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  • American Geophysical Union  (5,143)
  • Annual Reviews
  • BioMed Central
  • Copernicus
  • 2005-2009  (8,940)
  • 2005  (8,940)
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  • 2005-2009  (8,940)
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  • 1
    Publication Date: 2021-01-05
    Description: Destructive earthquakes are rare in France yet pose a sizable seismic hazard, especially when critical infrastructures are concerned. Only a few destructive events have occurred within the instrumental period, the most important being the 11 June 1909, Lambesc (Provence) earthquake. With a magnitude estimated at 6.2 [Rothé, 1942], the event was recorded by 30 observatories and produced intensity IX effects in the epicentral area, ~30 km north of Marseille. We collected 30 seismograms, leveling data and earthquake intensities to assess the magnitude and possibly the focal mechanism of this event. Following this multidisciplinary approach, we propose a source model where all relevant parameters are constrained by at least two of the input datasets. Our reappraisal of the seismological data yielded Mw 5.8-6.1 (6.0 preferred) and Ms 6.0, consistent with the magnitude from intensity data (Me 5.8) and with constraints derived from modeling of coseismic elevation changes. Hence, we found the Lambesc earthquake to have been somewhat smaller than previously reported. Our datasets also constrain the geometry and kinematics of faulting, suggesting that the earthquake was generated by reverse-right lateral slip on a WNW-striking, steeply north-dipping fault beneath the western part of the Trévaresse fold. This result suggests that the fold, located in front of the Lubéron thrust, plays a significant role in the region’s recent tectonic evolution. The sense of slip obtained for the 1909 rupture also agrees with the regional stress field obtained from earthquake focal mechanisms and microtectonic data as well as recent GPS data.
    Description: Published
    Description: 2454
    Description: partially_open
    Keywords: Lambesc earthquake ; France ; historical seismograms ; displacement modeling ; macroseismic data ; geodetic data ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.05. Historical seismology ; 04. Solid Earth::04.06. Seismology::04.06.09. Waves and wave analysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-04-07
    Description: The flow of ground water in a buried permeable paleochannel can be observed at the ground surface through its self-potential signature. We apply this method to delineate the Saint-Ferréol paleo-channel of the Rhone River located in Camargue, in the South East of France. Negative potentials, 30 mV (reference taken outside the paleochannel),are associated with ground water flow in this major sand-filled channel (500 m wide). Electrical resistivity is primarily controls by the salinity of the pore water. Electrical resistivity tomography and in situ sampling show the salinity of the water inside the paleo-channel is ten times smaller by comparison with the pore water of the surrounding sediments. Combining electrical resistivity surveys, self-potential data, and a minimum of drilling information, a 3-D reconstruction of the architecture of the paleo-channel is obtained showing the usefulness of this methodology for geomorphological reconstructions in this type of coastal environment.
    Description: - Observatoire de Recherche en Environnement (ORE)
    Description: Published
    Description: L07401
    Description: partially_open
    Keywords: Self-potential ; electrical resistivity tomography ; hydrogeology ; tomography ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 03. Hydrosphere::03.02. Hydrology::03.02.02. Hydrological processes: interaction, transport, dynamics ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 04. Solid Earth::04.02. Exploration geophysics::04.02.04. Magnetic and electrical methods ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy ; 05. General::05.02. Data dissemination::05.02.04. Hydrogeological data
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  • 3
    Publication Date: 2017-04-04
    Description: In this paper we provide a review of chemical and isotopic data gathered over the last three decades on Etna volcano's fluid emissions and we present a synthetic framework of their spatial and temporal relationships with the volcano-tectonic structures, groundwater circulation and eruptive activity. We show that the chemistry, intensity and spatial distribution of gas exhalations are strongly controlled by the main volcano-tectonic fault systems. The emission of mantle-derived magmatic volatiles, supplied by deep to shallow degassing of alkali-hawaiitic basalts, persistently occurs through the central conduits, producing a huge volcanic plume. The magmatic derivation of the hot gases is verified by their He, C and S isotopic ratios. Colder but widespread emanations of magma-derived CO2 and He also occur through the flanks of the volcano and through aquifers, mainly concentrated within two sectors of the south-southwest (Paternò-Belpasso) and eastern (Zafferana) flanks. In these two peripheral areas, characterized by intense local seismicity and gravity highs, magma-derived CO2 and helium are variably diluted by shallower crustal-derived fluids (organically-derived carbon, radiogenic helium). Thermal and geochemical anomalies recorded in groundwaters and soil gases within these two areas prior to the 1991-1993 eruption are consistent with an input of hot fluids released by ascending magma. Magmatic fluids interacted with the shallow aquifers, modifying their physico-chemical conditions, and led to strong variations of the soil CO2 flux. In addition to routine survey of the crater plume emissions, geochemical monitoring of remote soil gases and groundwaters may thus contribute to forecasting Etna's eruptions.
    Description: Published
    Description: 129-145
    Description: partially_open
    Keywords: Mt. Etna ; Geochemical surveillance ; Groundwaters ; Volcanic gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 4
    Publication Date: 2017-04-04
    Description: The western Mediterranean subduction zone (WMSZ) extends from the northern Apennine to southern Spain and turns around forming the narrow and tight Calabrian and Gibraltar Arcs. The evolution of the WMSZ is characterized by a first phase of orogenic wedging followed, from 30 Ma on, by trench retreat and back-arc extension. Combining new and previous geological data, new tomographic images of the western Mediterranean mantle, and plate kinematics, we describe the evolution of the WMSZ during the last 35 Myr. Our reconstruction shows that the two arcs form by fragmentation of the 1500 km long WMSZ in small, narrow slabs. Once formed, these two narrow slabs retreat outward, producing back-arc extension and large scale rotation of the flanks, shaping the arcs. The Gibraltar Arc first formed during the middle Miocene, while the Calabrian Arc formed later, during the late Miocene-Pliocene. Despite the different paleogeographic settings, the mechanism of rupture and backward migration of the narrow slabs presents similarities on both sides of the western Mediterranean, suggesting that the slab deformation is also driven by lateral mantle flow that is particularly efficient in a restricted (upper mantle) style of mantle convection.
    Description: Published
    Description: 1-21
    Description: reserved
    Keywords: Mediterranean ; subduction ; arcuate belt ; tomography ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 5
    Publication Date: 2017-04-04
    Description: The recent eruption of Mount Etna (July 2001) offered the opportunity to analyze magma-derived volatiles emitted during preand syn-eruptive phases, and to verify whether their composition is affected by changes in volcanic dynamics. This paper presents the results of analyses of F, Cl and S in the volcanic plume collected by filter-packs, and interprets variations in the composition based on contrasting solubility in magmas. A Rayleigh-type degassing mechanism was used to fit the acquired data and to estimate Henryâ s solubility constant ratios in Etnean basalt. This model provided insights into the dynamics of the volcano. Abundances of sulfur and halogens in eruptive plumes may help predict the temporal evolution of an ongoing effusive eruption.
    Description: -Gruppo Nazionale per la Vulcanologia.
    Description: Published
    Description: 1559
    Description: partially_open
    Keywords: magmatic degassing ; acidic gases ; plume chemistry ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 6
    Publication Date: 2017-04-04
    Description: A high-resolution environmental magnetic study of the Massignano section, Italy (Global Stratotype Section and Point for the Eocene-Oligocene boundary), has been performed to test whether a clear magnetic signature associated with climatic change is recognizable in this record. Our results reveal the existence of alternating intervals with high and low magnetic mineral concentrations similar to the pattern of rock magnetic property variations observed from an environmental magnetic study of the CIROS-1 sediment core from Antarctica. These results suggest that an external forcing mechanism drove the sedimentary response to global climate change prior to the major Oi-1 cooling event at the Eocene-Oligocene boundary.
    Description: Published
    Description: 601-605
    Description: reserved
    Keywords: Environmental magnetism ; Massignano ; 04. Solid Earth::04.05. Geomagnetism::04.05.07. Rock magnetism
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  • 7
    Publication Date: 2017-04-04
    Description: Mud volcanoes represent the largest expression of natural methane release into the atmosphere; however, the gas flux has never been investigated in detail. Methane output from vents and diffuse soil degassing is herewith reported for the first time. Measurements were carried out at 5 mud volcano fields around Sicily (Italy). Each mud volcano is characterized by tens of vents and bubbling pools. In the quiescent phase, methane emission from single vents ranges between 0.01 and 6.8 kg/day. Diffuse soil leakage around the vents is in the order of 102–104 mg m 2 d 1. An exceptional flux of 106 mg m 2 d 1 was recorded close to an everlasting fire. Soil CH4 flux is positive even at large distances from the mud volcano fields suggesting a diffuse microseepage over wider areas. A total of at least 400 tons CH4 per year can be estimated over the area investigated alone ( 1.5 km2).
    Description: Published
    Description: 1215
    Description: partially_open
    Keywords: methane ; flux measurements ; Sicily ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases
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  • 8
    Publication Date: 2017-04-04
    Description: Volcanic gas emissions from fumaroles on the rim of La Fossa crater, Vulcano Island, Italy, were measured simultaneously using direct sampling (for H2O, CO2, total sulfur, HCl and HF), filter packs (for SO2, HCl, HF) and short-path active-mode FTIR measurements (for H2O, CO2,SO2, HCl and HF) in an intercomparison study in May 2002. The results show that Cl/F ratios were in good agreement between all three methods, and that FTIR and direct sampling determined comparable proportions of CO2 and H2O. Amounts of total S observed in direct sampling data were approximately double the amounts of SO2 measured with filter packs and FTIR. This difference could be attributed either to the fact FTIR and filter packs do not measure reduced sulfur species (e.g., H2S) or to sublimation of elemental S upon exit from the fumarole, after collection by direct sampling but before detection with FTIR and filter packs.
    Description: Published
    Description: L02610
    Description: partially_open
    Keywords: volcanic gas techniques ; gas geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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  • 9
    Publication Date: 2017-04-04
    Description: Chemical and isotopic data have been used as geochemical tracers for a genetic characterization of hydrocarbon gases from a total of eleven manifestations located in Eastern and Central-Southern Sicily (Italy). The molecular analysis shows that almost all the samples are enriched in methane (up to 93.2% Vol.), with the exception of four gas samples collected around Mt. Etna showing high mantle-derived CO2 content. Methane isotope signatures suggest that these are thermogenic gases or a mixture between thermogenic gases and microbial gases. Although samples from some mud volcanoes in Southern Sicily (Macalube di Aragona) show isotope signatures consistent with a mixing model between thermogenic and microbial, by combining the molecular compositions (C1/(C2 + C3))and the methane isotope ratios (d13C1), such a process seems to be excluded. Therefore, the occurrence of secondary post-genetic processes should be invoked. Two main hypotheses have been considered: the first hypothesis includes that the gas is produced by microbial activity and altered post-genetically by microbial oxidation of methane, while according to the second hypothesis thermogenic gas have modified their molecular ratios due to vertical migration.
    Description: Published
    Description: L06607
    Description: partially_open
    Keywords: Isotopic composition/chemistry ; Organic geochemistry ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
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  • 10
    Publication Date: 2017-04-04
    Description: We study the dynamic traction behavior within the cohesive zone during the propagation of earthquake ruptures adopting rate and state dependent constitutive relations. The resulting slip weakening curve displays an equivalent slip weakening distance (D0_eq), which is different from the parameter L controlling the state variable evolution. The adopted constitutive parameters (a, b, L) control the slip weakening behavior and the absorbed fracture energy. The dimension of the nucleation patch scales with L and not with D0_eq. We propose a scaling relation between these two lengthscale parameters which prescribes that D0_eq/L ~ 15.
    Description: Published
    Description: 1-4
    Description: open
    Keywords: Earthquake dynamics and mechanics ; Earthquake parameters ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics
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  • 11
    Publication Date: 2017-04-04
    Description: Constraining fluxes of volcanic bromine and iodine to the atmosphere is important given the significant role these species play in ozone depletion. However, very few such measurements have been made hitherto, such that global volcanic fluxes are poorly constrained. Here we extend the data set of volcanic Br and I degassing by reporting the first measurements of bromine and iodine emissions from Mount Etna. These data were obtained using filter packs and contemporaneous ultraviolet spectroscopic SO2 flux measurements, resulting in time-averaged emission rates of 0.7 kt yr 1 and 0.01 kt yr 1 for Br and I, respectively, from April to October 2004, from which we estimate global Br and I fluxes of order 13 (range, 3â 40) and 0.11 (range, 0.04â 6.6) kt yr 1. Observed changes in plume composition highlight the coherent geochemical behavior of HCl, HF, HBr, and HI during magmatic degassing, and strong fractionation of these species with respect to SO2.
    Description: Published
    Description: Q08008
    Description: partially_open
    Keywords: bromine and iodine in volcanic gases ; halogen atmospheric chemistry ; volcanic degassing ; volcanic plumes ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 12
    Publication Date: 2017-04-04
    Description: A new method for extracting dissolved gases in natural waters has been developed and tested, both in the laboratory and in the field. The sampling device consists of a polytetrafluroethylene (PTFE) tube (waterproof and gas permeable) sealed at one end and connected to a glass sample holder at the other end. The device is pre-evacuated and subsequently dipped in water, where the dissolved gases permeate through the PTFE tube until the pressure inside the system reaches equilibrium. A theoretical model describing the time variation in partial gas pressure inside a sampling device has been elaborated, combining the mass balance and ‘‘Solution-Diffusion Model’’ which describes the gas permeation process through a PTFE membrane). This theoretical model was used to predict the temporal evolution of the partial pressure of each gas species in the sampling device. The model was validated by numerous laboratory tests. The method was applied to the groundwater of Vulcano Island (southern Italy). The results suggest that the new sampling device could easily extract the dissolved gases from water in order to determine their chemical and isotopic composition.
    Description: - European Social Fund.
    Description: Published
    Description: Q09005
    Description: partially_open
    Keywords: dissolved gases ; helium isotope ; PTFE membrane ; Vulcano Island ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.07. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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  • 13
    Publication Date: 2017-04-04
    Description: Ground-based measurements of volcanic sulfur dioxide fluxes are important indicators of volcanic activity, with application in hazard assessment, and understanding the impacts of volcanic emissions upon the environment and climate. These data are obtained by making traverses underneath the volcanic plume a few kilometers from source with an ultraviolet spectrometer, measuring integrated SO2 concentrations across the plume’s cross section, and multiplying by the plume’s transport speed. However, plume velocities are usually derived from ground-based anemometers, located many kilometers from the traverse route and hundreds of meters below plume altitude, complicating the experimental design and introducing large flux (can be 〉100%) errors. Here we present the first report of a single instrument capable of (accurate) volcanic SO2 flux measurements. This device records integrated SO2 concentrations and plume heights during traverses. Between traverses, two in-plume SO2 time series are measured from underneath the plume with the instrument, corresponding to zenith and inclined (user-specified angle from vertical in the direction of the volcano) fields of view, respectively. The distance between the points of intersection of the two views with the plume is found on the basis of the determined plume height, and the two signals are cross-correlated to determine the lag between them, enabling accurate derivation of the wind speed. We present flux data (with errors ±12%) obtained in this way at Mt. Etna during July 2004.
    Description: Published
    Description: Q02003
    Description: partially_open
    Keywords: DOAS ; volcanic SO2 emissions. ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 14
    Publication Date: 2017-04-04
    Description: The main goal of this work is to provide a probability map for the next moderate to large earthquakes (M 〉= 5.5) in Italy. For this purpose we apply a new nonparametric multivariate model to characterize the spatiotemporal distribution of earthquakes. The method is able to account for tectonics/physics parameters that can potentially influence the spatiotemporal variability and tests their relative importance; moreover, it allows straightforward testing of a variety of hypothesis, such as Seismic Gap, Cluster, and Poisson hypothesis. The method has been applied to Italian seismicity of the last four centuries for earthquakes with M 〉= 5.5. Italy has been divided into 61 irregular zones representing areas with homogeneous tectonic regime resulting from active stress data. Besides the magnitude and the time of the earthquakes, the model includes information on the tectonic stress regime, the homogeneity of its orientation, the number of active faults, the dimension of the area and the homogeneity of the topography. The time distribution of the M 〉= 5.5 earthquakes appears clustered in time for a few years after an event, and then the distribution becomes similar to a memoryless Poisson process, leading to a time-dependent probability map. This map shows that the most likely regions where the next moderate to large earthquakes may occur are Friuli, Umbria- Marche, and part of Southern Apennines and the Calabrian arc.
    Description: Published
    Description: 1-15
    Description: reserved
    Keywords: earthquake probability ; Italy ; seismotectonic regionalization ; statistical modeling ; 04. Solid Earth::04.06. Seismology::04.06.02. Earthquake interactions and probability
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  • 15
    Publication Date: 2012-02-03
    Description: Slow earthquakes and afterslips prove that the Earth does not have just two response time scales, i.e. that of tectonic loading and that of regular earthquakes. A swarm of slow earthquakes, with time constants of the order of hundreds of seconds, has been detected by a laser interferometer below the Gran Sasso massif (Italy). We analyse and model these observations to identify a very plausible source in a local fault, with no historic seismic behavior. While slow earthquakes occurring in subduction zones, and at the transition between locked and stably sliding segments of the San Andreas fault, are often associated with seismic events, in the case of the Apennines there is no correlation between local seismicity and slow earthquakes. Slow earthquakes, therefore, may also represent a specific failure behavior for a seismically locked fault, adding further complexity to the interpretation of geologic data for seismic hazard estimates.
    Description: Published
    Description: 2219
    Description: open
    Keywords: Earthquake dynamics and mechanics ; Seismic hazard assessment and prediction ; Seismicity and seismotectonics ; 04. Solid Earth::04.01. Earth Interior::04.01.05. Rheology ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics
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  • 16
    Publication Date: 2017-04-04
    Description: This paper reports the use of diffusive tubes in determining HF, HCl, and SO2 in the volcanic plume of Mount Etna in an attempt to highlight the potential of this method in studying volcanoes. In a first application a network of 18 diffusive tubes was installed on Etna flanks, aimed at evaluating the atmospheric dispersion of the volcanic plume on a local scale. Results showed a monotonic decrease in volatile air concentrations with distance from the craters (HF from 0.15 to 〈0.003 mmol m3, HCl from 2 to 〈0.01 mmol m3, and SO2 from 11 to 0.04 mmol m3), revealing the prevalently volcanic contribution. Matching of SO2/HCl and HCl/HF volatile ratios with contemporaneous measurements at the summit craters validated the use of diffusive tubes in tracing the chemical features of a volcanic plume from remote locations. A first tentative assessment of dry deposition rates of volcanogenic acidic gases was also made, yielding 2.5 74 t d1 (SO2), 0.6 17 t d1 (HCl), and 0.02 0.6 t d1 (HF) and revealing the potential environmental impact of gas emissions. In a second experiment, carried out during the recent October 2002 to February 2003 eruption of Etna, diffusive tubes provided a continuous record of the chemical composition of the eruptive plume from a safe distance of 1 km from the vents, thus considerably decreasing the risks involved in sampling. This highlighted a clear time decrease in SO2 concentrations and SO2/HCl ratios, which was interpreted as due to progressive exhaustion of volatile degassing and eruption energy.
    Description: Published
    Description: D21308
    Description: partially_open
    Keywords: volcanic plumes ; impact of volcanic emissions ; sulfur and halogens chemistry ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 17
    Publication Date: 2017-04-04
    Description: In the last 13 years gas emissions from both the summit and the flanks of Mount Etna volcano have been monitored using remote sensing techniques (COSPEC, and FTIR since 2000) and on-site monitoring devices. The SO2 flux variations (600 to 25,000 Mg/day) indicated: (i) low values coinciding with deep seismicity prior to eruptions or/and preceding increases in summit volcanic activity; (ii) increasing trends tracking the ascent of fresh magma within the shallow feeding system and whose rate seems proportional to the speed of magma rise; (iii) decreasing trends related to progressive degassing of magma batches; (iv) an imbalance between the amount of magma erupted and that which contributed the SO2 emission (~ 13 % of the degassing magma having been erupted during the studied period), implying that magma degassing is dominantly intrusive; (v) a seasonal component, probably due to variations in solar zenith angle, meteorological parameters and, possibly, tidal forces.FTIR monitoring allowed to recognize significant variations of SO2/HCl and SO2/HF ratios in the volcanic plume which, combined with COSPEC data, provided new insight into the dynamics of ascent and degassing of discrete magma bodies. Strong variations in CO2-rich soil degassing are interpreted as markers of gradual magma ascent from great depth (〉10 km) to the upper (〈5 km) feeding system of Mt. Etna. These changes appear to precede increases in SO2 plume flux at the craters and, so, provide additional constraints upon the interpretation of COSPEC data and the modeling of magma rise at that volcano.
    Description: Published
    Description: 111-128
    Description: partially_open
    Keywords: Gas emissions ; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases
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  • 18
    Publication Date: 2017-04-04
    Description: The Neapolitan volcanic region is located within the graben structure of the Campanian Plain (CP), which developed between the western sector of the Appenine Chain and the eastern margin of the Tyrrhenian Sea. Two volcanic areas, spaced less than 10 km apart, are situated within the CP: the Somma-Vesuvius Volcano (SVV) and the Phlegraean Volcanic District (PVD). SVV is a typical stratovolcano, whereas PVD, including Campi Flegrei, Procida, and Ischia, is composed mostly of monogenetic centers. This contrast is due to different magma supply systems: a widespread fissure-type system beneath the PVD and a central-type magma supply system for the SVV. Volcanological, geophysical, and geochemical data show that magma viscosity, magma supply rate, and depth of magma storage are comparable at PVD and SVV, whereas different structural arrangements characterize the two areas. On the basis of geophysical data and magma geochemistry, an oblique-extensional tectonic regime is proposed within the PVD, whereas in the SVVarea a compressive stress regime dominates over extension. Geophysical data suggest that the area with the maximum deformation rate extends between the EW-running 41st parallel and the NE-running Magnaghi-Sebeto fault systems. The PVD extensional area is a consequence of the Tyrrhenian Sea opening and is decoupled from the surrounding areas (Roccamonfina and Somma-Vesuvius) which are still dominated by Adriatic slab dynamics. Spatially, we argue that the contribution of the asthenospheric wedge become much less important from W-NW to E-SE in the CP. The development of the two styles of volcanism in the CP reflects the different tectonic regimes acting in the area.
    Description: Published
    Description: 1-25
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    Keywords: Volcanic styles ; Tectonic setting ; Neapolitan volcanic region ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
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  • 19
    Publication Date: 2017-04-04
    Description: From December 2002 to July 2003, Stromboli volcano was characterized by a new effusive stage of eruption after a period of extraordinary strombolian activity. Signals recorded in two continuous monitoring stations during the eruption, which have already been presented in very recent papers, evidenced anomalies in the CO2 flux just before the onset of the eruption. A more detailed analysis carried out on the data subset acquired during the eruption, integrated by daily field observations of the scientific personnel working at the volcanological observatory in Stromboli, showed that CO2 flux and soil temperature are strictly related to volcanic events. Furthermore, the relative minima and maxima of the two parameters showed a strong correlation with wind speed and direction. This fact was especially true at the summit station, whereas at the coastal sites seasonal and meteorological effects masked the volcanic signal. The analysis of the wind data, particularly the relationships between wind speed and direction, air and soil temperature, and local circulation of atmospheric air masses revealed that during the eruption, in the summit area of Stromboli air movements were not only related to atmospheric circulation but were also significantly affected, and in certain cases caused, by volcanic activity. This conclusion was reached by observing several anomalies, such as the discrepancies in the wind direction between the two stations, higher air temperatures at the summit site, and inversion of direction for wind before and after the reopening of the conduit in a major explosion on 5 April 2003. The relationships found between volcanic activity, soil temperatures, CO2 fluxes, and wind speed and direction indicate that soil temperature measurements, in an open conduit volcano such as in this case, could be used to monitor the level of volcanic activity, along with CO2 flux. Furthermore, the possible volcanic origin of a peculiar type of air circulation identified in the summit area of Stromboli suggests that the separation between volcanic and atmospheric signals might not be obvious, requiring monitoring over a wide area, rather than a single location.
    Description: Published
    Description: Q12001
    Description: partially_open
    Keywords: carbon dioxide flux ; continuous monitoring ; soil temperature ; wind ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 20
    Publication Date: 2017-04-04
    Description: Marked increases of CO2, H2 and He dissolved in thermal waters and changes in the dissolved carbon isotopic composition, were observed at Stromboli before the 28 December 2002 eruption and before a violent explosive paroxysm occurred on 5 April 2003. High anomalous CO2 flux values were recorded at the crater rim since a week before the eruption onset. The first anomalies in the thermal waters (dissolved CO2 amount) appeared some months before the eruption, when magma column rose at a very high level in the conduit. High peaks of dissolved H2 and He were recorded a few days before the paroxysm. Carbon isotopic composition indicates a magmatic origin of the dissolved CO2 whose increase, together with those of H2 and He, is attributed to an increasing output of deep gases likely produced by depressurization of a rising batch of a deep gas-rich magma, whose fragments have been emitted during the explosion.
    Description: Italian Civil Protection
    Description: Published
    Description: L07620
    Description: partially_open
    Keywords: Stromboli ; geochemical precursors ; CO2 flux ; pH ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 21
    Publication Date: 2017-04-04
    Description: The Jalisco Block (JB) is a geologically and tectonically complex part of northwestern Mexico characterized by active subduction-type volcanism, rifting, and old stable structures. Thermal springs and groups of springs are widely distributed over JB. Bubbling gas from seven thermal springs located within different tectonic environments of the JB was analyzed for He, 20Ne, and N2 concentrations and d15N ratios. All gases are N2-dominant (〉84%) with the exception of one sample (Rio´ Purificacio´n), which has a significant CH4 content (about 50%). All collected gas samples are relatively high in He, up to 1500 ppm vol and with 3He/4He values ranging from 0.6 to 4.5 Ra. All measured nitrogen isotope ratios are heavier than air with d15N values ranging from 0.5 to 5.0%. The relative N2 excess with respect to air-saturated water computed on the basis of N2 and 20Ne contents indicates the contribution of a nonatmospheric N2 source. All the samples show a good correlation between d15N and the relative excess of N2 with d15N +5.3% for the maximum N2 excess of 100%. Due to a presumed lack of seafloor sediment involved in the subduction process, such a d15N positive value seems to reflect the addition to the fluids of a heavy nitrogen originating from metamorphism processes of rocks occurring within the overlying continental crust.
    Description: Published
    Description: 1-9
    Description: partially_open
    Keywords: bubbling gases ; forearc region ; Jalisco Block-Mexico ; nitrogen isotopes ; subduction-related volcanism ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
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  • 22
    Publication Date: 2017-04-04
    Description: In this paper we present the first geochemical data set regarding long-term monitoring of dissolved gases in thermal waters from a seismic area. Three sites in Umbria (Central Apennines, Italy) were studied both for the chemical and for the helium isotopic composition of the dissolved gases. Data were collected during and after the seismic crisis that struck the region in 1997â 1998. The chemical composition of the dissolved gases revealed that a CO2-rich gas phase was always mixed with an atmospheric-derived component dominated by N2. A normal faulting marked the beginning of the seismic activity enhancing the release of CO2 on a regional scale. Variations in both the chemical and isotopic compositions of the dissolved gases were also observed as preseismic, synseismic, and postseismic phenomena related to the seismic shock of March 1998. Those geochemical modifications were interpreted as being the consequence of a drop in the CO2 degassing rate, in good agreement with the compressive focal mechanism of that seismic event. Furthermore, this interpretation was also consistent with the geologic and tectonic setting of the study area and induced us to postulate that changes in the local rock permeability, due to crustal deformations (i.e., coseismic deformation and postseismic release), were responsible for the geochemical modifications observed. On the basis of the foregoing, we have concluded that the geochemistry of dissolved gases in groundwaters represents a useful tool for the investigation of the relationships between circulating fluids and seismic activity.
    Description: Published
    Description: partially_open
    Keywords: dissolved gases ; geochemistry ; seismic areas ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.04. Hydrogeological data
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  • 23
    Publication Date: 2017-04-04
    Description: The performance of a newly-developed portable gas analyzer, capable of real-time measurement of CO2, SO2 and H2S concentrations in volcanic gases, was tested at La Fossa Crater, Vulcano Island. The gas analyzer was used to acquire about 3000 determinations over the fumarolic field, allowing the definition of its chemical structure and heterogeneity. Our high-resolution analysis reveals that, in December 2004, the La Fossa fumarolic field was characterized by an oxidized inner core (SO2/H2S ratios of 3), and by more reducing conditions on its northern edge (SO2/H2S ratios of 1; range: 0.2–3.3). CO2/(SO2+H2S) molar ratios averaged 35 ± 21, with overlapping compositions for rim and inner crater fumaroles. S-poor compositions (CO2/(SO2+H2S) 50) characterized the field margins, probably due to deposition of native sulfur. Based on the above data and an SO2 flux of 18 ± 3 t.d-1, we estimate CO2 and H2S output rates from the volcano of 420 ± 250 and 4 ± 2 t.d-1, respectively.
    Description: Published
    Description: L13309
    Description: partially_open
    Keywords: electrochemical sensors ; fumarolic gases ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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  • 24
    Publication Date: 2017-04-04
    Description: We present the first regional map of CO2 Earth degassing from a large area (most of central and south Italy) derived from the carbon of deep provenance dissolved in the main springs of the region. The investigation shows that a globally significant amount of deeply derived CO2 (10% of the estimated global CO2 emitted from subaerial volcanoes) is released by two large areas located in western Italy. The anomalous flux of CO2 suddenly disappears in the Apennine in correspondence to a narrow band where most of seismicity concentrates. Here, at depth, the gas accumulates in crustal traps generating CO2 overpressurized reservoirs which induce seismicity.
    Description: Published
    Description: 1-4
    Description: partially_open
    Keywords: Carbon dioxide ; Central Italy ; Southern Italy ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 25
    Publication Date: 2017-04-04
    Description: A major explosion occurred at Stromboli on April 5 2003, being the most powerful event over a period of exceptional eruptive activity lasting from December to July. Here, we describe results from a network of diffusive tubes set up on the Stromboli’s summit area, aimed at a characterisation of plume composition (SO2, HCl, HF) prior to and after April 5. Data analysis revealed anomalous sulphur degassing 2–3 days before the event, when SO2/HCl ratios (9) significantly higher than those typical of quiescent degassing (1) were recorded. We interpret this exceptional plume signature as an evidence of S-rich magmas ascending in the shallow plumbing system, and propose high SO2/HCl as a potential precursor of major explosions on the volcano. The post-April 5 phase was characterised by time-decreasing SO2/HCl and SO2/HF plume ratios, ascribed to declining magma feeding as a prelude to restoration of ‘‘normal’’ Strombolian activity.
    Description: Published
    Description: L14607
    Description: partially_open
    Keywords: magmatic degassing ; paroxysm ; Stromboli ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 26
    Publication Date: 2017-04-04
    Description: On 2nd/3rd November 2002, a huge amount of gas, mainly composed of CO2, was suddenly released from the sea bottom off the coast of Panarea, producing a ‘‘crater’’20 by 10 meters wide and 7 meters deep. The gas output was estimated to be 109 l/d, two orders of magnitude higher than that measured in the 1980s. The anomalous degassing rate lasted for some weeks, slowly decreasing to an almost constant rate of about 4 x 107 l/d after two months. The geothermo- barometric estimations revealed an increase of both the temperature and pressure in the geothermal system feeding the sampled vents. The 3He/4He ratios were similar to those measured in nearby Stromboli. We have monitored the area for the last two decades, and based on our intensive and extensive geochemical measurements, have ascertained that the geothermal reservoir has lost its steady state. We maintain that a new magmatic input caused these phenomena.
    Description: - Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy. - Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo, Palermo, Italy. - Dipartimento Chimica e Fisica della Terra ed Applicazioni, Palermo, Italy.
    Description: Published
    Description: L07619
    Description: partially_open
    Keywords: Submarine degassing ; magmatic fluids ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 27
    Publication Date: 2017-04-04
    Description: Five gas discharges in the area of Mount Etna volcano (Italy) and in the near Hyblean plateau have been monitored since 1996. All the emissions displayed low contributions from crustal fluids, whereas magmatic gases were the main component. Selective dissolution of these gases into hydrothermal aquifers has been recognized and modeled, allowing us to calculate the original composition of the magma-released gases. The inferred composition of the magmatic gases exhibits synchronous variations of He/Ne and He/CO2 ratios, which are coherent with the magma degassing process. On the basis of numerical simulations of volatile degassing from Etnean basalts we have computed the initial and final pressures of the magma batches feeding the emissions. We thus can define the levels of the Etna plumbing system where magmas are stored. Pressure values were around 360 and 160 MPa for initial and final stages, respectively, meaning related depths of about 10 and 3 km below sea level, matching those obtained by geophysical investigations for the deep and shallow magma reservoirs. In addition, we have been able to recognize episodes of magma migration from the deeper reservoir toward the shallow one. An important magma injection into the shallow storage volume was detected during the onset of the 2001 eruption (17 July). No further injection had taken place during this period until September 2001, providing a possible reason for the quick exhaustion of the eruption. In view of this we suggest that the sampled emissions are a powerful geochemical tool to investigate the Etna’s plumbing system and its magma dynamics, as well as the development of eruptive events.
    Description: Published
    Description: 2463
    Description: partially_open
    Keywords: gas geochemistry ; magma degassing ; modeling ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 28
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    American Geophysical Union
    In:  Etiope G., Caracausi A., Favara R., Italiano F., Baciu C. (2002) Methane emission from the mud volcanoes of Sicily (Italy). Geoph. Res. Letters 29, 14340-14343.
    Publication Date: 2017-04-04
    Description: The paper ‘‘Methane emission from the mud volcanoes of Sicily (Italy)’’ by Etiope et al. [2002] represents the first report ever done on experimental CH4 output data from subaerial mud volcanoes (MV). A review of available CH4 flux data and detailed discussion about the global implications of mud volcanic CH4 emission has been made elsewhere [Etiope and Klusman, 2002; Morner and Etiope, 2002]. [2] The comment by Kopf [2003] contributes to open discussions and to make the readership aware on how important this subject is. In this reply we wish to clarify that precise data of CH4 flux from geologic sources are beginning to be available only now. It would be opportune that the MV-expert community could agree in using a common unit for the gas flux. We propose t y 1 and Mt y 1, and not metres cubed, consistently with the data reported for the methane sources/sinks budget by the IPCC. [3] Sicilian MVs, the first to be measured in detail, are considerably much smaller than the Azeri Ashgil MV, mentioned by Kopf [2003], and it is therefore obvious to expect a lower gas flux. Anyway the Dashgil mud volcano flux data are not based on exact measurements but only on visual estimates of the bubbles [Hovland et al., 1997]. In order to fully reply to Kopf [2003], hereafter we briefly discuss the problem of how to estimate the total number of MVs in the world and present new data from other European MVs, recently investigated. Finally, we outline the global importance of mud volcanic CH4 emission, as Kopf [2003] and recent literature is stressing.
    Description: Published
    Description: 1094
    Description: partially_open
    Keywords: methane ; mud volcanoes ; helium ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 02. Cryosphere::02.03. Ice cores::02.03.02. Atmospheric Chemistry ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases
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  • 29
    Publication Date: 2017-04-04
    Description: Five years of gas monitoring from selected sites suggest that Mt Etna’s plumbing system is much more extensive than previously reported. It extends at least 40 km SW from the volcano’s boundary along the NE-SW regional fault, where it discharges about 200 tons/day of gas, containing helium with mantle-type isotopic composition. Synchronous variations of 3He/4He isotopic ratios in gas sampled at sites located 60 kilometers apart have allowed us to detect pulses of ascending magma in the plumbing system, thus providing a powerful tool for eruption forecasting. Following summer 2001 eruption, the still increasing trend of the 3He/4He ratios indicates that magma storage is even now occurring at a shallow depth. Hence, the volcano maintains a high capacity to re-erupt within the next few months.
    Description: Published
    Description: 1057
    Description: partially_open
    Keywords: helium isotopes ; geochemical monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 30
    Publication Date: 2017-04-04
    Description: We report results on the measured high 3He/4He isotope ratio in western Sicily, interpreted together with the heat data. The study of this sector of the Europe-Africa interaction is crucial to a better understanding of the tectonics and the geodynamical evolution of the central Mediterranean area. The estimated mantle-derived helium fluxes in the investigated areas are up to 2–3 orders of magnitude greater than those of a stable continental area. The highest flux, found in the southernmost area near the Sicily Channel, where recent eruptions of the Ferdinandea Island occurred 20 miles out to sea off Sciacca, has been associated with a clear excess of heat flow. Our results indicate that there is an accumulation of magma below the continental crust of western Sicily that is possibly intruding and out-gassing through roughly N-S trending deep fault systems linked to the mantle, that have an extensional component. Although the identification of these faults is not sufficiently constrained by our data, they could possibly be linked to the pre-existing faults that originated during the Mesozoic extensional-transtensional tectonic phases.
    Description: Published
    Description: L04312
    Description: partially_open
    Keywords: helium isotopes ; heat production ; tectonics ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 03. Hydrosphere::03.04. Chemical and biological::03.04.07. Radioactivity and isotopes ; 04. Solid Earth::04.02. Exploration geophysics::04.02.03. Heat flow ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.03. Heat generation and transport ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
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  • 31
    Publication Date: 2017-04-04
    Description: We analyse seismograms of the slump episodes at Stromboli on December 30, 2002. Using a simple single force model, we estimate the volume involved in the individual subevents and attempt a chronological reconstruction of the whole process. Our results indicate the occurrence of two main events that could be interpreted as a submarine slump, which caused the observed tsunami, and a subaerial slump, which did not produce destructive sea waves. A total volume of about 20 106 m3 results for the submarine event, which developed over about 2 minutes with several distinct detachments, the first and largest displacing a volume of 10.8 106 m3. The second, subaerial, slump involved at least 2.5 106 m3, in about 90 s. A large long period pulse is also recognizable in the seismograms of the Stromboli station. We tentatively interpret this feature as tilt caused by the water load associated with the inundation in the Ficogrande area, on the northeastern side of the island.
    Description: Published
    Description: (L02605)
    Description: reserved
    Keywords: Stromboli Volcano ; seismological description ; Fractures and faults ; Structural Geology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
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  • 32
    Publication Date: 2017-04-04
    Description: A field survey performed during the 1997 Umbria-Marche earthquake sequence led us to recognize ground and pavement ruptures associated with the three largest shocks (M〉= 5.7). The ruptures are concentrated in narrow bands that, in part, are on and near previously mapped high-angle normal fauts. The geometry of the ground deformation is consistent with the NE-trending extension indicated by CMT focal solutions of the mainshocks. The distribution of aftershocks suggests that the three mainshocks occurred on ~40 degree SW-dipping normal faults. Geological investigations, modelling of expected coseismic elevation changes, and seismic data, suggest that the surface deformation is not the direct result of primary rupture of faults at depth.
    Description: Published
    Description: 895-898
    Description: reserved
    Keywords: Structural geology ; Fractures and faults ; Seismology ; Seismicity and seismotectonics ; Europe ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology
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  • 33
    Publication Date: 2017-04-04
    Description: Recent examinations of the chemical fluxes through convergent plate margins suggest the existence of significant mass imbalances for many key species: only 20–30% of the to-the-trench inventory of large-ion lithophile elements (LILE) can be accounted for by the magmatic outputs of volcanic arcs. Active serpentinite mud volcanism in the shallow forearc region of the Mariana convergent margin presents a unique opportunity to study a new outflux: the products of shallow-level exchanges between the upper mantle and slab-derived fluids. ODP Leg 125 recovered serpentinized harzburgites and dunites from three sites on the crests and flanks of the active Conical Seamount. These serpentinites have U-shaped rare earth element (REE) patterns, resembling those of boninites. U, Th, and the high field strength elements (HFSE) are highly depleted and vary in concentration by up to 2 orders of magnitude. The low U contents and positive Eu anomalies indicate that fluids from the subducting Pacific slab were probably reducing in nature. On the basis of substantial enrichments of fluid-mobile elements in serpentinized peridotites, we calculated very large slab inventory depletions of B (79%), Cs (32%), Li (18%), As (17%), and Sb (12%). Such highly enriched serpentinized peridotites dragged down to depths of arc magma generation may represent an unexplored reservoir that could help balance the input-output deficit of these elements as observed by Plank and Langmuir (1993, 1998) and others. Surprisingly, many species thought to be mobile in fluids, such as U, Ba, Rb, and to a lesser extent Sr and Pb, are not enriched in the rocks relative to the depleted mantle peridotites, and we estimate that only 1–2% of these elements leave the subducting slabs at depths of 10 to 40 km. Enrichments of these elements in volcanic front and behind-the-front arc lavas point to changes in slab fluid composition at greater depths.
    Description: Published
    Description: 1-24
    Description: partially_open
    Keywords: Serpentinite ; Ocean Drilling Program ; Forearc ; Mantle ; Marianas ; Subduction ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.06. Subduction related processes
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  • 34
    Publication Date: 2017-04-04
    Description: We present an updated present-day stress data compilation for the Italian region and discuss it with respect to the geodynamic setting and the seismicity of the area. We collected and analyzed 190 new stress data from borehole breakouts, seismicity, and active faults and checked in detail the previous compilation [Montone et al., 1999]. Our improved data set consists of 542 data, 362 of which with a reliable quality for stress maps. The Italian region is well sampled, allowing the computation of constrained smoothed stress maps; for surrounding regions we added the World Stress Map 2003 release data. These maps depict the active stress conditions and, in the areas where the data are sparse, contribute to understand the relationship between active stress, past tectonic setting, and the seismicity of the study region. The new data are particularly representative along the northern Apennine front, from the Po Plain to offshore the Adriatic, and along the southern Tyrrhenian Sea, north of Sicily, where they point out a compressive tectonic regime. In the Alps both compressive and transcurrent regimes are observed. Our data also confirm that the whole Apenninic belt and the Calabrian arc are extending. Along the central Adriatic coast, changes from one stress regime to another are shown by abrupt variations in the minimum horizontal stress directions. Other gentler stress rotations, as, for instance, from the southern Apennines to the Calabrian arc or along the northern Apennines, follow the curvature of the arcs and are not associated to a stress regime variation.
    Description: Published
    Description: (B10410)
    Description: partially_open
    Keywords: active stress ; earthquakes ; borehole breakouts ; crust and lithosphere ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 35
    Publication Date: 2017-04-04
    Description: We defend the two statements of ours in Michelini and Lomax [2004] about Zhang and Thurber [2003] regarded by Thurber and Zhang as incorrect and misleading.
    Description: Published
    Description: partially_open
    Keywords: earthquake location ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 36
    Publication Date: 2017-04-04
    Description: The 1995–2004 seismicity in the Gargano Promontory (hereafter GP) foreland at the transition zone between Southern and Northern Apennine belts (Italy) is analyzed with the aim to put constraints on the present-day kinematics of this key-area of the foreland. The spatial distribution of earthquakes and 54 calculated focal mechanisms show that that the main GP ruptures develop along E-W striking, right-lateral strike-slip faults and NW- SE, normal to left-lateral second-order faults that move in response to a prevailing NW-SE compression (i.e. NE-SW extension). Tacking into account the depth of the relocated seismicity and the available geological information, we propose that the GP shear zone represents an E-W striking, major crustal discontinuity separating sectors of the foreland that move in response to the higher, northeastward propagation velocity of the thrust front of the Northern Apennines with respect to that of the Southern Apennines.
    Description: Published
    Description: open
    Keywords: Seismicity ; seismotectonics ; geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous
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  • 37
    Publication Date: 2021-05-19
    Description: The low frequency sea surface temperature (SST) variability in the North Atlantic is studied using the Center for Ocean-Land-Atmosphere Studies (COLA) anomaly coupled general circulation model. The main focus is placed on the relative roles of stable and unstable coupled feedbacks in inducing the low frequency SST variability in various regions of the North Atlantic. To examine this question, a recently developed coupling technique, interactive ensembles, is applied to reduce the strength of “weather noise” in the model and isolate the atmospheric feedback to boundary forcing.
    Description: Published
    Keywords: Sea surface temperature
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed , Article
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  • 38
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 20 (2005): PA4011, doi:10.1029/2005PA001150.
    Description: Monthly samples of stratified plankton tows taken from the slope waters off Cape Cod nearly 25 years ago are used to describe the seasonal succession of planktonic foraminifera and their oxygen isotope ratios. The 15°C seasonal cycle of sea surface temperature (SST) accounts for a diverse mixture of tropical to subpolar species. Summer samples include various Globigerinoides and Neogloboquadrina dutertrei, whereas winter and early spring species include Globigerina bulloides and Neogloboquadrina pachyderma (dextral). Globorotalia inflata lives all year but at varying water depths. Compared with the fauna in 1960–1961 (described by R. Cifelli), our samples seem warmer. Because sea surface salinity varies little during the year, δ18O is mostly a function of SST. Throughout the year, there are always species present with δ18O close to the calculated isotopic equilibrium of carbonate with surface seawater. This raises the possibility that seasonality can be estimated directly from the range of δ18O in a sediment sample provided that the δ18O-salinity relationship is the same as today.
    Description: Funding was provided by NSF grant OCE-0117149.
    Keywords: Plankton tow ; Foraminifera ; Stable isotopes
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  • 39
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
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  • 40
    Publication Date: 2022-05-25
    Description: Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.
    Description: Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.
    Description: This work was supported by NIH grant RO1 RR07861, the NASA Astrobiology Institute grant NCC2-1054, grants from the Edward Mallinckrodt, Jr Foundation and the Sinsheimer Foundation, and NSF grants NSF DBI - 9984882 and NSF IIS - 9996304.
    Keywords: Escherichia coli K-12
    Repository Name: Woods Hole Open Access Server
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  • 41
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 19 (2005): GB4006, doi:10.1029/2004GB002445.
    Description: We report iron measurements for water column and aerosol samples collected in the Sargasso Sea during July-August 2003 (summer 2003) and April-May 2004 (spring 2004). Our data reveal a large seasonal change in the dissolved iron (dFe) concentration of surface waters in the Bermuda Atlantic Time-series Study region, from ∼1–2 nM in summer 2003, when aerosol iron concentrations were high (mean 10 nmol m−3), to ∼0.1–0.2 nM in spring 2004, when aerosol iron concentrations were low (mean 0.64 nmol m−3). During summer 2003, we observed an increase of ∼0.6 nM in surface water dFe concentrations over 13 days, presumably due to eolian iron input; an estimate of total iron deposition over this same period suggests an effective solubility of 3–30% for aerosol iron. Our summer 2003 water column profiles show potentially growth-limiting dFe concentrations (0.02–0.19 nM) coinciding with a deep chlorophyll maximum at 100–150 m depth, where phytoplankton biomass is typically dominated by Prochlorococcus during late summer.
    Description: Funding for this work was provided by the U.S. National Science Foundation (OCE-0222053 to P. N. S., OCE-0222046 to T. M. C., and OCE-0241310 to D. J. M.), the U.S. National Aeronautics and Space Administration (NAG5-11265 to D. J. M.), the Australian Research Council (DP0342826 to A. R. B.), the Antarctic Climate and Ecosystems Cooperative Research Center, and the H. Unger Vetlesen Foundation.
    Keywords: Atmospheric deposition ; Iron ; Sargasso Sea
    Repository Name: Woods Hole Open Access Server
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  • 42
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 32 (2005): L19304, doi:10.1029/2005GL023457.
    Description: The effect of rheology on the evolution of the slab-tip during subduction initiation is analyzed using 2-D numerical flow models. Experimentally determined flow laws have both strong temperature- and stress-dependence, which leads to large local variations in viscosity with direct consequences for subduction initiation. We find that models with Newtonian viscosity lead to flat or coupled subduction due to hydrodynamic stresses that pull the slab-tip up towards the overriding plate. Non-Newtonian rheology reduces these hydrodynamic stresses by decreasing the wedge viscosity and the slab coupling to wedge-corner flow, rendering the small negative-slab buoyancy of the slab-tip sufficient to maintain its dip during the early stages of subduction.
    Keywords: Dynamics of lithosphere and mantle ; Plate boundary ; Rheology: mantle ; Subduction zone processes
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  • 43
    facet.materialart.
    Unknown
    American Geophysical Union
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q04009, doi:10.1029/2004GC000768.
    Description: The Hawaii-2 Observatory (H2O) is an excellent site for studying the source regions and propagation of microseisms since it is located far from shorelines and shallow water. During Leg 200 of the Ocean Drilling Program, the officers of the JOIDES Resolution took wind and wave measurements for comparison with double-frequency (DF) microseism data collected at nearby H2O. The DF microseism band can be divided into short period and long period bands, SPDF and LPDF, respectively. Comparison of the ship’s weather log with the seismic data in the SPDF band from about 0.20 to 0.45 Hz shows a strong correlation of seismic amplitude with wind speed and direction, implying that the energy reaching the ocean floor is generated locally by ocean gravity waves. Near-shore land seismic stations see similar SPDF spectra, also generated locally by wind seas. At H2O, SPDF microseism amplitudes lag sustained changes in wind speed and direction by several hours, with the lag increasing with wave period. This lag may be associated with the time necessary for the development of opposing seas for DF microseism generation. Correlation of swell height above H2O with the LPDF band from 0.085 to 0.20 Hz is often poor, implying that a significant portion of this energy originates at distant locations. Correlation of the H2O seismic data with NOAA buoy data, with hindcast wave height data from the North Pacific, and with seismic data from mainland and island stations, defines likely source areas of the LPDF signals. Most of the LPDF energy at H2O appears to be generated by high amplitude storm waves impacting long stretches of coastline nearly simultaneously, and the Hawaiian Islands appear to be a significant source of LPDF energy in the North Pacific when waves arrive from particular directions. The highest DF levels observed at mid-ocean site H2O occur in the SPDF band when two coincident nearby storm systems develop. Mid-ocean generated DF microseisms are not observed at interior continental sites, indicating high attenuation of these signals. At near-coastal seismic stations, both SPDF and LPDF microseism levels are generally dominated by local generation at nearby shorelines.
    Description: This work was supported by the U.S. Science Support Program (User Reference: 418920-BA372; Task Order F001602) associated with the Ocean Drilling Program and is sponsored by the National Science Foundation and the Joint Oceanographic Institutions, Inc. Additional support was provided by the California Energy Commission and the California Department of Boating and Waterways as part of their program to improve boating facilities, access, safety, and education. Support for Ralph Stephen was also provided by the National Science Foundation under Grant #OCE-0424633.
    Keywords: Microseisms ; Ocean gravity waves ; Seismic noise ; Rayleigh wave attenuation ; Oceanic Q ; Hawaii-2 Observatory
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  • 44
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 20 (2005): PA4005, doi:10.1029/2004PA001061.
    Description: Detailed deglacial and Holocene records of planktonic δ18O and Mg/Ca–based sea surface temperature (SST) from the Okinawa Trough suggest that at ∼18 to 17 thousand years before present (kyr B.P.), late spring/early summer SSTs were approximately 3°C cooler than today, while surface waters were up to 1 practical salinity unit saltier. These conditions are consistent with a weaker influence of the summer East Asian Monsoon (EAM) than today. The timing of suborbital SST oscillations suggests a close link with abrupt changes in the EAM and North Atlantic climate. A tropical influence, however, may have resulted in subtle decoupling between the North Atlantic and the Okinawa Trough/EAM during the deglaciation. Okinawa Trough surface water trends in the Holocene are consistent with model simulations of an inland shift of intense EAM precipitation during the middle Holocene. Millennial-scale alternations between relatively warm, salty conditions and relatively cold, fresh conditions suggest varying influence of the Kuroshio during the Holocene.
    Description: Funding for this research was provided by NSFC (grants 40106006 and 40206007), SKLLQG (grant LLQG0204), and the NSF (OCE-020776 to DWO). Y.S.'s visit to WHOI was supported via a NSF START Fellowship.
    Keywords: Okinawa Trough ; Deglaciation ; Holocene ; Kuroshio Current ; East Asian monsoon ; Mg/Ca ; Oxygen isotopes ; Foraminifera
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  • 45
    Publication Date: 2022-05-25
    Description: This paper is not subject to U.S. copyright. Published in 2005 by the American Geophysical Union. The definitive version was published in Journal of Geophysical Research 110 (2005): B06404, doi:10.1029/2004JB003459.
    Description: The Puerto Rico trench exhibits great water depth, an extremely low gravity anomaly, and a tilted carbonate platform between (reconstructed) elevations of +1300 m and −4000 m. I argue that these features are manifestations of large vertical movements of a segment of the Puerto Rico trench, its forearc, and the island of Puerto Rico that took place 3.3 m.y. ago over a time period as short as 14–40 kyr. I explain these vertical movements by a sudden increase in the slab's descent angle that caused the trench to subside and the island to rise. The increased dip could have been caused by shearing or even by a complete tear of the descending North American slab, although the exact nature of this deformation is unknown. The rapid (14–40 kyr) and uniform tilt along a 250 km long section of the trench is compatible with scales of mantle flow and plate bending. The proposed shear zone or tear is inferred from seismic, morphological, and gravity observations to start at the trench at 64.5°W and trend southwestwardly toward eastern Puerto Rico. The tensile stresses necessary to deform or tear the slab could have been generated by increased curvature of the trench following a counterclockwise rotation of the upper plate and by the subduction of a large seamount.
    Keywords: Dynamic topography ; Slab tear ; Puerto Rico trench ; Caribbean plate ; Challenger Deep ; Seamount subduction
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  • 46
    Publication Date: 2022-05-25
    Description: © 2005 Serres and Riley. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 6 (2005): 33, doi:10.1186/1471-2164-6-33.
    Description: Background: Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results: Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion: The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms.
    Description: The research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-01ER63202 and by National Aeronautics and Space Administration Astrobiology grant NCC2-1054.
    Keywords: Escherichia coli ; Multimodular proteins
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  • 47
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
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  • 48
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    Unknown
    American Geophysical Union
    In:  EPIC3Tectonics, American Geophysical Union, 24(TC4020), pp. 1-19
    Publication Date: 2019-07-17
    Description: Employing surface mapping of syntectonic sediments, interpretation of industry reflection-seismic profiles, gravity data, and isotopic age dating, we reconstruct the tectonic evolution of the southern Altiplano (∼20–22°S) between the cordilleras defining its margins. The southern Altiplano crust was deformed between the late Oligocene and the late Miocene with two main shortening stages in the Oligocene (33–27 Ma) and middle/late Miocene (19–8 Ma) that succeeded Eocene onset of shortening at the protoplateau margins. Shortening rates in the southern Altiplano ranged between 1 and 4.7 mm/yr with maximum rates in the late Miocene. Summing rates for the southern Altiplano and the Eastern Cordillera, we observe an increase from Eocene times to the late Oligocene to some 8 mm/yr, followed by fluctuation around this value during the Miocene prior to shutoff of deformation at 7–8 Ma and transfer of active shortening to the sub-Andean fold and thrust belt. Shortening inverted early Tertiary graben and half graben systems and was partitioned in three fault systems in the western, central, and eastern Altiplano, respectively. The east vergent fault systems of the western and central Altiplano were synchronously active with the west vergent Altiplano west flank fault system. From these data and from section balancing, we infer a kinematically linked western Altiplano thrust belt that accumulated a minimum of 65 km shortening. Evolution of this belt contrasts with the Eastern Cordillera, which reached peak shortening rates (8 mm/yr) in between the above two stages. Hence local shortening rates fluctuated across the plateau superimposed on a general trend of increasing bulk rate with no trend of lateral propagation. This observation is repeated at the shorter length and time scales of individual growth structures that show evidence for periods of enhanced local rates at a timescale of 1–3 Myr. We interpret this irregular pattern of deformation to reflect a plateau-style of shortening related to a self-organized state of a weak crust in the central South American back arc with a fault network that fluctuated around the critical state of mechanical failure. Tuning of this state may have occurred by changes in plate kinematics, during the Paleogene, initially reactivating crustal weak zones and by thermal weakening of the crust with active magmatism mainly in the Neogene stage.
    Repository Name: EPIC Alfred Wegener Institut
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  • 49
    Publication Date: 2022-05-26
    Description: © 2001 Samuel et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. The definitive version was published in BMC Microbiology 1 (2001): 4, doi:10.1186/1471-2180-1-4.
    Description: Many bacteria swim by rotating helical flagellar filaments. Waterbury et al. discovered an exception, strains of the cyanobacterium Synechococcus that swim without flagella or visible changes in shape. Other species of cyanobacteria glide on surfaces. The hypothesis that Synechococcus might swim using traveling surface waves prompted this investigation. Results Using quick-freeze electron microscopy, we have identified a crystalline surface layer that encloses the outer membrane of the motile strain Synechococcus sp. WH8113, the components of which are arranged in a rhomboid lattice. Spicules emerge in profusion from the layer and extend up to 150 nm into the surrounding fluid. These spicules also send extensions inwards to the inner cell membrane where motility is powered by an ion-motive force. Conclusion The envelope structure of Synechococcus sp. WH8113 provides new constraints on its motile mechanism. The spicules are well positioned to transduce energy at the cell membrane into mechanical work at the cell surface. One model is that an unidentified motor embedded in the cell membrane utilizes the spicules as oars to generate a traveling wave external to the surface layer in the manner of ciliated eukaryotes.
    Description: ADTS was supported by the Rowland Institute for Science and is an Amgen Fellow of the Life Sciences Research Foundation.
    Keywords: Synechococcus sp. ; Motile mechanism
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  • 50
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    Unknown
    American Geophysical Union
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q11007, doi:10.1029/2005GC000975.
    Description: Binary mixing is one of the most common models used to explain variations in geochemical data. When the data being modeled are ratios of elements or isotopes, the mixtures follow hyperbolic trends with curvatures that depend on a cross-term representing the relative concentrations of the elements or isotopes under consideration in the mixing components. The inverse problem of estimating mixing components is difficult because of the cross-term in the hyperbolic equation, which requires the use of nonlinear methods to estimate the mixing parameters, and because the end-member ratio values are intrinsically underdetermined unless the mixing proportions of the samples are known a priori, which is not generally the case. I use maximum likelihood methods to address these issues and derive a general inversion for binary mixing model parameters from ratio-ratio data. I apply the method to synthetic test data and a global compilation of 230Th/232Th versus 87Sr/86Sr data from oceanic basalts and find that the concentration ratio parameter is well-constrained by the inversion while the end-member ratio estimates are strongly dependent on the initial guesses used to start the iterative solver, reflecting the underdetermined nature of the end-member positions on the mixing hyperbola. Monte Carlo methods that randomly perturb the initial guesses can be used to improve error estimates, and goodness-of-fit statistics can be used to assess the performance of the mixing model for explaining data variance.
    Keywords: Inverse theory ; Isotopes ; Mixing
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  • 51
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 295-318 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 267-294 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 153-171 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 91-118 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
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    Annual Review of Materials Research 35 (2005), S. 127-142 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The preparation of skeletal catalysts is considered, with particular reference to the preparation of skeletal nickel and skeletal copper. Skeletal catalysts have physical properties that are highly desired for some industrial processes, and the means of controlling these properties to optimize performance is reviewed. The preparation can be affected by the initial alloy composition, the quenching process, the leaching procedure, aging and by the addition of promoters. These processes may affect either or both the chemical and physical characteristics of the catalysts. Preparation procedures need to be adjusted for individual reactions if optimal performance is required. The effect of the preparation conditions on the structure and catalytic performance of these systems is reviewed.
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    Annual Review of Materials Research 35 (2005), S. 167-207 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We review here the theory of the early stages of oxidation of the (110) surface of Ni1x Alx, based on ab initio calculations using a plane-wave pseudopotential method. The clean surface and several oxidized surfaces have been investigated, with oxygen coverages up to 2ML of oxygen (1ML = 3 O atoms per 2 surface Al atoms). The theory to date is a description in terms of equilibrium thermodynamics, with a comparison of the free energies of several surfaces of different composition, implemented at the atomic scale. Three environmental parameters are singled out as control variables in this treatment, namely the alloy composition x (assumed to be near 0.5), the temperature T and the partial pressure of oxygen pO2. With certain reasonable approximations an analytic formula for the surface energy ?? is derived in terms of these variables and some constants that are calculated ab initio together with others that are derived from experimental thermodynamic tables. At oxygen pressures just above the threshold for bulk oxidation of NiAl, the calculations explain the observed formation of a thin film of alumina in place of NiAl surface layers, with the consequent dissolution of Ni into the bulk. Ab initio calculations illustrate how the energetics of supplying Al to the surface depends on bulk stoichiometry, which alters the relative stability of different surface oxidation states so as to favour oxidation more if the alloy is Al-rich than if it is Ni-rich.
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    Annual Review of Materials Research 35 (2005), S. 315-350 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: There is a pressing need for cleaner fuels (free or aromatics and of minimal sulfur content) or ones that convert chemical energy directly to electricity, silently and without production of noxious oxides and particulates; chemical, petrochemical and pharmaceutical processes that may be conducted in a one-step, solvent-free manner and that use air as the preferred oxidant; and industrial processes that minimize consumption of energy, production of waste, or the use of corrosive, explosive, volatile, and nonbiodegradable materials. All these needs and other desiderata, such as the in situ production and containment of aggressive and hazardous reagents, and the avoidance of use of ecologically harmful elements, may be achieved by designing the appropriate heterogeneous inorganic catalyst, which ideally should be cheap, readily preparable and fully characterizable, preferably under in situ reaction conditions. A range of nanoporous and nanoparticle catalysts that meet most of the stringent demands of sustainable development and responsible (clean) technology is described. Specific examples that are highlighted include the production of adipic acid (precursor of polyamides and urethanes) without the use of concentrated nitric acid nor the production of greenhouse gases such as nitrous oxide; the production of caprolactam (precursor of nylon) without the use of oleum and hydroxylamine sulfate; and the terminal oxyfunctionalization of linear alkanes in air. The topic of biocatalysis and sustainable development is also briefly discussed for the epoxidation of terpenes and fatty acid methyl esters; for the generation of polymers, polylactides, and polyesters; and for the production of 1,3-propanediol from corn.
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    Annual Review of Materials Research 35 (2005), S. 351-395 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review covers the synthesis, characterization, and physico-chemical properties of microporous and mesoporous aluminophosphates and silicoaluminophosphates molecular sieves. Particular emphasis is given to the materials that have found applications as acid catalysts. We consider the evolution of the synthesis procedures from the first discoveries to the current methodologies and give perspectives for new possible synthesis strategies. Emphasis is given to the use of specially prepared precursors/reactants designed for the use as molecular sieves. Experimental (especially MAS-NMR and FTIR spectroscopy) and theoretical approaches to the description of the Si insertion into the ALPO framework and to the acidic properties of SAPOs and MeAPSOs materials are discussed.
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    Annual Review of Materials Research 35 (2005), S. 51-73 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The diffusion-multiple approachĐ??the creation of composition gradients and intermetallic phases by long-term annealing of junctions of three or more phases/alloysĐ??enables the generation of a large number of phases and compositions for efficient mapping of phase diagrams, phase properties, and kinetics. With an efficiency much higher than that of a conventional approach, many critical materials data, which otherwise would be too time-consuming and expensive to acquire, can be obtained and employed to accelerate alloy design. The critical data for structural materials design include phase diagrams, diffusion coefficients, precipitation kinetics, solution-strengthening effects, and precipitation-strengthening effects. All these data can be obtained from diffusion multiples. The combination of the diffusion-multiple approach with the CALPHAD approach can impact computational design of structural materials. The diffusion-multiple approach can also be applied to combinatorial screening of functional materials having unique physical, chemical, or other properties when micro-scale measurement techniques are available for these properties. Examples are shown to illustrate the progress made to date on applying the diffusion-multiple approach to accelerated design/discovery of materials.
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    Annual Review of Materials Research 35 (2005), S. 505-538 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Renewable energy resources, of which wind energy is prominent, are part of the solution to the global energy problem. Wind turbine and the rotorblade concepts are reviewed, and loadings by wind and gravity as important factors for the fatigue performance of the materials are considered. Wood and composites are discussed as candidates for rotorblades. The fibers and matrices for composites are described, and their high stiffness, low density, and good fatigue performance are emphasized. Manufacturing technologies for composites are presented and evaluated with respect to advantages, problems, and industrial potential. The important technologies of today are prepreg (pre-impregnated) technology and resin infusion technology. The mechanical properties of fiber composite materials are discussed, with a focus on fatigue performance. Damage and materials degradation during fatigue are described. Testing procedures for documentation of properties are reviewed, and fatigue loading histories are discussed, together with methods for data handling and statistical analysis of (large) amounts of test data. Future challenges for materials in the field of wind turbines are presented, with a focus on thermoplastic composites, new structural materials concepts, new structural design aspects, structural health monitoring, and the coming trends and markets for wind energy.
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    Annual Review of Materials Research 35 (2005), S. 397-426 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review illustrates how catalytically active molecular structures are created on oxide surfaces by attachment of metal complexes with subsequent structural transformation and molecular imprinting on the surfaces. Also discussed is how the designed surfaces are characterized in situ by physical techniques including conventional and time-resolved X-ray absorption fine structure. The structural transformation and molecular imprinting for attached metal complexes can provide a new class of catalytic materials with a high complexity for selective catalysis including shape-selective and asymmetric catalysis.
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    Annual Review of Materials Research 35 (2005), S. 29-49 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper describes the use of extended X-ray absorption fine structure spectroscopy (EXAFS) to examine the structure of molten salts and ionic liquids and species dissolved in them. The EXAFS theory is briefly described as are the methods by which EXAFS of these systems can be studied. A range of applications have used EXAFS to investigate the structure of metallic species in ionic liquids from extraction studies to catalysts. The area of structural investigations of ionic liquids is still being developed, although growing rapidly, whereas the structure of molten salts has been studied using EXAFS in more detail.
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    Annual Review of Materials Research 35 (2005), S. 539-569 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In the nanoscience era, the properties of many exciting new materials and devices will depend on the details of their composition down to the level of single atoms. Thus the characterization of the structure and electronic properties of matter at the atomic scale is becoming ever more vital for economic and technological as well as for scientific reasons. The combination of atomic-resolution Z-contrast scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) represents a powerful method to link the atomic and electronic structure to macroscopic properties, allowing materials, nanoscale systems, and interfaces to be probed in unprecedented detail. Z-contrast STEM uses electrons that have been scattered to large angles for imaging. The relative intensity of each atomic column is roughly proportional to Z2, where Z is the atomic number. Recent developments in correcting the aberrations of the lenses in the electron microscope have pushed the achievable spatial resolution and the sensitivity for imaging and spectroscopy in the STEM into the sub-A??ngstrom (sub-A??) regime, providing a new level of insight into the structure/property relations of complex materials. Images acquired with an aberration-corrected instrument show greatly improved contrast. The signal-to-noise ratio is sufficiently high to allow sensitivity even to single atoms in both imaging and spectroscopy. This is a key achievement because the detection and measurement of the response of individual atoms has become a challenging issue to provide new insight into many fields, such as catalysis, ceramic materials, complex oxide interfaces, or grain boundaries. In this article, the state-of-the-art for the characterization of all of these different types of materials by means of aberration-corrected STEM and EELS are reviewed.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 47-79 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 191-218 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, species identity, and the presence of keystone species have a strong impact on decomposition, whereas the importance of diversity within functional groups is not clear at present. In conclusion, litter species and decomposer diversity can significantly influence carbon and nutrient turnover rates; however, no general or predictable pattern has emerged. Proposed mechanisms for diversity effects need confirmation and a link to functional traits for a comprehensive understanding of how biodiversity interacts with decomposition processes and the consequences of ongoing biodiversity loss for ecosystem functioning.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 445-466 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 295-317 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: One of the greatest mass extinctions in Earth's history occurred at the end of the Cretaceous era, sixty-five million years (Myr) ago. Considerable evidence indicates that the impact of a large asteroid or comet was the ultimate cause of this extraordinary event. At the time of mass extinction, the organic flux to the deep sea collapsed, and production of calcium carbonate by marine plankton radically declined. These biogeochemical processes did not fully recover for a few million years. The drastic decline and long lag in final recovery of these processes are most simply explained as consequences of open-ocean ecosystem alteration by the mass extinction. If this explanation is correct, the extent and timing of marine biogeochemical recovery from the end-Cretaceous event was ultimately contingent on the extent and timing of open-ocean ecosystem recovery. The biogeochemical recovery may in turn have created new evolutionary opportunities for a diverse array of marine organisms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 1-21 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Variation in the subtle differences between right and left sides of bilateral characters, or fluctuating asymmetry (FA), has long been considered to be primarily environmental in origin, and this has promoted its use as a measure of developmental instability (DI) in populations. There is little evidence for specific genes that govern FA per se. Numerous studies show that FA levels in various characters are influenced by dominance and especially epistatic interactions among genes. An epistatic genetic basis for FA may complicate its primary use in comparisons of DI levels in outbred or wild populations subjected or not subjected to various environmental stressors. Although the heritability of FA typically is very low or zero, epistasis can generate additive genetic variation for FA that may allow it to evolve especially in populations subjected to bottlenecks, hybridizations, or periods of rapid environmental changes caused by various stresses.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 419-444 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Understanding and predicting the dynamics of multispecies systems generally require estimates of interaction strength among species. Measuring interaction strength is difficult because of the large number of interactions in any natural system, long-term feedback, multiple pathways of effects between species pairs, and possible nonlinearities in interaction-strength functions. Presently, the few studies that extensively estimate interaction strength suggest that distributions of interaction strength tend to be skewed toward few strong and many weak interactions. Modeling studies indicate that such skewed patterns tend to promote system stability and arise during assembly of persistent communities. Methods for estimating interaction strength efficiently from traits of organisms, such as allometric relationships, show some promise. Methods for estimating community response to environmental perturbations without an estimate of interaction strength may also be of use. Spatial and temporal scale may affect patterns of interaction strength, but these effects require further investigation and new multispecies modeling frameworks. Future progress will be aided by development of long-term multispecies time series of natural communities, by experimental tests of different methods for estimating interaction strength, and by increased understanding of nonlinear functional forms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 219-242 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 267-294 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: It has often been argued that conserving biodiversity is necessary for maintaining ecosystem functioning. We critically evaluate the current evidence for this argument. Although there is substantial evidence that diversity is able to affect function, particularly for plant communities, it is unclear if these patterns will hold for realistic scenarios of extinctions, multitrophic communities, or larger spatial scales. Experiments are conducted at small spatial scales, the very scales at which diversity tends to increase owing to exotics. Stressors may affect function by many pathways, and diversity-mediated effects on function may be a minor pathway, except in the case of multiple-stressor insurance effects. In general, the conservation case is stronger for stability measures of function than stock and flux measures, in part because it is easier to attribute value unambiguously to stability and in part because stock and flux measures of functions are anticipated to be more affected by multitrophic dynamics. Nor is biodiversity-ecosystem function theory likely to help conservation managers in practical decisions, except in the particular case of restoration. We give recommendations for increasing the relevance of this area of research for conservation.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 597-620 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.
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    Annual Review of Fluid Mechanics 37 (2005), S. 357-392 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The objective of this review is to critically assess the different approaches developed in recent years to understand the dynamics of open flows such as mixing layers, jets, wakes, separation bubbles, boundary layers, and so on. These complex flows develop in extended domains in which fluid particles are continuously advected downstream. They behave either as noise amplifiers or as oscillators, both of which exhibit strong nonlinearities ( Huerre & Monkewitz 1990 ). The local approach is inherently weakly nonparallel and it assumes that the basic flow varies on a long length scale compared to the wavelength of the instability waves. The dynamics of the flow is then considered as a superposition of linear or nonlinear instability waves that, at leading order, behave at each streamwise station as if the flow were homogeneous in the streamwise direction. In the fully global context, the basic flow and the instabilities do not have to be characterized by widely separated length scales, and the dynamics is then viewed as the result of the interactions between Global modes living in the entire physical domain with the streamwise direction as an eigendirection. This second approach is more and more resorted to as a result of increased computational capability. The earlier review of Huerre & Monkewitz (1990) emphasized how local linear theory can account for the noise amplifier behavior as well as for the onset of a Global mode. The present survey first adopts the opposite point of view by demonstrating how fully global theory accounts for the noise amplifier behavior of open flows. From such a perspective, there is strong emphasis on the very peculiar nonorthogonality of linear Global modes, which in turn allows a novel interpretation of recent numerical simulations and experimental observations. The nonorthogonality of linear Global modes also imposes severe constraints on the extension of linear global theory to the fully nonlinear re??gime. When the flow is weakly nonparallel, this limitation is so severe that the linear Global mode theory is of little help. It is then much more appropriate to develop a fully nonlinear formulation involving the presence of a front separating the base state region from the bifurcated state region.
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    Annual Review of Fluid Mechanics 37 (2005), S. 129-149 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We review the fluid mechanics and rheology of dense suspensions, emphasizing investigations of microstructure and total stress. "Dense" or "highly concentrated" suspensions are those in which the average particle separation distance is less than the particle radius. For these suspensions, multiple-body interactions as well as two-body lubrication play a significant role and the rheology is non-Newtonian. We include investigations of multimodal suspensions, but not those of suspensions with dominant nonhydrodynamic interactions. We consider results from both physical experiments and computer simulations and explore scaling theories and the development of constitutive equations.
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    Annual Review of Fluid Mechanics 37 (2005), S. 239-261 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Annual Review of Fluid Mechanics 37 (2005), S. 23-42 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: George Gabriel Stokes died just over 100 years ago, and it has been more than 150 years since he published his great 1847 paper on water waves. The work of Stokes' precursors, which informed his early publications of 1842Đ??50, is described in the previous volume of the Annual Review of Fluid Mechanics ( Craik 2004 ). Here I examine Stokes' papers and letters concerning water waves.
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    Annual Review of Fluid Mechanics 37 (2005), S. 295-328 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Chaotic advection and, more generally, ideas from dynamical systems, have been fruitfully applied to a diverse, and varied, collection of mixing and transport problems arising in engineering applications over the past 20 years. Indeed, the "dynamical systems approach" was developed, and tested, to the point where it can now be considered a standard tool for understanding mixing and transport issues in many disciplines. This success for engineering-type flows motivated an effort to apply this approach to transport and mixing problems in geophysical flows. However, there are fundamental difficulties arising in this endeavor that must be properly understood and overcome. Central to this approach is that the starting point for analysis is a velocity field (i.e., the "dynamical system"). In many engineering applications this can be obtained sufficiently accurately, either analytically or computationally, so that it describes particle trajectories for the actual flow. However, in geophysical flows (and we concentrate here almost exclusively on oceanographic flows), the wide range of dynamically significant time and length scales makes the justification of any velocity field, in the sense of reproducing particle trajectories for the actual flow, a much more difficult matter. Nevertheless, the case for this approach is compelling due to the advances in observational capabilities in oceanography (e.g., drifter deployments, remote sensing capabilities, satellite imagery, etc.), which reveal space-time structures that are highly suggestive of the structures one visualizes in the global, geometrical study of dynamical systems theory. This has been pursued in recent years through a combination of laboratory studies, kinematic models, and dynamically consistent models that have all been compared with observational data. During the course of these studies it has become apparent that a new type of dynamical system is necessary to consider in these studies (i.e., a finite time, aperiodically time-dependent velocity field defined as a data set), which requires the development of new analytical and computational tools, as well as the necessity to discard some of the standard ideas and results from dynamical systems theory. In this article we review a number of the key developments to date in this young, but rapidly developing, area at the interface between geophysical fluid dynamics and applied and computational mathematics. We also describe the wealth of new directions for research that this approach unlocks.
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    Annual Review of Genetics 39 (2005), S. 359-407 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Life is the interplay between structure and energy, yet the role of energy deficiency in human disease has been poorly explored by modern medicine. Since the mitochondria use oxidative phosphorylation (OXPHOS) to convert dietary calories into usable energy, generating reactive oxygen species (ROS) as a toxic by-product, I hypothesize that mitochondrial dysfunction plays a central role in a wide range of age-related disorders and various forms of cancer. Because mitochondrial DNA (mtDNA) is present in thousands of copies per cell and encodes essential genes for energy production, I propose that the delayed-onset and progressive course of the age-related diseases results from the accumulation of somatic mutations in the mtDNAs of post-mitotic tissues. The tissue-specific manifestations of these diseases may result from the varying energetic roles and needs of the different tissues. The variation in the individual and regional predisposition to degenerative diseases and cancer may result from the interaction of modern dietary caloric intake and ancient mitochondrial genetic polymorphisms. Therefore the mitochondria provide a direct link between our environment and our genes and the mtDNA variants that permitted our forbears to energetically adapt to their ancestral homes are influencing our health today.
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    Annual Review of Genetics 39 (2005), S. 69-94 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Cell-cycle control of transcription seems to be a universal feature of proliferating cells, although relatively little is known about its biological significance and conservation between organisms. The two distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have provided valuable complementary insight into the regulation of periodic transcription as a function of the cell cycle. More recently, genome-wide studies of proliferating cells have identified hundreds of periodically expressed genes and underlying mechanisms of transcriptional control. This review discusses the regulation of three major transcriptional waves, which roughly coincide with three main cell-cycle transitions (initiation of DNA replication, entry into mitosis, and exit from mitosis). I also compare and contrast the transcriptional regulatory networks between the two yeasts and discuss the evolutionary conservation and possible roles for cell cycle-regulated transcription.
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    Annual Review of Genetics 39 (2005), S. 23-46 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Three processes alter genomic sequence and structure at the immunoglobulin genes of B lymphocytes: gene conversion, somatic hypermutation, and class switch recombination. Though the molecular signatures of these processes differ, they occur by a shared pathway which is induced by targeted DNA deamination by a B cellĐ??specific factor, activation induced cytidine deaminase (AID). Ubiquitous factors critical for DNA repair carry out all downstream steps, creating mutations and deletions in genomic DNA. This review focuses on the genetic and biochemical mechanisms of diversification of immunoglobulin genes.
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    Annual Review of Genetics 39 (2005), S. 561-613 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The basic vertebrate body plan of the zebrafish embryo is established in the first 10 hours of development. This period is characterized by the formation of the anterior-posterior and dorsal-ventral axes, the development of the three germ layers, the specification of organ progenitors, and the complex morphogenetic movements of cells. During the past 10 years a combination of genetic, embryological, and molecular analyses has provided detailed insights into the mechanisms underlying this process. Maternal determinants control the expression of transcription factors and the location of signaling centers that pattern the blastula and gastrula. Bmp, Nodal, FGF, canonical Wnt, and retinoic acid signals generate positional information that leads to the restricted expression of transcription factors that control cell type specification. Noncanonical Wnt signaling is required for the morphogenetic movements during gastrulation. We review how the coordinated interplay of these molecules determines the fate and movement of embryonic cells.
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    Annual Review of Genetics 39 (2005), S. 481-501 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The zebrafish (Danio rerio) has emerged as an ideal organism for the study of hematopoiesis, the process by which all the cellular elements of the blood are formed. These elements, including erythrocytes, granulocytes, monocytes, lymphocytes, and thrombocytes, are formed through complex genetic signaling pathways that are highly conserved throughout phylogeny. Large-scale forward genetic screens have identified numerous blood mutants in zebrafish, helping to elucidate specific signaling pathways important for hematopoietic stem cells (HSCs) and the various committed blood cell lineages. Here we review both primitive and definitive hematopoiesis in zebrafish, discuss various genetic methods available in the zebrafish model for studying hematopoiesis, and describe some of the zebrafish blood mutants identified to date, many of which have known human disease counterparts.
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    Annual Review of Genetics 39 (2005), S. 339-358 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The moss Physcomitrella patens, like seed plants, shows alternation of generations, but its gametophyte, the haploid phase of the life cycle, is dominant, making it ideal for genetic studies. Crosses show direct segregations, so F2 or test crosses are unnecessary. Mutagenesis yields mutants, the phenotype of which is directly evident. Haploid tissue can be propagated vegetatively, allowing the maintenance of mutants blocked early in development. Protoplasts, isolated from filamentous gametophytic tissue, regenerate directly into filamentous tissue, providing an abundant supply of single haploid cells for transformation. Recombination occurs at a high frequency between genomic sequences in transforming DNA and the corresponding chromosomal sequences, allowing precise inactivation or modification of genes. RNAi technology allows the inactivation of the expression of gene families and the partial knockdown of essential genes. Over 100,000 ESTs have been sequenced and annotated, and sequencing of the genome should be completed by the end of 2005.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 319-349 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Progress in experimental and theoretical biology is likely to provide us with the opportunity to assemble detailed predictive models of mammalian cells. Using a functional format to describe the organization of mammalian cells, we describe current approaches for developing qualitative and quantitative models using data from a variety of experimental sources. Recent developments and applications of graph theory to biological networks are reviewed. The use of these qualitative models to identify the topology of regulatory motifs and functional modules is discussed. Cellular homeostasis and plasticity are interpreted within the framework of balance between regulatory motifs and interactions between modules. From this analysis we identify the need for detailed quantitative models on the basis of the representation of the chemistry underlying the cellular process. The use of deterministic, stochastic, and hybrid models to represent cellular processes is reviewed, and an initial integrated approach for the development of large-scale predictive models of a mammalian cell is presented.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 1-33 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: In this review I describe the several stages of my research career, all of which were driven by a desire to understand the basic mechanisms responsible for the complex and beautiful organization of the eukaryotic cell. I was originally trained as an electron microscopist in Argentina, and my first major contribution was the introduction of glutaraldehyde as a fixative that preserved the fine structure of cells, which opened the way for cytochemical studies at the EM level. My subsequent work on membrane-bound ribosomes illuminated the process of cotranslational translocation of polypeptides across the ER membrane and led to the formulation, with Gunter Blobel, of the signal hypothesis. My later studies with many talented colleagues contributed to an understanding of ER structure and function and aspects of the mechanisms that generate and maintain the polarity of epithelial cells. For this work my laboratory introduced the now widely adopted Madin-Darby canine kidney (MDCK) cell line, and demonstrated the polarized budding of envelope viruses from those cells, providing a powerful new system that further advanced the field of protein traffic.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 133-153 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Chromatin can be differentiated by the deposition of variant histones at centromeres, active genes, and silent loci. Variant histones are assembled into nucleosomes in a replication-independent manner, in contrast to assembly of bulk chromatin that is coupled to replication. Recent in vitro studies have provided the first glimpses of protein machines dedicated to building and replacing alternative nucleosomes. They deposit variant H2A and H3 histones and are targeted to particular functional sites in the genome. Differences between variant and canonical histones can have profound consequences, either for delivery of the histones to sites of assembly or for their function after incorporation into chromatin. Recent studies have also revealed connections between assembly of variant nucleosomes, chromatin remodeling, and histone post-translational modification. Taken together, these findings indicate that chromosome architecture can be highly dynamic at the most fundamental level, with epigenetic consequences.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 203-222 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Plants shape their organs with a precision demanded by optimal function; organ shaping requires control over cell wall expansion anisotropy. Focusing on multicellular organs, I survey the occurrence of expansion anisotropy and discuss its causes and proposed controls. Expansion anisotropy of a unit area of cell wall is characterized by the direction and degree of anisotropy. The direction of maximal expansion rate is usually regulated by the direction of net alignment among cellulose microfibrils, which overcomes the prevailing stress anisotropy. In some stems, the directionality of expansion of epidermal cells is controlled by that of the inner tissue. The degree of anisotropy can vary widely as a function of position and of treatment. The degree of anisotropy is probably controlled by factors in addition to the direction of microfibril alignment. I hypothesize that rates of expansion in maximal and minimal directions are regulated by distinct molecular mechanisms that regulate interactions between matrix and microfibrils.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 581-603 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Over the past decades, intravital microscopy (IVM), the imaging of cells in living organisms, has become a valuable tool for studying the molecular determinants of lymphocyte trafficking. Recent advances in microscopy now make it possible to image cell migration and cell-cell interactions in vivo deep within intact tissues. Here, we summarize the principal techniques that are currently used in IVM, discuss options and tools for fluorescence-based visualization of lymphocytes in microvessels and tissues, and describe IVM models used to explore lymphoid and non-lymphoid organs. The latter will be introduced according to the physiologic itinerary of developing and differentiating T and B lymphocytes as they traffic through the body, beginning with their development in bone marrow and thymus and continuing with their migration to secondary lymphoid organs and peripheral tissues.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 411-434 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Centrosomes, spindle pole bodies, and related structures in other organisms are a morphologically diverse group of organelles that share a common ability to nucleate and organize microtubules and are thus referred to as microtubule organizing centers or MTOCs. Features associated with MTOCs include organization of mitotic spindles, formation of primary cilia, progression through cytokinesis, and self-duplication once per cell cycle. Centrosomes bind more than 100 regulatory proteins, whose identities suggest roles in a multitude of cellular functions. In fact, recent work has shown that MTOCs are required for several regulatory functions including cell cycle transitions, cellular responses to stress, and organization of signal transduction pathways. These new liaisons between MTOCs and cellular regulation are the focus of this review. Elucidation of these and other previously unappreciated centrosome functions promises to yield exciting scientific discovery for some time to come.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 695-718 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The combined use of the new technologies of multiphoton-based intravital imaging, the chemotaxis-mediated collection of invasive cells, and high sensitivity expression profiling has allowed the correlation of the behavior of invasive tumor cells in vivo with their gene expression patterns. New insights have resulted including a gene expression signature for invasive cells and the tumor microenvironment invasion model. This model proposes that tumor invasion and metastasis can be studied as a problem resembling normal morphogenesis. We discuss how these new insights may lead to a better understanding of the molecular basis of the invasive behavior of tumor cells in vivo, which may result in new strategies for the diagnosis and treatment of metastasis.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 435-456 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Secretory and transmembrane proteins enter the secretory pathway through the protein-conducting Sec61 channel in the membrane of the endoplasmic reticulum. In the endoplasmic reticulum, proteins fold, are frequently covalently modified, and oligomerize before they are packaged into transport vesicles that shuttle them to the Golgi complex. Proteins that misfold in the endoplasmic reticulum are selectively transported back across the endoplasmic reticulum membrane to the cytosol for degradation by proteasomes. Depending on the topology of the defect in the protein, cytosolic or lumenal chaperones are involved in its targeting to degradation. The export channel for misfolded proteins is likely also formed by Sec61p. Export may be powered by AAA-ATPases of the proteasome 19S regulatory particle or Cdc48p/p97. Exported proteins are frequently ubiquitylated prior to degradation and are escorted to the proteasome by polyubiquitin-binding proteins.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 511-527 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Phagocytosis, the process by which cells engulf large particles, requires a substantial contribution of membranes. Recent studies have revealed that intracellular compartments, including endocytic organelles and the endoplasmic reticulum (ER), can engage in fusion events with the plasma membrane at the sites of nascent phagosomes. The finding that ER proteins are delivered to phagosomes, where degraded peptides are loaded onto major histocompatibility complex (MHC) class II molecules, has significantly enhanced our understanding of the immune functions associated with these organelles. Although it is well known that pathogens are killed in phagosomes, the contribution of ER proteins to phagosomes has provided a novel pathway for the loading of exogenous peptides onto MHC class I molecules, a process known as cross-presentation. Thus, phagocytosis has evolved from a nutritional function in unicellular organisms to play key roles in both innate and adaptive immunity in vertebrates.
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