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  • Articles  (149,589)
  • Wiley  (140,517)
  • Annual Reviews
  • SpaceNews Inc.
  • 2020-2022  (41,920)
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  • 1
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    Advances in understanding large-scale responses of the water cycle to climate change (2020)
    Wiley
    Details
    Publication Date: 2020-12-22
    Description: Globally, thermodynamics explains an increase in atmospheric water vapor with warming of around 7%/°C near to the surface. In contrast, global precipitation and evaporation are constrained by the Earth's energy balance to increase at ∼2-3%/°C. However, this rate of increase is suppressed by rapid atmospheric adjustments in response to greenhouse gases and absorbing aerosols that directly alter the atmospheric energy budget. Rapid adjustments to forcings, cooling effects from scattering aerosol, and observational uncertainty can explain why observed global precipitation responses are currently difficult to detect but are expected to emerge and accelerate as warming increases and aerosol forcing diminishes. Precipitation increases with warming are expected to be smaller over land than ocean due to limitations on moisture convergence, exacerbated by feedbacks and affected by rapid adjustments. Thermodynamic increases in atmospheric moisture fluxes amplify wet and dry events, driving an intensification of precipitation extremes. The rate of intensification can deviate from a simple thermodynamic response due to in-storm and larger-scale feedback processes, while changes in large-scale dynamics and catchment characteristics further modulate the frequency of flooding in response to precipitation increases. Changes in atmospheric circulation in response to radiative forcing and evolving surface temperature patterns are capable of dominating water cycle changes in some regions. Moreover, the direct impact of human activities on the water cycle through water abstraction, irrigation, and land use change is already a significant component of regional water cycle change and is expected to further increase in importance as water demand grows with global population.
    Description: Published
    Description: 49-75
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Keywords: climate change; land surface; precipitation; radiative forcing; water cycle
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Physical and geochemical record of an early Eocene carbon‐cycle perturbation on a turbiditic continental margin (2021)
    Wiley
    Details
    Publication Date: 2021-01-20
    Description: Multivariate analysis of the elemental composition of hemipelagic sedimentary successions has provided invaluable information about palaeoenvironmental evolution, including records of short-lived Eocene hyperthermal events. However, few studies have analyzed the sedimentary record of these climatic events in turbidite-rich continental margin successions. In order to test the usefulness of multivariate statistical techniques (factor and cluster analysis) in palaeonvironmental and palaeoclimatic research on turbiditic successions, the lowermost Eocene Solondota section, which accumulated on the North Iberian continental margin, was studied. A prominent negative carbon isotope excursion from Solondota was correlated with the Ypresian (early Eocene) hyperthermal event J, also known as C24n.2rH1. High-resolution sedimentological, geochemical (stable isotopes, major and trace elements) and mineralogical (bulk and clay mineralogy) data show that multivariate statistical analysis helps to manage large-sized quantitative datasets objectively, avoiding arbitrary choice of representative elements and identifying environmental factors (virtual variables) that may not be evident otherwise. Variations in major and minor elements from hemipelagic carbonates across the Solondota carbon isotope excursion suggest a temporarily more humid continental climate, which caused increased terrigenous material input into the marine environment. The finer grained fraction boosted hemipelagic carbonate dilution, whereas the coarser grained sediment was transported by temporarily more frequent and voluminous turbidity currents. Thus, the results from the Solondota carbon isotope excursion revealed similarities with deep marine records of other early Eocene minor hyperthermal events. This demonstrates the validity of deep-marine turbiditic successions for providing reliable sedimentological, mineralogical and geochemical records of global palaeoclimatic significance, complementing the information obtained from other sedimentary environments. Furthermore, the generally expanded nature of turbiditic successions can potentially provide palaeoclimatic information at very high resolution, enriching, and perhaps improving, the commonly condensed and sometimes discontinuous record of hemipelagic- only successions.
    Description: Published
    Description: 881-904
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    A minimum time control problem for aerobic degradation processes in biocell composting plants (2021)
    Wiley
    Details
    Publication Date: 2021-05-12
    Description: We introduce a mathematical model for the composting process in biocells. The model includes several phenomena, like the aerobic biodegradation of the soluble substrate by means of a bacterial population, the hydrolysis of insoluble substrate, and the biomass decay. We investigate the best strategies to reduce substrate components in minimal time by controlling the effects of cell oxygen concentration on the degradation phenomenon. It is shown that singular controls are not optimal for this model and the optimal control time profiles are of bang or bang-bang type. The occurrence of switching curves is discussed. In the case of a bang-bang control we prove that optimal control profiles have a unique switching time and the corresponding switching curve is determined.
    Description: Published
    Description: 1251-1266
    Description: 7A. Geofisica per il monitoraggio ambientale
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Integrated use of unmanned aerial vehicle photogrammetry and terrestrial laser scanning to support archaeological analysis: The Acropolis of Selinunte case (Sicily, Italy) (2021)
    Wiley
    Details
    Publication Date: 2021-06-14
    Description: Southwestern Sicily is an area of infrequent seismic activity; however, some studies carried out in the archaeological Selinunte site suggest that, between the fourth century BC and the early Middle Ages, probably at least two earthquakes strucked this area with enough energy to damage and cause the collapse and kinematics of much of the architecture of Selinunte. Take into account that, in 2008, a noninvasive archaeological prospection and traditional data gathering methods along the Acropolis north fortifications were carried out. Following these first studies, after about 10 years, a new geophysical campaign was carried out. This second campaign benefited from the application of modern technologies for the acquisition and processing of the point cloud data on the northern part of the Acropolis, like terrestrial laser scanning and unmanned aerial vehicle photogrammetry. In this paper, we present the application of these techniques and a strategy for their integration for the 3D modelling of buildings and cultural heritages. We show how the integration of data acquired independently by these two techniques is an added value able to overcome the intrinsic limits of the individual techniques. The application to Selinunte's Acropolis allowed it to highlight and measure with high accuracy fractures, dislocation, inclinations of walls, depressions of some areas and other interesting observations, which may be important starting points for future investigations.
    Description: Published
    Description: 153-165
    Description: 2IT. Laboratori analitici e sperimentali
    Description: JCR Journal
    Keywords: 3D reconstruction ; archaeological survey ; digital elevation model ; Selinunte Archaeological Park ; terrestrial laser scanning ; unmanned aerial vehicle photogrammetry ; 05.04. Instrumentation and techniques of general interest ; 04.02. Exploration geophysics ; 05.02. Data dissemination ; 05.06. Methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Empirical nonergodic shaking scenarios based on spatial correlation models: An application to central Italy (2021)
    Wiley
    Details
    Publication Date: 2021-01-18
    Description: This paper provides a new methodological framework to generate empirical ground shaking scenarios, designed for engineering applications and civil protection planning. The methodology is useful both to reconstruct the ground motion pattern of past events and to generate future shaking scenarios, in regions where strong-motion datasets from multiple events and multiple stations are available. The proposed methodology combines (1) an ad-hoc nonergodic ground motion model (GMM) with (2) a spatial correlation model for the source region-, site-, and path-systematic residual terms, and (3) a model of the remaining aleatory error to take into account for directivity effects. The associated variability is a function of the type of scenario generated (bedrock or site, past or future event) and it is minimal for source areas where several events have occurred and for sites where recordings are available. In order to develop the region-specific fully nonergodic GMM and to compute robust estimation of the residual terms, the approach is calibrated on a highly dense dataset compiled for the area of central Italy. Example tests demonstrate the validity of the approach, which allows to simulate acceleration response spectra at unsampled sites, as well as to capture peculiar physical features of ground motion patterns in the region. The proposed approach could be usefully adopted for data-driven simulations of ground shaking maps, as alternative or complementary tool to physic-based and stochastic-based approaches.
    Description: Published
    Description: 60-80
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Geolithological and anthropogenic controls on the hydrochemistry of the Volturno river (Southern Italy) (2021)
    Wiley
    Details
    Publication Date: 2021-03-03
    Description: The present work aims to study the main chemical and physical water parameters in the upper and middle Volturno river catchment (southern Italy), between the Capo Volturno springs and the confluence with the Calore river. This study makes use of morphology, geolithology, tectonic, land use, and physico‐chemical (pH, electrical conductivity, redox potential, temperature, major ions, and 222Rn) data for the identification of the main sources of surface and groundwaters in the Volturno catchment and of their evolution and mixing both in base flow and peak flow conditions. The study was also performed to assess whether the alteration due to potential anthropogenic contamination may hamper the identification of natural “primitive” sources of surface waters, especially in the populated and farmed plains far from the river headwaters. Our data suggest that water chemistry of this stretch of the Volturno river is dominated mainly by lithology and, only marginally, by the intense exogenous activities and that this trend is appreciable in both base flow and peak flow conditions. The proposed simple geochemical approach based on easy‐to‐sample matrices and on cost‐effective standard methods is a valuable tool to address catchment functionality especially in upland areas, where complex geologic and structural settings, heterogeneous groundwater flow, and logistical issues are the rule rather than the exception. Because the upper and middle Volturno catchment is comparable with numerous valleys of the Mediterranean area, this study could be a reference for analogous applications.
    Description: Published
    Description: 627–638
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
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  • 7
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    Hydrogeochemical dynamics affecting steam-heated pools at El Chichón Crater (Chiapas - Mexico) (2021)
    Wiley
    Details
    Publication Date: 2021-03-02
    Description: El Chichon is an active volcano located in the north-western Chiapas, southern Mexico. The crater hosts a lake, a spring, named Soap Pool, emerging from the underlying volcanic aquifer and several mud pools/hot springs on the internal flanks of the crater which strongly interact with the current fumarolic system (steam-heated pools). Some of these pools, the crater lake and a cold spring emerging from the 1982 pumice deposits, have been sampled and analysed. Water–volcanic gas interactions determine the heating (43–99°C) and acidification (pH 2–4) of the springs, mainly by H2S oxidation. Significantly, in the study area, a significant NH3 partial pressure has been also detected. Such a geochemically aggressive environment enhances alteration of the rock in situ and strongly increases the mineralization of the waters (and therefore their electrical conductivity). Two different mineralization systems were detected for the crater waters: the soap pool-lake (Na+/Cl = 0.4, Na/Mg〉10) and the crater mud pools (Na+/Cl 〉 10, Na/Mg 〈 4). A deep boiling, Na+-K+-Cl -rich water reservoir generally influences the Soap Pool-lake, while the mud pool is mainly dominated by water-gas–rock interactions. In the latter case, conductivity of sampled water is directly proportional to the presence of reactive gases in solution. Therefore, chemical evolution proceeds through neutralization due to both rock alteration and bacterial oxidation of ammonium to nitrate. The chemical compositions show that El Chichon aqueous fluids, within the crater, interact with gases fed by a geothermal reservoir, without clear additions of deep magmatic fluids. This new geochemical dataset, together with previously published data, can be used as a base line with which to follow-up the activity of this deadly volcano.
    Description: Published
    Description: 331–343
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
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  • 8
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    New Applications in Gas Geochemistry (2021)
    Wiley
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    Publication Date: 2021-02-03
    Description: Gases present in the Earth crust are important in various branches of human activities. Hydrocarbons are a significant energy resource, helium is applied in many high-tech instruments, and studies of crustal gas dynamics provide insight in the geodynamic processes and help monitor seismic and volcanic hazards. Quantitative analysis of methane and CO2 migration is important for climate change studies. Some of them are toxic (H2S, CO2, CO); radon is responsible for the major part of human radiation dose. The development of analytical techniques in gas geochemistry creates opportunities of applying this science in numerous fields. Noble gases, hydrocarbons, CO2, N2, H2, CO, and Hg vapor are measured by advanced methods in various environments and matrices including fluid inclusions. Following the “Geochemical Applications of Noble Gases”(2009), “Frontiers in Gas Geochemistry” (2013), and “Progress in the Application of Gas Geochemistry to Geothermal, Tectonic and Magmatic Studies” (2017) published as special issues of Chemical Geology and “Gas geochemistry: From conventional to unconventional domains” (2018) published as a special issue of Marine and Petroleum Geology, this volume continues the tradition of publishing papers reflecting the diversity in scope and application of gas geochemistry.
    Description: Published
    Description: 976190
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: geochemistry ; Atmosphere ; 03. Hydrosphere ; 04. Solid Earth
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  • 9
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    Arctic Sea Ice in CMIP6 (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, ISSN: 0094-8276
    Details
    Publication Date: 2020-05-04
    Description: We examine CMIP6 simulations of Arctic sea‐ice area and volume. We find that CMIP6 models produce a wide spread of mean Arctic sea‐ice area, capturing the observational estimate within the multi‐model ensemble spread. The CMIP6 multi‐model ensemble mean provides a more realistic estimate of the sensitivity of September Arctic sea‐ice area to a given amount of anthropogenic CO2 emissions and to a given amount of global warming, compared with earlier CMIP experiments. Still, most CMIP6 models fail to simulate at the same time a plausible evolution of sea‐ice area and of global mean surface temperature. In the vast majority of the available CMIP6 simulations, the Arctic Ocean becomes practically sea‐ice free (sea‐ice area 〈 1 million km2) in September for the first time before the year 2050 in each of the four emission scenarios SSP1‐1.9, SSP1‐2.6, SSP2‐4.5 and SSP5‐8.5 examined here.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 10
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    Circulation and Thermohaline Variability of the Hanna Shoal Region on the Northeastern Chukchi Sea Shelf (2020)
    Wiley
    In:  EPIC3Journal of Geophysical Research: Oceans, Wiley
    Details
    Publication Date: 2020-07-07
    Description: We analyzed velocity and hydrographic data from 23 moorings in the northeast Chukchi Sea from 2011 to 2014. In most years the eastern side of Hanna Shoal was strongly stratified year-round, while weakly stratified regions prevailed on the shelf south and west of the Shoal. Stratification differences cause differential vertical mixing rates, which in conjunction with advection of different bottom water properties resulted in seasonally-varying along-isobath density gradients. In agreement with numerical models, we find that bottom waters flow anticyclonically around the Shoal. Whereas most of the shelf responded barotropically to wind-forcing, there was a strong baroclinic component to the flow field northeast of Hanna Shoal, resulting in no net vertically-integrated transport on average. In contrast there is a net eastward transport from west of the Shoal, which implies convergence north of the Shoal. Convergence and along-isobath density gradients may foster cross-shelf exchange north of Hanna Shoal. Modal analyses indicate that the shelf south of the Shoal and Barrow Canyon responded coherently to local and remote winds, whereas the wind-current response around Hanna Shoal was less coherent. Barotropic topographic waves, of ~3-day period, were generated episodically northeast of the Shoal and propagate clockwise around Hanna Shoal, but are blocked from entering Barrow Canyon and are possibly scattered by the horizontally sheared flow and converging isobaths on the western side of the Shoal. Analysis of water properties on the western side of Hanna Shoal suggests that these include contributions from the western and southern portions of the Chukchi Sea.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Limited Retreat of the Wilkes Basin Ice Sheet during the Last Interglacial (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(13), ISSN: 0094-8276
    Details
    Publication Date: 2020-07-20
    Description: The response of the East Antarctic Ice Sheet to global warming represents a major source of uncertainty in sea level projections. Thinning of the East Antarctic George V and Sabrina Coast ice‐cover is currently taking place, and regional ice‐sheet instability episodes might have been triggered in past warm climates. However, the magnitude of ice retreat in the past can not yet be quantitatively derived from paleo‐proxy records alone. We propose that a runaway retreat of the George V coast grounding line and subsequent instability of the Wilkes Basin ice‐sheet would either leave a clear imprint on the water isotope composition in the Talos Dome region or prohibit a Talos Dome ice‐core record from the Last Interglacial altogether. Testing this hypothesis our ice sheet model simulations suggest, that Wilkes Basin ice‐sheet retreat remained relatively limited during the Last Interglacial and provide a constraint on Last Interglacial East Antarctic grounding line stability.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Extent and cessation of the mid-Cretaceous Hikurangi Plateau underthrusting: Impact on global plate tectonics and the submarine Chatham Rise (2020)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Solid Earth, Wiley, 125, ISSN: 0148-0227
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    Publication Date: 2020-08-21
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Evolution of the Upper Ocean Stratification in the Japan Sea Since the Last Glacial (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(16), pp. e2020GL088255, ISSN: 0094-8276
    Details
    Publication Date: 2021-08-05
    Description: Paleoceanographic evidence commonly indicates that Last Glacial Maximum surface temperatures in the Japan Sea were comparable to modern conditions, in striking difference to colder neighboring regions. Here, based on a core from the central Japan Sea, our results show similar UK′37‐ and TEXL86‐derived temperatures between 24.7 and 16.3 ka BP, followed by an abrupt divergence at ~16.3 ka BP and a weakening of divergence after ~8.7 ka BP. We attribute this process to a highly stratified glacial upper ocean controlled by the East Asian Summer Monsoon, increasing thermal gradient between surface and subsurface layers during the deglaciation and the intrusion of Tsushima Warm Current since the mid‐Holocene, respectively. Therefore, we suggest that threshold‐like changes in upper‐ocean temperatures linked to sea level rise and monsoon dynamics, rather than just sea surface temperatures, play a critical role in shaping the thermal and ventilation history of this NW Pacific marginal sea.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    AMOC recovery in a multi-centennial scenario using a coupled atmosphere-ocean-ice sheet model (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(16), pp. e2019GL086810, ISSN: 0094-8276
    Details
    Publication Date: 2020-09-14
    Description: We simulate the two Coupled Model Intercomparison Project scenarios RCP4.5 and RCP8.5, to assess the effects of melt‐induced fresh water on the Atlantic meridional overturning circulation (AMOC). We use a newly developed climate model with high resolution at the coasts, resolving the complex ocean dynamics. Our results show an AMOC recovery in simulations run with and without an included ice sheet model. We find that the ice sheet adds a strong decadal variability on the freshwater release, resulting in intervals in which it reduces the surface runoff by high accumulation rates. This compensating effect is missing in climate models without dynamic ice sheets. Therefore, we argue to assess those freshwater hosing experiments critically, which aim to parameterize Greenland's freshwater release. We assume the increasing net evaporation over the Atlantic and the resulting increase in ocean salinity, to be the main driver of the AMOC recovery.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Ocean Circulation and Variability Beneath Nioghalvfjerdsbræ (79 North Glacier) Ice Tongue (2020)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Oceans, Wiley, 125(8), ISSN: 0148-0227
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    Publication Date: 2020-11-30
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Spatial and Temporal variability of iodine in aerosol (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Atmospheres, Wiley, 126, pp. e2020JD034410, ISSN: 0148-0227
    Details
    Publication Date: 2021-05-10
    Description: In this work we describe the compilation and homogenization of an extensive dataset of aerosol iodine field observations in the period between 1963 and 2018 and we discuss the spatial and temporal dependences of total iodine in bulk aerosol by comparing the observations with CAM-Chem model imulations. Total iodine in aerosol shows a distinct latitudinal dependence, with an enhancement towards the northern hemisphere (NH) tropics and lower values towards the poles. This behavior, which has been predicted by atmospheric models to depend on the global distribution of the main ceanic iodine source (which in turn depends on the reaction of surface ozone with aqueous iodide on he sea water-air interface, generating gas-phase I2 and HOI), is confirmed here by field observations for the first time. Longitudinally, there is some indication of a wave-one profile in the Tropics, which peaks in the Atlantic and shows a minimum in the Pacific, following the wave-one longitudinal variation of tropical tropospheric ozone. New data from Antarctica show that the south polar seasonal variation of iodine in aerosol mirrors that observed previously in the Arctic, with two equinoctial maxima and the dominant maximum occurring in spring. While no clear seasonal variability is observed in NH middle latitudes, there is an indication of different seasonal cycles in the NH tropical Atlantic and Pacific. A weak positive long-term trend is observed in the tropical annual averages, which is consistent with an enhancement of the anthropogenic ozone-driven global oceanic source of iodine over the last 50 years.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Nonmonotonic Change of the Arctic Ocean Freshwater Storage Capability in a Warming Climate (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(10), pp. e2020GL090951, ISSN: 0094-8276
    Details
    Publication Date: 2021-07-01
    Description: Freshwater in the Arctic Ocean is one of the key climate components. It is not well understood how the capability of the Arctic Ocean to store freshwater will develop when freshwater supplies increase in a warming climate. By using numerical experiments, we find that this capability varies with the Arctic sea ice decline nonmonotonically, with the largest capability at intermediate strength of sea ice decline. Through enhancing the ocean surface stress, sea ice decline not only accumulates freshwater toward the Amerasian Basin but also tends to reduce the amount of freshwater in both the Eurasian and Amerasian basins by increasing the occupation of Atlantic-origin water in the upper ocean. An increase in river runoff modulates the counterbalance of the two competing effects, leading to the nonmonotonic changes of the Arctic freshwater storage capability in a warming climate.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    On the Cause of the Mid‐Pleistocene Transition (2021)
    Wiley
    In:  EPIC3Reviews of Geophysics, Wiley, 59(2), pp. e2020RG000727, ISSN: 8755-1209
    Details
    Publication Date: 2021-06-17
    Description: The Mid-Pleistocene Transition (MPT), where the Pleistocene glacial cycles changed from 41 to ∼100 kyr periodicity, is one of the most intriguing unsolved issues in the field of paleoclimatology. Over the course of over four decades of research, several different physical mechanisms have been proposed to explain the MPT, involving non-linear feedbacks between ice sheets and the global climate, the solid Earth, ocean circulation, and the carbon cycle. Here, we review these different mechanisms, comparing how each of them relates to the others, and to the currently available observational evidence. Based on this discussion, we identify the most important gaps in our current understanding of the MPT. We discuss how new model experiments, which focus on the quantitative differences between the different physical mechanisms, could help fill these gaps. The results of those experiments could help interpret available proxy evidence, as well as new evidence that is expected to become available.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    Dynamics of the African Plate 75 Ma: From Plate Kinematic Reconstructions to Intraplate Paleo-Stresses (2021)
    Wiley
    In:  EPIC3Tectonics, Wiley, 40(7), ISSN: 0278-7407
    Details
    Publication Date: 2021-07-26
    Description: Plate reconstruction studies show that the Neotethys Ocean was closing due to the convergence of Africa and Eurasia toward the end of the Cretaceous. The period around 75 Ma reflects the onset of continental collision between the two plates as convergence continued to be taken up mostly by subduction of the Neotethys slab beneath Eurasia. The Owen transform plate boundary in the northeast accommodated the fast northward motion of the Indian plate relative to the African plate. The rest of the plate was surrounded by mid-ocean ridges. Africa was experiencing continent-wide rifting related to northeast-southwest extension. We aim to quantify the forces and paleostresses that may have driven this continental extension. We use the latest plate kinematic reconstructions in a grid search to estimate horizontal gravitational stresses (HGSs), plate boundary forces, and the plate's interaction with the asthenosphere. The contribution of dynamic topography to HGSs is based on recent mantle convection studies. We model intraplate stresses and compare them with the strain observations. The fit to observations favors models where dynamic topography amplitudes are smaller than 300 m. The results also indicate that the net pull transmitted from slab to the surface African plate was low. To put this into context, we notice that available tectonic reconstructions show fragmented subduction zones and various colliding micro-continents along the northern margin of the African plate around this time. We therefore interpret a low net pull as resulting from either a small average slab length or from the micro-continents' resistance to subduction.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Global River Discharge and Floods in the Warmer Climate of the Last Interglacial (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(e2020G), ISSN: 0094-8276
    Details
    Publication Date: 2020-09-18
    Description: We investigate hydrology during a past climate slightly warmer than the present: the Last Interglacial (LIG). With daily output of pre‐industrial and LIG simulations from eight new climate models we force hydrological model PCR‐GLOBWB, and in turn hydrodynamic model CaMa‐Flood. Compared to pre‐industrial, annual mean LIG runoff, discharge, and 100‐year flood volume are considerably larger in the Northern Hemisphere, by 14%, 25% and 82%, respectively. Anomalies are negative in the Southern Hemisphere. In some boreal regions, LIG runoff and discharge are lower despite higher precipitation, due the higher temperatures and evaporation. LIG discharge is much higher for the Niger, Congo, Nile, Ganges, Irrawaddy, Pearl, and lower for the Mississippi, Saint Lawrence, Amazon, Paraná, Orange, Zambesi, Danube, Ob. Discharge is seasonally postponed in tropical rivers affected by monsoon changes. Results agree with published proxies on the sign of discharge anomaly in 15 of 23 sites where comparison is possible.
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    Necessary Conditions for Warm Inflow Toward the Filchner Ice Shelf, Weddell Sea (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(22), pp. 1-11, ISSN: 0094-8276
    Details
    Publication Date: 2020-11-18
    Description: Understanding changes in Antarctic ice shelf basal melting is a major challenge for predicting future sea level. Currently, warm Circumpolar Deep Water surrounding Antarctica has limited access to the Weddell Sea continental shelf; consequently, melt rates at Filchner‐Ronne Ice Shelf are low. However, large‐scale model projections suggest that changes to the Antarctic Slope Front and the coastal circulation may enhance warm inflows within this century. We use a regional high‐resolution ice shelf cavity and ocean circulation model to explore forcing changes that may trigger this regime shift. Our results suggest two necessary conditions for supporting a sustained warm inflow into the Filchner Ice Shelf cavity: (i) an extreme relaxation of the Antarctic Slope Front density gradient and (ii) substantial freshening of the dense shelf water. We also find that the on‐shelf transport over the western Weddell Sea shelf is sensitive to the Filchner Trough overflow characteristics.
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  • 22
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    A changing Arctic Ocean: How measured and modeled 129129I distributions indicate fundamental shifts in circulation between 1994 and 2015 (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Oceans, Wiley, 126(3), ISSN: 0148-0227
    Details
    Publication Date: 2021-03-11
    Description: 129I measurements on samples collected during GEOTRACES oceanographic missions in the Arctic Ocean in 2015 have provided the first detailed, synoptic 129I sections across the Eurasian, Canada and Makarov Basins. During the 1990s, increased discharges of 129I from European nuclear fuel reprocessing plants produced a large, tracer spike whose passage through the Arctic Ocean has been followed by 129I time series measurements over the past 25 years. Elevated 129I levels measured over the Lomonosov and Alpha-Mendeleyev Ridges in 2015 were associated with tracer labeled, Atlantic-origin water bathymetrically steered by the ridge systems through the central Arctic while lower 129I levels were evident in the more poorly ventilated basin interiors. 129I levels of 200-400 x 107 at/l measured in intermediate waters in 2015 had increased by a factor of 10 compared to results from the same locations in 1994-1996 owing to the circulation of the 1990s, 129I input spike mainly associated with enhanced discharges from the La Hague nuclear fuel reprocessing plant. Comparisons of the patterns of 129I distributions between the mid-1990s and 2015 delineate large scale circulation changes that occurred during the shift from a positive Arctic Oscillation and a cyclonic circulation regime in the mid-1990s to anticyclonic circulation in 2015. The latter is characterized by a broadened Beaufort Gyre in the upper ocean, a weakened boundary current and partial mid-depth, AW flow reversal in the southern Canada Basin. Tracer 129I simulations using the applied circulation model, NAOSIM agree with both historical 129I results and recent GEOTRACES data sets, thereby lending context and credibility to the interpretation of large scale changes in arctic circulation and their relationship to shifts in climate indices revealed by tracer 129I distributions. This paper reports measurements and simulation results for 129I for the 1990s and 2015, and interprets them in the context of ocean circulation responses to changing atmospheric forcing regimes.
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  • 23
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    New Magnetostratigraphic Insights From Iceberg Alley on the Rhythms of Antarctic Climate During the Plio-Pleistocene (2021)
    Wiley
    In:  EPIC3Paleoceanography and Paleoclimatology, Wiley, 36(2), pp. 1-27, ISSN: 0883-8305
    Details
    Publication Date: 2021-02-25
    Description: International Ocean Discovery Program (IODP) Expedition 382 in the Scotia Sea’s Iceberg Alley recovered among the most continuous and highest resolution stratigraphic records in the Southern Ocean near Antarctica spanning the last 3.3 Myr. Sites drilled in Dove Basin (U1536/U1537) have well‐resolved magnetostratigraphy and a strong imprint of orbital forcing in their lithostratigraphy. All magnetic reversals of the last 3.3 Myr are identified, providing a robust age model independent of orbital tuning. During the Pleistocene, alternation of terrigenous versus diatomaceous facies shows power in the eccentricity and obliquity frequencies comparable to the amplitude modulation of benthic δ18O records. This suggests that variations in Dove Basin lithostratigraphy during the Pleistocene reflect a similar history as globally integrated ice volume at these frequencies. However, power in the precession frequencies over the entire ∼3.3 Myr record does not match the amplitude modulation of benthic δ18O records, suggesting Dove Basin contains a unique record at these frequencies. Comparing the position of magnetic reversals relative to local facies changes in Dove Basin and the same magnetic reversals relative to benthic δ18O at North Atlantic IODP Site U1308, we demonstrate Dove Basin facies change at different times than benthic δ18O during intervals between ∼3 and 1 Ma. These differences are consistent with precession phase shifts and suggest climate signals with a Southern Hemisphere summer insolation phase were recorded around Antarctica. If Dove Basin lithology reflects local Antarctic ice volume changes, these signals could represent ice sheet precession‐paced variations not captured in benthic δ18O during the 41‐kyr world.
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    Climatically modulated dust inputs from New Zealand to the Southwest Pacific sector of the Southern Ocean over the last 410 kyr (2021)
    Wiley
    In:  EPIC3Paleoceanography and Paleoclimatology, Wiley, pp. e2020PA003949
    Details
    Publication Date: 2021-04-01
    Description: Eolian mineral dust is an active agent in the global climate system. It affects planetary albedo and can influence marine biological productivity and ocean‐atmosphere carbon dynamics. This makes understanding of the global dust cycle crucial for constraining the dust/climate relationship, which requires long‐term dust emission records for all major dust sources. Despite their importance, the sources of atmospheric dust deposited in the Southern Ocean remain poorly constrained. Eolian dust in the Pacific sector of the Southern Ocean is generally assumed to originate from Australia, with minor contributions from New Zealand. Here we present a high‐resolution elemental record of terrestrial inputs for the past ∼410 kyr from marine sediment core PS75/100‐4 recovered from east of South Island, New Zealand. Sediment grain size is slightly finer than that of loess deposits from South Island, New Zealand, and is coarser than that of marine sediments in the Tasman Sea to the west of New Zealand, which indicates that the dust originated mainly from New Zealand and not only from Australia. Core PS75/100‐4 records lithogenic mass accumulation rates ranging from ∼0.01 to 0.69 g/cm2/kyr (∼0.20 g/cm2/kyr average), with variations over a factor of ∼3‐4 over glacial versus interglacial timescales for the past 410 kyr. Our geochemical data correlate well with Southern Ocean and Antarctic eolian dust records and suggest a westerly wind‐supplied dust signal from New Zealand. Our findings, therefore, suggest that New Zealand should be considered an important long‐term regional dust source in global dust cycle models.
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    Evidence for a highly dynamic West Antarctic Ice Sheet during the Pliocene (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48, ISSN: 0094-8276
    Details
    Publication Date: 2021-07-20
    Repository Name: EPIC Alfred Wegener Institut
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    Detailed Seismic Bathymetry Beneath Ekström Ice Shelf, Antarctica: Implications for Glacial History and Ice‐Ocean Interaction (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47, pp. e2019G, ISSN: 0094-8276
    Details
    Publication Date: 2020-08-03
    Description: The shape of ice shelf cavities are a major source of uncertainty in understanding ice‐ocean interactions. This limits assessments of the response of the Antarctic ice sheets to climate change. Here we use vibroseis seismic reflection surveys to map the bathymetry beneath the Ekström Ice Shelf, Dronning Maud Land. The new bathymetry reveals an inland‐sloping trough, reaching depths of 1,100 m below sea level, near the current grounding line, which we attribute to erosion by palaeo‐ice streams. The trough does not cross‐cut the outer parts of the continental shelf. Conductivity‐temperature‐depth profiles within the ice shelf cavity reveal the presence of cold water at shallower depths and tidal mixing at the ice shelf margins. It is unknown if warm water can access the trough. The new bathymetry is thought to be representative of many ice shelves in Dronning Maud Land, which together regulate the ice loss from a substantial area of East Antarctica.
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    Wintertime Airborne Measurements of Ice Nucleating Particles in the High Arctic: A Hint to a Marine, Biogenic Source for Ice Nucleating Particles (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47, pp. 1-11, ISSN: 0094-8276
    Details
    Publication Date: 2020-09-14
    Description: Ice nucleating particles (INPs) affect the radiative properties of cold clouds. Knowledge concerning their concentration above ground level and their potential sources is scarce. Here we present the first highly temperature resolved ice nucleation spectra of airborne samples from an aircraft campaign during late winter in 2018. Most INP spectra featured low concentration levels (〈3 · 10−4 L−1 at −15°C). −2 −1 However, we also found INP concentrations of up to 1.8·10 L at −15°C and freezing onsets as high as −7.5°C for samples mainly from the marine boundary layer. Shape and onset temperature of the ice nucleation spectra of those samples as well as heat sensitivity hint at biogenic INP. Colocated measurements additionally indicate a local marine influence rather than long‐range transport. Our results suggest that even in late winter above 80°N a local marine source for biogenic INP, which can efficiently nucleate ice at high temperatures, is present. Clouds are a key factor in the energy budget of the Arctic atmosphere. Ice nucleating particles (INPs) can modify the radiation properties and lifetime of clouds by affecting the relative abundance of liquid and frozen droplets in a cloud. Despite this important ability, knowledge about the INP concentration above ground level is limited as airborne INP measurements are very scarce in the Arctic. Here we present results from an aircraft campaign, which took place during the late winter of 2018 in latitudes above 80°N. We found INP concentrations at above −15°C, which are similar to those found in midlatitudes. These INPs also initiate freezing already at high temperatures. We found indications that the INPs are biogenic and originate from a local, marine source, rather than being transported from midlatitudes into the Arctic. Due to the presence of numerous cracks, open leads and polynyas in the sea ice in the investigation area, the ocean may provide a source for these biogenic INP in an environment, where sources on land are still shrouded in snow and ice. However, in a warming Arctic contributions from different sources might change, making the characterization of the current state important.
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    Deposition history and paleo-current activity on the southeastern Lomonosov Ridge and its Eurasian flank based on seismic data (2020)
    Wiley
    In:  EPIC3Geochemistry, Geophysics, Geosystems, Wiley, 21, pp. #e2020GC009133
    Details
    Publication Date: 2020-11-01
    Description: A regional seismic survey on the southeastern Lomonosov Ridge and adjacent basins provides constraints on the coupled evolution of ocean circulations, depositional regime and tectonic processes. First, Mesozoic strata on the Lomonosov Ridge, its faulted flanks and the initial Amundsen Basin were covered with syn-rift sediments of Paleocene to early Eocene age. Numerous vertical faults indicate differential compaction of possibly anoxic sediments deposited in the young, still isolated Eurasian Basin. The second stage, as indicated by a prominent high-amplitude-reflector sequence (HARS) covering the ridge, was a time of widespread changes in deposition conditions, likely controlled by the ongoing subsidence of the Lomonosov Ridge and gradual opening of the Fram Strait. Episodic incursions of water masses from the North Atlantic probably were the consequences, and led to the deposition of thin sedimentary layers of different lithology. The third stage is marked by continuous deposition since the early Miocene (20 Ma). At that time, the ridge no longer posed an obstacle between the Amerasia and Eurasia Basins and pelagic sedimentation was established. Drift bodies, sediment waves, and erosional structures indicate the onset of circulation. Faulting on the ridge slope has led to a series of terraces where sediment drifts have accumulated since the early Miocene. It is suggested that ongoing sagging of the ridge and currents may have shaped the steep sediment free flanks of the terraces. Lastly, a sequence of high-amplitude reflectors marks the transition to the early Pliocene large-scale Northern Hemisphere glaciations.
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    Amplified Arctic Surface Warming and Sea Ice Loss Due to Phytoplankton and Colored Dissolved Material (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47, pp. e2020GL088795, ISSN: 0094-8276
    Details
    Publication Date: 2020-11-16
    Description: Optically active water constituents attenuate solar radiation and hence affect the vertical distribution of energy in the upper ocean. To understand their implications, we operate an ocean biogeochemical model coupled to a general circulation model with sea ice. Incorporating the effect of phytoplankton and colored dissolved organic matter (CDOM) on light attenuation in the model increases the sea surface temperature in summer and decreases sea ice concentration in the Arctic Ocean. Locally, the sea ice season is reduced by up to one month. CDOM drives a significant part of these changes, suggesting that an increase of this material will amplify the observed Arctic surface warming through its direct thermal effect. Indirectly, changing advective processes in the Nordic Seas may further intensify this effect. Our results emphasize the phytoplankton and CDOM feedbacks on the Arctic ocean and sea ice system and underline the need to consider these effects in future modeling studies to enhance their plausibility.
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    COVID-19 crisis reduces free tropospheric ozone across the northern hemisphere (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(5), ISSN: 0094-8276
    Details
    Publication Date: 2021-03-04
    Description: Throughout spring and summer 2020, ozone stations in the northern extratropics recorded unusually low ozone in the free troposphere. From April to August, and from 1 to 8 kilometers altitude, ozone was on average 7% (≈4 nmol/mol) below the 2000 to 2020 climatological mean. Such low ozone, over several months, and at so many stations, has not been observed in any previous year since at least 2000. Atmospheric composition analyses from the Copernicus Atmosphere Monitoring Service and simulations from the NASA GMI model indicate that the large 2020 springtime ozone depletion in the Arctic stratosphere contributed less than one quarter of the observed tropospheric anomaly. The observed anomaly is consistent with recent chemistry-climate model simulations, which assume emissions reductions similar to those caused by the COVID-19 crisis. COVID-19 related emissions reductions appear to be the major cause for the observed reduced free tropospheric ozone in 2020.
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    Evolution of (Bio-)geochemical Processes and Diagenetic Alteration of Sediments Along the Tectonic Migration of Ocean Floor in the Shikoku Basin off Japan (2021)
    Wiley
    In:  EPIC3Geochemistry, Geophysics, Geosystems, Wiley
    Details
    Publication Date: 2021-06-30
    Description: Biogeochemical processes in subseafloor sediments are closely coupled to global element cycles. To improve the understanding of changes in biogeochemical conditions on geological timescales, we investigate sediment cores from a 1180 m deep hole in the Nankai Trough offshore Japan (Site C0023) drilled during International Ocean Discovery Program Expedition 370. During its tectonic migration from the Shikoku Basin to the Nankai Trough over the past 15 Ma, Site C0023 has experienced significant changes in depositional, thermal, and geochemical conditions. By combining pore-water, solid-phase, and rock magnetic data, we demonstrate that a transition from organic carbon-starved conditions with predominantly aerobic respiration to an elevated carbon burial environment with increased sedimentation occurred at ∼2.5 Ma. Higher rates of organic carbon burial in consequence of increased nutrient supply and productivity likely stimulated the onset of anaerobic electron-accepting processes during organic carbon degradation. A significant temperature increase by ∼50°C across the sediment column associated with trench-style sedimentation since ∼0.5 Ma could increase the bioavailability of organic matter and enhance biogenic methanogenesis. The resulting shifts in reaction fronts led to diagenetic transformation of iron (oxyhydr)oxides into pyrite in the organic carbon-starved sediments several millions of years after burial. We also show that high amounts of reducible iron(III) which can serve as electron acceptor for microbial iron(III) reduction are preserved and still available as phyllosilicate-bound Fe. This is the first study that shows the evolution of long-term variations of (bio-)geochemical processes along tectonic migration of ocean floor, thereby altering the primary sediment composition long after deposition.
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    Bathymetry beneath ice shelves of western Dronning Maud Land, East Antarctica, and implications on ice shelf stability (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(12), pp. e2019GL086724, ISSN: 0094-8276
    Details
    Publication Date: 2020-09-06
    Description: Antarctica's ice shelves play a key role in stabilizing the ice streams that feed them. Since basal melting largely depends on ice‐ocean interactions, it is vital to attain consistent bathymetry models to estimate water and heat exchange beneath ice shelves. We have constructed bathymetry models beneath the ice shelves of western Dronning Maud Land by inverting airborne gravity data, and incorporating seismic, multibeam and radar depth references. Our models reveal deep glacial troughs beneath the ice shelves and terminal moraines close to the continental shelf breaks, which currently limit the entry of Warm Deep Water from the Southern Ocean. The ice shelves buttress a catchment that comprises an ice volume equivalent to nearly 1 meter of eustatic sea level rise, partly susceptible to ocean forcing. Changes in water temperature and thermocline depth may accelerate marine based ice sheet drainage and constitute an underestimated contribution to future global sea level rise.
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    Antarctic Sea Ice Area in CMIP6 (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(9), ISSN: 0094-8276
    Details
    Publication Date: 2020-06-02
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    Regionally coupled atmosphere - ocean - marine biogeochemistry model ROM: 2. Studying the climate change signal in the North Atlantic and Europe (2020)
    Wiley
    In:  EPIC3Journal of Advances in Modeling Earth Systems, Wiley, n/a(n/a), pp. e2019MS001646, ISSN: 1942-2466
    Details
    Publication Date: 2020-07-06
    Description: Climate simulations for the North Atlantic and Europe for recent and future conditions simulated with the regionally coupled ROM model are analyzed and compared to the results from the MPI‐ESM. The ROM simulations also include a biogeochemistry and ocean tides. For recent climate conditions, ROM generally improves the simulations compared to the driving model MPI‐ESM. Reduced oceanic biases in the Northern Atlantic are found, as well as a better simulation of the atmospheric circulation, notably storm tracks and blocking. Regarding future climate projections for the 21st century following the RCP 4.5 and 8.5 scenarios, MPI‐ESM and ROM largely agree qualitatively on the climate change signal over Europe. However, many important differences are identified. For example, ROM shows an SST cooling in the Subpolar Gyre which is not present in MPI‐ESM. Under the RCP8.5 scenario, ROM Arctic sea ice cover is thinner and reaches the seasonally ice‐free state by 2055, well before MPI‐ESM. This shows the decisive importance of higher ocean resolution and regional coupling for determining the regional responses to global warming trends. Regarding biogeochemistry, both ROM and MPI‐ESM simulate a widespread decline in winter nutrient concentration in the North Atlantic of up to ~35%. On the other hand, the phytoplankton spring bloom in the Arctic and in the North‐Western Atlantic starts earlier and the yearly primary production is enhanced in the Arctic in the late 21st century. These results clearly demonstrate the added value of ROM to determine more detailed and more reliable climate projections at the regional scale.
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    Eddy Kinetic Energy in the Arctic Ocean From a Global Simulation With a 1‐km Arctic (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(14), ISSN: 0094-8276
    Details
    Publication Date: 2020-07-28
    Description: Simulating Arctic Ocean mesoscale eddies in ocean circulation models presents a great challenge because of their small size. This study employs an unstructured‐mesh ocean‐sea ice model to conduct a decadal‐scale global simulation with a 1‐km Arctic. It provides a basinwide overview of Arctic eddy energetics. Increasing model resolution from 4 to 1 km increases Arctic eddy kinetic energy (EKE) and total kinetic energy (TKE) by about 40% and 15%, respectively. EKE is the highest along main currents over topography slopes, where strong conversion from available potential energy to EKE takes place. It is high in halocline with a maximum typically centered in the depth range of 70–110 m, and in the Atlantic Water layer of the Eurasian Basin as well. The seasonal variability of EKE along the continental slopes of southern Canada and eastern Eurasian basins is similar, stronger in fall and weaker in spring.
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    Meta-analysis of multiple driver effects on marine phytoplankton highlights modulating role of pCO2 (2020)
    Wiley
    In:  EPIC3Global Change Biology, Wiley, 26(12), pp. 6787-6804
    Details
    Publication Date: 2020-11-23
    Description: Responses of marine primary production to a changing climate are determined by a concert of multiple environmental changes, for example in temperature, light, pCO2, nutrients, and grazing. To make robust projections of future global marine primary production, it is crucial to understand multiple driver effects on phytoplankton. This meta-analysis quantifies individual and interactive effects of dual driver combinations on marine phytoplankton growth rates. Almost 50% of the single-species laboratory studies were excluded because central data and metadata (growth rates, carbonate system, experimental treatments) were insufficiently reported. The remaining data (42 studies) allowed for the analysis of interactions of pCO2 with temperature, light, and nutrients, respectively. Growth rates mostly respond non-additively, whereby the interaction with increased pCO2 profusely dampens growth-enhancing effects of high temperature and high light. Multiple and single driver effects on coccolithophores differ from other phytoplankton groups, especially in their high sensitivity to increasing pCO2. Polar species decrease their growth rate in response to high pCO2, while temperate and tropical species benefit under these conditions. Based on the observed interactions and projected changes, we anticipate primary productivity to: (a) first increase but eventually decrease in the Arctic Ocean once nutrient limitation outweighs the benefits of higher light availability; (b) decrease in the tropics and mid-latitudes due to intensifying nutrient limitation, possibly amplified by elevated pCO2; and (c) increase in the Southern Ocean in view of higher nutrient availability and synergistic interaction with increasing pCO2. Growth-enhancing effect of high light and warming to coccolithophores, mainly Emiliania huxleyi, might increase their relative abundance as long as not offset by acidification. Dinoflagellates are expected to increase their relative abundance due to their positive growth response to increasing pCO2 and light levels. Our analysis reveals gaps in the knowledge on multiple driver responses and provides recommendations for future work on phytoplankton.
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    Dropstones in the Mar del Plata Canyon Area (SW Atlantic): Evidence for Provenance, Transport, Distribution, and Oceanographic Implications (2020)
    Wiley
    In:  EPIC3Geochemistry Geophysics Geosystems, Wiley, 22, ISSN: 1525-2027
    Details
    Publication Date: 2021-01-28
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    Ammonium in Antarctic aerosol: Marine biological activity versus long-range transport of biomass burning (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48, pp. e2021GL092826, ISSN: 0094-8276
    Details
    Publication Date: 2021-06-14
    Description: Year-round records of the ionic composition of Antarctic aerosol were obtained at the inland Dome C (DC) and coastal Neumayer (NM) sites, with additional observations of black carbon at NM. Discussions focus on the origin of ammonium in Antarctica. This first Antarctic atmospheric study of several species emitted by biomass burning indicates that black carbon, oxalate, and fine potassium reach a maximum in October in relation to biomass burning activity in the southern hemisphere. Ammonium reaches a maximum two months later, suggesting that biomass burning remains a minor ammonium source there. The ammonium maximum in December coincides with the occurrence of diatom blooms in the austral ocean, suggesting that oceanic ammonia emissions are the main source of ammonium in Antarctica. The ammonium to sulfur-derived biogenic species molar ratio of 0.15 in summer suggests far lower ammonia emissions from the Antarctic oceans than mid-latitude southern oceans.
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    Seasonality in Saharan Dust Across the Atlantic Ocean: From Atmospheric Transport to Seafloor Deposition (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Atmospheres, Wiley, 126, ISSN: 0148-0227
    Details
    Publication Date: 2021-06-25
    Description: Saharan dust is transported in great quantities from the North African continent every year, most of which is deposited across the North Atlantic Ocean. This dust impacts regional and global climate by affecting the atmospheric radiation balance and altering ocean carbon budgets. However, little research has been carried out on time series of Saharan dust collected in situ across the open Atlantic. Here, we present a unique three-year time series of Saharan dust along a trans-Atlantic transect, sampled by moored surface buoys and subsurface sediment traps. Results show a good correlation between the particle-size distributions of atmospheric dust and the lithogenic particles settling to the deep ocean floor, confirming the aeolian origin of the lithogenic particles intercepted by the subsurface sediment traps, even in the distal western part of the Atlantic Ocean. Dust from both dry and wet deposition as collected by the sediment traps, shows increased deposition fluxes and coarser grain size in summer and/or autumn that coincides with increased precipitation at the sampling sites as derived from satellite data. In contrast, both buoys that sampled dust during transport at sea level show little seasonal variation in both concentration and particle size, as the large amounts of dust transported in summer and early autumn at high altitudes are far above their sampling range. This implies that wet deposition in summer and autumn defines the typical seasonal trends of both the dust deposition flux and its particle-size distribution observed in the sediment traps.
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    New Developments in the PuffinPlot Paleomagnetic Data Analysis Program (2020)
    Wiley
    Details
    Publication Date: 2020-03-06
    Description: PuffinPlot is a program for paleomagnetic data analysis and plotting, first released in 2012 and under continuous development since then. It is free, cross‐platform software and provides both a graphical desktop interface for interactive use and an application‐programmer interface for scripting. We present a major new release of the program, describe significant new features added since the first release, and demonstrate their application to real‐world data. New features include automatic magnetic declination realignment, relative paleointensity calculation, virtual geomagnetic pole determination, calculation of inclination‐only statistics, support for reproducible research via the export of self‐contained data bundles, and support for reading a number of popular paleomagnetic file formats. We also discuss the application of unit tests in ensuring PuffinPlot's long‐term reliability and outline directions for future development of the software.
    Description: Published
    Description: 5578-5587
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
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    Fine‐Scale Structure of the 2016–2017 Central Italy Seismic Sequence From Data Recorded at the Italian National Network (2020)
    Wiley
    Details
    Publication Date: 2020-05-25
    Description: We explore the three‐dimensional structure of the 2016–2017 Central Italy sequence using ~34,000 ML ≥ 1.5 earthquakes that occurred between August 2016 and January 2018. We applied cross‐correlation and double‐difference location methods to waveform and parametric data routinely produced at the Italian National Institute of Geophysics and Volcanology. The sequence activated an 80 km long system of normal faults and near‐horizontal detachment faults through the MW 6.0 Amatrice, the MW 5.9 Visso, and the MW 6.5 Norcia mainshocks and aftershocks. The system has an average strike of N155°E and dips 38°–55° southwestward and is segmented into 15–30 km long faults individually activated by the cascade of MW ≥ 5.0 shocks. The two main normal fault segments, Mt. Vettore‐Mt. Bove to the North and Mt. della Laga to the South, are separated by an NNE‐SSW‐trending lateral ramp of the Sibillini thrust, a regional structure inherited from the previous compressional tectonic phase putting into contact diverse lithologies with different seismicity patterns. Space‐time reconstruction of the fault system supports a composite rupture scenario previously proposed for the MW 6.5 Norcia earthquake, where the rupture possibly propagated also along an oblique portion of the Sibillini thrust. This dissected set of normal fault segments is bounded at 8–10 km depth by a continuous 2 km thick seismicity layer of extensional nature slightly dipping eastward and interpreted as a shear zone. All three mainshocks in the sequence nucleated along the high‐angle planes at significant distance from the shear zone, thus complicating the interpretation of the mechanisms driving strain partitioning between these structures.
    Description: Published
    Description: e2019JB018440
    Description: 3T. Sorgente sismica
    Description: JCR Journal
    Keywords: normal fault ; shear zone ; fault segmentation ; apennines ; 04.06. Seismology
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  • 42
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    Active Extension in a Foreland Trapped Between Two Contractional Chains: The South Apulia Fault System (SAFS) (2020)
    Wiley
    Details
    Publication Date: 2020-07-08
    Description: The response of continental forelands to subduction and collision is a widely investigated topic in geodynamics. The deformation occurring within a foreland shared by two opposite‐verging chains, however, is uncommon and poorly understood. The Apulia Swell in the southern end of the Adria microplate (Africa‐Europe plate boundary, central Mediterranean Sea) represents one of these cases, as it is the common foreland of the SW verging Albanides‐Hellenides and the NE verging Southern Apennines merging into the SSE verging Calabrian Arc. We investigated the internal deformation of the Apulia Swell using multiscale geophysical data: multichannel seismic profiles recording up to 12‐s two‐way time (TWT) for a consistent image of the upper crust; high‐resolution multichannel seismic profiles, high‐resolution multibeam bathymetry, and CHIRP profiles acquired by R/V OGS Explora to constrain the Quaternary geological record. The results of our analyses characterize the geometry of the South Apulia Fault System (SAFS), a 100‐km‐long and 12‐km‐wide structure attesting an extensional (and possibly transtensional) response of the foreland to the two contractional fronts. The SAFS consists of two NW‐SE right‐stepping master faults and several secondary structures. The SAFS activity spans from the Early Pleistocene through the Holocene, as testified by the bathymetric and high‐resolution seismic data, with long‐term slip rates in the range of 0.2–0.4 mm/yr. Considering the position within an area with few or none other active faults in the surroundings, the dimension, and the activity rates, the SAFS can be a candidate causative fault of the 20 February 1743, M 6.7, earthquake.
    Description: Italian Ministry for Education, University, and Research (MIUR), Premiale 2014 D. M. 291 03/05/2016.
    Description: Published
    Description: e2020TC006116
    Description: 2T. Deformazione crostale attiva
    Description: 2TR. Ricostruzione e modellazione della struttura crostale
    Description: JCR Journal
    Keywords: active tectonics ; apulia ; south apulia fault system ; 1743 earthquake ; marine geology ; stable continental region ; ionian sea ; active faults ; subsurface geology ; seismic interpretation ; 04.04. Geology ; 04.07. Tectonophysics ; 04.02. Exploration geophysics
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  • 43
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    Climate change and Arctic ecosystems: 2. Modeling, paleodata‐model comparisons, and future projections (2003)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Atmospheres, Wiley, 8171 p., ISSN: 0148-0227
    Details
    Publication Date: 2019-08-23
    Repository Name: EPIC Alfred Wegener Institut
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  • 44
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    Reservoir Structure and Hydraulic Properties of the Campi Flegrei Geothermal System Inferred by Audiomagnetotelluric, Geochemical, and Seismicity Study (2020)
    Wiley
    Details
    Publication Date: 2020-01-23
    Description: The Campi Flegrei caldera is a large volcanic complex lying in the Campanian Plain, Southern Italy. During its history the caldera experienced episodes of bradyseism and intense swarm seismicity. The mechanism leading to unrest episodes is still debated, and great efforts are ongoing to improve the knowledge of this structure and its evolution due to the high volcanic risk in such a densely populated area. Here we present a resistivity model from a two‐dimensional inversion of audiomagnetotelluric data acquired along an approximately 5.6‐km long profile crosscutting the Solfatara‐Pisciarelli district and the Agnano plain. The resistivity model shows (1) very low resistivity values confined in the first 500 m of depth both in correspondence of the Solfatara‐Pisciarelli districts and the Agnano depression; (2) a resistive plume that extends underneath the Solfatara crater down to 2,000‐ to 3,000‐m depth, and (3) an adjoining relative conductive unit eastward. We discuss the resistivity structures in a multidisciplinary framework integrating inedited geochemical and seismological observations with existing surface geology and subsurface information. The Solfatara‐Pisciarelli district and the Agnano plain, both being expression of intense hydrothermal activity, show different characteristics. Below the Solfatara‐Pisciarelli area, the shallow conductive zone is interpreted as a faulted clay cap that overlies a highly active vapor‐dominated reservoir characterized by a convective mechanism. Conversely, below the Agnano plain, a liquid phase seems to prevail in the reservoir. The spatiotemporal variations of seismicity imply a combined action of preexisting tectonic lineaments and fluid interaction between the gas/steam reservoir and the outflow zone.
    Description: Published
    Description: 5336-5356
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
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  • 45
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    Insight Into Campi Flegrei Caldera Unrest Through Seismic Tremor Measurements at Pisciarelli Fumarolic Field (2020)
    Wiley
    Details
    Publication Date: 2020-01-23
    Description: Within a general volcanic unrest in the densely urbanized area of Campi Flegrei caldera (Italy) an increase in the activity of Pisciarelli hydrothermal area is occurring. The seismic amplitude of Pisciarelli fumarolic tremor is a proxy for the fluid emission rate of the entire Solfatara‐Pisciarelli hydrothermal system. The long‐term analysis indicates a significant increase, by a factor of ~3 of the fumarolic tremor amplitude since May 2017. This increment matches with the trend of geochemical and seismic parameters observed in Campi Flegrei, therefore highlighting that Pisciarelli is a key site to monitor the volcanic unrest underway in this high‐risk caldera. The analysis of data from three closely spaced seismic stations provided new clues about the source mechanism of the tremor. Analyzing the fumarolic tremor amplitude we could also identify an episode of enlargement of the emission area close to the main fumarole of Pisciarelli. We propose a monitoring system based on the fumarolic tremor analysis, which provides real‐time information on the Pisciarelli hydrothermal activity and therefore on the current unrest in Campi Flegrei caldera.
    Description: Published
    Description: 5544-5555
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
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  • 46
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    Water Availability and Deformation Processes in Smectite‐Rich Gouges During Seismic Slip (2020)
    Wiley
    Details
    Publication Date: 2020-02-10
    Description: Smectite clays occur in subduction zone fault cores at shallow depth (approximately 1 km; e.g., Japan Trench) and landslide décollements (e.g., Vajont, Italy, 1963). The availability of pore fluids affects the likelihood that seismic slip propagates from deeper to shallow fault depths or that a landslide accelerates to its final collapse. To investigate the deformation processes active during seismic faulting we performed friction experiments with a rotary machine on 2‐mm‐thick smectite‐rich gouge layers (70/30 wt % Ca‐montmorillonite/opal) sheared at 5‐MPa normal stress, at slip rates of 0.001, 0.01, 0.1, and 1.3 m/s, and total displacement of 3 m. Experiments were performed on predried gouges under vacuum, under room humidity and under partly saturated conditions. The fault shear strength measured in the experiments was included in a one‐dimensional numerical model incorporating frictional heating, thermal, and thermochemical pressurization. Quantitative X‐ray powder diffraction and scanning electron microscopy investigations were performed on pristine and deformed smectite‐rich gouges. Under dry conditions, cataclasis and amorphization dominated at slip rates of 0.001–0.1 m/s, whereas grain size sensitive flow and, under vacuum, frictional melting occurred at fast slip rates (1.3 m/s). Under partly saturated conditions, frictional slip in a smectite foliation occurred in combination with pressurization of water by shear‐enhanced compaction and, for V = 0.01–1.3 m/s, with thermal pressurization. Pseudotachylytes, the only reliable microstructural markers for seismic slip, formed only with large frictional power (〉2 MW/m2), which could be achieved at shallow depth with high slip rates, or, at depth, with high shear stress in dehydrated smectites.
    Description: Published
    Description: 10855-10876
    Description: 3T. Sorgente sismica
    Description: JCR Journal
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  • 47
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    The evolving paleobathymetry of the circum-Antarctic Southern Ocean since 34 Ma – A key to understanding past cryosphere-ocean developments (2020)
    Wiley
    In:  EPIC3Geochemistry Geophysics Geosystems, Wiley, 21, ISSN: 1525-2027
    Details
    Publication Date: 2021-07-19
    Description: The Southern Ocean is a key player in the climate, ocean and atmospheric system. As the only direct connection between all three major oceans since the opening of the Southern Ocean gateways, the development of the Southern Ocean and its relationship with the Antarctic cryosphere has influenced the climate of the entire planet. Although the depths of the ocean floor have been recognized as an important factor in climate and paleoclimate models, appropriate paleobathymetric models including a detailed analysis of the sediment cover are not available. Here, we utilize more than 40 years of seismic reflection data acquisition along the margins of Antarctica and its conjugate margins, along with multiple drilling campaigns by the International Ocean Discovery Program (IODP) and its predecessor programs. We combine and update the seismic stratigraphy across the regions of the Southern Ocean and calculate ocean-wide paleobathymetry grids via a backstripping method. We present a suite of high-resolution paleobathymetric grids from the Eocene-Oligocene Boundary to modern times. The grids reveal the development of the Southern Ocean from isolated basins to an interconnected ocean affected by the onset and vigor of an Antarctic Circumpolar Current, as well as the glacial sedimentation and erosion of the Antarctic continent. The ocean-wide comparison through time exposes patterns of ice sheet development such as switching of glacial outlets and the change from wet-based to dry-based ice sheets. Ocean currents and bottom-water production interact with the sedimentation along the continental shelf and slope and profit from the opening of the ocean gateways.
    Repository Name: EPIC Alfred Wegener Institut
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    Plio‐Pleistocene variability of the East Pacific thermocline and atmospheric systems (2020)
    Wiley
    In:  EPIC3Paleoceanography, Wiley, 35, pp. 1-7, ISSN: 0883-8305
    Details
    Publication Date: 2020-03-13
    Description: The transition from the Pliocene to the Pleistocene was accompanied by major tectonic reorganizations of key oceanic gateways. In particular, the gradual closure of the Panama Gateway and the constriction of the Indonesian Gateway significantly affected the structure of the Pacific thermocline. In the East Pacific, the thermocline shoaled from an early Pliocene El Niño‐like depth to its modern state, which had significant implications for global climate. Here we use Mg/Ca temperature estimates from subsurface and thermocline dwelling foraminifera to reconstruct the meridional Plio‐Pleistocene evolution of the Southeast Pacific thermocline, in relation to atmospheric circulation changes. In combination with similar reconstructions from the north‐equatorial Pacific, our data indicate a change in the thermocline, responding to the northward displacement of the Intertropical Convergence Zone/South Pacific High system between ~3.8 and 3.5 Ma. After 3.5 Ma, we record a second major phase of thermocline shoaling, which points to the Intertropical Convergence Zone/South Pacific High‐system movement toward its modern position along with the gradual cooling of the Northern Hemisphere and its associated glaciation. These findings highlight that a warming globe may affect equatorial regions more intensively due to the potential temperature‐driven movement of the Intertropical Convergence Zone/South Pacific High and their associated oceanic systems.
    Repository Name: EPIC Alfred Wegener Institut
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    Radiocarbon evidence for the contribution of the Southern Indian Ocean to the evolution of atmospheric CO2 over the last 32,000 years (2020)
    Wiley
    In:  EPIC3Paleoceanography, Wiley, 35, pp. PA003733, ISSN: 0883-8305
    Details
    Publication Date: 2020-03-13
    Description: It is widely assumed that the ventilation of the Southern Ocean played a crucial role in driving glacial‐interglacial atmospheric CO2 levels. So far, however, ventilation records from the Indian sector of the Southern Ocean are widely missing. Here we present reconstructions of water residence times (depicted as ΔΔ14C and Δδ13C) for the last 32,000 years on sediment records from the Kerguelen Plateau and the Conrad Rise (~570‐ to 2,500‐m water depth), along with simulated changes in ocean stratification from a transient climate model experiment. Our data indicate that Circumpolar Deep Waters in the Indian Ocean were part of the glacial carbon pool. At our sites, close to or bathed by upwelling deep waters, we find two pulses of decreasing ΔΔ14C and δ13C values (~21–17 ka; ~15–12 ka). Both transient pulses precede a similar pattern in downstream intermediate waters in the tropical Indian Ocean as well as rising atmospheric CO2 values. These findings suggest that 14C‐depleted, CO2‐rich Circumpolar Deep Water from the Indian Ocean contributed to the rise in atmospheric CO2 during Heinrich Stadial 1 and also the Younger Dryas and that the southern Indian Ocean acted as a gateway for sequestered carbon to the atmosphere and tropical intermediate waters.
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  • 50
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    Intensification of the Atlantic Water Supply to the Arctic Ocean Through Fram Strait Induced by Arctic Sea Ice Decline (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(3), pp. e2019GL086682, ISSN: 0094-8276
    Details
    Publication Date: 2020-03-23
    Repository Name: EPIC Alfred Wegener Institut
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    Assessment of sea ice extent in CMIP6 with comparison to observations and CMIP5 (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(9), pp. e2020GL087965, ISSN: 0094-8276
    Details
    Publication Date: 2020-05-04
    Description: Both the Arctic and Antarctic sea ice extents (SIE) from 44 coupled models in the Coupled Model Intercomparison Project Phase 6 (CMIP6) are evaluated by comparing them with observations and CMIP5 results. The CMIP6 multi‐model mean can adequately reproduce the seasonal cycles of both the Arctic and Antarctic SIE. The observed Arctic September SIE declining trend (−0.82±0.18 million km2/decade) between 1979 and 2014 is slightly underestimated in CMIP6 models (−0.70±0.06 million km2/decade). The observed weak but significant upward trend of the Antarctic SIE is not captured, which was an issue already in the CMIP5 phase. Compared with CMIP5 models, CMIP6 models have lower inter‐model spreads in SIE mean values and trends, although their SIE biases are relatively larger. The CMIP6 models did not reproduce the new summer tendencies after 2000, including the faster decline of Arctic SIE and the larger interannual variability in Antarctic SIE.
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    SoilTemp: a global database of near‐surface temperature (2020)
    Wiley
    In:  EPIC3Global Change Biology, Wiley, ISSN: 1354-1013
    Details
    Publication Date: 2020-04-22
    Description: Current analyses and predictions of spatially‐explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long‐term average thermal conditions at coarse spatial resolutions only. Hence, many climate‐forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing, or cold‐air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free‐air temperatures, microclimatic ground and near‐surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near‐surface temperature data from all over the world. Currently this database contains time series from 7538 temperature sensors from 51 countries across all key biomes. The database will pave the way towards an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
    Repository Name: EPIC Alfred Wegener Institut
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    Constraining the age and evolution of the Tuaheni Landslide Complex, Hikurangi Margin, New Zealand, using pore-water geochemistry and numerical modeling (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47, ISSN: 0094-8276
    Details
    Publication Date: 2020-06-05
    Repository Name: EPIC Alfred Wegener Institut
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  • 54
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    Back-Arc Extension of the Central Bransfield Basin Induced by Ridge–Trench Collision: Implications From Ambient Noise Tomography and Stress Field Inversion (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(21), ISSN: 0094-8276
    Details
    Publication Date: 2021-11-02
    Description: The Bransfield Basin is a young (∼4 Ma) back-arc basin related to the remnant subduction of the Phoenix Plate that once existed along the entire Pacific margin of the Antarctic Peninsula. Based on a recently deployed amphibious seismic network, we use ambient noise tomography to obtain the S-wave velocity structure in the Central Bransfield Basin (CBB). Combining with the stress field inverted from focal mechanisms, our images reveal that the CBB suffers a significant extension in the northwest-southeast direction. The extension is strongest in the northeastern CBB with associated mantle exhumation and weakens to the southwest with decoupled deformations between the upper crust and lithospheric mantle. Such an along-strike variation of extension can be explained by slab window formation and forearc rotation, which are associated with the Phoenix Plate detachment during the ridge–trench collisions at the southwest of the Hero Fracture Zone.
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  • 55
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    Restoring shellfish reefs: Global guidelines for practitioners and scientists (2020)
    Wiley
    In:  EPIC3Conservation Science and Practice, Wiley, e198, pp. 1-11
    Details
    Publication Date: 2020-03-27
    Description: Widespread global declines in shellfish reefs (ecosystem-forming bivalves such as oysters and mussels) have led to growing interest in their restoration and protection. With restoration projects now occurring on four continents and in at least seven countries, global restoration guidelines for these ecosystems have been developed based on experience over the past two decades. The following key elements of the guidelines are outlined: (a) the case for shellfish reef resto- ration and securing financial resources; (b) planning, feasibility, and goal set- ting; (c) biosecurity and permitting; (d) restoration in practice; (e) scaling up from pilot to larger scale restoration, (f) monitoring, (g) restoration beyond oyster reefs (specifically mussels), and (h) successful communication for shell- fish reef restoration projects.
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    Poleward shift of the major ocean gyres detected in a warming climate (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(5), pp. e2019GL085868, ISSN: 0094-8276
    Details
    Publication Date: 2020-09-17
    Description: Recent evidence shows that wind‐driven ocean currents, like the western boundary currents, are strongly affected by global warming. However, due to insufficient observations both on temporal and spatial scales, the impact of climate change on large‐scale ocean gyres is still not clear. Here, based on satellite observations of sea surface height and sea surface temperature, we find a consistent poleward shift of the major ocean gyres. Due to strong natural variability, most of the observed ocean gyre shifts are not statistically significant, implying that natural variations may contribute to the observed trends. However, climate model simulations forced with increasing greenhouse gases suggest that the observed shift is most likely to be a response of global warming. The displacement of ocean gyres, which is coupled with the poleward shift of extratropical atmospheric circulation, has broad impacts on ocean heat transport, regional sea level rise, and coastal ocean circulation.
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    Statistical Uncertainty in Paleoclimate Proxy Reconstructions (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48, pp. e2021GL092773, ISSN: 0094-8276
    Details
    Publication Date: 2021-08-23
    Description: A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.
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    Stable nitrogen isotope analysis of amino acids as a new tool to clarify complex parasite–host interactions within food webs (2021)
    Wiley
    In:  EPIC3Oikos, Wiley, ISSN: 0030-1299
    Details
    Publication Date: 2021-08-26
    Description: Traditional bulk isotopic analysis is a pivotal tool for mapping consumer–resource interactions in food webs but has largely failed to adequately describe parasite–host relationships. Thus, parasite–host interactions remain undescribed in food web frameworks despite these relationships increasing linkage density, connectance and ecosystem biomass. Compound-specific stable isotopes from amino acids provides a promising novel approach that may aid in mapping parasite–host relationships in food webs. Here we apply a combination of traditional bulk stable isotope analyses and compound-specific isotopic analysis of nitrogen in amino acids to examine resource use and trophic interactions of five parasites from three hosts from a marine coastal food web (Wadden Sea, European Atlantic). By comparing isotopic compositions of bulk and amino acid nitrogen, we aimed to characterize isotopic fractionation occurring between parasites and their hosts and to clarify parasite trophic positions. Our results indicate that parasitic trophic interactions were more accurately identified using compound-specific stable isotope analysis due to removal of underlying source isotopic variation for both parasites and hosts. The compound-specific method provided clearer trophic discrimination factors in comparison to bulk isotope methods. Amino acid compound specific isotope analysis has widely been applied to examine trophic position within food webs, but our analyses suggest that the method is particularly useful for clarifying the feeding strategies for parasitic species. Baseline isotopic information provided by source amino acids allows clear identification of the fractionation from parasite metabolism by integrating underlying isotopic variations from the host tissues. However, like for bulk isotope analysis, the application of a universal trophic discrimination factor to parasite–host relationships remains inappropriate for compound-specific stable isotope analysis. Despite this limitation, compound-specific stable isotope analysis is and will continue to be a valuable tool to increase our understanding of parasitic interactions in marine food webs.
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    Seasonality of Mesoscale Phytoplankton Control in Eastern Fram Strait (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research: Oceans, Wiley, 126(10), ISSN: 2169-9275
    Details
    Publication Date: 2021-12-08
    Description: Globally, mesoscale processes create a rich and filamented pattern in biological productivity. Despite of remoteness and a harsh environment, observations likewise show an impact of mesoscale processes on phytoplankton growth in the Arctic. Observations of sufficiently high resolution are, however, difficult to carry out. Large-scale models are another way to gain knowledge about the system. In the current study, we use a global sea ice-ocean biogeochemical model, which is eddy resolving in Fram Strait, to show that the mesoscale dynamics has a strong effect on shaping phytoplankton growth. For the year 2009, we demonstrate that the growth season in the West Spitzbergen Current can be divided into two regimes; during Regime I, which takes place in May and June before and during the spring bloom, high chlorophyll concentrations are associated with areas of positive vorticity and a shallow mixed layer, pointing toward light limitation controlling growth. During Regime II, which occurs after the bloom from mid-July to late August, the highest chlorophyll concentration is found in areas of negative vorticity. Here, upwelling of nutrient-rich water occurs, through doming isopycnals, acting to raise the nutricline, may also play a role in alleviating nutrient limitation in the surface water. The study suggests that the mesoscale eddy environment locally modulates the seasonal cycle of light and nutrient limitation. Knowledge of the eddy field should be taken into consideration for making conclusions from point-wise measurements in Fram Strait.
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    Sensitivity to changes in the surface-layer turbulence parameterization for stable conditions in winter: A case study with a regional climate model over the Arctic (2021)
    Wiley
    In:  EPIC3Atmospheric Science Letters, Wiley, e1066, pp. 1-10
    Details
    Publication Date: 2021-12-16
    Description: The modeling of the atmospheric boundary layer over sea ice is still challenging because of the complex interaction between clouds, radiation and turbulence over the often inhomogeneous sea ice cover. There is still much uncertainty concerning sea ice roughness, near-surface thermal stability and related processes, and their accurate parameterization. Here, a regional Arctic climate model forced by ERA-interim data was used to test the sensitivity of climate simulations to a modified surface flux parameterization for wintertime conditions over the Arctic. The reference parameterization as well as the modified one is based on Monin–Obukhov similarity theory, but different roughness lengths were prescribed and the stability dependence of the transfer coefficients for momentum, heat and moisture differed from each other. The modified parameterization accounts for the most compre- hensive observations that are presently available over sea ice in the inner Arctic. Independent of the parameterization used, the model was able to reproduce the two observed dominant winter states with respect to cloud cover and longwave radiation. A stepwise use of the different parameterization assumptions showed that modifications of both surface roughness and stability dependence had a considerable impact on quantities such as air pressure, wind and near-surface turbulent fluxes. However, the reduction of surface roughness to values agreeing with those observed during t he Surface Heat Budget of the Arctic Ocean campaign led to an improvement in the western Arctic, while the modified stability parameteri- zation had only a minor impact. The latter could be traced back to the model's underestimation of the strength of stability over sea ice. Future work should concentrate on possible reasons for this underestimation and on the question of generality of the results for other climate models
    Repository Name: EPIC Alfred Wegener Institut
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    Bathymetric Control on Borchgrevink and Roi Baudouin Ice Shelves in East Antarctica (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Earth Surface, Wiley, 126(10), ISSN: 0148-0227
    Details
    Publication Date: 2021-10-18
    Description: The stability of ice shelves and drainage of ice sheets they buttress is largely determined by melting at their atmospheric and oceanic interfaces. Subglacial bathymetry can impact ice shelf stability because it influences the onset and the pattern of warm ocean water incursions into the cavities between them and the seafloor. Bathymetry is further important at pinning points, which significantly retard the flow of ice shelves. This effect can be lost instantaneously if basal and surface melting cause an ice sheet to thin and lift off its pinning points. With all this in mind, we have developed a model of bathymetry beneath the western Roi Baudouin and central and eastern Borchgrevink ice shelves in Dronning Maud Land based on inversion from gravity data and tied to available depth references offshore and subglacial topography inland of the grounding line. The model shows deep glacial troughs beneath the ice shelves and bathymetric sills close to the continental shelf. The central Borchgrevink Ice Shelf overhangs the continental slope by around 50km, exposing its northern parts to the open ocean and higher ocean temperatures. Continuous troughs traverse the central Borchgrevink and western Roi Baudouin ice shelves at depths greater than the offshore thermocline and thus present a risk of Warm Deep Water intrusions into their cavities under the current and future oceanographic regimes. Differing bathymetric characteristics might explain the ice shelves' contrasting dominant mass loss processes.
    Repository Name: EPIC Alfred Wegener Institut
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    Evidence of Cascading Subglacial Water Flow at Jutulstraumen Glacier (Antarctica) Derived From Sentinel-1 and ICESat-2 Measurements (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(20), ISSN: 0094-8276
    Details
    Publication Date: 2021-10-22
    Description: Migration of subglacial water underneath thick Antarctic ice is difficult to observe directly but is known to influence ice flow dynamics. Here, we analyze a 6-year time series of displacement maps from differential Sentinel-1 SAR interferometry (DInSAR) in the upstream region of Jutulstraumen Glacier. Our results reveal short-term (between 12 days and 1 year) interconnected subsidence- and uplift events of the ice surface, which we interpret as a pressure response to the drainage and filling of subglacial lakes. This indicates an episodic cascade-like water transport with longer quiescent phases in a dynamically stable glacial setting. Abrupt events appear in the DInSAR time series and are confirmed by ICESat-2 altimetry. The events can be traced for a 1-year period along a urn:x-wiley:00948276:media:grl63164:grl63164-math-0001175 km flow path. We are able to observe the migration of subglacial water with unprecedented spatial and temporal resolution, providing a new observational baseline to further develop subglacial hydrological models.
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    Influence of Early Low-Temperature and Later High-Temperature Diagenesis on Magnetic Mineral Assemblages in Marine Sediments from the Nankai Trough (2021)
    Wiley
    In:  EPIC3Geochemistry Geophysics Geosystems, Wiley, ISSN: 1525-2027
    Details
    Publication Date: 2021-10-21
    Description: Diagenesis can have a major impact on sedimentary mineralogy. Primary magnetic mineral assemblages can be modified significantly by dissolution or by formation of new magnetic minerals during early or late diagenesis. At International Ocean Discovery Program Site C0023, which was drilled in the protothrust zone of the Nankai Trough during Expedition 370, offshore of Shikoku Island, Japan, non-steady state conditions have produced a complex sequence of magnetic overprints. Detailed rock magnetic measurements, which characterize magnetic mineral assemblages in terms of abundance, grain size, and composition, were conducted to assess magnetic mineral alteration and diagenetic overprinting. Four magnetic zones (MZs) are identified down-core from ∼200 to 1100 meters below sea floor based on rock magnetic variations. MZ 1 is a high magnetic intensity zone that contains ferrimagnetic greigite, which formed at shallow depths and is preserved because of rapid sedimentation. MZs 2 and 4 are low magnetic intensity zones with fewer magnetic minerals, mainly coarse-grained (titano-)magnetite and hematite. This magnetic mineral assemblage is a remnant of a more complex assemblage that was altered diagenetically a few million years after deposition when the site entered the Nankai Trough. MZ 3 is a high magnetic intensity zone between MZs 2 and 4. It contains authigenic single-domain magnetic particles that probably formed from fluids that circulated through faults in the accretionary prism. Varying sediment supply and organic matter input through time, burial temperature, and tectonic fluid circulation are the primary drivers of magnetic mineral assemblage variations.
    Repository Name: EPIC Alfred Wegener Institut
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    Palaeoclimate reconstruction on Big Lyakhovsky Island, north Siberia—hydrogen and oxygen isotopes in ice wedges (2002)
    Wiley
    In:  EPIC3Permafrost and Periglacial Processes, Wiley, 13(2), pp. 91-105, ISSN: 1045-6740
    Details
    Publication Date: 2023-07-06
    Description: Late Quaternary permafrost deposits on Big Lyakhovsky Island (New Siberian Islands, Russian Arctic) were studied with the aim of reconstructing the palaeoclimatic and palaeoenvironmental conditions of northern Siberia. Hydrogen and oxygen stable isotope analyses are presented for six different generations of ice wedges as well as for recent ice wedges and precipitation. An age of about 200 ka BP was determined for an autochtonous peat layer in ice-rich deposits by U/Th method, containing the oldest ice wedges ever analysed for hydrogen and oxygen isotopes. The palaeoclimatic reconstruction revealed a period of severe winter temperatures at that time. After a gap in the sedimentation history of several tens of thousands of years, ice-wedge growth was re-initiated around 50 ka BP by a short period of extremely cold winters and rapid sedimentation leading to ice-wedge burial and characteristic ice-soil wedges (‘polosatics’). This corresponds to the initial stage for the Late Weichselian Ice Complex, a peculiar cryolithogenic periglacial formation typical of the lowlands of northern Siberia. The Ice Complex ice wedges reflect cold winters and similar climatic conditions as around 200 ka BP. With a sharp rise in υ18O of 6‰ and υD of 40‰, the warming trend between Pleistocene and Holocene ice wedges is documented. Stable isotope data of recent ice wedges show that Big Lyakhovsky Island has never been as warm in winter as today.
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    Late Saalian and Eemian palaeoenvironmental history of the Bol'shoy Lyakhovsky Island (Laptev Sea region, Arctic Siberia) (2004)
    Wiley
    In:  EPIC3Boreas, Wiley, 33(4), pp. 319-348, ISSN: 0300-9483
    Details
    Publication Date: 2024-04-25
    Description: Palaeoenvironmental records from permafrost sequences complemented by infrared stimulated luminescence (IRSL) and 230Th/U dates from Bol'shoy Lyakhovsky Island (73°20′N, 141°30′E) document the environmental history in the region for at least the past 200 ka. Pollen spectra and insect fauna indicate that relatively wet grasssedge tundra habitats dominated during an interstadial c. 200-170 ka BP. Summers were rather warm and wet, while stable isotopes reflect severe winter conditions. The pollen spectra reflect sparser grass-sedge vegetation during a Taz (Late Saalian) stage, c. 170-130 ka BP, with environmental conditions much more severe compared with the previous interstadial. Open Poaceae and Artemisia plant associations dominated vegetation at the beginning of the Kazantsevo (Eemian) c. 130 ka BP. Some shrubs (Alnus fruticosa, Salix, Betula nana) grew in more protected and wetter places as well. The climate was relatively warm during this time, resulting in the melting of Saalian ice wedges. Later, during the interglacial optimum, shrub tundra with Alnus fruticosa and Betula nana s.l. dominated vegetation. Climate was relatively wet and warm. Quantitative pollen-based climate reconstruction suggests that mean July temperatures were 4-5°C higher than the present during the optimum of the Eemian, while late Eemian records indicate significant climate deterioration. © 2004 Taylor & Francis.
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    STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 27-47 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Owing to the rapid development of in vivo applications for non-viral gene delivery vectors, it is necessary to have a better understanding of how the structure-activity relationships of these lipid-DNA complexes are affected by their environment. Indeed, research in gene therapy first focused on in vitro cell culture studies to determine the mechanisms involved in the delivery of DNA into the cell. New biophysical techniques such as electron microscopy and X-ray diffraction have been developed to discern the structure of the lipid-DNA complex. However, further studies have revealed discrepancies between optimal lipid-DNA formulations for in vitro transfection and for in vivo administration of these vectors. Furthermore, some immune stimulatory effects have been associated with in vivo lipid-DNA administration. This review summarizes the current state of knowledge on in vitro and in vivo lipid-DNA complex transfections. New prospects of vectors for in vivo gene transfer are also discussed.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.27
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    GCN5-RELATED N-ACETYLTRANSFERASES: A Structural Overview (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 81-103 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Hundreds of acetyltransferases exist. All use a common acetyl donor-acetyl coenzyme A-and each exhibits remarkable specificity for acetyl acceptors, which include small molecules and proteins. Analysis of the primary sequences of these enzymes indicates that they can be sorted into several superfamilies. This review covers the three-dimensional structures of members of one of these superfamilies, now referred to in the literature as the GCN5-related N-acetyltransferases (GNAT), reflecting the importance of one functional category, the histone acetyltransferases. Despite the diversity of substrate specificities, members of the GNAT superfamily demonstrate remarkable similarity in protein topology and mode of acetyl coenzyme A binding, likely reflecting a conserved catalytic mechanism.
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    SIGNALING AND SUBCELLULAR TARGETING BY MEMBRANE-BINDING DOMAINS1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 49-79 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Protein kinase C homology-1 and -2, FYVE, and pleckstrin homology domains are ubiquitous in eukaryotic signal transduction and membrane-trafficking proteins. These domains regulate subcellular localization and protein function by binding to lipid ligands embedded in cell membranes. Structural and biochemical analysis of these domains has shown that their molecular mechanisms of membrane binding depend on a combination of specific and nonspecific interactions with membrane lipids. In vivo studies of green fluorescent protein fusions have highlighted the key roles of these domains in regulating protein localization to plasma and internal membranes in cells.
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    MEASURING THE FORCES THAT CONTROL PROTEIN INTERACTIONS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 1-26 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Although the force fields and interaction energies that control protein behavior can be inferred indirectly from equilibrium and kinetic measurements, recent developments have made it possible to quantify directly (a) the ranges, magnitudes, and time dependence of the interaction energies and forces between biological materials; (b) the mechanical properties of isolated proteins; and (c) the strength of single receptor-ligand bonds. This review describes recent results obtained by using the atomic force microscope, optical tweezers, the surface force apparatus, and micropipette aspiration to quantify short-range protein-ligand interactions and the long-range, nonspecific forces that together control protein behavior. The examples presented illustrate the power of force measurements to quantify directly the force fields and energies that control protein behavior.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.1
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    DNA RECOGNITION BY Cys2His2 ZINC FINGER PROTEINS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 183-212 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cys2His2 zinc fingers are one of the most common DNA-binding motifs found in eukaryotic transcription factors. These proteins typically contain several fingers that make tandem contacts along the DNA. Each finger has a conserved betabetaalpha structure, and amino acids on the surface of the alpha-helix contact bases in the major groove. This simple, modular structure of zinc finger proteins, and the wide variety of DNA sequences they can recognize, make them an attractive framework for attempts to design novel DNA-binding proteins. Several studies have selected fingers with new specificities, and there clearly are recurring patterns in the observed side chain-base interactions. However, the structural details of recognition are intricate enough that there are no general rules (a "recognition code") that would allow the design of an optimal protein for any desired target site. Construction of multifinger proteins is also complicated by interactions between neighboring fingers and the effect of the intervening linker. This review analyzes DNA recognition by Cys2His2 zinc fingers and summarizes progress in generating proteins with novel specificities from fingers selected by phage display.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.183
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    FAST KINETICS AND MECHANISMS IN PROTEIN FOLDING1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 327-359 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review describes how kinetic experiments using techniques with dramatically improved time resolution have contributed to understanding mechanisms in protein folding. Optical triggering with nanosecond laser pulses has made it possible to study the fastest-folding proteins as well as fundamental processes in folding for the first time. These include formation of alpha-helices, beta-sheets, and contacts between residues distant in sequence, as well as overall collapse of the polypeptide chain. Improvements in the time resolution of mixing experiments and the use of dynamic nuclear magnetic resonance methods have also allowed kinetic studies of proteins that fold too fast (〉 103 s-1) to be observed by conventional methods. Simple statistical mechanical models have been extremely useful in interpreting the experimental results. One of the surprises is that models originally developed for explaining the fast kinetics of secondary structure formation in isolated peptides are also successful in calculating folding rates of single domain proteins from their native three-dimensional structure.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.327
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    A DECADE OF CLC CHLORIDE CHANNELS: Structure, Mechanism, and Many Unsettled Questions (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 411-438 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract ClC-type chloride channels are ubiquitous throughout the biological world. Expressed in nearly every cell type, these proteins have a host of biological functions. With nine distinct homologues known in eukaryotes, the ClCs represent the only molecularly defined family of chloride channels. ClC channels exhibit features of molecular architecture and gating mechanisms unprecedented in other types of ion channels. They form two-pore homodimers, and their voltage-dependence arises not from charged residues in the protein, but rather via coupling of gating to the movement of chloride ions within the pore. Because the functional characteristics of only a few ClC channels have been studied in detail, we are still learning which properties are general to the whole family. New approaches, including structural analyses, will be crucial to an understanding of ClC architecture and function.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.411
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    DESIGNED SEQUENCE-SPECIFIC MINOR GROOVE LIGANDS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 439-461 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract In the past decade, a general design for sequence-specific minor groove ligands has evolved, based on the natural products distamycin and netropsin. By utilizing a basic set of design rules for connecting pyrrole, imidazole, and hydroxypyrrole modules, new ligands can be prepared to target almost any sequence of interest with both high affinity and specificity. In this review we present the design rules with a brief history of how they evolved. The structural basis for sequence-specific recognition is explained, together with developments that allow linking of recognition modules that enable targeting of long DNA sequences. Examples of the affinity and specificity that can be achieved with a number of variations on the basic design are given. Recently these molecules have been used to compete with proteins both in vitro and in vivo, and a brief description of the experimental results are given.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.439
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    NMR PROBES OF MOLECULAR DYNAMICS: Overview and Comparison with Other Techniques (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 129-155 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.
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    STRUCTURE OF PROTEINS INVOLVED IN SYNAPTIC VESICLE FUSION IN NEURONS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 157-171 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor SNAP, and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models.
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    AB INITIO PROTEIN STRUCTURE PREDICTION: Progress and Prospects (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 173-189 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.
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    STRUCTURAL RELATIONSHIPS AMONG REGULATED AND UNREGULATED PHOSPHORYLASES (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 191-209 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Species and tissue-specific isozymes of phosphorylase display differences in regulatory properties consistent with their distinct roles in particular organisms and tissues. In this review, we compare crystallographic structures of regulated and unregulated phosphorylases, including maltodextrin phosphorylase (MalP) from Escherichia coli, glycogen phosphorylase from yeast, and mammalian isozymes from muscle and liver tissues. Mutagenesis and functional studies supplement the structural work and provide insights into the structural basis for allosteric control mechanisms. MalP, a simple, unregulated enzyme, is contrasted with the more complicated yeast and mammalian phosphorylases that have evolved regulatory sites onto the basic catalytic architecture. The human liver and muscle isozymes show differences structurally in their means of invoking allosteric activation. Phosphorylation, though common to both the yeast and mammalian enzymes, occurs at different sites and activates the enzymes by surprisingly different mechanisms.
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    BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 211-243 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.
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    CHAPERONIN-MEDIATED PROTEIN FOLDING (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 245-269 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Molecular chaperones are required to assist folding of a subset of proteins in Escherichia coli. We describe a conceptual framework for understanding how the GroEL-GroES system assists misfolded proteins to reach their native states. The architecture of GroEL consists of double toroids stacked back-to-back. However, most of the fundamentals of the GroEL action can be described in terms of the single ring. A key idea in our framework is that, with coordinated ATP hydrolysis and GroES binding, GroEL participates actively by repeatedly unfolding the substrate protein (SP), provided that it is trapped in one of the misfolded states. We conjecture that the unfolding of SP becomes possible because a stretching force is transmitted to the SP when the GroEL particle undergoes allosteric transitions. Force-induced unfolding of the SP puts it on a higher free-energy point in the multidimensional energy landscape from which the SP can either reach the native conformation with some probability or be trapped in one of the competing basins of attraction (i.e., the SP undergoes kinetic partitioning). The model shows, in a natural way, that the time scales in the dynamics of the allosteric transitions are intimately coupled to folding rates of the SP. Several scenarios for chaperonin-assisted folding emerge depending on the interplay of the time scales governing the cycle. Further refinement of this framework may be necessary because single molecule experiments indicate that there is a great dispersion in the time scales governing the dynamics of the chaperonin cycle.
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    MY ROAD TO BIOPHYSICS: Picking Flowers on the Way to Photosynthesis (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 1-44 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134147
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    PROPERTIES AND BIOLOGICAL ACTIVITIES OF THIOREDOXINS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 421-455 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The mammalian thioredoxins are a family of small (approximately 12 kDa) redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase and in turn reduce oxidized cysteine groups on proteins. The two main thioredoxins are thioredoxin-1, a cytosolic and nuclear form, and thioredoxin-2, a mitochondrial form. Thioredoxin-1 has been studied more. It performs many biological actions including the supply of reducing equivalents to thioredoxin peroxidases and ribonucleotide reductase, the regulation of transcription factor activity, and the regulation of enzyme activity by heterodimer formation. Thioredoxin-1 stimulates cell growth and is an inhibitor of apoptosis. Thioredoxins may play a role in a variety of human diseases including cancer. An increased level of thioredoxin-1 is found in many human tumors, where it is associated with aggressive tumor growth. Drugs are being developed that inhibit thioredoxin and that have antitumor activity.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.421
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    NMR STUDIES OF LIPOPROTEIN STRUCTURE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 177-206 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Early NMR structural studies of serum lipoproteins were based on 1H, 13C, 31P, and 2H studies of lipid components. From the early studies information on composition, lipid chain dynamics and order parameters, and monolayer organization resulted. More recently, selective or complete isotopic labeling techniques, combined with multidimensional NMR spectroscopy, have resulted in structural information of apoprotein fragments. Finally, use of heteronuclear three- and four-dimensional experiments have yielded solution structures and protein-lipid interactions of intact apolipoproteins C-I, C-II, and A-I.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140910
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    THE LINKAGE BETWEEN PROTEIN FOLDING AND FUNCTIONAL COOPERATIVITY: Two Sides of the Same Coin? (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 235-256 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract During the course of their biological function, proteins undergo different types of structural rearrangements ranging from local to large-scale conformational changes. These changes are usually triggered by their interactions with small-molecular-weight ligands or other macromolecules. Because binding interactions occur at specific sites and involve only a small number of residues, a chain of cooperative interactions is necessary for the propagation of binding signals to distal locations within the protein structure. This process requires an uneven structural distribution of protein stability and cooperativity as revealed by NMR-detected hydrogen/deuterium exchange experiments under native conditions. The distribution of stabilizing interactions does not only provide the architectural foundation to the three-dimensional structure of a protein, but it also provides the required framework for functional cooperativity. In this review, the statistical thermodynamic linkage between protein stability, functional cooperativity, and ligand binding is discussed.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134215
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    INTERPRETING THE EFFECTS OF SMALL UNCHARGED SOLUTES ON PROTEIN-FOLDING EQUILIBRIA (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 271-306 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Proteins are designed to function in environments crowded by cosolutes, but most studies of protein equilibria are conducted in dilute solution. While there is no doubt that crowding changes protein equilibria, interpretations of the changes remain controversial. This review combines experimental observations on the effect of small uncharged cosolutes (mostly sugars) on protein stability with a discussion of the thermodynamics of cosolute-induced nonideality and critical assessments of the most commonly applied interpretations. Despite the controversy surrounding the most appropriate manner for interpreting these effects of thermodynamic nonideality arising from the presence of small cosolutes, experimental advantage may still be taken of the ability of the cosolute effect to promote not only protein stabilization but also protein self-association and complex formation between dissimilar reactants. This phenomenon clearly has potential ramifications in the cell, where the crowded environment could well induce the same effects.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.271
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    BINDING OF LIGANDS AND ACTIVATION OF TRANSCRIPTION BY NUCLEAR RECEPTORS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 329-359 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Nuclear receptors (NRs) form a superfamily of ligand-inducible transcription factors composed of several domains. Recent structural studies focused on domain E, which harbors the ligand-binding site and the ligand-dependent transcription activation function AF-2. Structures of single representatives in an increasing number of various complexes as well as new structures of further NRs addressed issues such as discrimination of ligands, superagonism, isotype specificity, and partial agonism. Until today, one unique transcriptionally active form of domain E was determined; however, divergent tertiary structures of apo-forms and transcriptionally inactive forms are known. Thus, recent results link the transformation of NRs upon ligand binding to principles of protein folding. Furthermore, the ensemble of NR structures, including those of DNA-binding domains, provides one of the foundations for the understanding of interactions with transcription intermediary factors up to the characterization of the link between NR complexes and the basal transcriptional machinery at the structural level.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.329
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    STRUCTURAL INSIGHTS INTO MICROTUBULE FUNCTION (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 397-420 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Microtubules are polymers that are essential for, among other functions, cell transport and cell division in all eukaryotes. The regulation of the microtubule system includes transcription of different tubulin isotypes, folding of alpha/beta-tubulin heterodimers, post-translation modification of tubulin, and nucleotide-based microtubule dynamics, as well as interaction with numerous microtubule-associated proteins that are themselves regulated. The result is the precise temporal and spatial pattern of microtubules that is observed throughout the cell cycle. The recent high-resolution analysis of the structure of tubulin and the microtubule has brought new insight to the study of microtubule function and regulation, as well as the mode of action of antimitotic drugs that disrupt normal microtubule behavior. The combination of structural, genetic, biochemical, and biophysical data should soon give us a fuller understanding of the exquisite details in the regulation of the microtubule cytoskeleton.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.397
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    RIBOZYME STRUCTURES AND MECHANISMS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 457-475 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.457
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    MAGNETIC RESONANCE STUDIES OF THE BACTERIORHODOPSIN PUMP CYCLE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 73-95 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134233
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    PIP2 AND PROTEINS: Interactions, Organization, and Information Flow (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 151-175 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134259
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    STRUCTURAL AND THERMODYNAMIC CORRELATES OF T CELL SIGNALING (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 121-149 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134423
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    THE alpha-HELIX AND THE ORGANIZATION AND GATING OF CHANNELS (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 207-233 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The structures of an increasing number of channels and other alpha-helical membrane proteins have been determined recently, including the KcsA potassium channel, the MscL mechanosensitive channel, and the AQP1 and GlpF members of the aquaporin family. In this chapter, the orientation and packing characteristics of bilayer-spanning helices are surveyed in integral membrane proteins. In the case of channels, alpha-helices create the sealed barrier that separates the hydrocarbon region of the bilayer from the permeation pathway for solutes. The helices surrounding the permeation pathway tend to be rather steeply tilted relative to the membrane normal and are consistently arranged in a right-handed bundle. The helical framework further provides a supporting scaffold for nonmembrane-spanning structures associated with channel selectivity. Although structural details remain scarce, the conformational changes associated with gating transitions between closed and open states of channels are reviewed, emphasizing the potential roles of helix-helix interactions in this process.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134329
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    PRINCIPLES AND BIOPHYSICAL APPLICATIONS OF LANTHANIDE-BASED PROBES (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 275-302 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Using luminescent lanthanides, instead of conventional fluorophores, as donor molecules in resonance energy transfer measurements offers many technical advantages and opens up a wide range of new applications. Advantages include farther measurable distances (~100 A) with greater accuracy, insensitivity to incomplete labeling, and the ability to use generic relatively large labels, when necessary. Applications highlighted include the study of ion channels in living cells, protein-protein interaction in cells, DNA-protein complexes, and high-throughput screening assays to measure peptide dimerization associated with DNA transcription factors and ligand-receptor interactions.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140927
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    SINGLE-PARTICLE IMAGING OF MACROMOLECULES BY CRYO-ELECTRON MICROSCOPY (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 303-319 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134202
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    RHODOPSIN: Insights from Recent Structural Studies (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 443-484 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134348
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    CONFORMATIONAL REGULATION OF INTEGRIN STRUCTURE AND FUNCTION (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 485-516 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (〈1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
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    OPTICAL SINGLE TRANSPORTER RECORDING: Transport Kinetics in Microarrays of Membrane Patches (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 47-67 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Optical single transporter recording (OSTR) is an emerging technique for the fluorescence microscopic measurement of transport kinetics in membrane patches. Membranes are attached to transparent microarrays of cylindrical test compartments (TCs) ~0.1-100 mum in diameter and ~10-100 mum in depth. Transport across membrane patches that may contain single transporters or transporter populations is recorded by confocal microscopy. By these means transport of proteins through single nuclear pore complexes has been recorded at rates of 〈1 translocation/s. In addition to the high sensitivity in terms of measurable transport rates OSTR features unprecedented spatial selectivity and parallel processing. This article reviews the conceptual basis of OSTR and its realization. Applications to nuclear transport are summarized. The further development of OSTR is discussed and its extension to a diversity of transporters, including translocases and ATP-binding cassette (ABC) pumps, projected.
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    STRUCTURE AND FUNCTION OF NATURAL KILLER CELL SURFACE RECEPTORS* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 93-114 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Since mid-1990, with cloning and identification of several families of natural killer (NK) receptors, research on NK cells began to receive appreciable attention. Determination of structures of NK cell surface receptors and their ligand complexes led to a fast growth in our understanding of the activation and ligand recognition by these receptors as well as their function in innate immunity. Functionally, NK cell surface receptors are divided into two groups, the inhibitory and the activating receptors. Structurally, they belong to either the immunoglobulin (Ig)-like receptor superfamily or the C-type lectin-like receptor (CTLR) superfamily. Their ligands are either members of class I major histocompatibility complexes (MHC) or homologs of class I MHC molecules. The inhibitory form of NK receptors provides the protective immunity through recognizing class I MHC molecules with self-peptides on healthy host cells. The activating, or the noninhibitory, NK receptors mediate the killing of tumor or virally infected cells through their specific ligand recognition. The structures of activating and inhibitory NK cell surface receptors and their complexes with the ligands determined to date, including killer immunoglobulin-like receptors (KIRs) and their complexes with HLA molecules, CD94, Ly49A, and its complex with H-2Dd, and NKG2D receptors and their complexes with class I MHC homologs, are reviewed here.
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    THE POWER AND PROSPECTS OF FLUORESCENCE MICROSCOPIES AND SPECTROSCOPIES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 161-182 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142525
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    NEW INSIGHT INTO SITE-SPECIFIC RECOMBINATION FROM FLP RECOMBINASE-DNA STRUCTURES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 135-159 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The lamba integrase, or tyrosine-based family of site-specific recombinases, plays an important role in a variety of biological processes by inserting, excising, and inverting DNA segments. Flp, encoded by the yeast 2-mum plasmid, is the best-characterized eukaryotic member of this family and is responsible for maintaining the copy number of this plasmid. Over the past several years, structural and biochemical studies have shed light on the details of a common catalytic scheme utilized by these enzymes with interesting variations under different biological contexts. The emergence of new Flp structures and solution data provides insights not only into its unique mechanism of active site assembly and activity regulation but also into the specific contributions of certain protein residues to catalysis.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.141732
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    X-RAY CRYSTALLOGRAPHIC ANALYSIS OF LIPID-PROTEIN INTERACTIONS IN THE BACTERIORHODOPSIN PURPLE MEMBRANE* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 285-310 
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    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past decade has witnessed increasingly detailed insights into the structural mechanism of the bacteriorhodopsin photocycle. Concurrently, there has been much progress within our knowledge pertaining to the lipids of the purple membrane, including the discovery of new lipids and the overall effort to localize and identify each lipid within the purple membrane. Therefore, there is a need to classify this information to generalize the findings. We discuss the properties and roles of haloarchaeal lipids and present the structural data as individual case studies. Lipid-protein interactions are discussed in the context of structure-function relationships. A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented.
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    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142516
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