and MLS), grants from the WM Keck Foundation and the G Unger Vetlesen Foundation (to MLS), and a National Research Council Research Associateship Award (to JAH).
    Repository Name: Woods Hole Open Access Server
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  • 17
    Publication Date: 2022-05-25
    Description: © 2008 Salvador-Recatalà et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Physiology 8 (2008): 6, doi:10.1186/1472-6793-8-6.
    Description: The function of voltage-gated calcium (Cav) channels greatly depends on coupling to cytoplasmic accessory β subunits, which not only promote surface expression, but also modulate gating and kinetic properties of the α1 subunit. Schistosomes, parasitic platyhelminths that cause schistosomiasis, express two β subunit subtypes: a structurally conventional β subunit and a variant β subunit with unusual functional properties. We have previously characterized the functional properties of the variant Cavβ subunit. Here, we focus on the modulatory phenotype of the conventional Cavβ subunit (SmCavβ) using the human Cav2.3 channel as the substrate for SmCavβ and the whole-cell patch-clamp technique. The conventional Schistosoma mansoni Cavβ subunit markedly increases Cav2.3 currents, slows macroscopic inactivation and shifts steady state inactivation in the hyperpolarizing direction. However, currents produced by Cav2.3 in the presence of SmCavβ run-down to approximately 75% of their initial amplitudes within two minutes of establishing the whole-cell configuration. This suppressive effect was independent of Ca2+, but dependent on intracellular Mg2+-ATP. Additional experiments revealed that SmCavβ lends the Cav2.3/SmCavβ complex sensitivity to Na+ ions. A mutant version of the Cavβ subunit lacking the first forty-six amino acids, including a string of twenty-two acidic residues, no longer conferred sensitivity to intracellular Mg2+-ATP and Na+ ions, while continuing to show wild type modulation of current amplitude and inactivation of Cav2.3. The data presented in this article provide insights into novel mechanisms employed by platyhelminth Cavβ subunits to modulate voltage-gated Ca2+ currents that indicate interactions between the Ca2+ channel complex and chelated forms of ATP as well as Na+ ions. These results have potentially important implications for understanding previously unknown mechanisms by which platyhelminths and perhaps other organisms modulate Ca2+ currents in excitable cells.
    Description: This work was supported by NIH grant #s R01 AI-40522 and R01 AI-73660 to RMG and by NIH-NCRR grant # P41 RR001395 to the Biocurrents Research Center (BRC) at MBL.
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    Publication Date: 2022-05-25
    Description: © 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 9 (2008): 210, doi:10.1186/1471-2164-9-210.
    Description: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.
    Description: MR acknowledges support from DE-FG02-04ER63940. JTS acknowledges the support from the University of Washington NASA NAI program and the NSF Astrobiology IGERT program. TZW acknowledges support from a grant from the Fondation Fourmentin-Guilbert and AD acknowledges support from the European Union BioSapiens Network of Excellence, Grant LSHG CT-2003-503265
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    Publication Date: 2022-05-25
    Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 10 (2009): 11, doi:10.1186/1471-2164-10-11.
    Description: Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. Current results provide quantitative substitution preferences (or avoidance) of amino acids that lead to the adaptation of proteins to cold temperatures. These finding would help future efforts in selecting mutations for rational design of proteins with enhanced psychrophilic properties.
    Description: This work was supported by a grant from Howard Hughes Medical Institute to Queens College, CUNY, and Queens College Research Enhancement Grant.
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    Publication Date: 2022-05-25
    Description: © 2009 Sarkar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 2 (2009): 101, doi:10.1186/1756-0500-2-101.
    Description: GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.
    Description: INS and HM are funded in part by a research grant from the Ellison Medical Foundation and National Library of Medicine award R01LM009725 to INS.
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    Publication Date: 2022-05-25
    Description: © 2009 Reitzel and Tarrant. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 230, doi:10.1186/1471-2148-9-230.
    Description: Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Sequenced genomes from an increasing number of bilaterians have provided a more complete picture of duplication and loss of nuclear receptors in protostomes and deuterostomes but have left open the question of which nuclear receptors were present in the cnidarian-bilaterian ancestor. In addition, nuclear receptor expression and function are largely uncharacterized within cnidarians, preventing determination of conserved and novel nuclear receptor functions in the context of animal evolution. Here we report the first complete set of nuclear receptors from a cnidarian, the starlet sea anemone Nematostella vectensis. Genomic searches using conserved DNA- and ligand-binding domains revealed seventeen nuclear receptors in N. vectensis. Phylogenetic analyses support N. vectensis orthologs of bilaterian nuclear receptors in four nuclear receptor subfamilies within nuclear receptor family 2 (COUP-TF, TLL, HNF4, TR2/4) and one putative ortholog of GCNF (nuclear receptor family 6). Other N. vectensis genes grouped well with nuclear receptor family 2 but represented lineage-specific duplications somewhere within the cnidarian lineage and were not clear orthologs of bilaterian genes. Three nuclear receptors were not well-supported within any particular nuclear receptor family. The seventeen nuclear receptors exhibited distinct developmental expression patterns, with expression of several nuclear receptors limited to a subset of developmental stages. N. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation for mechanistic characterization of cnidarian nuclear receptor function.
    Description: We are grateful for financial support from the Woods Hole Oceanographic Institution (WHOI) through the Tropical Research Initiative, the Ocean Life Institute (AMT), the Academic Programs Office, and to the Beacon Institute for Rivers and Estuaries (AMR).
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    Publication Date: 2022-05-25
    Description: Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
    Description: Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.
    Description: This work was supported by NIH grant RO1 RR07861, the NASA Astrobiology Institute grant NCC2-1054, grants from the Edward Mallinckrodt, Jr Foundation and the Sinsheimer Foundation, and NSF grants NSF DBI - 9984882 and NSF IIS - 9996304.
    Keywords: Escherichia coli K-12
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    Publication Date: 2022-05-25
    Description: From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.
    Description: © 2006 Nahum et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Description: EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs.
    Description: This work was partly funded by the National Institutes of Health (R22/R33 Innovation and Development grant to David Pollock), the National Science Foundation (CBM2/EPSCOR), and the State of Louisiana (Biological Computation and Visualization Center, Governor's iotechnology Initiative, and startup funds to David Pollock).
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    Publication Date: 2022-05-25
    Description: © 2006 Erdner and Anderson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 7 (2006): 88, doi:10.1186/1471-2164-7-88.
    Description: Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS).
    Description: This work was funded by National Science Foundation OCE-0136861 and OCE-0430724, National Institute of Environmental Health Sciences 1 P50 ES012742-01, and a grant from the Woods Hole Oceanographic Institution Ocean Life Institute.
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    Publication Date: 2022-05-25
    Description: © 2003 BioMed Central. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 4 (2003): 235, doi:10.1186/gb-2003-4-11-235.
    Description: One of the challenges for ‘post-genomic’ biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors.
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    Publication Date: 2022-05-25
    Description: © 2006 Hutt and Albertini. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Journal of Experimental & Clinical Assisted Reproduction 3 (2006): 6, doi:10.1186/1743-1050-3-6.
    Description: The publication of a report in Nature in 2004 by the Tilly group suggesting that mouse ovaries are capable of generating oocytes de novo post-natally, has sparked interest in a problem long thought to have been resolved from classical studies in a variety of mammalian species. Within a nearly two year time period, laboratories around the world have taken up the challenge to dogma raised by this initial report, either to test this concept in an experimental basic science setting or give direction to clinical applications that could result, were the original premises of this work in the mouse valid for extrapolation to humans. This review provides a status report for this promising area of research, (1) to summarize recent findings in the literature with respect to the validity of the original hypothesis proffered by the Tilly group, and, (2) to gauge the potential utility of ovarian stem cells as a treatment for certain forms of human infertility.
    Description: Support and the funding provided from the Hall Family Foundation.
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    Publication Date: 2022-05-25
    Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S3, doi:10.1186/1476-069X-7-S2-S3.
    Description: Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.
    Description: The Oceans and Human Health Initiative research described within this paper is supported by the National Science Foundation, The National Institute for Environmental Health Sciences and the National Oceanic and Atmospheric Administration. Grant numbers are: NIEHS P50 ES012742 and NSF OCE- 043072 (RJG, LAA-Z, MFP), NSF OCE04-32479 and NIEHS P50 ES012740 (RSF), NSF OCE-0432368 and NIEHS P50 ES12736 (HMS-G), NIEHS P50 ES012762 and NSF OCE-0434087 (JSM).
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    Publication Date: 2022-05-25
    Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S6, doi:10.1186/1476-069X-7-S2-S6.
    Description: We review the major linkages between the oceans and public health, focusing on exposures and potential health effects due to anthropogenic and natural factors including: harmful algal blooms, microbes, and chemical pollutants in the oceans; consumption of seafood; and flooding events. We summarize briefly the current state of knowledge about public health effects and their economic consequences; and we discuss priorities for future research. We find that: • There are numerous connections between the oceans, human activities, and human health that result in both positive and negative exposures and health effects (risks and benefits); and the study of these connections comprises a new interdisciplinary area, "oceans and human health." • The state of present knowledge about the linkages between oceans and public health varies. Some risks, such as the acute health effects caused by toxins associated with shellfish poisoning and red tide, are relatively well understood. Other risks, such as those posed by chronic exposure to many anthropogenic chemicals, pathogens, and naturally occurring toxins in coastal waters, are less well quantified. Even where there is a good understanding of the mechanism for health effects, good epidemiological data are often lacking. Solid data on economic and social consequences of these linkages are also lacking in most cases. • The design of management measures to address these risks must take into account the complexities of human response to warnings and other guidance, and the economic tradeoffs among different risks and benefits. Future research in oceans and human health to address public health risks associated with marine pathogens and toxins, and with marine dimensions of global change, should include epidemiological, behavioral, and economic components to ensure that resulting management measures incorporate effective economic and risk/benefit tradeoffs.
    Description: Funding was provided in part by the NSF-NIEHS Oceans Centers at Woods Hole, University of Hawaii, University of Miami, and University of Washington, and the NOAA Oceans and Human Health Initiative Centers of Excellent in Charleston, Seattle and Milwaukee, the National Center for Environmental Health (NCEH) of the Centers for Disease Control and Prevention (CDC), and the WHOI Marine Policy Center. Grant numbers are: NIEHS P50 ES012742 and NSF OCE-043072 (HLKP, RJG, PH); NSF OCE 0432368 and NIEHS P50 ES12736 (LEF); NIEHS P50 ES012762 and NSF OCE-0434087 (EMF, AT, LRY); NSF OCE04-32479 and NIEHS P50 ES012740 (BAW)
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    Publication Date: 2022-05-25
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2004): 1448–1461, doi:10.1175/1520-0426(2004)021〈1448:AOAPAD〉2.0.CO;2.
    Description: The accuracy of velocities measured by a pulse-coherent acoustic Doppler profiler (PCADP) in the bottom boundary layer of a wave-dominated inner-shelf environment is evaluated. The downward-looking PCADP measured velocities in eight 10-cm cells at 1 Hz. Velocities measured by the PCADP are compared to those measured by an acoustic Doppler velocimeter for wave orbital velocities up to 95 cm s−1 and currents up to 40 cm s−1. An algorithm for correcting ambiguity errors using the resolution velocities was developed. Instrument bias, measured as the average error in burst mean speed, is −0.4 cm s−1 (standard deviation = 0.8). The accuracy (root-mean-square error) of instantaneous velocities has a mean of 8.6 cm s−1 (standard deviation = 6.5) for eastward velocities (the predominant direction of waves), 6.5 cm s−1 (standard deviation = 4.4) for northward velocities, and 2.4 cm s−1 (standard deviation = 1.6) for vertical velocities. Both burst mean and root-mean-square errors are greater for bursts with ub ≥ 50 cm s−1. Profiles of burst mean speeds from the bottom five cells were fit to logarithmic curves: 92% of bursts with mean speed ≥ 5 cm s−1 have a correlation coefficient R2 〉 0.96. In cells close to the transducer, instantaneous velocities are noisy, burst mean velocities are biased low, and bottom orbital velocities are biased high. With adequate blanking distances for both the profile and resolution velocities, the PCADP provides sufficient accuracy to measure velocities in the bottom boundary layer under moderately energetic inner-shelf conditions.
    Description: This work was funded by the U.S. Geological Survey as part of the Southwest Washington Coastal Erosion Study
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    Publication Date: 2022-05-25
    Description: © 2007 Dietz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Ecology 7 (2007): 14, doi:10.1186/1472-6785-7-14.
    Description: Free-ranging narwhals (Monodon monoceros) were instrumented in Admiralty Inlet, Canada with both satellite tags to study migration and stock separation and short-term, high-resolution digital archival tags to explore diving and feeding behaviour. Three narwhals were equipped with an underwater camera pod (Crittercam), another individual was equipped with a digital archival tag (DTAG), and a fifth with both units during August 2003 and 2004. Crittercam footage indicated that of the combined 286 minutes of recordings, 12% of the time was spent along the bottom. When the bottom was visible in the camera footage, the narwhals were oriented upside-down 80% of the time (range: 61 100%). The DTAG data (14.6 hours of recordings) revealed that during time spent below the surface, the two tagged narwhals were supine an average of 13% (range: 9–18%) of the time. Roughly 70% of this time spent in a supine posture occurred during the descent. Possible reasons for this upside-down swimming behaviour are discussed. No preference for a clockwise or counter-clockwise direction of roll was observed, discounting the possibility that rolling movements contribute to the asymmetric left-handed helical turns of the tusk.
    Description: This study was funded by the National Environmental Research Institute, the Greenland Institute of Natural Resources (organized by Mads Peter Heide-Jørgensen), the Department of Fisheries and Oceans, the Nunavut Wildlife Research Trust Fund and the Danish Cooperation for the Environment in the Arctic (DANCEA). Ari D. Shapiro received financial support from the WHOI Academic Programs Office, the National Science Foundation Research Fellowship and the National Defense Science & Engineering Graduate Fellowship.
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    Publication Date: 2022-05-25
    Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S1, doi:10.1186/1476-069X-7-S2-S1.
    Description: The oceans are the dominant feature of the planet and are fundamentally linked to human history and to human health. Concerns about the impact of the oceans on human health can be traced to ancient times. Jewish law prohibited the consumption of shellfish, probably reflecting the fact that filter-feeding bivalves can accumulate pathogens and toxins. The Portuguese explorer Pedro Fernandes de Queirós described symptoms associated with ciguatera fish poisoning after eating Caribbean sea bream in 1606, and several of British explorer James Cook's crew experienced similar symptoms after eating fish off the coast of Vanuatu in 1774 [1]. Roughly 1,200 people died from the consumption of fish and shellfish contaminated with methyl mercury in Minamata (Japan) during the 20th century; an even larger number were affected by chronic long-term neurotoxicological impacts [2]. A tsunami caused by an undersea earthquake on December 26, 2004 killed more than 225,000 people in eleven countries bordering the Indian Ocean; and more than 1,400 people died within a single day when the storm surge generated by Hurricane Katrina overwhelmed the New Orleans levee system on August 29, 2005 [3]. Looking ahead, the International Panel on Climate Change has projected a sea level rise of as much as 88 cm during the 21st century as a result of global warming [4], with major implications for the welfare and sustainability of coastal communities.
    Description: The support of the National Science Foundation (US) and the National Institute of Environmental Health Sciences (US) is gratefully acknowledged: Grant numbers NSF OCE04- 32479 and NIEHS P50 ES012740 (EAL), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), and NIEHS P50 ES012742 and NSF OCE-043072 (JJS).
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  • 32
    Publication Date: 2022-05-25
    Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S2, doi:10.1186/1476-069X-7-S2-S2.
    Description: Harmful algal blooms (HABs) are one focus of the national research initiatives on Oceans and Human Health (OHH) at NIEHS, NOAA and NSF. All of the OHH Centers, from the east coast to Hawaii, include one or more research projects devoted to studying HAB problems and their relationship to human health. The research shares common goals for understanding, monitoring and predicting HAB events to protect and improve human health: understanding the basic biology of the organisms; identifying how chemistry, hydrography and genetic diversity influence blooms; developing analytical methods and sensors for cells and toxins; understanding health effects of toxin exposure; and developing conceptual, empirical and numerical models of bloom dynamics. In the past several years, there has been significant progress toward all of the common goals. Several studies have elucidated the effects of environmental conditions and genetic heterogeneity on bloom dynamics. New methods have been developed or implemented for the detection of HAB cells and toxins, including genetic assays for Pseudo-nitzschia and Microcystis, and a biosensor for domoic acid. There have been advances in predictive models of blooms, most notably for the toxic dinoflagellates Alexandrium and Karenia. Other work is focused on the future, studying the ways in which climate change may affect HAB incidence, and assessing the threat from emerging HABs and toxins, such as the cyanobacterial neurotoxin β-N-methylamino-L-alanine. Along the way, many challenges have been encountered that are common to the OHH Centers and also echo those of the wider HAB community. Long-term field data and basic biological information are needed to develop accurate models. Sensor development is hindered by the lack of simple and rapid assays for algal cells and especially toxins. It is also critical to adequately understand the human health effects of HAB toxins. Currently, we understand best the effects of acute toxicity, but almost nothing is known about the effects of chronic, subacute toxin exposure. The OHH initiatives have brought scientists together to work collectively on HAB issues, within and across regions. The successes that have been achieved highlight the value of collaboration and cooperation across disciplines, if we are to continue to advance our understanding of HABs and their relationship to human health.
    Description: This work was funded through grants from the NSF/NIEHS Centers for Oceans and Human Health, NIEHS P50 ES012742 and NSF OCE-043072 (DLE and DMA), NSF OCE04-32479 and NIEHS P50 ES012740 (PB and RRB), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), NIEHS P50 ES012762 and NSF OCE-0434087 (RCS, KAL, MSP, MLW, and KAH). Additional support was provided by the ECOHAB Grant program NSF Grant OCE-9808173 and NOAA Grant NA96OP0099 (DMA), NOAA OHHI NA04OAR4600206 (RRB) and Washington State Sea Grant NA16RG1044 (RCS). KAL and VLT were supported in part by the West Coast Center for Oceans and Human Health (WCCOHH) as part of the NOAA Oceans and Human Health Initiative.
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  • 33
    Publication Date: 2022-05-25
    Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S5, doi:10.1186/1476-069X-7-S2-S5.
    Description: Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.
    Description: The authors acknowledge the financial support for the NSF/NIEHS and NOAA Centers for Oceans and Human Health
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  • 34
    Publication Date: 2022-05-25
    Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Direct 4 (2009): 46, doi:10.1186/1745-6150-4-46.
    Description: Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes. Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.
    Description: This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-08ER64511.
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  • 35
    Publication Date: 2022-05-25
    Description: © 2005 Serres and Riley. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 6 (2005): 33, doi:10.1186/1471-2164-6-33.
    Description: Background: Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results: Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion: The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms.
    Description: The research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-01ER63202 and by National Aeronautics and Space Administration Astrobiology grant NCC2-1054.
    Keywords: Escherichia coli ; Multimodular proteins
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  • 36
    Publication Date: 2022-05-25
    Description: © 2007 Huang and Gogarten. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R99, doi:10.1186/gb-2007-8-6-r99.
    Description: Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria. We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont. Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.
    Description: This work was performed while JH held a National Research Council Associateship Award at the NASA Astrobiology Institute at the Marine Biological Laboratory in Woods Hole, Massachusetts (NCC2-1054). Additional support was provided through NSF (MCB-0237197) and NASA AISR (NNG04GP90G) grants to JPG.
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  • 37
    Publication Date: 2022-05-26
    Description: This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Evolutionary Biology 8 (2008): 14, doi:10.1186/1471-2148-8-14.
    Description: Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches.
    Description: This project was made possible by a collaborative grant from the National Science Foundation Assembling the Tree of Life program (EF 04-31117) that was awarded to L.A.K., D.B., J.L., D.J.P., and to the ATCC
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  • 38
    Publication Date: 2022-05-26
    Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 7 (2009): 72, doi:10.1186/1741-7007-7-72.
    Description: Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.
    Description: The International Census of Marine Microbes and the W.M. Keck Foundation award to the Marine Biological Laboratory at Woods Hole (MA) supported the pyrosequencing part of this study. Further financial support came from a grant from the Deutsche Forschungsgemeinschaft to TS (STO414/3-1). Support for the unpublished work on Cariaco Basin protists came from NSF MCB-0348407 to VE (collaborative project with S Epstein at Northeastern University, Boston, MA, USA). Financial support to AC was provided by NSF MCB-0348045. Financial support to RC was provided by the ANR-Biodiversité project Aquaparadox.
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  • 39
    Publication Date: 2022-05-26
    Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Microbiology 9 (2009): 16, doi:10.1186/1471-2180-9-16.
    Description: The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades – euglenids, kinetoplastids and diplonemids – that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond. We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 – 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world. Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".
    Description: This work was supported by grants to BSL from the Tula Foundation (Centre for Microbial Diversity and Evolution), the National Science and Engineering Research Council of Canada (NSERC 283091-04) and the Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity. Funding for the collection of sediments and participation of VPE and JMB in this research was provided by the US National Science Foundation grant MCB-060484.
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  • 40
    Publication Date: 2022-05-26
    Description: © 2001 Samuel et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. The definitive version was published in BMC Microbiology 1 (2001): 4, doi:10.1186/1471-2180-1-4.
    Description: Many bacteria swim by rotating helical flagellar filaments. Waterbury et al. discovered an exception, strains of the cyanobacterium Synechococcus that swim without flagella or visible changes in shape. Other species of cyanobacteria glide on surfaces. The hypothesis that Synechococcus might swim using traveling surface waves prompted this investigation. Results Using quick-freeze electron microscopy, we have identified a crystalline surface layer that encloses the outer membrane of the motile strain Synechococcus sp. WH8113, the components of which are arranged in a rhomboid lattice. Spicules emerge in profusion from the layer and extend up to 150 nm into the surrounding fluid. These spicules also send extensions inwards to the inner cell membrane where motility is powered by an ion-motive force. Conclusion The envelope structure of Synechococcus sp. WH8113 provides new constraints on its motile mechanism. The spicules are well positioned to transduce energy at the cell membrane into mechanical work at the cell surface. One model is that an unidentified motor embedded in the cell membrane utilizes the spicules as oars to generate a traveling wave external to the surface layer in the manner of ciliated eukaryotes.
    Description: ADTS was supported by the Rowland Institute for Science and is an Amgen Fellow of the Life Sciences Research Foundation.
    Keywords: Synechococcus sp. ; Motile mechanism
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  • 41
    Publication Date: 2022-05-26
    Description: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 8 (2008): 144, doi:10.1186/1471-2148-8-144.
    Description: Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. From the over 10.7 million taxonomic names that are part of the uBio system, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.
    Description: The work presented here was funded in part by the MBLWHOI Library and the DAB Lindberg Research Fellowship from the Medical Library Association to INS.
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  • 42
    Publication Date: 2022-05-26
    Description: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Bioinformatics 9 (2008): 103, doi:10.1186/1471-2105-9-103.
    Description: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.
    Description: This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation.
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  • 43
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 13(10), ISSN: 1942-2466
    Publication Date: 2023-06-21
    Description: We propose to make the damping time scale, which governs the decay of pseudo-elastic waves in the Elastic Viscous Plastic (EVP) sea-ice solvers, independent of the external time step and large enough to warrant numerical stability for a moderate number of internal time steps. A necessary condition is that the forcing on sea ice varies slowly on the damping time scale, in which case an EVP solution may still approach a Viscous Plastic one, but on a time scale longer than a single external time step. In this case, the EVP method becomes very close to the recently proposed modified EVP (mEVP) method in terms of stability and simulated behavior. In a simple test case dealing with sea ice breaking under the forcing of a moving cyclone, the EVP method with an enlarged damping time scale can simulate linear kinematic features which are very similar to those from the traditional EVP implementation, although a much smaller number of internal time steps is used. There is more difference in sea-ice thickness and linear kinematic features simulated in a realistic Arctic configuration between using the traditional and our suggested choices of EVP damping time scales, but it is minor considering model uncertainties associated with choices of many other parameters in sea-ice models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 44
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 127(10), ISSN: 2169-8953
    Publication Date: 2023-06-21
    Description: Zooplankton plays a notable role in ocean biogeochemical cycles. However, it is often simulated as one generic group and top closure term in ocean biogeochemical models. This study presents the description of three zooplankton functional types (zPFTs, micro-, meso- and macrozooplankton) in the ocean biogeochemical model FESOM-REcoM. In the presented model, microzooplankton is a fast-growing herbivore group, mesozooplankton is another major consumer of phytoplankton, and macrozooplankton is a slow-growing group with a low temperature optimum. Meso- and macrozooplankton produce fast-sinking fecal pellets. With three zPFTs, the annual mean zooplankton biomass increases threefold to 210 Tg C. The new food web structure leads to a 25% increase in net primary production and a 10% decrease in export production globally. Consequently, the export ratio decreases from 17% to 12% in the model. The description of three zPFTs reduces model mismatches with observed dissolved inorganic nitrogen and chlorophyll concentrations in the South Pacific and the Arctic Ocean, respectively. Representation of three zPFTs also strongly affects phytoplankton phenology: Fast nutrient recycling by zooplankton sustains higher chlorophyll concentrations in summer and autumn. Additional zooplankton grazing delays the start of the phytoplankton bloom by 3 weeks and controls the magnitude of the bloom peak in the Southern Ocean. As a result, the system switches from a light-controlled Sverdrup system to a dilution-controlled Behrenfeld system. Overall, the results suggest that representation of multiple zPFTs is important to capture underlying processes that may shape the response of ecosystems and ecosystem services to on-going and future environmental change in model projections.
    Repository Name: EPIC Alfred Wegener Institut
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  • 45
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 12(12), ISSN: 1942-2466
    Publication Date: 2023-06-21
    Description: Ocean models at eddy-permitting resolution are generally overdissipative, damping the intensity of the mesoscale eddy field. To reduce overdissipation, we propose a simplified, kinematic energy backscatter parametrization built into the viscosity operator in conjunction with a new flow-dependent coefficient of viscosity based on nearest neighbor velocity differences. The new scheme mitigates excessive dissipation of energy and improves global ocean simulations at eddy-permitting resolution. We find that kinematic backscatter substantially raises simulated eddy kinetic energy, similar to an alternative, previously proposed dynamic backscatter parametrization. While dynamic backscatter is scale aware and energetically more consistent, its implementation is more complex. Furthermore, it turns out to be computationally more expensive, as it applies, among other things, an additional prognostic subgrid energy equation. The kinematic backscatter proposed here, by contrast, comes at no additional computational cost, following the principle of simplicity. Our primary focus is the discretization on triangular unstructured meshes with cell placement of velocities (an analog of B-grids), as employed by the Finite-volumE Sea ice-Ocean Model (FESOM2). The kinematic backscatter scheme with the new viscosity coefficient is implemented in FESOM2 and tested in the simplified geometry of a zonally reentrant channel as well as in a global ocean simulation on a 1/4° mesh. This first version of the new kinematic backscatter needs to be tuned to the specific resolution regime of the simulation. However, the tuning relies on a single parameter, emphasizing the overall practicality of the approach.
    Repository Name: EPIC Alfred Wegener Institut
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  • 46
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(4), ISSN: 0094-8276
    Publication Date: 2023-06-23
    Description: Climate change in the Arctic has substantial impacts on human life and ecosystems both within and beyond the Arctic. Our analysis of CMIP6 simulations shows that some climate models project much larger Arctic climate change than other models, including changes in sea ice, ocean mixed layer, air-sea heat flux, and surface air temperature in wintertime. In particular, dramatic enhancement of Arctic Ocean convection down to a few hundred meters is projected in these models but not in others. Interestingly, these models employ the same ocean model family (NEMO) while the choice of models for the atmosphere and sea ice varies. The magnitude of Arctic climate change is proportional to the strength of the increase in poleward ocean heat transport, which is considerably higher in this group of models. Establishing the plausibility of this group of models with high Arctic climate sensitivity to anthropogenic forcing is imperative given the implied ramifications.
    Repository Name: EPIC Alfred Wegener Institut
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  • 47
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 14(12), ISSN: 1942-2466
    Publication Date: 2023-06-23
    Description: A new version of the AWI Coupled Prediction System is developed based on the Alfred Wegener Institute Climate Model v3.0. Both the ocean and the atmosphere models are upgraded or replaced, reducing the computation time by a factor of 5 at a given resolution. This allowed us to increase the ensemble size from 12 to 30, maintaining a similar resolution in both model components. The online coupled data assimilation scheme now additionally utilizes sea-surface salinity and sea-level anomaly as well as temperature and salinity profile observations. Results from the data assimilation demonstrate that the sea-ice and ocean states are reasonably constrained. In particular, the temperature and salinity profile assimilation has mitigated systematic errors in the deeper ocean, although issues remain over polar regions where strong atmosphere-ocean-ice interaction occurs. One-year-long sea-ice forecasts initialized on 1 January, 1 April, 1 July and 1 October from 2003 to 2019 are described. To correct systematic forecast errors, sea-ice concentration from 2011 to 2019 is calibrated by trend-adjusted quantile mapping using the preceding forecasts from 2003 to 2010. The sea-ice edge raw forecast skill is within the range of operational global subseasonal-to-seasonal forecast systems, outperforming a climatological benchmark for about 2 weeks in the Arctic and about 3 weeks in the Antarctic. The calibration is much more effective in the Arctic: Calibrated sea-ice edge forecasts outperform climatology for about 45 days in the Arctic but only 27 days in the Antarctic. Both the raw and the calibrated forecast skill exhibit strong seasonal variations.
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  • 48
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    Unknown
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Atmospheres, American Geophysical Union (AGU), ISSN: 2169-897X
    Publication Date: 2023-06-23
    Description: Sea ice leads play an important role in energy exchange between the ocean and atmosphere in polar regions, and therefore must be considered in weather and climate models. As sea ice leads are not explicitly resolved in such models, lead-averaged surface heat flux is of considerable interest for the parameterization of energy exchange. Measurements and numerical studies have established that the lead-averaged surface heat flux depends not only on meteorological parameters, but also on lead width. Nonetheless, few studies to date have investigated the dependency of surface heat flux on lead width. Most findings on that dependency are based on observations with lead widths smaller than a few hundred meters, but leads can have widths from a few meters to several kilometers. In this parameter study, we present the results of three series of large-eddy simulations of turbulent exchange processes above leads. We varied the lead width and air temperature, as well as the roughness length. As this study focused on conditions without background wind, ice-breeze circulation occurred, and was the main driver of the adjustment of surface heat flux. A previous large-eddy simulation study with uncommonly large roughness length found that lead-averaged surface heat flux exhibited a distinct maximum at lead widths of about 3 km, while our results show the largest heat fluxes for the smallest leads simulated (lead width of 50 m). At more realistic roughness lengths, we observed monotonously increasing heat fluxes with increasing lead width. Further, new scaling laws for the ice-breeze circulation are proposed.
    Repository Name: EPIC Alfred Wegener Institut
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  • 49
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    American Meteorological Society
    In:  EPIC3Journal of Climate, American Meteorological Society, 35(23), pp. 7811-7831, ISSN: 0894-8755
    Publication Date: 2023-06-23
    Description: Numerical simulations allow us to gain a comprehensive understanding of the underlying mechanisms of past, present, and future climate changes. The mid-Holocene (MH) and the last interglacial (LIG) were the two most recent warm episodes of Earth’s climate history and are the focus of paleoclimate research. Here, we present results of MH and LIG simulations with two versions of the state-of-the-art Earth system model AWI-ESM. Most of the climate changes in MH and LIG compared to the preindustrial era are agreed upon by the two model versions, including 1) enhanced seasonality in surface temperature that is driven by the redistribution of seasonal insolation; 2) a northward shift of the intertropical convergence zone (ITCZ) and tropical rain belt; 3) a reduction in annual mean Arctic sea ice concentration; 4) weakening and northward displacement of the Northern Hemisphere Hadley circulation, which is related to the decrease and poleward shift of the temperature gradient from the subtropical to the equator in the Northern Hemisphere; 5) a westward shift of the Indo-Pacific Walker circulation due to anomalous warming over the Eurasia and North Africa during boreal summer; and 6) an expansion and intensification of Northern Hemisphere summer monsoon rainfall, with the latter being dominated by the dynamic component of moisture budget (i.e., the strengthening of wind circulation). However, the simulated responses of the Atlantic meridional overturning circulation (AMOC) in the two models yield different results for both the LIG and the MH. AMOC anomalies between the warm interglacial and preindustrial periods are associated with changes in North Atlantic westerly winds and stratification of the water column at the North Atlantic due to changes in ocean temperature, salinity, and density.
    Repository Name: EPIC Alfred Wegener Institut
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  • 50
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    Unknown
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(3), ISSN: 2169-9275
    Publication Date: 2023-06-23
    Description: The Arctic is warming much faster than the global average. This is known as Arctic Amplification and is caused by feedbacks in the local climate system. In this study, we explore a previously proposed hypothesis that an associated wind feedback in the Barents Sea could play an important role by increasing the warm water inflow into the Barents Sea. We find that the strong recent decrease in Barents Sea winter sea ice cover causes enhanced ocean-atmosphere heat flux and a local air temperature increase, thus a reduction in sea level pressure and a local cyclonic wind anomaly with eastward winds in the Barents Sea Opening. By investigating various reanalysis products and performing high-resolution perturbation experiments with the ocean and sea ice model FESOM2.1, we studied the impact of cyclonic atmospheric circulation changes on the warm Atlantic Water import into the Arctic via the Barents Sea and Fram Strait. We found that the observed wind changes do not significantly affect the warm water transport into the Barents Sea, which rejects the wind-feedback hypothesis. At the same time, the cyclonic wind anomalies in the Barents Sea increase the amount of Atlantic Water recirculating westwards in Fram Strait by a downslope shift of the West Spitsbergen Current, and thus reduce Atlantic Water reaching the Arctic basin via Fram Strait. The resulting warm-water anomaly in the Greenland Sea Gyre drives a local anticyclonic circulation anomaly.
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  • 51
    Publication Date: 2023-03-13
    Description: Goniodomin A (GDA, 1) is a phycotoxin produced by at least four species of Alexandrium dinoflagellates that are found globally in brackish estuaries and lagoons. It is a linear polyketide with six oxygen heterocyclic rings that is cyclized into a macrocyclic structure via lactone formation. Two of the oxygen heterocycles in 1 comprise a spiro-bis-pyran, whereas goniodomin B (GDB) contains a 2,7-dioxabicyclo[3.3.1]nonane ring system fused to a pyran. When H2O is present, 1 undergoes facile conversion to isomer GDB and to an α,β-unsaturated ketone, goniodomin C (GDC, 7). GDB and GDC can be formed from GDA by cleavage of the spiro-bis-pyran ring system. GDA, but not GDB or GDC, forms a crown ether-type complex with K+. Equilibration of GDA with GDB and GDC is observed in the presence of H+ and of Na+, but the equilibrated mixtures revert to GDA upon addition of K+. Structural differences have been found between the K+ and Na+ complexes. The association of GDA with K+ is strong, while that with Na+ is weak. The K+ complex has a compact, well-defined structure, whereas Na+ complexes are an ill-defined mixture of species. Analyses of in vitro A. monilatum and A. hiranoi cultures indicate that only GDA is present in the cells; GDB and GDC appear to be postharvest transformation products.
    Repository Name: EPIC Alfred Wegener Institut
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  • 52
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(22), ISSN: 0094-8276
    Publication Date: 2023-11-25
    Description: Given the role played by the historical and extensive coverage of sea ice concentration (SIC) observations in reconstructing the long‐term variability of Antarctic sea ice, and the limited attention given to model‐dependent parameters in current sea ice data assimilation studies, this study focuses on enhancing the performance of the Data Assimilation System for the Southern Ocean in assimilating SIC through optimizing the localization and observation error estimate, and two assimilation experiments were conducted from 1979 to 2018. By comparing the results with the sea ice extent of the Southern Ocean and the sea ice thickness in the Weddell Sea, it becomes evident that the experiment with optimizations outperforms that without optimizations due to achieving more reasonable error estimates. Investigating uncertainties of the sea ice volume anomaly modeling reveals the importance of the sea ice‐ocean interaction in the SIC assimilation, implying the necessity of assimilating more oceanic and sea‐ice observations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 53
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(20), ISSN: 0094-8276
    Publication Date: 2023-11-20
    Description: Surface processes alter the water stable isotope signal of the surface snow after deposition. However, it remains an open question to which extent surface post-depositional processes should be considered when inferring past climate information from ice core records. Here, we present simulations for the Greenland Ice Sheet, combining outputs from two climate models with an isotope-enabled snowpack model. We show that surface vapor exchange and associated fractionation imprint a climate signal into the firn, resulting in an increase in the annual mean value of δ18O by +2.3‰ and a reduction in d-excess by −6.3‰. Further, implementing isotopic fractionation during surface vapor exchange improves the representation of the observed seasonal amplitude in δ18O from 65.0% to 100.2%. Our results stress that surface vapor exchange is important in the climate proxy signal formation and needs consideration when interpreting ice core climate records.
    Repository Name: EPIC Alfred Wegener Institut
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  • 54
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(4), ISSN: 0094-8276
    Publication Date: 2023-02-23
    Description: Comparing helicopter-borne surface temperature maps in winter and optical orthomosaics in summer from the year-long Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition, we find a strong geometric correlation between warm anomalies in winter and melt pond location the following summer. Warm anomalies are associated with thinner snow and ice, that is, surface depression and refrozen leads, that allow for water accumulation during melt. Warm surface temperature anomalies in January were 0.3–2.5 K warmer on sea ice that later formed melt ponds. A one-dimensional steady-state thermodynamic model shows that the observed surface temperature differences are in line with the observed ice thickness and snow depth. We demonstrate the potential of seasonal prediction of summer melt pond location and coverage from winter surface temperature observations. A threshold-based classification achieves a correct classification for 41% of the melt ponds.
    Repository Name: EPIC Alfred Wegener Institut
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  • 55
    Publication Date: 2023-02-25
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(11), (2022): 2841–2852, https://doi.org/10.1175/jpo-d-22-0025.1.
    Description: Prediction of rapid intensification in tropical cyclones prior to landfall is a major societal issue. While air–sea interactions are clearly linked to storm intensity, the connections between the underlying thermal conditions over continental shelves and rapid intensification are limited. Here, an exceptional set of in situ and satellite data are used to identify spatial heterogeneity in sea surface temperatures across the inner core of Hurricane Sally (2020), a storm that rapidly intensified over the shelf. A leftward shift in the region of maximum cooling was observed as the hurricane transited from the open gulf to the shelf. This shift was generated, in part, by the surface heat flux in conjunction with the along- and across-shelf transport of heat from storm-generated coastal circulation. The spatial differences in the sea surface temperatures were large enough to potentially influence rapid intensification processes suggesting that coastal thermal features need to be accounted for to improve storm forecasting as well as to better understand how climate change will modify interactions between tropical cyclones and the coastal ocean.
    Description: This research was made possible by the NOAA RESTORE Science Program (NA17NOS4510101 and NA19NOS4510194) and the NASA Physical Oceanography program (80NSSC21K0553 and WBS 281945.02.25.04.67) and NOAA IOOS program via GCOOS (NA16NOS0120018). The authors declare that they have no competing interests.
    Keywords: Seas/gulfs/bays ; Atmosphere–ocean interaction ; Currents ; Tropical cyclones ; Buoy observations ; In situ oceanic observations
    Repository Name: Woods Hole Open Access Server
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  • 56
    Publication Date: 2023-02-25
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(8), (2022): 1797–1815, https://doi.org/10.1175/JPO-D-21-0288.1.
    Description: Intruding slope water is a major source of nutrients to sustain the high biological productivity in the Gulf of Maine (GoM). Slope water intrusion into the GoM is affected by Gulf Stream warm-core rings (WCRs) impinging onto the nearby shelf edge. This study combines long-term mooring measurements, satellite remote sensing data, an idealized numerical ocean model, and a linear coastal-trapped wave (CTW) model to examine the impact of WCRs on slope water intrusion into the GoM through the Northeast Channel. Analysis of satellite sea surface height and temperature data shows that the slope sea region off the GoM is a hotspot of ring activities. A significant linear relationship is found between interannual variations of ring activities in the slope sea region off the GoM and bottom salinity at the Northeast Channel, suggesting the importance of WCRs in modulating variability of intruding slope water. Analysis of the mooring data reveals enhanced slope water intrusion through bottom-intensified along-channel flow following impingements of WCRs on the nearby shelf edge. Numerical simulations qualitatively reproduce the observed WCR impingement processes and associated episodic enhancement of slope water intrusion in the Northeast Channel. Diagnosis of the model result indicates that baroclinic CTWs excited by the ring–topography interaction are responsible for the episodically intensified subsurface along-channel inflow, which carries more slope water into the GoM. A WCR that impinges onto the shelf edge to the northeast of the Northeast Channel tends to generate stronger CTWs and cause stronger enhancement of the slope water intrusion into the GoM.
    Description: This study is supported by the National Science Foundation through Grant OCE-1634965.
    Keywords: Continental shelf/slope ; Channel flows ; Mesoscale processes ; In situ oceanic observations ; Satellite observations ; Numerical analysis/modeling
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  • 57
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    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), 38, 22 p., pp. e2022PA004439-e2022PA004439, ISSN: 2572-4517
    Publication Date: 2023-08-30
    Description: Atmospheric carbon dioxide concentrations (pCO2) beyond ice core records have been reconstructed from δ11B derived from planktic foraminifera found in equatorial sediment cores. Here, I applied a carbon cycle model over the Plio-Pleistocene to evaluate the assumptions leading to these numbers. During glacials times, simulated atmospheric pCO2 was unequilibrated with pCO2 in the equatorial surface ocean by up to 35 ppm while the δ11B-based approaches assume unchanged (quasi)equilibrium between both. In the Pliocene, δ11B-based estimates of surface ocean pH are lower in the Pacific than in the Atlantic resulting in higher calculated pCO2. This offset in pH between ocean basins is not supported by models. To calculate pCO2 in surface waters out of the δ11B-based pH some assumptions on either total alkalinity or dissolved inorganic carbon are necessary. However, the assumed values of these under-constrained variables were according to my results partly inconsistent with chemically possible combinations within the marine carbonate system. The model results show glacial/interglacial variability in total alkalinity of the order of 100 μmol/kg, which is rarely applied to proxy reconstructions. Simulated atmospheric pCO2 is tightly (r2 〉 0.9) related to equatorial surface-ocean pH, which can be used for consistency checks. Long-term trends in volcanic CO2 outgassing and the strength of the continental weathering fluxes are still unconstrained, allowing for a wide range of possible atmospheric pCO2 across the Plio-Pleistocene. Nevertheless, this carbon cycle analysis suggests that reported atmospheric pCO2 above 500 ppm in the Pliocene might, for various reasons, need to be revised to smaller numbers.
    Repository Name: EPIC Alfred Wegener Institut
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  • 58
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(12), ISSN: 0094-8276
    Publication Date: 2023-09-01
    Description: Aquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the “methane paradox.” In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formation observed in the SML of oceans and lakes.
    Repository Name: EPIC Alfred Wegener Institut
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  • 59
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 15(9), ISSN: 1942-2466
    Publication Date: 2023-09-04
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Most viscous‐plastic sea ice models use the elliptical yield curve. This yield curve has a fundamental flaw: it excludes acute angles between deformation features at high resolution. Conceptually, the teardrop (TD) and parabolic lens (PL) yield curves offer an attractive alternative. These yield curves feature a non‐symmetrical shape, a Coulombic behavior for the low‐medium compressive stress, and a continuous transition to the ridging‐dominant mode, but their published formulation leads to negative or zero bulk and shear viscosities and, consequently, poor numerical convergence with stress states at times outside the yield curve. These issues are a consequence of the original assumption that the constitutive equations of the commonly used elliptical yield curve are also applicable to non‐symmetrical yield curves and yield curves with tensile strength. We derive a corrected formulation for the constitutive relations of the TD and PL yield curves. Results from simple uni‐axial loading experiments show that with the new formulation the numerical convergence of the solver improves and much smaller nonlinear residuals after a smaller number of total solver iterations can be reached, resulting in significant improvements in numerical efficiency and representation of the stress and deformation fields. The TD and PL yield curves lead to smaller angles of failure that better agree with observations. They are promising candidates to replace the elliptical yield curve in high‐resolution pan‐Arctic sea ice simulations.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 60
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    American Meteorological Society
    In:  EPIC3Journal of Climate, American Meteorological Society, pp. 1-40, ISSN: 0894-8755
    Publication Date: 2023-09-04
    Description: 〈jats:title〉Abstract〈/jats:title〉 〈jats:p〉Tipping points in the Earth system describe critical thresholds beyond which a single component, part of the system, or the system as a whole changes from one stable state to another. In the present-day Southern Ocean, the Weddell Sea constitutes an important dense-water formation site, associated with efficient deep-ocean carbon and oxygen transfer and low ice-shelf basal melt rates. Here, a regime shift will occur when continental shelves are continuously flushed with warm, oxygen-poor offshore waters from intermediate depth, leading to less efficient deep-ocean carbon and oxygen transfer and higher ice-shelf basal melt rates. We use a global ocean–biogeochemistry model including ice-shelf cavities and an eddy-permitting grid in the southern Weddell Sea to address the susceptibility of this region to such a system change for four 21〈jats:sup〉st〈/jats:sup〉-century emission scenarios. Assessing the projected changes in shelf–open ocean density gradients, bottom-water properties, and on-shelf heat transport, our results indicate that the Weddell Sea undergoes a regime shift by 2100 in the highest-emission scenario SSP5-8.5, but not yet in the lower-emission scenarios. The regime shift is imminent by 2100 in the scenarios SSP3-7.0 and SSP2-4.5, but avoidable under the lowest-emission scenario SSP1-2.6. While shelf-bottom waters freshen and acidify everywhere, bottom waters in the Filchner Trough undergo accelerated warming and deoxygenation following the system change, with implications for local ecosystems and ice-shelf basal melt. Additionally, deep-ocean carbon and oxygen transfer decline, implying that the local changes ultimately affect ocean circulation, climate, and ecosystems globally.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 61
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    American Geophysical Union (AGU)
    In:  EPIC3Reviews of Geophysics, American Geophysical Union (AGU), 61(3), ISSN: 8755-1209
    Publication Date: 2023-10-09
    Description: Knowledge of Antarctica's sedimentary basins builds our understanding of the coupled evolution of tectonics, ice, ocean, and climate. Sedimentary basins have properties distinct from basement-dominated regions that impact ice-sheet dynamics, potentially influencing future ice-sheet change. Despite their importance, our knowledge of Antarctic sedimentary basins is restricted. Remoteness, the harsh environment, the overlying ice sheet, ice shelves, and sea ice all make fieldwork challenging. Nonetheless, in the past decade the geophysics community has made great progress in internationally coordinated data collection and compilation with parallel advances in data processing and analysis supporting a new insight into Antarctica's subglacial environment. Here, we summarize recent progress in understanding Antarctica's sedimentary basins. We review advances in the technical capability of radar, potential fields, seismic, and electromagnetic techniques to detect and characterize basins beneath ice and advances in integrated multi-data interpretation including machine-learning approaches. These new capabilities permit a continent-wide mapping of Antarctica's sedimentary basins and their characteristics, aiding definition of the tectonic development of the continent. Crucially, Antarctica's sedimentary basins interact with the overlying ice sheet through dynamic feedbacks that have the potential to contribute to rapid ice-sheet change. Looking ahead, future research directions include techniques to increase data coverage within logistical constraints, and resolving major knowledge gaps, including insufficient sampling of the ice-sheet bed and poor definition of subglacial basin structure and stratigraphy. Translating the knowledge of sedimentary basin processes into ice-sheet modeling studies is critical to underpin better capacity to predict future change.
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  • 62
    Publication Date: 2023-04-26
    Description: Mechanisms behind the phenomenon of Arctic amplification are widely discussed. To contribute to this debate, the (AC)3 project was established in 2016 (www.ac3-tr.de/). It comprises modeling and data analysis efforts as well as observational elements. The project has assembled a wealth of ground-based, airborne, shipborne, and satellite data of physical, chemical, and meteorological properties of the Arctic atmosphere, cryosphere, and upper ocean that are available for the Arctic climate research community. Short-term changes and indications of long-term trends in Arctic climate parameters have been detected using existing and new data. For example, a distinct atmospheric moistening, an increase of regional storm activities, an amplified winter warming in the Svalbard and North Pole regions, and a decrease of sea ice thickness in the Fram Strait and of snow depth on sea ice have been identified. A positive trend of tropospheric bromine monoxide (BrO) column densities during polar spring was verified. Local marine/biogenic sources for cloud condensation nuclei and ice nucleating particles were found. Atmospheric–ocean and radiative transfer models were advanced by applying new parameterizations of surface albedo, cloud droplet activation, convective plumes and related processes over leads, and turbulent transfer coefficients for stable surface layers. Four modes of the surface radiative energy budget were explored and reproduced by simulations. To advance the future synthesis of the results, cross-cutting activities are being developed aiming to answer key questions in four focus areas: lapse rate feedback, surface processes, Arctic mixed-phase clouds, and airmass transport and transformation.
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  • 63
    Publication Date: 2023-06-01
    Repository Name: EPIC Alfred Wegener Institut
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  • 64
    Publication Date: 2023-01-27
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(8), (2022): 1705-1730, https://doi.org/10.1175/jpo-d-21-0243.1.
    Description: Formation and evolution of barrier layers (BLs) and associated temperature inversions (TIs) were investigated using a 1-yr time series of oceanic and air–sea surface observations from three moorings deployed in the eastern Pacific fresh pool. BL thickness and TI amplitude showed a seasonality with maxima in boreal summer and autumn when BLs were persistently present. Mixed layer salinity (MLS) and mixed layer temperature (MLT) budgets were constructed to investigate the formation mechanism of BLs and TIs. The MLS budget showed that BLs were initially formed in response to horizontal advection of freshwater in boreal summer and then primarily maintained by precipitation. The MLT budget revealed that penetration of shortwave radiation through the mixed layer base is the dominant contributor to TI formation through subsurface warming. Geostrophic advection is a secondary contributor to TI formation through surface cooling. When the BL exists, the cooling effect from entrainment and the warming effect from detrainment are both significantly reduced. In addition, when the BL is associated with the presence of a TI, entrainment works to warm the mixed layer. The presence of BLs makes the shallower mixed layer more sensitive to surface heat and freshwater fluxes, acting to enhance the formation of TIs that increase the subsurface warming via shortwave penetration.
    Description: SK is supported by JSPS Overseas Research Fellowships. JS and SK are supported by NASA Grant 80NSSC18K1500. JTF and the mooring deployment were funded by NASA Grants NNX15AG20G and 80NSSC18K1494. DZ is supported by NASA Grant 80NSSC18K1499. This publication is partially funded by the Cooperative Institute for Climate, Ocean, and Ecosystem Studies (CICOES) under NOAA Cooperative Agreement NA20OAR4320271, Contribution 2021-1152. This is PMEL Contribution 5268.
    Description: 2023-01-27
    Keywords: Ocean ; North Pacific Ocean ; Tropics ; Entrainment ; Oceanic mixed layer ; Salinity
    Repository Name: Woods Hole Open Access Server
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  • 65
    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(8), (2022): 1927-1943, https://doi.org/10.1175/jpo-d-21-0124.1.
    Description: The Galápagos Archipelago lies on the equator in the path of the eastward flowing Pacific Equatorial Undercurrent (EUC). When the EUC reaches the archipelago, it upwells and bifurcates into a north and south branch around the archipelago at a latitude determined by topography. Since the Coriolis parameter (f) equals zero at the equator, strong velocity gradients associated with the EUC can result in Ertel potential vorticity (Q) having sign opposite that of planetary vorticity near the equator. Observations collected by underwater gliders deployed just west of the Galápagos Archipelago during 2013–16 are used to estimate Q and to diagnose associated instabilities that may impact the Galápagos Cold Pool. Estimates of Q are qualitatively conserved along streamlines, consistent with the 2.5-layer, inertial model of the EUC by Pedlosky. The Q with sign opposite of f is advected south of the Galápagos Archipelago when the EUC core is located south of the bifurcation latitude. The horizontal gradient of Q suggests that the region between 2°S and 2°N above 100 m is barotropically unstable, while limited regions are baroclinically unstable. Conditions conducive to symmetric instability are observed between the EUC core and the equator and within the southern branch of the undercurrent. Using 2-month and 3-yr averages, e-folding time scales are 2–11 days, suggesting that symmetric instability can persist on those time scales.
    Description: This work was supported by the National Science Foundation (Grants OCE-1232971 and OCE-1233282), the NASA Earth and Space Science Fellowship Program (Grant 80NSSC17K0443), and the Global Ocean Monitoring and Observing Program of the National Oceanographic and Atmospheric Administration (NA13OAR4830216). Color maps are from Thyng et al. (2016).
    Description: 2023-02-01
    Keywords: Currents ; In situ oceanic observations ; Instability ; Mixing ; Ocean dynamics ; Pacific Ocean ; Potential vorticity ; Tropics
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  • 66
    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(8), (2022): 1183-1198, https://doi.org/10.1175/jtech-d-21-0068.1.
    Description: Horizontal kinematic properties, such as vorticity, divergence, and lateral strain rate, are estimated from drifter clusters using three approaches. At submesoscale horizontal length scales O(1–10)km, kinematic properties become as large as planetary vorticity f, but challenging to observe because they evolve on short time scales O(hourstodays). By simulating surface drifters in a model flow field, we quantify the sources of uncertainty in the kinematic property calculations due to the deformation of cluster shape. Uncertainties arise primarily due to (i) violation of the linear estimation methods and (ii) aliasing of unresolved scales. Systematic uncertainties (iii) due to GPS errors, are secondary but can become as large as (i) and (ii) when aspect ratios are small. Ideal cluster parameters (number of drifters, length scale, and aspect ratio) are determined and error functions estimated empirically and theoretically. The most robust method—a two-dimensional, linear least squares fit—is applied to the first few days of a drifter dataset from the Bay of Bengal. Application of the length scale and aspect-ratio criteria minimizes errors (i) and (ii), and reduces the total number of clusters and so computational cost. The drifter-estimated kinematic properties map out a cyclonic mesoscale eddy with a surface, submesoscale fronts at its perimeter. Our analyses suggest methodological guidance for computing the two-dimensional kinematic properties in submesoscale flows, given the recently increasing quantity and quality of drifter observations, while also highlighting challenges and limitations.
    Description: This research was supported by the Office of Naval Research (ONR) Departmental Research Initiative ASIRI under Grant N00014-13-1-0451 (SE and AM) and Grant N00014-13-1-0477 (VH and LC). The authors thank the captain and crew of the R/V Roger Revelle, and Andrew Lucas with the Multiscale Ocean Dynamics group at the Scripps Institution for Oceanography for providing the FastCTD data collected in 2015, which was supported by ONR Grant N00014-13-1-0489, as well as Eric D’Asaro for helpful discussions and Lance Braasch for assistance with the drifter dataset. AM and SE further thank NSF (Grant OCE-I434788) and ONR (Grant N00014-16-1-2470) for support. VH and LC were additionally supported by ONR Grants N00014-15-1-2286, N00014-14-1-0183, N00014-19-1-26-91 and NOAA Global Drifter Program (GDP) Grant NA15OAR4320071.
    Description: 2023-02-01
    Keywords: Indian Ocean ; Eddies ; Frontogenesis/frontolysis ; Fronts ; Lagrangian circulation/transport ; Ocean circulation ; Ocean dynamics
    Repository Name: Woods Hole Open Access Server
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  • 67
    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 35(17), (2022): 5465-5482, https://doi.org/10.1175/jcli-d-21-0671.1.
    Description: Understanding the contribution of ocean circulation to glacial–interglacial climate change is a major focus of paleoceanography. Specifically, many have tried to determine whether the volumes and depths of Antarctic- and North Atlantic–sourced waters in the deep ocean changed at the Last Glacial Maximum (LGM; ∼22–18 kyr BP) when atmospheric pCO2 concentrations were 100 ppm lower than the preindustrial. Measurements of sedimentary geochemical proxies are the primary way that these deep ocean structural changes have been reconstructed. However, the main proxies used to reconstruct LGM Atlantic water mass geometry provide conflicting results as to whether North Atlantic–sourced waters shoaled during the LGM. Despite this, a number of idealized modeling studies have been advanced to describe the physical processes resulting in shoaled North Atlantic waters. This paper aims to critically assess the approaches used to determine LGM Atlantic circulation geometry and lay out best practices for future work. We first compile existing proxy data and paleoclimate model output to deduce the processes responsible for setting the ocean distributions of geochemical proxies in the LGM Atlantic Ocean. We highlight how small-scale mixing processes in the ocean interior can decouple tracer distributions from the large-scale circulation, complicating the straightforward interpretation of geochemical tracers as proxies for water mass structure. Finally, we outline promising paths toward ascertaining the LGM circulation structure more clearly and deeply.
    Description: S.K.H. was supported by the Investment in Science Fund at WHOI and the John E. and Anne W. Sawyer Endowed Fund in Support of Scientific Staff. F.J.P. was supported by a Stanback Postdoctoral Fellowship at Caltech.
    Description: 2023-02-01
    Keywords: Diapycnal mixing ; Meridional overturning circulation ; Ocean circulation
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  • 68
    Publication Date: 2023-02-17
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(10), (2022): 1525–1539, https://doi.org/10.1175/jtech-d-21-0186.1.
    Description: The static and dynamic performances of the RBRargo3 are investigated using a combination of laboratory-based and in situ datasets from floats deployed as part of an Argo pilot program. Temperature and pressure measurements compare well to co-located reference data acquired from shipboard CTDs. Static accuracy of salinity measurements is significantly improved using 1) a time lag for temperature, 2) a quadratic pressure dependence, and 3) a unit-based calibration for each RBRargo3 over its full pressure range. Long-term deployments show no significant drift in the RBRargo3 accuracy. The dynamic response of the RBRargo3 demonstrates the presence of two different adjustment time scales: a long-term adjustment O(120) s, driven by the temperature difference between the interior of the conductivity cell and the water, and a short-term adjustment O(5–10) s, associated to the initial exchange of heat between the water and the inner ceramic. Corrections for these effects, including dependence on profiling speed, are developed.
    Keywords: Data processing/distribution ; In situ oceanic observations ; Profilers ; Oceanic
    Repository Name: Woods Hole Open Access Server
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  • 69
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(22), ISSN: 0094-8276
    Publication Date: 2023-06-21
    Description: Based on the ERA5 reanalysis, we report on statistically significant impacts of transient cyclones on sea ice concentration (SIC) in the Atlantic sector of the Arctic Ocean in winter under “New Arctic” conditions (2000–2020). This includes a pattern of reduced SIC prior to and during cyclones for the whole study domain, while a regional difference between increased SIC in the Barents Sea and reduced SIC in the Greenland Sea is found as the net effect from 3 days prior to 5 days after the cyclone passage. Generally, locally low to medium SIC conditions combined with intense cyclones drive highest SIC changes. There are indications that both thermodynamic and dynamic effects contribute to the SIC changes, but a detailed quantification is required in future research. We provide evidence that cyclone impacts on SIC have amplified compared to the “Old Arctic” (1979–1999), particularly in the Barents Sea.
    Repository Name: EPIC Alfred Wegener Institut
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  • 70
    Publication Date: 2023-01-16
    Description: The uptake ability toward arsenic(V), chromium(VI), and boron(III) ions of ad hoc functionalized magnetic nanostructured devices has been investigated. To this purpose, ligands based on meglumine have been synthesized and used to coat magnetite nanoparticles (Fe3O4) obtained by the co-precipitation methodology. The as-prepared hybrid material was characterized by infrared spectroscopy (IR), X-ray diffraction, thermogravimetric analysis, and scanning electron microscopy combined with energy-dispersive X-ray analysis. Moreover, its magnetic hysteresis properties were measured to evaluate its magnetic properties, and the adsorption kinetics and isothermal models were applied to discern between the different adsorption phenomena. Specifically, the better fitting was observed by the Langmuir isotherm model for all metal ions tested, highlighting a higher uptake in arsenic (28.2 mg/g), chromium (12.3 mg/g), and boron (23.7 mg/g) sorption values if compared with other magnetic nanostructured materials. After adsorption, an external magnetic stimulus can be used to efficiently remove nanomaterials from the water. Finally the nanomaterial can be reused up to five cycles and regenerated for another three cycles.
    Description: Published
    Description: 10775–10788
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 71
    Publication Date: 2023-02-28
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(12),(2022): 3199-3219, https://doi.org/10.1175/jpo-d-22-0009.1.
    Description: The abyssal overturning circulation is thought to be primarily driven by small-scale turbulent mixing. Diagnosed water-mass transformations are dominated by rough topography “hotspots,” where the bottom enhancement of mixing causes the diffusive buoyancy flux to diverge, driving widespread downwelling in the interior—only to be overwhelmed by an even stronger upwelling in a thin bottom boundary layer (BBL). These water-mass transformations are significantly underestimated by one-dimensional (1D) sloping boundary layer solutions, suggesting the importance of three-dimensional physics. Here, we use a hierarchy of models to generalize this 1D boundary layer approach to three-dimensional eddying flows over realistically rough topography. When applied to the Mid-Atlantic Ridge in the Brazil Basin, the idealized simulation results are roughly consistent with available observations. Integral buoyancy budgets isolate the physical processes that contribute to realistically strong BBL upwelling. The downward diffusion of buoyancy is primarily balanced by upwelling along the sloping canyon sidewalls and the surrounding abyssal hills. These flows are strengthened by the restratifying effects of submesoscale baroclinic eddies and by the blocking of along-ridge thermal wind within the canyon. Major topographic sills block along-thalweg flows from restratifying the canyon trough, resulting in the continual erosion of the trough’s stratification. We propose simple modifications to the 1D boundary layer model that approximate each of these three-dimensional effects. These results provide local dynamical insights into mixing-driven abyssal overturning, but a complete theory will also require the nonlocal coupling to the basin-scale circulation.
    Description: We acknowledge funding support from National Science Foundation Awards 1536515, 1736109, and 2149080. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant 174530.
    Description: 2023-05-18
    Keywords: Abyssal circulation ; Diapycnal mixing ; Meridional overturning circulation ; Topographic effects ; Upwelling/downwelling ; Bottom currents/bottom water
    Repository Name: Woods Hole Open Access Server
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  • 72
    Publication Date: 2023-02-28
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(6), (2022): 1091–1110, https://doi.org/10.1175/JPO-D-21-0068.1.
    Description: Hundreds of full-depth temperature and salinity profiles collected by Deepglider autonomous underwater vehicles (AUVs) in the North Atlantic reveal robust signals in eddy isopycnal vertical displacement and horizontal current throughout the entire water column. In separate glider missions southeast of Bermuda, subsurface-intensified cold, fresh coherent vortices were observed with velocities exceeding 20 cm s−1 at depths greater than 1000 m. With vertical resolution on the order of 20 m or less, these full-depth glider slant profiles newly permit estimation of scaled vertical wavenumber spectra from the barotropic through the 40th baroclinic mode. Geostrophic turbulence theory predictions of spectral slopes associated with the forward enstrophy cascade and proportional to inverse wavenumber cubed generally agree with glider-derived quasi-universal spectra of potential and kinetic energy found at a variety of locations distinguished by a wide range of mean surface eddy kinetic energy. Water-column average spectral estimates merge at high vertical mode number to established descriptions of internal wave spectra. Among glider mission sites, geographic and seasonal variability implicate bottom drag as a mechanism for dissipation, but also the need for more persistent sampling of the deep ocean.
    Description: This work was funded by NSF Grant 1736217 and would not have been possible without the help of Kirk O’Donnell, James Bennett, Noel Pelland, and all contributors to Deepglider development. We additionally thank the captain crew of the R/V Atlantic Explorer and the BATS team at the Bermuda Institute of Ocean Sciences, particularly Rod Johnson, as well as Seakeepers International for their professionalism, capability, and generous assistance in deploying and recovering gliders.
    Keywords: North Atlantic Ocean ; Eddies ; Mesoscale processes ; Turbulence ; Energy transport ; In situ oceanic observations ; Oceanic variability
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  • 73
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    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), ISSN: 2572-4517
    Publication Date: 2023-02-03
    Repository Name: EPIC Alfred Wegener Institut
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  • 74
    Publication Date: 2023-03-02
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(12), (2022): 3221–3240, https://doi.org/10.1175/jpo-d-22-0010.1.
    Description: Small-scale mixing drives the diabatic upwelling that closes the abyssal ocean overturning circulation. Indirect microstructure measurements of in situ turbulence suggest that mixing is bottom enhanced over rough topography, implying downwelling in the interior and stronger upwelling in a sloping bottom boundary layer. Tracer release experiments (TREs), in which inert tracers are purposefully released and their dispersion is surveyed over time, have been used to independently infer turbulent diffusivities—but typically provide estimates in excess of microstructure ones. In an attempt to reconcile these differences, Ruan and Ferrari derived exact tracer-weighted buoyancy moment diagnostics, which we here apply to quasi-realistic simulations. A tracer’s diapycnal displacement rate is exactly twice the tracer-averaged buoyancy velocity, itself a convolution of an asymmetric upwelling/downwelling dipole. The tracer’s diapycnal spreading rate, however, involves both the expected positive contribution from the tracer-averaged in situ diffusion as well as an additional nonlinear diapycnal distortion term, which is caused by correlations between buoyancy and the buoyancy velocity, and can be of either sign. Distortion is generally positive (stretching) due to bottom-enhanced mixing in the stratified interior but negative (contraction) near the bottom. Our simulations suggest that these two effects coincidentally cancel for the Brazil Basin Tracer Release Experiment, resulting in negligible net distortion. By contrast, near-bottom tracers experience leading-order distortion that varies in time. Errors in tracer moments due to realistically sparse sampling are generally small (〈20%), especially compared to the O(1) structural errors due to the omission of distortion effects in inverse models. These results suggest that TREs, although indispensable, should not be treated as “unambiguous” constraints on diapycnal mixing.
    Description: We acknowledge funding support from National Science Foundation Awards 1536515 and 1736109. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant 174530. This research is also supported by the NOAA Climate and Global Change Postdoctoral Fellowship Program, administered by UCAR’s Cooperative Programs for the Advancement of Earth System Science (CPAESS) under Award NA18NWS4620043B.
    Description: 2023-05-18
    Keywords: Diapycnal mixing ; Diffusion ; Upwelling/downwelling ; Bottom currents/bottom water ; Tracers
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  • 75
    Publication Date: 2024-02-27
    Description: Significant progress in permafrost carbon science made over the past decades include the identification of vast permafrost carbon stocks, the development of new pan‐Arctic permafrost maps, an increase in terrestrial measurement sites for CO〈jats:sub〉2〈/jats:sub〉 and methane fluxes, and important factors affecting carbon cycling, including vegetation changes, periods of soil freezing and thawing, wildfire, and other disturbance events. Process‐based modeling studies now include key elements of permafrost carbon cycling and advances in statistical modeling and inverse modeling enhance understanding of permafrost region C budgets. By combining existing data syntheses and model outputs, the permafrost region is likely a wetland methane source and small terrestrial ecosystem CO〈jats:sub〉2〈/jats:sub〉 sink with lower net CO〈jats:sub〉2〈/jats:sub〉 uptake toward higher latitudes, excluding wildfire emissions. For 2002–2014, the strongest CO〈jats:sub〉2〈/jats:sub〉 sink was located in western Canada (median: −52 g C m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉) and smallest sinks in Alaska, Canadian tundra, and Siberian tundra (medians: −5 to −9 g C m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉). Eurasian regions had the largest median wetland methane fluxes (16–18 g CH〈jats:sub〉4〈/jats:sub〉 m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉). Quantifying the regional scale carbon balance remains challenging because of high spatial and temporal variability and relatively low density of observations. More accurate permafrost region carbon fluxes require: (a) the development of better maps characterizing wetlands and dynamics of vegetation and disturbances, including abrupt permafrost thaw; (b) the establishment of new year‐round CO〈jats:sub〉2〈/jats:sub〉 and methane flux sites in underrepresented areas; and (c) improved models that better represent important permafrost carbon cycle dynamics, including non‐growing season emissions and disturbance effects.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 76
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    American Geophysical Union (AGU)
    In:  EPIC3Geochemistry Geophysics Geosystems, American Geophysical Union (AGU), 25(1), ISSN: 1525-2027
    Publication Date: 2024-03-04
    Description: Mineral dust accumulated on the ocean floor is an important archive for reconstructing past atmospheric circulation changes and climatological conditions in the source areas. Dust emitted from Southern Hemisphere dust sources is widely deposited over the oceans. However, there are few records of dust deposition over the open ocean, and a large need for extended geographical coverage exists. We present a large data set (134 surface sediment samples) of Late Holocene dust deposition from seafloor surface sediments covering the entire South Atlantic Ocean. Polymodal grain-size distributions of the lithogenic fraction indicate that the sediments are composed of multiple sediment components. By using end-member modeling, we attempt to disentangle the dust signal from non-aeolian sediments. Combined with 230Th-normalized lithogenic fluxes, we quantified the specific deposition fluxes for mineral dust, crrent-sorted sediments and ice-rafted debris (IRD). Although the method could not completely separate the different components in every region, it shows that dust deposition off the most prominent dust source for the South Atlantic Ocean—southern South America—amounts up to approximately 0.7 g cm−2 Kyr−1 and decreases downwind. Bottom-current-sorted sediments and IRD are mostly concentrated around the continental margins. The ratio of the coarse to fine dust end members reveals input from north African dust sources to the South Atlantic. The majority of the observations are in good agreement with new model simulations. This extensive and relevant data set of dust grain size and deposition fluxes to the South Atlantic could be used to calibrate and validate further model simulations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 77
    Publication Date: 2024-02-13
    Description: The availability of silicon (Si) in the ocean plays an important role in regulating biogeochemical and ecological processes. The Si budget of the Arctic Ocean appears balanced, with inputs equivalent to outputs, though it is unclear how a changing climate might aggravate this balance. In this study, we focus on Si cycling in Arctic coastal areas and continental shelf sediments to better constrain the Arctic Ocean Si budget. We provide the first estimate of amorphous Si (ASi) loading from erosion of coastal Yedoma deposits (30–90 Gmol yr−1), demonstrating comparable rates to particulate Si loading from rivers (10–90 Gmol yr−1). We found a positive relationship between surface sediment ASi and organic matter content on continental shelves. Combining these values with published Arctic shelf sediment properties and burial rates we estimate 70 Gmol Si yr−1 is buried on Arctic continental shelves, equivalent to 4.5% of all Si inputs to the Arctic Ocean. Sediment dissolved Si fluxes increased with distance from river mouths along cruise transects of shelf regions influenced by major rivers in the Laptev and East Siberian seas. On an annual basis, we estimate that Arctic shelf sediments recycle approximately up to twice as much DSi (680 Gmol Si) as is loaded from rivers (340–500 Gmol Si).
    Repository Name: EPIC Alfred Wegener Institut
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  • 78
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    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 38(1), ISSN: 0886-6236
    Publication Date: 2024-02-13
    Description: The coastal ocean contributes to regulating atmospheric greenhouse gas concentrations by taking up carbon dioxide (CO2) and releasing nitrous oxide (N2O) and methane (CH4). In this second phase of the Regional Carbon Cycle Assessment and Processes (RECCAP2), we quantify global coastal ocean fluxes of CO2, N2O and CH4 using an ensemble of global gap-filled observation-based products and ocean biogeochemical models. The global coastal ocean is a net sink of CO2 in both observational products and models, but the magnitude of the median net global coastal uptake is ∼60% larger in models (−0.72 vs. −0.44 PgC year−1, 1998–2018, coastal ocean extending to 300 km offshore or 1,000 m isobath with area of 77 million km2). We attribute most of this model-product difference to the seasonality in sea surface CO2 partial pressure at mid- and high-latitudes, where models simulate stronger winter CO2 uptake. The coastal ocean CO2 sink has increased in the past decades but the available time-resolving observation-based products and models show large discrepancies in the magnitude of this increase. The global coastal ocean is a major source of N2O (+0.70 PgCO2-e year−1 in observational product and +0.54 PgCO2-e year−1 in model median) and CH4 (+0.21 PgCO2-e year−1 in observational product), which offsets a substantial proportion of the coastal CO2 uptake in the net radiative balance (30%–60% in CO2-equivalents), highlighting the importance of considering the three greenhouse gases when examining the influence of the coastal ocean on climate.
    Repository Name: EPIC Alfred Wegener Institut
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  • 79
    Publication Date: 2024-02-08
    Description: Shells of the giant clam Tridacna can provide decade-long records of past environmental conditions via their geochemical composition and structurally through growth banding. Counting the daily bands can give an accurate internal age model with high temporal resolution, but daily banding is not always visually retrievable, especially in fossil specimens. We show that daily geochemical cycles (e.g., Mg/Ca) are resolvable via highly spatially resolved laser-ablation inductively coupled plasma mass spectrometry (LA-ICPMS; 3 \xc3\x97 33 \xce\xbcm laser slit) in our Miocene (\xe2\x88\xbc10 Ma) specimen, even in areas where daily banding is not visually discernible. By applying wavelet transformation on the measured daily geochemical cycles, we quantify varying daily growth rates throughout the shell. These growth rates are thus used to build an internal age model independent of optical daily band countability. Such an age model can be used to convert the measured elemental ratios from a function of distance to a function of time, which helps evaluate paleoenvironmental proxy data, for example, regarding the timing of sub-seasonal events. Furthermore, the quantification of daily growth rates across the shell facilitates the evaluation of (co)dependencies between growth rates and corresponding elemental compositions.
    Keywords: Tridacna
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 80
    Publication Date: 2024-01-26
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Erosion of permafrost coasts due to climate warming releases large quantities of organic carbon (OC) into the Arctic Ocean. While burial of permafrost OC in marine sediments potentially limits degradation, resuspension of sediments in the nearshore zone potentially enhances degradation and greenhouse gas production, adding to the “permafrost carbon feedback.” Recent studies, focusing on bulk sediments, suggest that permafrost OC derived from coastal erosion is predominantly deposited close to shore. However, bulk approaches disregard sorting processes in the coastal zone, which strongly influence the OC distribution and fate. We studied soils and sediments along a transect from the fast‐eroding shoreline of Herschel Island—〈jats:italic〉Qikiqtaruk〈/jats:italic〉 (Yukon, Canada) to a depositional basin offshore. Sample material was fractionated by density (1.8 g cm〈jats:sup〉−3〈/jats:sup〉) and size (63 μm), separating loose OC from mineral‐associated OC. Each fraction was analyzed for element content (TOC, TN), carbon isotopes (δ〈jats:sup〉13〈/jats:sup〉C, Δ〈jats:sup〉14〈/jats:sup〉C), molecular biomarkers (〈jats:italic〉n〈/jats:italic〉‐alkanes, 〈jats:italic〉n〈/jats:italic〉‐alkanoic acids, lignin phenols, cutin acids), and mineral surface area. The OC partitioning between fractions changes considerably along the transect, highlighting the importance of hydrodynamic sorting in the nearshore zone. Additionally, OC and biomarker loadings decrease along the land‐ocean transect, indicating significant loss of OC during transport. However, molecular proxies for degradation show contrasting trends, suggesting that OC losses are not always well reflected in its degradation state. This study, using fraction partitioning that crosses land‐ocean boundaries in a way not done before, aids to disentangle sorting processes from degradation patterns, and provides quantitative insight into losses of thawed and eroded permafrost OC.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 81
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    American Chemical Society
    In:  EPIC3Environmental Science & Technology Letters, American Chemical Society
    Publication Date: 2024-01-24
    Repository Name: EPIC Alfred Wegener Institut
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  • 82
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(21), ISSN: 0094-8276
    Publication Date: 2023-11-01
    Description: Molybdenum (Mo) is a trace element sensitive to oceanic redox conditions. The fidelity of sedimentary Mo as a paleoredox proxy of coeval seawater depends on the extent of Mo remobilization during postdepositional processes. Here we present the Mo content and isotope profiles for deep sediments from the Nankai Trough, Japan. The Mo signature suggests that these sediments have experienced extensive early diagenesis and hydrothermal alteration at depth. Iron (Fe)‐manganese (Mn) (oxyhydr)oxide alteration combined with Mo thiolation leads to a more than twenty‐fold enrichment of Mo within the sulfate reduction zone. Hydrothermal fluids and Mo adsorption onto Fe‐Mn (oxyhydr)oxides cause extremely negative Mo‐isotope values at the underthrust zone. These postdepositional Mo signals might be misinterpreted as expanded anoxia in the water column. Our findings highlight the importance of constraining postdepositional effects on Mo‐based proxies during paleoredox reconstruction.
    Repository Name: EPIC Alfred Wegener Institut
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  • 83
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(23), ISSN: 0094-8276
    Publication Date: 2023-09-19
    Description: The strong cooling during the Last Glacial Maximum (LGM, 21 ka BP) provides a rigorous test of climate models' ability to simulate past and future climate changes. We force an atmospheric general circulation model with two recent global LGM sea surface temperature (SST) reconstructions, one suggesting a weak and the other a more pronounced cooling, and compare the simulated land surface temperatures (LSTs) to reconstructed data. Our results do not confirm either SST reconstruction. The cold SST data set leads to good agreement between simulated and observed LSTs at low latitudes, but is systematically too cold at mid-latitudes. The opposite is true for the warm SST data set. Differences between the simulated LSTs are caused by varying land surface albedos, which is lower for the warmer SST reconstruction. The inconsistency between reconstructed and simulated climate points to a potentially significant bias in the proxy reconstructions and/or the climate sensitivity of current climate models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 84
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(17), ISSN: 0094-8276
    Publication Date: 2023-09-08
    Description: We quantify sea ice concentration (SIC) changes related to synoptic cyclones separately for each month of the year in the Greenland, Barents and Kara Seas for 1979–2018. We find that these SIC changes can be statistically significant throughout the year. However, their strength varies from region to region and month to month, and their sign strongly depends on the considered time scale (before/during vs. after cyclone passages). Our results show that the annual cycle of cyclone impacts on SIC is related to varying cyclone intensity and traversed sea ice conditions. We further show that significant changes in these cyclone impacts have manifested in the last 40 years, with the strongest changes occurring in October and November. For these months, SIC decreases before/during cyclones have more than doubled in magnitude in the Barents and Kara Seas, while SIC increases following cyclones have weakened (intensified) in the Barents Sea (Kara Sea).
    Repository Name: EPIC Alfred Wegener Institut
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  • 85
    Publication Date: 2023-12-19
    Description: As a contribution to the Regional Carbon Cycle Assessment and Processes phase 2 (RECCAP2) project, we present synthesized estimates of Arctic Ocean sea-air CO2 fluxes and their uncertainties from surface ocean pCO2-observation products, ocean biogeochemical hindcast and data assimilation models, and atmospheric inversions. For the period of 1985–2018, the Arctic Ocean was a net sink of CO2 of 116 ± 4 TgC yr−1 in the pCO2 products, 92 ± 30 TgC yr−1 in the models, and 91 ± 21 TgC yr−1 in the atmospheric inversions. The CO2 uptake peaks in late summer and early autumn, and is low in winter when sea ice inhibits sea-air fluxes. The long-term mean CO2 uptake in the Arctic Ocean is primarily caused by steady-state fluxes of natural carbon (70% ± 15%), and enhanced by the atmospheric CO2 increase (19% ± 5%) and climate change (11% ± 18%). The annual mean CO2 uptake increased from 1985 to 2018 at a rate of 31 ± 13 TgC yr−1 dec−1 in the pCO2 products, 10 ± 4 TgC yr−1 dec−1 in the models, and 32 ± 16 TgC yr−1 dec−1 in the atmospheric inversions. Moreover, 77% ± 38% of the trend in the net CO2 uptake over time is caused by climate change, primarily due to rapid sea ice loss in recent years. Furthermore, true uncertainties may be larger than the given ensemble standard deviations due to common structural biases across all individual estimates.
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  • 86
    Publication Date: 2024-01-06
    Description: The seasonal cycle is the dominant mode of variability in the air-sea CO2 flux in most regions of the global ocean, yet discrepancies between different seasonality estimates are rather large. As part of the Regional Carbon Cycle Assessment and Processes Phase 2 project (RECCAP2), we synthesize surface ocean pCO2 and air-sea CO2 flux seasonality from models and observation-based estimates, focusing on both a present-day climatology and decadal changes between the 1980s and 2010s. Four main findings emerge: First, global ocean biogeochemistry models (GOBMs) and observation-based estimates (pCO2 products) of surface pCO2 seasonality disagree in amplitude and phase, primarily due to discrepancies in the seasonal variability in surface DIC. Second, the seasonal cycle in pCO2 has increased in amplitude over the last three decades in both pCO2 products and GOBMs. Third, decadal increases in pCO2 seasonal cycle amplitudes in subtropical biomes for both pCO2 products and GOBMs are driven by increasing DIC concentrations stemming from the uptake of anthropogenic CO2 (Cant). In subpolar and Southern Ocean biomes, however, the seasonality change for GOBMs is dominated by Cant invasion, whereas for pCO2 products an indeterminate combination of Cant invasion and climate change modulates the changes. Fourth, biome-aggregated decadal changes in the amplitude of pCO2 seasonal variability are largely detectable against both mapping uncertainty (reducible) and natural variability uncertainty (irreducible), but not at the gridpoint scale over much of the northern subpolar oceans and over the Southern Ocean, underscoring the importance of sustained high-quality seasonally resolved measurements over these regions.
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  • 87
    Publication Date: 2024-01-06
    Description: This contribution to the RECCAP2 (REgional Carbon Cycle Assessment and Processes) assessment analyzes the processes that determine the global ocean carbon sink, and its trends and variability over the period 1985–2018, using a combination of models and observation-based products. The mean sea-air CO2 flux from 1985 to 2018 is −1.6 ± 0.2 PgC yr−1 based on an ensemble of reconstructions of the history of sea surface pCO2 (pCO2 products). Models indicate that the dominant component of this flux is the net oceanic uptake of anthropogenic CO2, which is estimated at −2.1 ± 0.3 PgC yr−1 by an ensemble of ocean biogeochemical models, and −2.4 ± 0.1 PgC yr−1 by two ocean circulation inverse models. The ocean also degasses about 0.65 ± 0.3 PgC yr−1 of terrestrially derived CO2, but this process is not fully resolved by any of the models used here. From 2001 to 2018, the pCO2 products reconstruct a trend in the ocean carbon sink of −0.61 ± 0.12 PgC yr−1 decade−1, while biogeochemical models and inverse models diagnose an anthropogenic CO2-driven trend of −0.34 ± 0.06 and −0.41 ± 0.03 PgC yr−1 decade−1, respectively. This implies a climate-forced acceleration of the ocean carbon sink in recent decades, but there are still large uncertainties on the magnitude and cause of this trend. The interannual to decadal variability of the global carbon sink is mainly driven by climate variability, with the climate-driven variability exceeding the CO2-forced variability by 2–3 times. These results suggest that anthropogenic CO2 dominates the ocean CO2 sink, while climate-driven variability is potentially large but highly uncertain and not consistently captured across different methods.
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  • 88
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    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(24), ISSN: 0094-8276
    Publication Date: 2024-04-22
    Description: Statistical analysis of reanalysis and observed data reveals that high dust surface mass concentration in northern Greenland is associated with a Pacific Decadal Oscillation like pattern in its negative phase in the North Pacific as well as with La Niña conditions in the tropical Pacific region. The sea surface temperature anomalies in the Pacific realm resemble the Interdecadal Pacific Oscillation (IPO). The associated atmospheric circulation pattern, in the form of a wave-train from the North Pacific to the Eurasian continent, favors enhanced dust uptake and transport toward the northern Greenland. Similar patterns are associated with a low-resolution stacked record of five Ca2+ ice cores, that is, ngt03C93.2 (B16), ngt14C93.2 (B18), ngt27C94.2 (B21), GISP2−B, and NEEM-2011-S1, from northern Greenland, a proxy for regional dust concentration, during the last 400 years. We argue that northern Greenland ice core dust records could be used as proxies for the IPO and related teleconnections.
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  • 89
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), 129(3), ISSN: 2169-9313
    Publication Date: 2024-04-24
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Extensive investigation of continental rift systems has been fundamental for advancing the understanding of extensional tectonics and modes of formation of new ocean basins. However, current rift classification schemes do not account for conjugate end members formed by Large Igneous Province crust, referring to thick mafic crust, sometimes including continental fragments. Here, we investigate the rifting of William's Ridge (Kerguelen Plateau) and Broken Ridge, components of the Kerguelen Large Igneous Province now situated in the Southeast Indian Ocean, and incorporate these end members into the deformation migration concept for rifted margins. We use multichannel seismic reflection profiles and data from scientific drill cores acquired on both conjugate margins to propose, for the first time, a combined tectono‐stratigraphic framework. We interpret seismic patterns, tectonic features, and magnetic anomaly picks to determine an across‐strike structural domain classification. This interpretation considers the rift system overall to be “magma‐poor” despite being located proximal to the Kerguelen plume but suggests that syn‐rift interaction between the Kerguelen mantle plume and the lithospheric structure of William's Ridge and Broken Ridge has controlled the along‐strike segmentation of both conjugates. We integrate seismic reflection and bathymetric data to test the hypothesis of predominantly transform motion, between the Australian and Antarctic plates, in Late Cretaceous and Paleogene time.〈/jats:p〉
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  • 90
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    American Meteorological Society
    In:  EPIC3Journal of Physical Oceanography, American Meteorological Society, 54(4), pp. 1003-1018, ISSN: 0022-3670
    Publication Date: 2024-04-25
    Description: Coastal upwelling, driven by alongshore winds and characterized by cold sea surface temperatures and high upper-ocean nutrient content, is an important physical process sustaining some of the oceans’ most productive ecosystems. To fully understand the ocean properties in eastern boundary upwelling systems, it is important to consider the depth of the source waters being upwelled, as it affects both the SST and the transport of nutrients toward the surface. Here, we construct an upwelling source depth distribution for parcels at the surface in the upwelling zone. We do so using passive tracers forced at the domain boundary for every model depth level to quantify their contributions to the upwelled waters. We test the dependence of this distribution on the strength of the wind stress and stratification using high-resolution regional ocean simulations of an idealized coastal upwelling system. We also present an efficient method for estimating the mean upwelling source depth. Furthermore, we show that the standard deviation of the upwelling source depth distribution increases with increasing wind stress and decreases with increasing stratification. These results can be applied to better understand and predict how coastal upwelling sites and their surface properties have and will change in past and future climates.
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  • 91
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(1), ISSN: 2169-9275
    Publication Date: 2024-05-08
    Description: We assessed the spatial and temporal variability of the Arctic Boundary Current (ABC) using seven oceanographic moorings, deployed across the continental slope north of Severnaya Zemlya in 2015–2018. Transports and individual water masses were quantified based on temperature and salinity recorders and current profilers. Our results were compared with observations from the northeast Svalbard and the central Laptev Sea continental slopes to evaluate the hydrographic transformation along the ABC pathway. The highest velocities (〉0.30 m s−1) of the ABC occurred at the upper continental slope and decreased offshore to below 0.03 m s−1 in the deep basin. The ABC showed seasonal variability with velocities two times higher in winter than in summer. Compared to upstream conditions in Svalbard, water mass distribution changed significantly within 20 km of the shelf edge due to mixing with- and intrusion of shelf waters. The ABC transported 4.15 ± 0.3 Sv in the depth range 50–1,000 m, where 0.88 ± 0.1, 1.5 ± 0.2, 0.61 ± 0.1 and 1.0 ± 0.15 Sv corresponded to Atlantic Water (AW), Dense Atlantic Water (DAW), Barents Sea Branch Water (BSBW) and Transformed Atlantic Water (TAW). 62–70% of transport was constrained to within 30–40 km of the shelf edge, and beyond 84 km, transport increases were estimated to be 0.54 Sv. Seasonality of TAW derived from local shelf-processes and advection of seasonal-variable Fram Strait waters, while BSBW transport variability was dominated by temperature changes with maximum transport coinciding with minimum temperatures. Further Barents Sea warming will likely reduce TAW and BSBW transport leading to warmer conditions along the ABC pathway.
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  • 92
    Publication Date: 2023-12-20
    Description: We assess the Southern Ocean CO2 uptake (1985–2018) using data sets gathered in the REgional Carbon Cycle Assessment and Processes Project Phase 2. The Southern Ocean acted as a sink for CO2 with close agreement between simulation results from global ocean biogeochemistry models (GOBMs, 0.75 ± 0.28 PgC yr−1) and pCO2-observation-based products (0.73 ± 0.07 PgC yr−1). This sink is only half that reported by RECCAP1 for the same region and timeframe. The present-day net uptake is to first order a response to rising atmospheric CO2, driving large amounts of anthropogenic CO2 (Cant) into the ocean, thereby overcompensating the loss of natural CO2 to the atmosphere. An apparent knowledge gap is the increase of the sink since 2000, with pCO2-products suggesting a growth that is more than twice as strong and uncertain as that of GOBMs (0.26 ± 0.06 and 0.11 ± 0.03 Pg C yr−1 decade−1, respectively). This is despite nearly identical pCO2 trends in GOBMs and pCO2-products when both products are compared only at the locations where pCO2 was measured. Seasonal analyses revealed agreement in driving processes in winter with uncertainty in the magnitude of outgassing, whereas discrepancies are more fundamental in summer, when GOBMs exhibit difficulties in simulating the effects of the non-thermal processes of biology and mixing/circulation. Ocean interior accumulation of Cant points to an underestimate of Cant uptake and storage in GOBMs. Future work needs to link surface fluxes and interior ocean transport, build long overdue systematic observation networks and push toward better process understanding of drivers of the carbon cycle.
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  • 93
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 128(10), ISSN: 2169-9003
    Publication Date: 2024-03-14
    Description: Radio Echo Sounding (RES) surveys conducted in May 2010 and April 2011 revealed a 2 km2 flat area with increased bed reflectivity at the base of Isunnguata Sermia at the western margin of the Greenland Ice Sheet. This flat reflector was located within a localized subglacial hydraulic potential (hydropotential) minimum, as part of a complex and elongated trough system. By analogy with comparable features in Antarctica, the initial interpretation of such a feature was a potential subglacial lake. In September 2013 a co-located seismic survey revealed a 1,750 m by 540 and 37 m thick stratified lens-shaped bedform at the base of a subglacial trough system. Amplitude Versus Angle (AVA) analysis yields a derived reflection coefficient R = 0.09 ± 0.14 indicative of consolidated sediments possibly overlain by dilatant till. The bed and flank on the northern side of the trough consist of unconsolidated, possibly water-bearing sediments with R = −0.10 ± 0.08, whereas on the southern side it consists of more consolidated material. We interpret the trough as a key component of the wider subglacial drainage network, for which the sediments on its northern side act as a localized water-storage reservoir. Given the observation of seasonally forming and rapidly draining supraglacial meltwater lakes in this area, we interpret the lens-shaped bedform as deposited by episodically ponding meltwater within the subglacial trough system. Our results highlight the importance of transient subglacial hydrological and sedimentological processes such as drainage events for the interaction of ice sheets and their substrates, to understand ice dynamics in a warming climate.
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  • 94
    Publication Date: 2024-03-14
    Description: The presence of clouds in the Arctic regulates the surface energy budget (SEB) over the sea-ice surface and the ice-free ocean. Following several previous field campaigns, the cloud-radiation relationship, including cloud vertical structure and phase, has been elucidated; however, modeling of this relationship has matured slowly. In recognition of the recent decline in the Arctic sea-ice extent, representation of the cloud system in numerical models should consider the effects of areas covered by sea ice and ice-free areas. Using an in situ stationary meteorological observation data set obtained over the ice-free Arctic Ocean by the Japanese Research Vessel Mirai (September 2014), coordinated evaluation of six regional climate models (RCMs) with nine model runs was performed by focusing on clouds and the SEB. The most remarkable findings were as follows: (1) reduced occurrence of unstable stratification with low-level cloud water in all models in comparison to the observations, (2) significant differences in cloud water representations between single- and double-moment cloud schemes, (3) extensive differences in partitioning of hydrometeors including solid/liquid precipitation, and (4) pronounced lower-tropospheric air temperature biases. These issues are considered as the main sources of SEB uncertainty over ice-free areas of the Arctic Ocean. The results from a coupled RCM imply that the SEB is constrained by both the atmosphere and the ocean (and sea ice) with considerable feedback. Coordinated improvement of both stand-alone atmospheric and coupled RCMs would promote a more comprehensive and improved understanding of the Arctic air-ice-sea coupled system.
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  • 95
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 126(12), ISSN: 2169-9003
    Publication Date: 2024-03-14
    Description: Bedforms of Thwaites Glacier, West Antarctica both record and affect ice flow, as shown by geophysical data and simple models. Thwaites Glacier flows across the tectonic fabric of the West Antarctic rift system with its bedrock highs and sedimentary basins. Swath radar and seismic surveys of the glacier bed have revealed soft-sediment flutes 100 m or more high extending 15 km or more across basins downglacier from bedrock highs. Flutes end at prominent hard-bedded moats on stoss sides of the next topographic highs. We use simple models to show that ice flow against topography increases pressure between ice and till upglacier along the bed over a distance that scales with the topography. In this basal zone of high pressure, ice-contact water would be excluded, thus increasing basal drag by increasing ice-till coupling and till flux, removing till to allow bedrock erosion that creates moats. Till carried across highlands would then be deposited in lee-side positions forming bedforms that prograde downglacier over time, and that remain soft on top through feedbacks that match till-deformational fluxes from well upglacier of the topography. The bedforms of the part of Thwaites surveyed here are prominent because ice flow has persisted over a long time on this geological setting, not because ice flow is anomalous. Bedform development likely has caused evolution of ice flow over time as till and lubricating water were redistributed, moats were eroded and bedforms grew.
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  • 96
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    American Meteorological Society
    In:  EPIC3Journal of Climate, American Meteorological Society, 37(6), pp. 2059-2080, ISSN: 0894-8755
    Publication Date: 2024-04-22
    Description: Heat stress is projected to intensify with global warming, causing significant socioeconomic impacts and threatening human health. Wet-bulb temperature (WBT), which combines temperature and humidity effects, is a useful indicator for assessing regional and global heat stress variability and trends. However, the variations of European WBT and their underlying mechanisms remain unclear. Using observations and reanalysis datasets, we demonstrate a remarkable warming of summer WBT during the period 1958–2021 over Europe. Specifically, the European summer WBT has increased by over 1.08C in the past 64 years. We find that the increase in European summer WBT is driven by both near-surface warming temperatures and increasing atmospheric moisture content. We identify four dominant modes of European summer WBT variability and investigate their linkage with the large-scale atmospheric circulation and sea surface temperature anomalies. The first two leading modes of the European WBT variability exhibit prominent interdecadal to long-term variations, mainly driven by a circumglobal wave train and concurrent sea surface temperature variations. The last two leading modes of European WBT variability mainly show interannual variations, indicating a direct and rapid response to large-scale atmospheric dynamics and nearby sea surface temperature variations. Further analysis shows the role of global warming and changes in midlatitude circulations in the variations of summer WBT. Our findings can enhance the understanding of plausible drivers of heat stress in Europe and provide valuable insights for regional decision-makers and climate adaptation planning.
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  • 97
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 128(2), ISSN: 2169-9003
    Publication Date: 2024-04-29
    Description: The stable water isotopic composition in firn and ice cores provides valuable information on past climatic conditions. Because of uneven accumulation and post-depositional modifications on local spatial scales up to hundreds of meters, time series derived from adjacent cores differ significantly and do not directly reflect the temporal evolution of the precipitated snow isotopic signal. Hence, a characterization of how the isotopic profile in the snow develops is needed to reliably interpret the isotopic variability in firn and ice cores. By combining digital elevation models of the snow surface and repeated high-resolution snow sampling for stable water isotope measurements of a transect at the East Greenland Ice-core Project campsite on the Greenland Ice Sheet, we are able to visualize the buildup and post-depositional changes of the upper snowpack across one summer season. To this end, 30 cm deep snow profiles were sampled on six dates at 20 adjacent locations along a 40 m transect. Near-daily photogrammetry provided snow height information for the same transect. Our data shows that erosion and redeposition of the original snowfall lead to a complex stratification in the δ18O signature. Post-depositional processes through vapor-snow exchange affect the near surface snow with d-excess showing a decrease in surface and near-surface layers. Our data suggests that the interplay of stratigraphic noise, accumulation intermittency, and local post-depositional processes form the proxy signal in the upper snowpack.
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  • 98
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(2), ISSN: 2169-9275
    Publication Date: 2024-05-01
    Description: We present a 700 km airborne electromagnetic survey of late-spring fast ice and sub-ice platelet layer (SIPL) thickness distributions from McMurdo Sound to Cape Adare, providing a first-time inventory of fast ice thickness close to its annual maximum. The overall mode of the consolidated ice (including snow) thickness was 1.9 m, less than its mean of 2.6 ± 1.0 m. Our survey was partitioned into level and rough ice, and SIPL thickness was estimated under level ice. Although level ice, with a mode of 2.0 m and mean of 2.0 ± 0.6 m, was prevalent, rough ice occupied 41% of the transect by length, 50% by volume, and had a mode of 3.3 m and mean of 3.2 ± 1.2 m. The thickest 10% of rough ice was almost 6 m on average, inclusive of a 2 km segment thicker than 8 m in Moubray Bay. The thickest ice occurred predominantly along the northwestern Ross Sea, due to compaction against the coast. The adjacent pack ice was thinner (by ∼1 m) than the first-year fast ice. In Silverfish Bay, offshore Hells Gate Ice Shelf, New Harbor, and Granite Harbor, the SIPL transect volume was a significant fraction (0.30) of the consolidated ice volume. The thickest 10% of SIPLs averaged nearly 3 m thick, and near Hells Gate Ice Shelf the SIPL was almost 10 m thick, implying vigorous heat loss to the ocean (∼90 W m −2). We conclude that polynya-induced ice deformation and interaction with continental ice influence fast ice thickness in the western Ross Sea.
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  • 99
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 125(2), ISSN: 2169-8953
    Publication Date: 2024-01-30
    Description: Climate change in the Arctic leads to permafrost degradation and to associated changes infreshwater geochemistry. There is a limited understanding of how disturbances such as active layerdetachments or retrogressive thaw slumps impact water quality on a catchment scale. This study investigateshow permafrost degradation affects concentrations of dissolved organic carbon (DOC), total dissolvedsolids (TDS), suspended sediment, and stable water isotopes in adjacent Low Arctic watersheds. Weincorporated data on disturbance between 1952 and 2015, as well as sporadic runoff and geochemistry dataof streams nearby. Our results show that the total disturbed area decreased by 41% between 1952 and 2015,whereas the total number of disturbances increased by 66% in all six catchments. The spatial variabilityof hydrochemical parameters is linked to catchment properties and not necessarily reflected at the outflow.Degrading ice‐wedge polygons were found to increase DOC concentrations upstream in Ice Creek West,whereas hydrologically connected disturbances were linked to increases in TDS and suspended sediment.Although we found a great spatial variability of hydrochemical concentrations along the paired watershed,there was a linear relationship between catchment size and daily DOC, total dissolved nitrogen, and TDSfluxes for all six streams. Suspended sedimentflux on the contrary did not show a clear relationship as onehydrologically connected retrogressive thaw slump impacted the overallflux in one of the streams.Understanding the spatial variability of water quality will help to model the lateral geochemicalfluxes fromArctic catchments
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  • 100
    Publication Date: 2024-01-31
    Description: In this study, we used stable isotopes of oxygen (δ18O), deuterium (δD), and dissolved inorganic carbon (δ13CDIC) in combination with temperature, salinity, oxygen, and nutrient concentrations to characterize the coastal (71°–78°W) and an oceanic (82°–98°W) water masses (SAAW—Subantarctic Surface Water; STW—Subtropical Water; ESSW—Equatorial Subsurface water; AAIW—Antarctic Intermediate Water; PDW—Pacific Deep Water) of the Southeast Pacific (SEP). The results show that δ18O and δD can be used to differentiate between SAAW-STW, SAAW-ESSW, and ESSW-AAIW. δ13CDIC signatures can be used to differentiate between STW-ESSW (oceanic section), SAAW-ESSW, ESSW-AAIW, and AAIW-PDW. Compared with the oceanic section, our new coastal section highlights differences in both the chemistry and geometry of water masses above 1,000 m. Previous paleoceanographic studies using marine sediments from the SEP continental margin used the present-day hydrological oceanic transect to compare against, as the coastal section was not sufficiently characterized. We suggest that our new results of the coastal section should be used for past characterizations of the SEP water masses that are usually based on continental margin sediment samples.
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