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  • Geodynamics and Tectonics  (182)
  • Biotechnology & Synthetic Biology  (41)
  • 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
  • 04.02. Exploration geophysics
  • JSTOR Archive Collection Business II
  • Textbook of informatics
  • Oxford University Press  (228)
  • Wiley  (10)
  • American Chemical Society (ACS)
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  • 1
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    Integrated use of unmanned aerial vehicle photogrammetry and terrestrial laser scanning to support archaeological analysis: The Acropolis of Selinunte case (Sicily, Italy) (2021)
    Wiley
    Details
    Publication Date: 2021-06-14
    Description: Southwestern Sicily is an area of infrequent seismic activity; however, some studies carried out in the archaeological Selinunte site suggest that, between the fourth century BC and the early Middle Ages, probably at least two earthquakes strucked this area with enough energy to damage and cause the collapse and kinematics of much of the architecture of Selinunte. Take into account that, in 2008, a noninvasive archaeological prospection and traditional data gathering methods along the Acropolis north fortifications were carried out. Following these first studies, after about 10 years, a new geophysical campaign was carried out. This second campaign benefited from the application of modern technologies for the acquisition and processing of the point cloud data on the northern part of the Acropolis, like terrestrial laser scanning and unmanned aerial vehicle photogrammetry. In this paper, we present the application of these techniques and a strategy for their integration for the 3D modelling of buildings and cultural heritages. We show how the integration of data acquired independently by these two techniques is an added value able to overcome the intrinsic limits of the individual techniques. The application to Selinunte's Acropolis allowed it to highlight and measure with high accuracy fractures, dislocation, inclinations of walls, depressions of some areas and other interesting observations, which may be important starting points for future investigations.
    Description: Published
    Description: 153-165
    Description: 2IT. Laboratori analitici e sperimentali
    Description: JCR Journal
    Keywords: 3D reconstruction ; archaeological survey ; digital elevation model ; Selinunte Archaeological Park ; terrestrial laser scanning ; unmanned aerial vehicle photogrammetry ; 05.04. Instrumentation and techniques of general interest ; 04.02. Exploration geophysics ; 05.02. Data dissemination ; 05.06. Methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    Active Extension in a Foreland Trapped Between Two Contractional Chains: The South Apulia Fault System (SAFS) (2020)
    Wiley
    Details
    Publication Date: 2020-07-08
    Description: The response of continental forelands to subduction and collision is a widely investigated topic in geodynamics. The deformation occurring within a foreland shared by two opposite‐verging chains, however, is uncommon and poorly understood. The Apulia Swell in the southern end of the Adria microplate (Africa‐Europe plate boundary, central Mediterranean Sea) represents one of these cases, as it is the common foreland of the SW verging Albanides‐Hellenides and the NE verging Southern Apennines merging into the SSE verging Calabrian Arc. We investigated the internal deformation of the Apulia Swell using multiscale geophysical data: multichannel seismic profiles recording up to 12‐s two‐way time (TWT) for a consistent image of the upper crust; high‐resolution multichannel seismic profiles, high‐resolution multibeam bathymetry, and CHIRP profiles acquired by R/V OGS Explora to constrain the Quaternary geological record. The results of our analyses characterize the geometry of the South Apulia Fault System (SAFS), a 100‐km‐long and 12‐km‐wide structure attesting an extensional (and possibly transtensional) response of the foreland to the two contractional fronts. The SAFS consists of two NW‐SE right‐stepping master faults and several secondary structures. The SAFS activity spans from the Early Pleistocene through the Holocene, as testified by the bathymetric and high‐resolution seismic data, with long‐term slip rates in the range of 0.2–0.4 mm/yr. Considering the position within an area with few or none other active faults in the surroundings, the dimension, and the activity rates, the SAFS can be a candidate causative fault of the 20 February 1743, M 6.7, earthquake.
    Description: Italian Ministry for Education, University, and Research (MIUR), Premiale 2014 D. M. 291 03/05/2016.
    Description: Published
    Description: e2020TC006116
    Description: 2T. Deformazione crostale attiva
    Description: 2TR. Ricostruzione e modellazione della struttura crostale
    Description: JCR Journal
    Keywords: active tectonics ; apulia ; south apulia fault system ; 1743 earthquake ; marine geology ; stable continental region ; ionian sea ; active faults ; subsurface geology ; seismic interpretation ; 04.04. Geology ; 04.07. Tectonophysics ; 04.02. Exploration geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
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    Present-day velocity field and block kinematics of Tibetan Plateau from GPS measurements (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-01
    Description: In this study, we present a new synthesis of GPS velocities for tectonic deformation within the Tibetan Plateau and its surrounding areas, a combined data set of ~1854 GPS-derived horizontal velocity vectors. Assuming that crustal deformation is localized along major faults, a block modelling approach is employed to interpret the GPS velocity field. We construct a 30-element block model to describe present-day deformation in western China, with half of them located within the Tibetan Plateau, and the remainder located in its surrounding areas. We model the GPS velocities simultaneously for the effects of block rotations and elastic strain induced by the bounding faults. Our model yields a good fit to the GPS data with a mean residual of 1.08 mm a –1 compared to the mean uncertainty of 1.36 mm a –1 for each velocity component, indicating a good agreement between the predicted and observed velocities. The major strike-slip faults such as the Altyn Tagh, Xianshuihe, Kunlun and Haiyuan faults have relatively uniform slip rates in a range of 5–12 mm a –1 along most of their segments, and the estimated fault slip rates agree well with previous geologic and geodetic results. Blocks having significant residuals are located at the southern and southeastern Tibetan Plateau, suggesting complex tectonic settings and further refinement of accurate definition of block geometry in these regions.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Preserved history of global mean spreading rate: 83 Ma to present (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-07
    Description: Using an up-to-date global plate rotation model, applied to the endpoints of preserved major spreading ridge isochrons, we have calculated the explicitly reconstructable length-weighted mean global half-spreading rate (HSR), ridge length and area production as a function of time since the end of the Cretaceous Normal Superchron at 83.0 Ma. Our calculations integrate uncertainties in rotation parameters and chron boundary ages with the partial sampling uncertainties arising from progressive subduction of older oceanic lithosphere and its preserved spreading record. This record of directly reconstructable oceanic ridge production provides a well-constrained baseline that can be compared to reconstructions that include the largely unconstrained extrapolated histories of entirely subducted oceanic plates. The directly reconstructable global mean HSR has not varied by more than ±15 per cent about an average rate of 28.4 ± 4.6 mm a –1 since 83 Ma. No long-term secular trend is evident: a maximum global mean half-rate of 32 ± 6 mm a –1 occurred from 33.1 Ma to about 25.8 Ma, with minima of 26 ± 5 mm a –1 between about 56 and 40.2 Ma, and 24 ± 1 mm a –1 since 3.2 Ma. Only this most recent interval has a rate that differs significantly (at ±2) from the long-term mean. The global, reconstructable ridge length at 56 Ma decreases by less than 15 per cent relative to the modern ridge system; by 83 Ma it has decreased by 38 per cent. These relatively high preserved ridge fractions mean that the estimated uncertainty due to partial sampling stays roughly equivalent to the estimated rotation model uncertainties, allowing long-term spreading rate variations of 〉20 per cent since the Late Cretaceous to be ruled out. In contrast, prior to 83 Ma too little oceanic lithosphere is preserved to reliably reconstruct global spreading rates.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
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    Numerical studies on convective stability and flow pattern in three-dimensional spherical mantle of terrestrial planets (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-13
    Description: We explore thermal convection of a fluid with a temperature-dependent viscosity in a basally heated 3-D spherical shell using linear stability analyses and numerical experiments, while considering the application of our results to terrestrial planets. The inner to outer radius ratio of the shell f assumed in the linear stability analyses is in the range of 0.11–0.88. The critical Rayleigh number R c for the onset of thermal convection decreases by two orders of magnitude as f increases from 0.11 to 0.88, when the viscosity depends sensitively on the temperature, as is the case for real mantle materials. Numerical simulations carried out in the range of f  = 0.11–0.55 show that a thermal boundary layer (TBL) develops both along the surface and bottom boundaries to induce cold and hot plumes, respectively, when f is 0.33 or larger. However, for smaller f values, a TBL develops only on the bottom boundary. Convection occurs in the stagnant-lid regime where the root mean square velocity on the surface boundary is less than 1 per cent of its maximum at depth, when the ratio of the viscosity at the surface boundary to that at the bottom boundary exceeds a threshold that depends on f . The threshold decreases from 10 6.5 at f  = 0.11 to 10 4 at f  = 0.55. If the viscosity at the base of the convecting mantle is 10 20 –10 21  Pa s, the Rayleigh number exceeds R c for Mars, Venus and the Earth, but does not for the Moon and Mercury; convection is unlikely to occur in the latter planets unless the mantle viscosity is much lower than 10 20  Pa s and/or the mantle contains a strong internal heat source.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
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    A hybrid boundary-integral/thin-sheet equation for subduction modelling (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-13
    Description: Subducting oceanic lithosphere is an example of a thin sheet-like object whose characteristic lateral dimension greatly exceeds its thickness. Here we exploit this property to derive a new hybrid boundary-integral/thin sheet (BITS) representation of subduction that combines in a single equation all the forces acting on the sheet: gravity, internal resistance to bending and stretching, and the tractions exerted by the ambient mantle. For simplicity, we limit ourselves to 2-D. We solve the BITS equations using a discrete Lagrangian approach in which the sheet is represented by a set of vertices connected by edges. Instantaneous solutions for the sinking speed of a slab attached to a trailing flat sheet obey a scaling law of the form V / V Stokes  = fct(St), where V Stokes is a characteristic Stokes sinking speed and St is the sheet's flexural stiffness. Time-dependent solutions for the evolution of the sheet's shape and thickness show that these are controlled by the viscosity ratio between the sheet and its surroundings. An important advantage of the BITS approach is the possibility of generalizing the sheet's rheology, either to a viscosity that varies along the sheet or to a non-Newtonian shear-thinning rheology.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    The great 1933 Sanriku-oki earthquake: reappraisal of the main shock and its aftershocks and implications for its tsunami using regional tsunami and seismic data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-16
    Description: The aftershock distribution of the 1933 Sanriku-oki outer trench earthquake is estimated by using modern relocation methods and a newly developed velocity structure to examine the spatial extent of the source-fault and the possibility of a triggered interplate seismicity. In this study, we first examined the regional data quality of the 1933 earthquake based on smoked-paper records and then relocated the earthquakes by using the 3-D velocity structure and double-difference method. The improvements of hypocentre locations using these methods were confirmed by the examination of recent earthquakes that are accurately located based on ocean bottom seismometer data. The results show that the 1933 aftershocks occurred under both the outer- and inner-trench-slope regions. In the outer-trench-slope region, aftershocks are distributed in a ~280-km-long area and their depths are shallower than 50 km. Although we could not constrain the fault geometry from the hypocentre distribution, the depth distribution suggests the whole lithosphere is probably not under deviatoric tension at the time of the 1933 earthquake. The occurrence of aftershocks under the inner trench slope was also confirmed by an investigation of waveform frequency difference between outer and inner trench earthquakes as recorded at Mizusawa. The earthquakes under the inner trench slope were shallow (depth less double equals30 km) and the waveforms show a low-frequency character similar to the waveforms of recent, precisely located earthquakes in the same area. They are also located where recent activity of interplate thrust earthquakes is high. These suggest that the 1933 outer-trench-slope main shock triggered interplate earthquakes, which is an unusual case in the order of occurrence in contrast with the more common pairing of a large initial interplate shock with subsequent outer-slope earthquakes. The off-trench earthquakes are distributed about 80 km width in the trench perpendicular direction. This wide width cannot be explained from a single high-angle fault confined at a shallow depth (depth less double equals50 km). The upward motion of the 1933 tsunami waveform records observed at Sanriku coast also cannot be explained from a single high-angle west-dipping normal fault. If we consider additional fault, involvement of high-angle, east-dipping normal faults can better explain the tsunami first motion and triggering of the aftershock in a wide area under the outer trench slope. Therefore multiple off-trench normal faults may have activated during the 1933 earthquake. We also relocated recent (2001–2012) seismicity by the same method. The results show that the present seismicity in the outer-trench-slope region can be divided into several groups along the trench. Comparison of the 1933 rupture dimensions based on our aftershock relocations with the morphologies of fault scarps in the outer trench slope suggest that the rupture was limited to the region where fault scarps are largely trench parallel and cross cut the seafloor spreading fabric. These findings imply that bending geometry and structural segmentation of the incoming plate largely controls the spatial extent of the 1933 seismogenic faulting. In this shallow rupture model for this largest outer trench earthquake, triggered seismicity in the forearc and structural control of faulting represent an important deformation styles for off-trench and shallow megathrust zones.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
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    Contemporary deformation in the Yakima fold and thrust belt estimated with GPS (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-05
    Description: Geodetic, geologic and palaeomagnetic data reveal that Oregon (western USA) rotates clockwise at 0.3 to 1.0° Ma –1 (relative to North America) about an axis near the Idaho–Oregon–Washington border, while northeast Washington is relatively fixed. This rotation has been going on for at least 15 Ma. The Yakima fold and thrust belt (YFTB) forms the boundary between northern Oregon and central Washington where convergence of the clockwise-rotating Oregon block is apparently accommodated. North–south shortening across the YFTB has been thought to occur in a fan-like manner, increasing in rate to the west. We obtained high-accuracy, high-density geodetic GPS measurements in 2012–2014 that are used with earlier GPS measurements from the 1990s to characterize YFTB kinematics. The new results show that the deformation associated with the YFTB starts at the Blue Mountains Anticline in northern Oregon and extends north beyond the Frenchman Hills in Washington, past the epicentre of the 1872 M w 7.0 Entiat earthquake to 49°N. The north–south strain rate across the region is 2 to 3 x 10 –9 yr –1 between the volcanic arc and the eastern edge of the YFTB (241.0°E); east of there it drops to about 10 –9 yr –1 . At the eastern boundary of the YFTB, faults and earthquake activity are truncated by a north-trending, narrow zone of deformation that runs along the Pasco Basin and Moses Lake regions near 240.9°E. This zone, abutting the Department of Energy Hanford Nuclear Reservation, accommodates about 0.5 mm yr –1 of east to northeast shortening. A similar zone of N-trending transpression is seen along 239.9°E where there is a change in the strike of the Yakima folds. The modern deformation of the YFTB is about 600 km wide from south to north and internally may be controlled by pre-existing crustal structure.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
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    Present-day dynamic and residual topography in Central Anatolia (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of ‘dynamic topography’. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N–S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ~1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 10
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    Role of source-layer tilts in the axi-asymmetric growth of diapirs triggered by a Rayleigh-Taylor instability (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-25
    Description: In many geological systems, inversion of density stratification sets in Rayleigh–Taylor (RT) instabilities, leading to an ascent of relatively low-density materials through the high-density overburden in the form of diapirs. These diapirs often originate from dipping low-density layers. This study aims to show how the initial tilt of such source layers can control the ascent behaviour of diapirs initiated by RT instabilities. Using two-layer viscous models we produced RT instabilities in physical experiments, and investigated the effects of source-layer tilts ( β ). Our experiments suggest that these diapirs ascend with contrasting lateral spreading rates in the up and down slope directions, resulting in their axi-asymmetric geometry. However, their heads retain a circular outline on the horizontal top surface, where the upwelling axis is located away from their geometric centre in the upslope direction. In this paper, we present a series of experimental models to demonstrate the spectrum of axi-symmetric to -asymmetric geometrical transitions with increasing β . Our experiments also reveal that when β is large (〉4°) the diapirs become unstable, resulting in a continuous migration of their stems in the upslope direction. Using the volume of fluid method we ran computational fluid dynamic (CFD) simulations to study the underlying hydrodynamics of axi-asymmetric diapiric growth. The CFD simulations show that β 〉 0° conditions develop stronger flow vortices on the downslope side of an ascending diapir, leading to a pressure difference between the up- and downslope flanks. Such a differential pressure causes the diapir head to spread at a faster rate in the tilt direction. An estimate of the asymmetric spreading rates is given as a function of β . Our present study provides a fundamental understanding of the hydrodynamic flow structure responsible for the asymmetric growth of RT instabilities on tilted source layers, as applicable to a wide range of large-scale geological settings, such as sedimentary basins and subduction zones.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 11
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    On the importance of the heterogeneity assumption in the characterization of reservoir geomechanical properties (2016)
    Oxford University Press
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    Publication Date: 2016-08-05
    Description: The geomechanical analysis of a highly compartmentalized reservoir is performed to simulate the seafloor subsidence due to gas production. The available observations over the hydrocarbon reservoir consist of bathymetric surveys carried out before and at the end of a 10-yr production life. The main goal is the calibration of the reservoir compressibility c M , that is, the main geomechanical parameter controlling the surface response. Two conceptual models are considered: in one (i) c M varies only with the depth and the vertical effective stress (heterogeneity due to lithostratigraphic variability); in another (ii) c M varies also in the horizontal plane, that is, it is spatially distributed within the reservoir stratigraphic units. The latter hypothesis accounts for a possible partitioning of the reservoir due to the presence of sealing faults and thrusts that suggests the idea of a block heterogeneous system with the number of reservoir blocks equal to the number of uncertain parameters. The method applied here relies on an ensemble-based data assimilation (DA) algorithm (i.e. the ensemble smoother, ES), which incorporates the information from the bathymetric measurements into the geomechanical model response to infer and reduce the uncertainty of the parameter c M . The outcome from conceptual model (i) indicates that DA is effective in reducing the c M uncertainty. However, the maximum settlement still remains underestimated, while the areal extent of the subsidence bowl is overestimated. We demonstrate that the selection of the heterogeneous conceptual model (ii) allows to reproduce much better the observations thus removing a clear bias of the model structure. DA allows significantly reducing the c M uncertainty in the five blocks (out of the seven) characterized by large volume and large pressure decline. Conversely, the assimilation of land displacements only partially constrains the prior c M uncertainty in the reservoir blocks marginally contributing to the cumulative seafloor subsidence, that is, blocks with low pressure.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 12
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    Persistent Scatterer Interferometry analysis of ground deformation in the Po Plain (Piacenza-Reggio Emilia sector, Northern Italy): seismo-tectonic implications (2016)
    Oxford University Press
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    Publication Date: 2016-07-08
    Description: This work aims to explore the ongoing tectonic activity of structures in the outermost sector of the Northern Apennines, which represents the active leading edge of the thrust belt and is dominated by compressive deformation. We have applied the Persistent Scatterer Interferometry (PSI) technique to obtain new insights into the present-day deformation pattern of the frontal area of the Northern Apennine. PSI has proved to be effective in detecting surface deformation of wide regions involved in low tectonic movements. We used 34 Envisat images in descending geometry over the period of time between 2004 and 2010, performing about 300 interferometric pairs. The analysis of the velocity maps and of the PSI time-series has allowed to observe ground deformation over the sector of the Po Plain between Piacenza and Reggio Emilia. The time-series of permanent GPS stations located in the study area, validated the results of the PSI technique, showing a good correlation with the PS time-series. The PS analysis reveals the occurrence of a well-known subsidence area on the rear of the Ferrara arc, mostly connected to the exploitation of water resources. In some instances, the PS velocity pattern reveals ground uplift (with mean velocities ranging from 1 to 2.8 mm yr –1 ) above active thrust-related anticlines of the Emilia and Ferrara folds, and part of the Pede-Apennine margin. We hypothesize a correlation between the observed uplift deformation pattern and the growth of the thrust-related anticlines. As the uplift pattern corresponds to known geological features, it can be used to constrain the seismo-tectonic setting, and a working hypothesis may involve that the active Emilia and Ferrara thrust folds would be characterized by interseismic periods possibly dominated by aseismic creep.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 13
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    Neotectonic deformation models for probabilistic seismic hazard: a study in the External Dinarides (2016)
    Oxford University Press
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    Publication Date: 2016-05-05
    Description: In Europe, common input data types for seismic hazard evaluation include earthquake catalogues, seismic zonation models and ground motion models, all with well-constrained epistemic uncertainties. In contrast, neotectonic deformation models and their related uncertainties are rarely considered in earthquake forecasting and seismic hazard studies. In this study, for the first time in Europe, we developed a seismic hazard model based exclusively on active fault and geodynamic deformation models. We applied it to the External Dinarides, a slow-deforming fold-and-thrust belt in the Central Mediterranean. The two deformation models furnish consistent long-term earthquake rates above the M w 4.7 threshold on a latitude/longitude grid with 0.2° spacing. Results suggest that the use of deformation models is a valid alternative to empirical-statistical approaches in earthquake forecasting in slow-deforming regions of Europe. Furthermore, we show that the variability of different deformation models has a comparable effect on the peak ground motion acceleration uncertainty as do the ground motion prediction equations.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 14
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    Breakdown of doublet recirculation and direct line drives by far-field flow in reservoirs: implications for geothermal and hydrocarbon well placement (2016)
    Oxford University Press
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    Publication Date: 2016-05-11
    Description: An important real world application of doublet flow occurs in well design of both geothermal and hydrocarbon reservoirs. A guiding principle for fluid management of injection and extraction wells is that mass balance is commonly assumed between the injected and produced fluid. Because the doublets are considered closed loops, the injection fluid is assumed to eventually reach the producer well and all the produced fluid ideally comes from stream tubes connected to the injector of the well pair making up the doublet. We show that when an aquifer background flow occurs, doublets will rarely retain closed loops of fluid recirculation. When the far-field flow rate increases relative to the doublet's strength, the area occupied by the doublet will diminish and eventually vanishes. Alternatively, rather than using a single injector (source) and single producer (sink), a linear array of multiple injectors separated by some distance from a parallel array of producers can be used in geothermal energy projects as well as in waterflooding of hydrocarbon reservoirs. Fluid flow in such an arrangement of parallel source-sink arrays is shown to be macroscopically equivalent to that of a line doublet. Again, any far-field flow that is strong enough will breach through the line doublet, which then splits into two vortices. Apart from fundamental insight into elementary flow dynamics, our new results provide practical clues that may contribute to improve the planning and design of doublets and direct line drives commonly used for flow management of groundwater, geothermal and hydrocarbon reservoirs.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 15
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    Endophytic fungi associated with Sudanese medicinal plants show cytotoxic and antibiotic potential (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-12
    Description: In this study, we isolated 15 endophytic fungi from five Sudanese medicinal plants. Each fungal endophytic strain was identified by sequencing of internal transcribed spacer (ITS) regions of rDNA. Ethyl acetate extracts were prepared from each endophyte cultivated in vitro and tested for their respective antibacterial activities and antiproliferative activities against human cancer cells. Antibacterial screening was carried out against two bacterial strains: Gram-negative Escherichia coli and Gram-positive methicillin-resistant Staphylococcus aureus , by the broth dilution method. Cell viability was evaluated by the MTT procedure after exposure of MCF7 breast cancer cells and HT29 or HCT116 human colon adenocarcinoma cells to each endophytic extract. Of interest, Byssochlamys spectabilis isolated from Euphorbia prostata showed cytotoxicity (IC 50 = 1.51 ± 0.2 μg mL –1 ) against MCF7 cells, but had a low effect against HT29 or HCT116 cells (IC 50 〉 20 μg mL –1 ). Cladosporium cladosporioides 2, isolated from Vernonia amygdalina leaves, showed antiproliferative activities against MCF7 cells (IC 50 = 10.5 ± 1.5 μg mL –1 ) only. On the other hand, B. spectabilis and Alternaria sp. extract had antibacterial activities against the S. aureus strain. The findings of this work revealed that endophytic fungi associated with medicinal plants from Sudan could be considered as an attractive source of new therapeutic compounds.
    Keywords: Biotechnology & Synthetic Biology
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    Seafloor spreading event in western Gulf of Aden during the November 2010-March 2011 period captured by regional seismic networks: evidence for diking events and interactions with a nascent transform zone (2016)
    Oxford University Press
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    Publication Date: 2016-04-07
    Description: In November 2010, intense seismic activity including 29 events with a magnitude above 5.0, started in the western part of the Gulf of Aden, where the structure of the oceanic spreading ridge is characterized by a series of N115°-trending slow-spreading segments set within an EW-trending rift. Using signals recorded by permanent and temporary networks in Djibouti and Yemen, we located 1122 earthquakes, with a magnitude ranging from 2.1 to 5.6 from 2010 November 1 to 2011 March 31. By looking in detail at the space–time distribution of the overall seismicity, and both the frequency and the moment tensor of large earthquakes, we re-examine the chronology of this episode. In addition, we also interpret the origin of the activity using high-resolution bathymetric data, as well as from observations of seafloor cable damage caused by high temperatures and lava flows. The analysis allows us to identify distinct active areas. First, we interpret that this episode is mainly related to a diking event along a specific ridge segment, located at E044°. In light of previous diking episodes in nearby subaerial rift segments, for which field constraints and both seismic and geodetic data exist, we interpret the space–time evolution of the seismicity of the first few days. Migration of earthquakes suggests initial magma ascent below the segment centre. This is followed by a southeastward dike propagation below the rift immediately followed by a northwestward dike propagation below the rift ending below the northern ridge wall. The cumulative seismic moment associated with this sequence reaches 9.1 x 10 17 Nm, and taking into account a very low seismic versus geodetic moment, we estimate a horizontal opening of ~0.58–2.9 m. The seismic activity that followed occurred through several bursts of earthquakes aligned along the segment axis, which are interpreted as short dike intrusions implying fast replenishment of the crustal magma reservoir feeding the dikes. Over the whole period, the opening is estimated to be ~1.76–8.8 m across the segment. A striking feature of this episode is that the seismicity remained confined within one individual segment, whereas the adjacent en-echelon segments were totally quiescent, suggesting that the magma supply system of one segment is disconnected from those of the neighbouring segments. Second, we identify activity induced by the first intrusion with epicentres aligned along an N035°E-trending, ~30 km long at the northwestern end of the active opening segment. This group encompasses more than seven earthquakes with magnitude larger than 5.0, and with strike-slip focal mechanisms consistent with the faults identified in the bathymetry and the structural pattern of the area. We propose that a transform fault is currently in formation which indicates an early stage of the ridge segmentation, at the locus of the trend change of the spreading ridge, which also corresponds to the boundary between a clear oceanic lithosphere and the zone of transform between continental and oceanic crust.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Residual polar motion caused by coseismic and interseismic deformations from 1900 to present (2016)
    Oxford University Press
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    Publication Date: 2016-04-07
    Description: We challenge the perspective that seismicity could contribute to polar motion by arguing quantitatively that, in first approximation and on the average, interseismic deformations can compensate for it. This point is important because what we must simulate and observe in Earth Orientation Parameter time-series over intermediate timescales of decades or centuries is the residual polar motion resulting from the two opposing processes of coseismic and interseismic deformations. In this framework, we first simulate the polar motion caused by only coseismic deformations during the longest period available of instrumental seismicity, from 1900 to present, using both the CMT and ISC-GEM catalogues. The instrumental seismicity covering a little longer than one century does not represent yet the average seismicity that we should expect on the long term. Indeed, although the simulation shows a tendency to move the Earth rotation pole towards 133°E at the average rate of 16.5 mm yr –1 , this trend is still sensitive to individual megathrust earthquakes, particularly to the 1960 Chile and 1964 Alaska earthquakes. In order to further investigate this issue, we develop a global seismicity model (GSM) that is independent from any earthquake catalogue and that describes the average seismicity along plate boundaries on the long term by combining information about present-day plate kinematics with the Anderson theory of faulting, the seismic moment conservation principle and a few other assumptions. Within this framework, we obtain a secular polar motion of 8 mm yr –1 towards 112.5°E that is comparable with that estimated from 1900 to present using the earthquake catalogues, although smaller by a factor of 2 in amplitude and different by 20° in direction. Afterwards, in order to reconcile the idea of a secular polar motion caused by earthquakes with our simplest understanding of the seismic cycle, we adapt the GSM in order to account for interseismic deformations and we use it to quantify, for the first time ever, their contribution to polar motion. Taken together, coseismic and interseismic deformations make the rotation pole wander around the north pole with maximum polar excursions of about 1 m. In particular, the rotation pole moves towards about Newfoundland when the interseismic contribution dominates over the coseismic ones (i.e. during phases of low seismicity or, equivalently, when most of the fault system associated with plate boundaries is locked). When megathrust earthquakes occur, instead, the rotation pole is suddenly shifted in an almost opposite direction, towards about 133°E.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    The role of elasticity in simulating long-term tectonic extension (2016)
    Oxford University Press
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    Publication Date: 2016-03-09
    Description: While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U x L . When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U x L favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    De novo biosynthesis of resveratrol by site-specific integration of heterologous genes in Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: Resveratrol is a well-known triphenolic natural product present in red wine. For its contribution to human health, the demand for resveratrol as a food and nutrition supplement has increased significantly. In recent years, the rapid development of synthetic biology has promoted extensive work to increase the production of resveratrol in microbes. However, supplementation of expensive phenylpropanoic precursors was required in current engineered strains. Here, we first utilized the site-specific integration strategy to produce resveratrol in Escherichia coli . The genes tal , 4cl and sts were site-specific integrated into the loci of genes tyrR and trpED in the chromosome of E. coli BW25113 (DE3). The final strain was capable of producing 4.612 mg L –1 of resveratrol from glucose.
    Keywords: Biotechnology & Synthetic Biology
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    Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: While extensively studied in several model organisms, the role of small, non-coding RNAs in the stress response remains largely unexplored in Clostridium organisms. About 100 years after the first industrial Acetone–Butanol–Ethanol fermentation process, based on the Weizmann Clostridium acetobutylicum strain, strain tolerance to butanol remains a crucial factor limiting the economics of the process. Several studies have examined the response of this organism to metabolite stress, and several genes have been engaged to impart enhanced tolerance, but no sRNAs have yet been directly engaged in this task. We show that the two stress-responsive sRNAs, 6S and tmRNA, upon overexpression impart tolerance to butanol as assessed by viability assays under process-relevant conditions. 6S overexpression enhances cell densities as well as butanol titres. We discuss the likely mechanisms that these two sRNAs might engage in this tolerance phenotype. Our data support the continued exploration of sRNAs as a basis for engineering enhanced tolerance and enhanced solvent production, especially because sRNA-based strategies impose a minimal metabolic burden on the cells.
    Keywords: Biotechnology & Synthetic Biology
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    Neofiscalin A and fiscalin C are potential novel indole alkaloid alternatives for the treatment of multidrug-resistant Gram-positive bacterial infections (2016)
    Oxford University Press
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    Publication Date: 2016-07-02
    Description: Ten indole alkaloids were obtained from the marine sponge-associated fungus Neosartorya siamensis KUFA 0017. We studied the antimicrobial properties of these and of three other compounds previously isolated from the soil fungus N. siamensis KUFC 6349. Only neofiscalin A showed antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE); with a minimum inhibitory concentration (MIC) of 8 μg mL –1 against both strains. Another compound, fiscalin C, presented synergistic activity against MRSA when combined with oxacillin, although alone showed no antibacterial effect. Moreover, neofiscalin A, when present at sub-MICs, hampered the ability of both MRSA and VRE strains to form a biofilm. Additionally, the biofilm inhibitory concentration values of neofiscalin A against the MRSA and VRE isolates were 96 and 80 μg mL –1 , respectively. At a concentration of 200 μg mL –1 , neofiscalin A was able to reduce the metabolic activity of the biofilms by ~50%. One important fact is that our results also showed that neofiscalin A had no cytotoxicity against a human brain capillary endothelial cell line.
    Keywords: Biotechnology & Synthetic Biology
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    The unconventional secretion of PepN is independent of a functional autophagy machinery in the filamentous fungus Aspergillus niger (2016)
    Oxford University Press
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    Publication Date: 2016-07-02
    Description: During unconventional protein secretion (UPS), proteins do not pass through the classical endoplasmic reticulum (ER)–Golgi-dependent pathway, but are transported to the cell membrane via alternative routes. One type of UPS is dependent on several autophagy-related (Atg) proteins in yeast and mammalian cells, but mechanisms for unconventional secretion are largely unknown for filamentous fungi. In this study, we investigated whether the autophagy machinery is used for UPS in the filamentous fungus Aspergillus niger . An aspartic protease, which we called PepN, was identified as being likely to be secreted unconventionally, as this protein is highly abundant in culture filtrates during carbon starvation while it lacks a conventional N-terminal secretion sequence. We analysed the presence of PepN in the culture filtrates of carbon starved wild-type, atg1 and atg8 deletion mutant strains by Western blot analysis and by secretome analysis using nanoLC-ESI-MS/MS (wild-type and atg8 deletion mutant). Besides the presence of carbohydrate-active enzymes and other types of proteases, PepN was abundantly found in culture filtrates of both wild-type and atg deletion strains, indicating that the secretion of PepN is independent of the autophagy machinery in A. niger and hence most likely occurs via a different mechanism.
    Keywords: Biotechnology & Synthetic Biology
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    Horizontal and vertical velocities derived from the IDS contribution to ITRF2014, and comparisons with geophysical models (2016)
    Oxford University Press
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    Publication Date: 2016-08-25
    Description: In the context of the 2014 realization of the International Terrestrial Reference Frame, the International DORIS (Doppler Orbitography Radiopositioning Integrated by Satellite) Service (IDS) has delivered to the IERS a set of 1140 weekly SINEX files including station coordinates and Earth orientation parameters, covering the time period from 1993.0 to 2015.0. From this set of weekly SINEX files, the IDS combination centre estimated a cumulative DORIS position and velocity solution to obtain mean horizontal and vertical motion of 160 stations at 71 DORIS sites. The main objective of this study is to validate the velocities of the DORIS sites by comparison with external models or time-series. Horizontal velocities are compared with two recent global plate models (GEODVEL 2010 and NNR-MORVEL56). Prior to the comparisons, DORIS horizontal velocities were corrected for Global Isostatic Adjustment from the ICE-6G (VM5a) model. For more than half of the sites, the DORIS horizontal velocities differ from the global plate models by less than 2–3 mm yr –1 . For five of the sites (Arequipa, Dionysos/Gavdos, Manila and Santiago) with horizontal velocity differences with respect to these models larger than 10 mm yr –1 , comparisons with GNSS estimates show the veracity of the DORIS motions. Vertical motions from the DORIS cumulative solution are compared with the vertical velocities derived from the latest GPS cumulative solution over the time span 1995.0–2014.0 from the University of La Rochelle solution at 31 co-located DORIS-GPS sites. These two sets of vertical velocities show a correlation coefficient of 0.83. Vertical differences are larger than 2 mm yr –1 at 23 percent of the sites. At Thule, the disagreement is explained by fine-tuned DORIS discontinuities in line with the mass variations of outlet glaciers. Furthermore, the time evolution of the vertical time-series from the DORIS station in Thule show similar trends to the GRACE equivalent water height.
    Keywords: Geodynamics and Tectonics
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    Gravity anomalies, flexure and mantle rheology seaward of circum-Pacific trenches (2016)
    Oxford University Press
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    Publication Date: 2016-08-27
    Description: We have used ensemble averages of satellite-derived free-air gravity anomaly data, together with inverse modelling techniques, to determine the effective elastic thickness, T e , of circum-Pacific subducting oceanic lithosphere and its relationship to plate age. Synthetic modelling tests show that T e can be recovered best using gravity anomaly, rather than bathymetry, data and profiles that are at least 750 km long. Inverse modelling based on a uniform T e elastic plate suggests that T e increases with age of the subducting oceanic lithosphere and is given approximately by the depth to the 390 ± 10 °C oceanic isotherm based on a cooling plate model. Misfits between the observed and calculated gravity anomalies are significantly improved if a mechanically weak zone is included between the trench axis and the outer rise. This weak zone is coincident with observations of bend-faulting and seismicity. Inverse modelling shows that T e landward of the outer rise is generally 40–65 per cent less than the T e seaward of the outer rise. Both landward and seaward T e increases with age of the lithosphere and are given by the depth to the 342–349 °C and 671–714 °C oceanic isotherm, respectively. A dependence of T e on age is consistent with models for the cooling of oceanic lithosphere as it moves away from a mid-ocean ridge and the temperature-dependent ductile creep of oceanic lithospheric minerals such as olivine. By comparing the observed T e to the predicted T e based on laboratory-derived yield strength envelopes and an assumption of elastic-perfectly plastic deformation, we have attempted to constrain the rheology of oceanic lithosphere. Regardless of the assumed friction coefficient, the dry-olivine low-temperature plasticity flow laws of Goetze, Evans & Goetze, Raterron et al . and Mei et al . all provide quite a good fit to the observed T e at circum-Pacific subduction zones. This result contrasts with the Hawaiian Islands, where these flow laws are generally too strong to fit the observations. The discrepancy in rheology within Pacific plate may be caused by differences in the timescale of loading and therefore the amount of viscoelastic stress relaxation that has occurred. Other possibilities include thermal rejuvenation and magma-assisted flexure at the Hawaiian Islands.
    Keywords: Geodynamics and Tectonics
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    High-resolution estimates of Nubia-Somalia plate motion since 20 Ma from reconstructions of the Southwest Indian Ridge, Red Sea and Gulf of Aden (2016)
    Oxford University Press
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    Publication Date: 2016-08-28
    Description: Large gaps and inconsistencies remain in published estimates of Nubia–Somalia plate motion based on reconstructions of seafloor spreading data around Africa. Herein, we use newly available reconstructions of the Southwest Indian Ridge at ~1-Myr intervals since 20 Ma to estimate Nubia–Somalia plate motion farther back in time than previously achieved and with an unprecedented degree of temporal resolution. At the northern end of the East African rift, our new estimates of Nubia–Somalia motion for six times from 0.78 Ma to 5.2 Ma differ by only 2 per cent from the rift-normal component of motion that is extrapolated from a recently estimated GPS angular velocity. The rate of rift-normal extension thus appears to have remained steady since at least 5.2 Ma. Our new rotations indicate that the two plates have moved relative to each other since at least 16 Ma and possibly longer. Motion has either been steady since at least 16 Ma or accelerated modestly between 6 and 5.2 Ma. Our Nubia–Somalia rotations predict 42.5 ± 3.8 km of rift-normal extension since 10.6 Ma across the well-studied, northern segment of the Main Ethiopian Rift, consistent with 40–50 km estimates for extension since 10.6 Myr based on seismological surveys of this narrow part of the plate boundary. Nubia–Somalia rotations are also derived by combining newly estimated Somalia–Arabia rotations that reconstruct the post-20-Ma opening of the Gulf of Aden with Nubia–Arabia rotations estimated via a probabilistic analysis of plausible opening scenarios for the Red Sea. These rotations predict Nubia–Somalia motion since 5.2 Myr that is consistent with that determined from Southwest Indian Ridge data and also predict 40 ± 3 km of rift-normal extension since 10.6 Ma across the Main Ethiopian Rift, consistent with our 42.5 ± 3.8 km Southwest Indian Ridge estimate. Our new rotations exclude at high confidence level previous estimates of 12 ± 13 and 123 ± 14 km for rift-normal extensions across the Main Ethiopian Rift since 10.6 Ma based on reconstructions of Chron 5n.2 along the Southwest Indian Ridge. Sparse coverage of magnetic reversals older than 16 Ma along the western third of the Southwest Indian Ridge precludes reliable determinations of Nubia–Somalia plate motion before 16 Ma, leaving unanswered the key question of when the motion between the two plates began.
    Keywords: Geodynamics and Tectonics
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    Crustal structure and kinematics of the TAMMAR propagating rift system on the Mid-Atlantic Ridge from seismic refraction and satellite altimetry gravity (2016)
    Oxford University Press
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    Publication Date: 2016-07-04
    Description: The TAMMAR segment of the Mid-Atlantic Ridge forms a classic propagating system centred about two degrees south of the Kane Fracture Zone. The segment is propagating to the south at a rate of 14 mm yr –1 , 15 per cent faster than the half-spreading rate. Here, we use seismic refraction data across the propagating rift, sheared zone and failed rift to investigate the crustal structure of the system. Inversion of the seismic data agrees remarkably well with crustal thicknesses determined from gravity modelling. We show that the crust is thickened beneath the highly magmatic propagating rift, reaching a maximum thickness of almost 8 km along the seismic line and an inferred (from gravity) thickness of about 9 km at its centre. In contrast, the crust in the sheared zone is mostly 4.5–6.5 km thick, averaging over 1 km thinner than normal oceanic crust, and reaching a minimum thickness of only 3.5 km in its NW corner. Along the seismic line, it reaches a minimum thickness of under 5 km. The PmP reflection beneath the sheared zone and failed rift is very weak or absent, suggesting serpentinisation beneath the Moho, and thus effective transport of water through the sheared zone crust. We ascribe this increased porosity in the sheared zone to extensive fracturing and faulting during deformation. We show that a bookshelf-faulting kinematic model predicts significantly more crustal thinning than is observed, suggesting that an additional mechanism of deformation is required. We therefore propose that deformation is partitioned between bookshelf faulting and simple shear, with no more than 60 per cent taken up by bookshelf faulting.
    Keywords: Geodynamics and Tectonics
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    Effects of MreB paralogs on poly-{gamma}-glutamic acid synthesis and cell morphology in Bacillus amyloliquefaciens (2016)
    Oxford University Press
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    Publication Date: 2016-08-27
    Description: Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly--glutamic acid (-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens , CwlO and LytE can degrade -PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of -PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the -PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the -PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, -PGA molecular weight and titer. In the mreBH inhibition mutant, -PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce -PGA degradation, and that improving the cell size could strengthen -PGA synthesis. This is the first report of enhanced -PGA production via suppression of actin-like MreB paralogs.
    Keywords: Biotechnology & Synthetic Biology
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    Industrial production of acetone and butanol by fermentation--100 years later (2016)
    Oxford University Press
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    Publication Date: 2016-06-08
    Description: Microbial production of acetone and butanol was one of the first large-scale industrial fermentation processes of global importance. During the first part of the 20th century, it was indeed the second largest fermentation process, superseded in importance only by the ethanol fermentation. After a rapid decline after the 1950s, acetone-butanol-ethanol (ABE) fermentation has recently gained renewed interest in the context of biorefinery approaches for the production of fuels and chemicals from renewable resources. The availability of new methods and knowledge opens many new doors for industrial microbiology, and a comprehensive view on this process is worthwhile due to the new interest. This thematic issue of FEMS Microbiology Letters, dedicated to the 100th anniversary of the first industrial exploitation of Chaim Weizmann's ABE fermentation process, covers the main aspects of old and new developments, thereby outlining a model development in biotechnology. All major aspects of industrial microbiology are exemplified by this single process. This includes new technologies, such as the latest developments in metabolic engineering, the exploitation of biodiversity and discoveries of new regulatory systems such as for microbial stress tolerance, as well as technological aspects, such as bio- and down-stream processing.
    Keywords: Biotechnology & Synthetic Biology
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    A new lactobacilli in vivo expression system for the production and delivery of heterologous proteins at mucosal surfaces (2016)
    Oxford University Press
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    Publication Date: 2016-06-02
    Description: Food-grade lactic acid bacteria, such as lactobacilli, represent good candidates for the development of mucosal vectors. Indeed, they are generally recognized as safe microorganisms and some strains display beneficial effects (probiotics). In this study, we described a new lactobacilli in vivo expression (LIVE) system for the production and delivery of therapeutic molecules at mucosal surfaces. The versatility and functionality of this system was successfully validated in several lactobacilli species; furthermore, we assessed in vivo LIVE system in two different mouse models of human pathologies: (i) a model of therapy against intestinal inflammation (inflammatory bowel diseases) and (ii) a model of vaccination against dental caries. We demonstrated that Lactobacillus gasseri expressing the anti-inflammatory cytokine IL-10 under LIVE system efficiently delivered the recombinant protein at mucosal surfaces and display anti-inflammatory effects. In the vaccination model against caries, LIVE system allowed the heterologous expression of Streptococcus mutans antigen GbpB by L. gasseri , leading to a stimulation of the host immune response.
    Keywords: Biotechnology & Synthetic Biology
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    Bioreactors and in situ product recovery techniques for acetone-butanol-ethanol fermentation (2016)
    Oxford University Press
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    Publication Date: 2016-06-02
    Description: The microbial fermentation process is one of the sustainable and environment-friendly ways to produce 1-butanol and other bio-based chemicals. The success of the fermentation process greatly relies on the choice of bioreactors and the separation methods. In this review, the history and the performance of bioreactors for the acetone–butanol–ethanol (ABE) fermentation is discussed. The subject is then focused on in situ product recovery (ISPR) techniques, particularly for the integrated extraction-gas stripping. The usefulness of this promising hybrid ISPR device is acknowledged by its incorporation with batch, fed-batch and continuous processes to improve the performance of ABE fermentation.
    Keywords: Biotechnology & Synthetic Biology
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    The Manihiki Plateau--a key to missing hotspot tracks? (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-29
    Description: A Neogene magmatic reactivation of the Manihiki Plateau, a large igneous province (LIP) in the central Pacific, is studied using seismic reflection data. Igneous diapirs have been identified exclusively within a narrow WNW–ESE striking corridor in the southern High Plateau (HP), which is parallel to the Neogene Pacific Plate motion and overlaps with an extrapolation of the Society Islands Hotspot (SIH) path. The igneous diapirs are characterized by a narrow width (〉5 km), penetration of the Neogene sediments, and they become progressively younger towards the East (23–10 Ma). The magmatic source appears to be of small lateral extent, which leads to the conclusion that the diapirs represent Neogene hotspot volcanism within a LIP, and thus may be an older, previously unknown extension of the SIH track (〉4.5 Ma). Comparing hotspot volcanism within oceanic and continental lithosphere, we further conclude that hotspot volcanism within LIP crust has similarities to tectonically faulted continental crust.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    Understanding lithospheric stresses: systematic analysis of controlling mechanisms with applications to the African Plate (2016)
    Oxford University Press
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    Publication Date: 2016-09-02
    Description: Many mechanisms control the state of stress within Earth plates. First-order well-known mechanisms include stresses induced by lateral variations of lithospheric density structure, sublithospheric tractions, ridge push and subduction pull. In this study, we attempt to quantify the influence of these mechanisms to understand the origin of stresses in the lithosphere, choosing the African plate (TAP) as an example. A finite-element based suite, Proshell, was developed to combine several data sets, to estimate the gravitational potential energy (GPE) of the lithosphere and to calculate stresses acting on the real (non-planar) geometry of TAP. We introduce several quantitative parameters to measure the degree of fit between the model and observations. Our modelling strategy involves nine series of numerical experiments. We start with the simplest possible model and then, step by step, build it up to be a more physically realistic model, all the while discussing the influence of each additional component. The starting (oversimplified) model series (1) is based on the CRUST2 data set for the crust and a half-space-cooling approximation of the lithospheric mantle. We then describe models (series 2–5) that account for lithospheric mantle density heterogeneities to build a more reliable GPE model. The consecutive series involve basal traction from the convective mantle (series A, C) and the rheological heterogeneity of the TAP via variations in its effective elastic thickness (series B, C). The model quality reflects the increase in complexity between series with an improving match to observed stress regimes and directions. The most complex model (series D) also accounts for the bending stresses in the elastic lithosphere and achieves a remarkably good fit to observations. All of our experiments were based on the iteration of controlling parameters in order to achieve the best fit between modelled and observed stresses, always considering physically feasible values. This gives us confidence that our methodology appropriately models the stress pattern of Africa, and that it may be further applied to other plates on Earth. Our modelling approach allows us to quantify several important features controlling the lithospheric stress pattern. Even though the initial oversimplified model does not fit the observations satisfactorily, it shows how ridge push may create significant compressive stresses in the lithosphere. More complex models show the importance of the density structure of the lithosphere, specifically in the subcrustal lithosphere. The stress regime within the TAP mainly results from a global balance of masses and mass moments between continental and oceanic parts of the plate. The orientation of stresses, in turn, is influenced more by local features expressed by topographic and crustal density variations, whereas existent subcrustal density variations appear to be smoothed by the crust above. The models show that accounting separately for either basal tractions or rheological heterogeneities brings moderate improvement, but the combination of these two mechanisms results in a substantially better match between model and observations. The bending stresses caused by isostatical re-adjustment improve the model match, but they have to be analysed with caution because of their depth-dependent nature.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Recent kinematics of the tectonic plates surrounding the Red Sea and Gulf of Aden (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-03
    Description: The Red Sea and Gulf of Aden represent two young basins that formed between Africa and Arabia since the early Oligocene, floored by oceanic crust or by transitional and thinned continental crust. While in the easternmost Gulf of Aden, the rift–drift transition can be dated chron C6 (~20.1 Ma), here we show that in the Red Sea the first pulse of seafloor spreading occurred during chron C3n.2n (~4.6 Ma) around ~17.1°N (present-day coordinates) and propagated southwards from this location, separating the Danakil microplate from Arabia. It is also shown that seafloor spreading between Arabia and Nubia started later, around chron 2A (~2.58 Ma), and propagated northwards. At present, there is no magnetic evidence for the existence of a linear spreading centre in the northern Red Sea at latitudes higher than ~24°N and in the southern Red Sea below ~14.8°N. The present-day plate kinematics of this region can be described with high accuracy by a network of five interacting plates (Nubia, Arabia, Somalia, Sinai and Danakil) and six triple junctions. For times older than anomaly 2A (~2.58 Ma) and up to anomaly 3, the absence of marine magnetic anomalies between Arabia and Nubia prevents a rigorous kinematic description of the five-plates system. However, there is strong evidence that the unique changes in plate motions during the last 5 Myr were a dramatic slowdown at chron C2 (~1.77 Ma) in the spreading or extension rates along the ridge and rift axes, thereby a good representation of the real plate motions can be obtained anyway by backward extension of the oldest Arabia–Nubia and Arabia–Danakil stage rotations determined on the basis of marine magnetic anomalies, respectively, C2–C2A and C2A–C3. The proposed kinematic reconstructions are accompanied by a geodynamic explanation for the genesis of large continent–continent fracture zones at the rift–drift transition and by an analysis of the strain associated with plate motions in Afar, northeastern Egypt and Sinai.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Tomography of the source zone of the 2016 South Taiwan earthquake (2016)
    Oxford University Press
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    Publication Date: 2016-09-07
    Description: On 2016 February 6 the South Taiwan earthquake ( M w 6.4) occurred in the Meinong District of Kaohsiung, southern Taiwan, at a depth of 17 km. It caused 117 fatalities and widespread damage to infrastructures, especially in the Tainan city. To clarify the generating mechanism of this damaging earthquake, we determined high-resolution 3-D images of P - and S -wave velocity ( V P , V S ) and Poisson's ratio ( ) in the epicentral area. We used 105 712 P - and 61 250 S -wave arrival times of 8279 local earthquakes (1.5 ≤ M ≤ 6.4) recorded at 41 seismic stations in South Taiwan during 2000–2011. In the upper crust (depth ≤ 10 km), the most remarkable feature is low- V P , low- V S and high- anomalies in areas with known active faults in the southwestern and easternmost parts of Taiwan. In contrast, high- V P , high- V S and low- anomalies become dominant in the lower crust. The hypocentre of the 2016 South Taiwan earthquake is located in a boundary zone where seismic velocity and Poisson's ratio change drastically in both the horizontal and vertical directions. Furthermore, the hypocentre is underlain by a vertically elongated high- anomaly at depths of 23–40 km, which may reflect ascending fluids from the upper (or uppermost) mantle. The low- V and high- anomalies in the upper crust coincide with areas of low heat flow, negative Bouguer gravity anomaly, and low magnetotelluric resistivity, which may reflect crustal fluids contained in the young fold-and-thrust belt. These results suggest that the 2016 South Taiwan earthquake was triggered by ascending fluids from dehydration of the subducting Eurasian slab, invading into active faults with a high loading rate.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Metabolic modeling of clostridia: current developments and applications (2016)
    Oxford University Press
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    Publication Date: 2016-01-29
    Description: Anaerobic Clostridium spp. is an important bioproduction microbial genus that can produce solvents and utilize a broad spectrum of substrates including cellulose and syngas. Genome-scale metabolic (GSM) models are increasingly being put forth for various clostridial strains to explore their respective metabolic capabilities and suitability for various bioconversions. In this study, we have selected representative GSM models for six different clostridia ( Clostridium acetobutylicum , C. beijerinckii , C. butyricum , C. cellulolyticum , C. ljungdahlii and C. thermocellum ) and performed a detailed model comparison contrasting their metabolic repertoire. We also discuss various applications of these GSM models to guide metabolic engineering interventions as well as assessing cellular physiology.
    Keywords: Biotechnology & Synthetic Biology
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    Electronic ISSN: 1574-6968
    Topics: Biology
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    Structure of a mushy layer under hypergravity with implications for Earth's inner core (2016)
    Oxford University Press
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    Publication Date: 2016-02-03
    Description: Crystallization experiments in the dendritic regime have been carried out in hypergravity conditions (from 1 to 1300 g) from an ammonium chloride solution (NH 4 Cl and H 2 O). A commercial centrifuge was equipped with a slip ring so that electric power (needed for a Peltier device and a heating element), temperature and ultrasonic signals could be transmitted between the experimental setup and the laboratory. Ultrasound measurements (2–6 MHz) were used to detect the position of the front of the mushy zone and to determine attenuation in the mush. Temperature measurements were used to control a Peltier element extracting heat from the bottom of the setup and to monitor the evolution of crystallization in the mush and in the liquid. A significant increase of solid fraction and attenuation in the mush is observed as gravity is increased. Kinetic undercooling is significant in our experiments and has been included in a macroscopic mush model. The other ingredients of the model are conservation of energy and chemical species, along with heat/species transfer between the mush and the liquid phase: boundary-layer exchanges at the top of the mush and bulk convection within the mush (formation of chimneys). The outputs of the model compare well with our experiments. We have then run the model in a range of parameters suitable for the Earth's inner core. This has shown the role of bulk mush convection for the inner core and the reason why a solid fraction very close to unity should be expected. We have also run melting experiments: after crystallization of a mush, the liquid has been heated from above until the mush started to melt, while the bottom cold temperature was maintained. These melting experiments were motivated by the possible local melting at the inner core boundary that has been invoked to explain the formation of the anomalously slow F-layer at the bottom of the outer core or inner core hemispherical asymmetry. Oddly, the consequences of melting are an increase in solid fraction and a decrease in attenuation. It is hence possible that surface seismic velocity and attenuation of the inner core are strongly affected by melting.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    A free surface capturing discretization for the staggered grid finite difference scheme (2016)
    Oxford University Press
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    Publication Date: 2016-02-05
    Description: The coupling that exists between surface processes and deformation within both the shallow crust and the deeper mantle-lithosphere has stimulated the development of computational geodynamic models that incorporate a free surface boundary condition. We introduce a treatment of this boundary condition that is suitable for staggered grid, finite difference schemes employing a structured Eulerian mesh. Our interface capturing treatment discretizes the free surface boundary condition via an interface that conforms with the edges of control volumes (e.g. a ‘staircase’ representation) and requires only local stencil modifications to be performed. Comparisons with analytic solutions verify that the method is first-order accurate. Additional intermodel comparisons are performed between known reference models to further validate our free surface approximation. Lastly, we demonstrate the applicability of a multigrid solver to our free surface methodology and demonstrate that the local stencil modifications do not strongly influence the convergence of the iterative solver.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    The crustal structure of Ellesmere Island, Arctic Canada--teleseismic mapping across a remote intraplate orogenic belt (2016)
    Oxford University Press
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    Publication Date: 2016-01-30
    Description: Ellesmere Island in Arctic Canada displays a complex geological evolution. The region was affected by two distinct orogenies, the Palaeozoic Ellesmerian orogeny (the Caledonian equivalent in Arctic Canada and Northern Greenland) and the Palaeogene Eurekan orogeny, related to the opening of Baffin Bay and the consequent convergence of the Greenland plate. The details of this complex evolution and the present-day deep structure are poorly constrained in this remote area and deep geophysical data are sparse. Receiver function analysis of seven temporary broad-band seismometers of the Ellesmere Island Lithosphere Experiment complemented by two permanent stations provides important data on the crustal velocity structure of Ellesmere Island. The crustal expression of the northernmost tectonic block of Ellesmere Island (~82°–83°N), Pearya, which was accreted during the Ellesmerian orogeny, is similar to that at the southernmost part, which is part of the Precambrian Laurentian (North America-Greenland) craton. Both segments have thick crystalline crust (~35–36 km) and comparable velocity–depth profiles. In contrast, crustal thickness in central Ellesmere Island decreases from ~24–30 km in the Eurekan fold and thrust belt (~79.7°–80.6°N) to ~16–20 km in the Hazen Stable Block (HSB; ~80.6°–81.4°N) and is covered by a thick succession of metasediments. A deep crustal root (~48 km) at ~79.6°N is interpreted as cratonic crust flexed beneath the Eurekan fold and thrust belt. The Carboniferous to Palaeogene sedimentary succession of the Sverdrup Basin is inferred to be up to 1–4 km thick, comparable to geologically-based estimates, near the western margin of the HSB.
    Keywords: Geodynamics and Tectonics
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    Joint analysis of GOCE gravity gradients data of gravitational potential and of gravity with seismological and geodynamic observations to infer mantle properties (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-20
    Description: Joint analysis of the seismic velocities and geoid, gravity and gravity gradients are used to constrain the viscosity profile within the mantle as well as the lateral density variations. Recent ESA's Gravity field and steady-state Ocean Circulation Explorer measurements of the second-order derivatives of the Earth's gravity potential give new possibilities to determine these mantle properties. Using a simple mantle model and seismic tomography results, we investigate how the gravitational potential, the three components of the gravity vector and the gravity gradients can bring information on the radial viscosity profile and on the mantle mass anomalies. We start with lateral density variations in the Earth's mantle based either on slab history or deduced from seismic tomography. The main uncertainties are: for the latter case, the relationship between seismic velocity and density—the so-called density/velocity scaling factor—and for the former case, the variation with depth of the density contrast between the cold slabs and the surrounding mantle. We perform a Monte Carlo search for the viscosity and the density/velocity scaling factor profiles within the mantle, which allows to fit the observed geoid, gravity and gradients of gravity. We compute the posterior probability distribution of the unknown parameters, and find that the gravity gradients improve the estimate of the scaling factor within the upper mantle, because of their sensitivity to the masses within the upper mantle, whereas the geoid and the gravity better constrain the scaling factor in the lower mantle. In the upper mantle, it is less than 0.02 in the upper part and about 0.08–0.14 in the lower part, and it is significantly larger for depths greater than 1200 km (about 0.32–0.34). In any case, the density/velocity scaling factor between 670 and 1150 km depth is not well constrained. We show that the viscosity of the upper part of the mantle is strongly correlated with the viscosity of the lower part of the mantle and that the viscosity profile is characterized by a decrease in the lower part of the upper mantle (about 10 20 –2  x  10 20 Pa s) and by an increase (about 10 23 –2  x  10 23 Pa s) at the top of the lower mantle (between 670 and 1150 km). The viscosity of the mantle below 1150 km depth is well estimated in our Monte Carlo search and is about 10 22 –4  x  10 22 Pa s.
    Keywords: Geodynamics and Tectonics
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    Acetone-butanol-ethanol fermentation of corn stover: current production methods, economic viability and commercial use (2016)
    Oxford University Press
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    Publication Date: 2016-03-02
    Description: Biobutanol is a next-generation liquid biofuel with properties akin to those of gasoline. There is a widespread effort to commercialize biobutanol production from agricultural residues, such as corn stover, which do not compete with human and animal foods. This pursuit is backed by extensive government mandates to expand alternative energy sources. This review provides an overview of research on biobutanol production using corn stover feedstock. Structural composition, pretreatment, sugar yield (following pretreatment and hydrolysis) and generation of lignocellulose-derived microbial inhibitory compounds (LDMICs) from corn stover are discussed. The review also discusses different Clostridium species and strains employed for biobutanol production from corn stover-derived sugars with respect to solvent yields, tolerance to LDMICs and in situ solvent recovery (integrated fermentation). Further, the economics of cellulosic biobutanol production are highlighted and compared to corn starch-derived ethanol and gasoline. As discussed herein, the economic competitiveness of biobutanol production from corn stover largely depends on feedstock processing and fermentation process design.
    Keywords: Biotechnology & Synthetic Biology
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    Topics: Biology
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    Topography caused by mantle density variations: observation-based estimates and models derived from tomography and lithosphere thickness (2016)
    Oxford University Press
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    Publication Date: 2016-03-02
    Description: Large-scale topography may be due to several causes, including (1) variations in crustal thickness and density structure, (2) oceanic lithosphere age differences, (3) subcrustal density variations in the continental lithosphere and (4) convective flow in the mantle beneath the lithosphere. The last contribution in particular may change with time and be responsible for continental inundations; distinguishing between these contributions is therefore important for linking Earth's history to its observed geological record. As a step towards this goal, this paper aims at such distinction for the present-day topography: the approach taken is deriving a ‘model’ topography due to contributions (3) and (4), along with a model geoid, using a geodynamic mantle flow model. Both lithosphere thickness and density anomalies beneath the lithosphere are inferred from seismic tomography. Density anomalies within the continental lithosphere are uncertain, because they are probably due to variations in composition and temperature, making a simple scaling from seismic to density anomalies inappropriate. Therefore, we test a number of different assumptions regarding these. As a reality check, model topography is compared, in terms of both correlation and amplitude ratio, to ‘residual’ topography, which follows from observed topography after subtracting contributions (1) and (2). The model geoid is compared to observations as well. Comparatively good agreement is found if there is either an excess density of 0.2 per cent in the lithosphere above 150 km depth, with anomalies below as inferred from tomography, or if the excess density is 0.4 per cent in the entire lithosphere. Further, a good fit is found for viscosity 10 20 Pa s in the asthenosphere, increasing to 10 23 Pa s in the lower mantle above D'. Results are quite dependent on which tomography models they are based on; for some recent ones, topography correlation is 0.6, many smaller scale features are matched, topography amplitude is less than 30 per cent too large, while geoid variance reduction exceeds 70 per cent—overall a considerable improvement compared to previous models. Correlation becomes less if smaller scale features (corresponding to spherical harmonic degrees 15 and higher), which are probably largely due to anomalies in the lithosphere, are also considered. Comparison of results with different viscosity structures, and a regional comparison of amplitude ratios, indicates that lateral viscosity variations can be quite strong, but only leading to moderate variations in model topography of a factor probably less than two.
    Keywords: Geodynamics and Tectonics
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    A Pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Biological production in heterologous hosts is of interest for the production of the C4 alcohol (butanol) and other chemicals. However, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. Pseudomonas putida is a potential host for solvent production; in order to further adapt P. putida to this role, we generated mini-Tn 5 mutant libraries in strain BIRD-1 that do not consume butanol. We analyzed the insertion site of the mini-Tn 5 in a mutant that was deficient in assimilation of butanol using arbitrary PCR followed by Sanger sequencing and found that the transposon was inserted in the malate synthase B gene. Here, we show that in a second round of mutagenesis a double mutant unable to take up butanol had an insertion in a gene coding for a multisensor hybrid histidine kinase. The genetic context of the histidine kinase sensor revealed the presence of a set of genes potentially involved in butanol assimilation; qRT-PCR analysis showed induction of this set of genes in the wild type and the malate synthase mutant but not in the double mutant.
    Keywords: Biotechnology & Synthetic Biology
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    Frontiers in microbial 1-butanol and isobutanol production (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: The heavy dependence on petroleum-derived fuel has raised concerns about energy sustainability and climate change, which have prompted researchers to explore fuel production from renewable sources. 1-Butanol and isobutanol are promising biofuels that have favorable properties and can also serve as solvents or chemical feedstocks. Microbial production of these alcohols provides great opportunities to access a wide spectrum of renewable resources. In recent years, research has improved the native 1-butanol production and has engineered isobutanol production in various organisms to explore metabolic diversity and a broad range of substrates. This review focuses on progress in metabolic engineering for the production of these two compounds using various resources.
    Keywords: Biotechnology & Synthetic Biology
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    Recent progress in biobutanol tolerance in microbial systems with an emphasis on Clostridium (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Biobased production of butanol promises a more sustainable route for industrial production. However, butanol toxicity remains a barrier for achieving high product titers. Investigation into butanol stress has shed some light on its modes of toxicity. Unfortunately, there still remain significant shortfalls in our understanding of the complex interactions of butanol with cells. To address this knowledge gap, a diverse range of tools have been employed to gain a better understanding of the adverse effects of butanol on the cell. These findings have lead to the identification of possible molecular mechanisms associated with butanol tolerance, which can be harnessed for future strain development efforts. This review focuses on recent efforts to address the toxicity of butanol in microbial producers and offers some perspectives on the future direction of this research sector.
    Keywords: Biotechnology & Synthetic Biology
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    Synergistic effect of calcium and zinc on glucose/xylose utilization and butanol tolerance of Clostridium acetobutylicum (2016)
    Oxford University Press
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    Publication Date: 2016-02-25
    Description: Biobutanol outperforms bioethanol as an advanced biofuel, but is not economically competitive in terms of its titer, yield and productivity associated with feedstocks and energy cost. In this work, the synergistic effect of calcium and zinc was investigated in the acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum using glucose, xylose and glucose/xylose mixtures as carbon source(s). Significant improvements associated with enhanced glucose/xylose utilization, cell growth, acids re-assimilation and butanol biosynthesis were achieved. Especially, the maximum butanol and ABE production of 16.1 and 25.9 g L –1 were achieved from 69.3 g L –1 glucose with butanol/ABE productivities of 0.40 and 0.65 g L –1 h –1 compared to those of 11.7 and 19.4 g/L with 0.18 and 0.30 g L –1 h –1 obtained in the control respectively without any supplement. More importantly, zinc was significantly involved in the butanol tolerance based on the improved xylose utilization under various butanol-shock conditions (2, 4, 6, 8 and 10 g L –1 butanol). Under the same conditions, calcium and zinc co-supplementation led to the best xylose utilization and butanol production. These results suggested that calcium and zinc could play synergistic roles improving ABE fermentation by C. acetobutylicum .
    Keywords: Biotechnology & Synthetic Biology
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    Along-strike variations of the partitioning of convergence across the Haiyuan fault system detected by InSAR (2016)
    Oxford University Press
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    Publication Date: 2016-03-03
    Description: Oblique convergence across Tibet leads to slip partitioning with the coexistence of strike-slip, normal and thrust motion on major fault systems. A key point is to understand and model how faults interact and accumulate strain at depth. Here, we extract ground deformation across the Haiyuan Fault restraining bend, at the northeastern boundary of the Tibetan plateau, from Envisat radar data spanning the 2001–2011 period. We show that the complexity of the surface displacement field can be explained by the partitioning of a uniform deep-seated convergence. Mountains and sand dunes in the study area make the radar data processing challenging and require the latest developments in processing procedures for Synthetic Aperture Radar interferometry. The processing strategy is based on a small baseline approach. Before unwrapping, we correct for atmospheric phase delays from global atmospheric models and digital elevation model errors. A series of filtering steps is applied to improve the signal-to-noise ratio across high ranges of the Tibetan plateau and the phase unwrapping capability across the fault, required for reliable estimate of fault movement. We then jointly invert our InSAR time-series together with published GPS displacements to test a proposed long-term slip-partitioning model between the Haiyuan and Gulang left-lateral Faults and the Qilian Shan thrusts. We explore the geometry of the fault system at depth and associated slip rates using a Bayesian approach and test the consistency of present-day geodetic surface displacements with a long-term tectonic model. We determine a uniform convergence rate of 10 [8.6–11.5] mm yr –1 with an N89 [81–97]°E across the whole fault system, with a variable partitioning west and east of a major extensional fault-jog (the Tianzhu pull-apart basin). Our 2-D model of two profiles perpendicular to the fault system gives a quantitative understanding of how crustal deformation is accommodated by the various branches of this thrust/strike-slip fault system and demonstrates how the geometry of the Haiyuan fault system controls the partitioning of the deep secular motion.
    Keywords: Geodynamics and Tectonics
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    Stability of the rate, state and temperature dependent friction model and its applications (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-03
    Description: In this paper, we study stability of the rate, state and temperature friction (RSTF) model. The Segall and Rice approach is used to model heat transfer at the sliding interface with its surroundings. The effect of pore pressure is not considered in the model to avoid the complex expression for critical stiffness. Linear stability analysis of the spring-mass sliding system is carried out with the ageing law under the quasistatic conditions in order to determine the critical stiffness above which sliding behaviour changes from unstable to stable or vice versa. Our numerical simulations establish that critical stiffness of the heated surface may increase or decrease from corresponding to the critical stiffness of the unheated surface depending on the relative values of two contradictory parameters related with velocity effect and temperature effect. Parametric studies are also carried out to understand shear velocity and temperature of the sliding surface dependence of steady friction. The RSTF model is also used to study the gravity induced failure of a creeping rock slope and the results are justified.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    Pseudomonas putida KT2440 markerless gene deletion using a combination of {lambda} Red recombineering and Cre/loxP site-specific recombination (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-07
    Description: Pseudomonas putida KT2440 is a saprophytic, environmental microorganism that plays important roles in the biodegradation of environmental toxic compounds and production of polymers, chemicals and secondary metabolites. Gene deletion of KT2440 usually involves cloning of the flanking homologous fragments of the gene of interest into a suicide vector followed by transferring into KT2440 via triparental conjugation. Selection and counterselection steps are then employed to generate gene deletion mutant. However, these methods are tedious and are not suitable for the manipulation of multiple genes simultaneously. Herein, a two-step, markerless gene deletion method is presented. First, homologous armsflanked loxP-neo-loxP was knocked-in to replace the gene of interest, then the kanamycin resistance marker is removed by Cre recombinase catalyzed site-specific recombination. Both two-plasmid and one-plasmid gene systems were established. MekR/P mekA regulated gene expression system was found to be suitable for tight Cre expression in one-plasmid deletion system. The straightforward, time saving and highly efficient markerless gene deletion strategy has the potential to facilitate the genetics and functional genomics study of P. putida KT2440.
    Keywords: Biotechnology & Synthetic Biology
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    Topics: Biology
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    Evaluation of viability, metabolic activity and spore quantity in clostridial cultures during ABE fermentation (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-02
    Description: Flow cytometry, in combination with fluorescent staining, was used to evaluate population heterogeneity in acetone-butanol–ethanol fermentation that was carried out with type strain Clostridium beijerinckii NCIMB 8052 and non-type C. pasteurianum NRRL B-598. A combination of propidium iodide (PI) and carboxyfluorescein diacetate (CFDA), PI plus Syto-9 and bis-oxonol (BOX) alone were employed to distinguish between active and damaged cells together with simultaneous detection of spores. These strategies provided valuable information on the physiological state of clostridia. CFDA and PI staining gave the best separation of four distinct subpopulations of enzymatically active cells, doubly stained cells, damaged cells and spores. Proportional representation of cells in particular sub-regions correlated with growth characteristics, fermentation parameters such as substrate consumption and product formation in both species under different cultivation conditions.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
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    Glacial isostatic adjustment in response to changing Late Holocene behaviour of ice streams on the Siple Coast, West Antarctica (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-08
    Description: The Siple Coast region of Antarctica contains a number of fast-flowing ice streams, which control the dynamics and mass balance of the region. These ice streams are known to undergo stagnation and reactivation cycles, which lead to ice thickness changes that may be sufficient to excite a viscous solid Earth response (glacial isostatic adjustment; GIA). This study aims to quantify Siple Coast ice thickness changes during the last 2000 yr in order to determine the degree to which they might contribute to GIA and associated present-day bedrock uplift rates. This is important because accurate modelling of GIA is necessary to determine the rate of present-day ice-mass change from satellite gravimetry. Recently-published reconstructions of ice-stream variability were used to create a suite of kinematic models for the stagnation-related thickening of Kamb Ice Stream since ~1850 AD, and a GIA model was used to predict present-day deformation rates in response to this thickening. A number of longer-term loading scenarios, which include the stagnation and reactivation of ice streams across the Siple Coast over the past 2000 yr, were also constructed, and used to investigate the longer term GIA signal in the region. Uplift rates for each of the ice loading histories, based on a range of earth models, were compared with regional GPS-observed uplift rates and an empirical GIA estimate. We estimate Kamb Ice Stream to have thickened by 70–130 m since stagnation ~165 years ago. Modelled present-day vertical motion in response to this load increase peaks at –17 mm yr –1 (i.e. 17 mm yr –1 subsidence) for the weakest earth models tested here. Comparison of the solid Earth response to ice load changes throughout the last glacial cycle, including ice stream stagnation and reactivation across the Siple Coast during the last 2000 yr, with an empirical GIA estimate suggests that the upper mantle viscosity of the region is greater than 1 x 10 20 Pa s. When upper mantle viscosity values of 1 x 10 20  Pa s or smaller are combined with our suite of ice-load scenarios we predict uplift rates across Siple Coast that are at least 4 mm yr –1 smaller than those predicted by the empirical GIA estimate. GPS data are unable to further constrain model parameters due to the distance of the GPS sites from the study area. Our results demonstrate that Late Holocene ice load changes related to the stagnation and reactivation of ice streams on the Siple Coast may play a dominant role in defining the present-day uplift signal. However, both the detailed Earth structure and deglacial history of the region need to be better constrained in order to reduce uncertainties associated with the GIA signal of this region.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    Simultaneous saccharification and fermentation of dilute alkaline-pretreated corn stover for enhanced butanol production by Clostridium saccharobutylicum DSM 13864 (2016)
    Oxford University Press
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    Publication Date: 2016-02-03
    Description: Simultaneous saccharification and fermentation (SSF) process was applied for biobutanol production by Clostridium saccharobutylicum DSM 13864 from corn stover (CS). The key influential factors in SSF process, including corn steep liquor concentration, dry biomass and enzyme loading, SSF temperature, inoculation size and pre-hydrolysis time were optimized. In 5-L bioreactor with SSF process, butanol titer and productivity of 12.3 g/L and 0.257 g/L/h were achieved at 48 h, which were 20.6% and 21.2% higher than those in separate hydrolysis and fermentation (SHF), respectively. The butanol yield reached 0.175 g/g pretreated CS in SSF, representing 50.9% increase than that in SHF (0.116 g/g pretreated CS). This study proves the feasibility of efficient and economic production of biobutanol from CS by SSF.
    Keywords: Biotechnology & Synthetic Biology
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    A glacial isostatic adjustment model for the central and northern Laurentide Ice Sheet based on relative sea level and GPS measurements (2016)
    Oxford University Press
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    Publication Date: 2016-04-29
    Description: The thickness and equivalent global sea level contribution of an improved model of the central and northern Laurentide Ice Sheet is constrained by 24 relative sea level histories and 18 present-day GPS-measured vertical land motion rates. The final model, termed Laur16, is derived from the ICE-5G model by holding the timing history constant and iteratively adjusting the thickness history, in four regions of northern Canada. In the final model, the last glacial maximum (LGM) thickness of the Laurentide Ice Sheet west of Hudson Bay was ~3.4–3.6 km. Conversely, east of Hudson Bay, peak ice thicknesses reached ~4 km. The ice model thicknesses inferred for these two regions represent, respectively, a ~30 per cent decrease and an average ~20–25 per cent increase to the load thickness relative to the ICE-5G reconstruction, which is generally consistent with other recent studies that have focussed on Laurentide Ice Sheet history. The final model also features peak ice thicknesses of 1.2–1.3 km in the Baffin Island region, a modest reduction relative to ICE-5G and unchanged thicknesses for a region in the central Canadian Arctic Archipelago west of Baffin Island. Vertical land motion predictions of the final model fit observed crustal uplift rates well, after an adjustment is made for the elastic crustal response to present-day ice mass changes of regional ice cover. The new Laur16 model provides more than a factor of two improvement of the fit to the RSL data ( 2 measure of misfit) and a factor of nine improvement to the fit of the GPS data (mean squared error measure of fit), compared to the ICE-5G starting model. Laur16 also fits the regional RSL data better by a factor of two and gives a slightly better fit to GPS uplift rates than the recent ICE-6G model. The volume history of the Laur16 reconstruction corresponds to an up to 8 m reduction in global sea level equivalent compared to ICE-5G at LGM.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Seismotectonics and rupture process of the MW 7.1 2011 Van reverse-faulting earthquake, eastern Turkey, and implications for hazard in regions of distributed shortening (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-23
    Description: The 2011 October 23 M W 7.1 Van earthquake in eastern Turkey caused ~600 deaths and caused widespread damage and economic loss. The seismogenic rupture was restricted to 10–25 km in depth, but aseismic surface creep, coincident with outcrop fault exposures, was observed in the hours to months after the earthquake. We combine observations from radar interferometry, seismology, geomorphology and Quaternary dating to investigate the geological slip rate and seismotectonic context of the Van earthquake, and assess the implications for continuing seismic hazard in the region. Transient post-seismic slip on the upper Van fault started immediately following the earthquake, and decayed over a period of weeks; it may not fully account for our long-term surface slip-rate estimate of ≥0.5 mm yr –1 . Post-seismic slip on the Bostanici splay fault initiated several days to weeks after the main shock, and we infer that it may have followed the M W  5.9 aftershock on the 9th November. The Van earthquake shows that updip segmentation can be important in arresting seismic ruptures on dip-slip faults. Two large, shallow aftershocks show that the upper 10 km of crust can sustain significant earthquakes, and significant slip is observed to have reached the surface in the late Quaternary, so there may be a continuing seismic hazard from the upper Van fault and the associated splay. The wavelength of folding in the hanging wall of the Van fault is dominated by the structure in the upper 10 km of the crust, masking the effect of deeper seismogenic structures. Thus, models of subsurface faulting based solely on surface folding and faulting in regions of reverse faulting may underestimate the full depth extent of seismogenic structures in the region. In measuring the cumulative post-seismic offsets to anthropogenic structures, we show that Structure-from-Motion can be rapidly deployed to create snapshots of post-seismic displacement. We also demonstrate the utility of declassified Corona mission imagery (1960s–1970s) for geomorphic mapping in areas where recent urbanization has concealed the geomorphic markers.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Construction and characterization of three protein-targeting expression system in Lactobacillus casei (2016)
    Oxford University Press
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    Publication Date: 2016-03-13
    Description: We previously reported that the β-1,4-Mannanase ( manB ) gene from Bacillus pumilus functions as a good reporter gene in Lactobacillus casei . Two vectors were constructed. One carries the signal peptide of secretion protein Usp45 (SP Usp45 ) from Lactococcus lactis (pELSH), and the other carries the full-length S-layer protein, SlpA, from L. acidophilus (pELWH). In this work, another vector, pELSPH, was constructed to include the signal peptide of protein SlpA (SP SlpA ), and the capacity of all three vectors to drive expression of the manB gene in L. casei was evaluated. The results showed that SP Usp45 is functionally recognized and processed by the L. casei secretion machinery. The SP Usp45 -mediated secretion efficiency was ~87%, and SP SlpA drove the export of secreted ManB with ~80% efficiency. SP SlpA secretion was highly efficient, and expressed SlpA was anchored to the cell wall by an unknown secretion mechanism. Full-length SlpA drove the cell wall-anchored expression of an SlpA-ManB fusion protein but at a much lower level than that of protein SlpA.
    Keywords: Biotechnology & Synthetic Biology
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    Lateral detachment in progress within the Vrancea slab (Romania): inferences from intermediate-depth seismicity patterns (2016)
    Oxford University Press
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    Publication Date: 2016-03-18
    Description: Within a slab experiencing present-day lateral break-off, a particular type of earthquakes is expected to cluster at the detachment horizon tip: namely, events generated by reverse faulting, with the approximately horizontal compression involved acting along the strike of the slab. Such a cluster of moderate magnitude earthquakes (4.7 ≤  m b ≤ 5.0) was identified in this study at the 160–175 km depth range of the Vrancea seismogenic body, in the Southeast Carpathians mountains collision environment. The corresponding cluster epicentres were systematically positioned at the boundary between a region being subject ( cf. published GPS records), to present-day upward movements, and another one that underwent present-day subsidence. Such an overall setting seems to suggest that a lateral break-off is currently developing at the indicated depth within the Vrancea slab, leading to topographic uplift above the already detached slab section, and to enhanced subsidence above the section to which the gravitational slab pull was being transferred. In addition, by taking into account some systematic time correspondence which we documented between moderate magnitude events of the 160–175 km depth cluster and the subsequent strong Vrancea shocks ( M w ≥ 6.9), it appears that the latter, although occurring at much shallower depths (roughly, in the 80–140 km range), were also controlled by the break-off progress.
    Keywords: Geodynamics and Tectonics
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    Circular structures of Bajada del Diablo (Argentina): geophysical signatures (2016)
    Oxford University Press
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    Publication Date: 2016-03-18
    Description: Bajada del Diablo is located in the Northern Patagonian Massif, Chubut, Argentina. The study area includes several circular structures found in Miocene olivine basalts of the Quiñelaf Eruptive Complex and in the Late Pliocene/Early Pleistocene Pampa Sastre conglomerates. An impact origin has been proposed for these circular structures. With the aim of further investigate the proposed impact origin, topographic, gravimetric, magnetic, resistivity, palaeomagnetic and electromagnetic surveys in two circular structures (‘8’ and ‘G’) located in Pampa Sastre conglomerates and in basalts of the Quiñelaf Eruptive Complex were carried out. The new geophysical results support the hypothesis of an impact origin. However, the confirmation of such an origin through the findings of shock metamorphism evidences and/or the recovery of meteorites remains elusive.
    Keywords: Geodynamics and Tectonics
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    Hetero-oligomeric MspA pores in Mycobacterium smegmatis (2016)
    Oxford University Press
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    Publication Date: 2016-03-13
    Description: The porin MspA of Mycobacterium smegmatis is a biological nanopore used for DNA sequencing. The octameric MspA pore can be isolated from M. smegmatis in milligram quantities, is extremely stable against denaturation and rapidly inserts into lipid membranes. Here, we show that MspA pores composed of different Msp subunits are formed in M. smegmatis and that hetero-oligomers of different Msp monomers increase the heterogeneity of MspA pores designed for DNA sequencing. To improve the quality of preparations of mutant MspA proteins, all four msp genes were deleted from the M. smegmatis genome after insertion of an inducible porin gene from M. tuberculosis. In the msp quadruple mutant M. smegmatis ML712 no Msp porins were detected and mutant MspA proteins were produced at wild-type levels. Lipid bilayer experiments demonstrated that MspA pores isolated from ML712 formed functional channels and had a narrower conductance distribution than pores purified from M. smegmatis with background msp expression. Thus, the M. smegmatis msp quadruple mutant improves the homogeneity of MspA pores designed for DNA sequencing and might also facilitate the identification and functional characterization of other mycobacterial pore proteins.
    Keywords: Biotechnology & Synthetic Biology
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    Butanol formation from gaseous substrates (2016)
    Oxford University Press
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    Publication Date: 2016-03-04
    Description: Mostly, butanol is formed as a product by saccharolytic anaerobes, employing the so-called ABE fermentation (for acetone–butanol–ethanol). However, this alcohol can also be produced from gaseous substrates such as syn(thesis) gas (major components are carbon monoxide and hydrogen) by autotrophic acetogens. In view of economic considerations, a biotechnological process based on cheap and abundant gases such as CO and CO 2 as a carbon source is preferable to more expensive sugar or starch fermentation. In addition, any conflict for use of substrates that can also serve as human nutrition is avoided. Natural formation of butanol has been found with, e.g. Clostridium carboxidivorans , while metabolic engineering for butanol production was successful using, e.g. C. ljungdahlii . Production of butanol from CO 2 under photoautotrophic conditions was also possible by recombinant DNA construction of a respective cyanobacterial Synechococcus sp. PCC 7942 strain.
    Keywords: Biotechnology & Synthetic Biology
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    A reassessment of in situ stress determination by hydraulic fracturing (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Estimating in situ stress based on hydraulic fracturing data typically depends on interpretation of the breakdown, secondary breakdown (‘reopening’) and shut-in pressure. While it has been recognized that the near-wellbore stress field should be taken into account and that the compressibility of the injection system and the viscous flow of the fluid can diminish the accuracy of stress estimates, these issues have not been well quantified. A coupled numerical model that includes the compressibility of the injection system and the flow of a viscous fluid in a plane-strain hydraulic fracture extending from a wellbore, in an impermeable rock, and in the presence of a non-isotropic in situ stress field provides a basic tool for estimating the order of the error associated with hydraulic fracturing stress measurements under non-ideal conditions. The main findings of this work are model-based guidelines on the values of relevant dimensionless parameter groups to ensure sufficient accuracy of stress estimates that use idealized models. When these guidelines cannot be met under field conditions, the model can be further applied to obtain first-order corrections that account for compressibility, viscosity and near-wellbore effects.
    Keywords: Geodynamics and Tectonics
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    Robust seismic velocity change estimation using ambient noise recordings (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: We consider the problem of seismic velocity change estimation using ambient noise recordings. Motivated by Zhan et al. , we study how the velocity change estimation is affected by seasonal fluctuations in the noise sources. More precisely, we consider a numerical model and introduce spatio-temporal seasonal fluctuations in the noise sources. We show that indeed, as pointed out by Zhan et al. , the stretching method is affected by these fluctuations and produces misleading apparent velocity variations which reduce dramatically the signal to noise ratio of the method. We also show that these apparent velocity variations can be eliminated by an adequate normalization of the cross-correlation functions. Theoretically we expect our approach to work as long as the seasonal fluctuations in the noise sources are uniform, an assumption which holds for closely located seismic stations. We illustrate with numerical simulations in homogeneous and scattering media that the proposed normalization significantly improves the accuracy of the velocity change estimation. Similar behaviour is also observed with real data recorded in the Aegean volcanic arc. We study in particular the volcano of Santorini during the seismic unrest of 2011–2012 and observe a decrease in the velocity of seismic waves which is correlated with GPS measured elevation.
    Keywords: Geodynamics and Tectonics
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    Lichen-forming fungus Caloplaca flavoruscens inhibits transcription factors and chromatin remodeling system in fungi (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Lichen-forming fungi and extracts derived from them have been used as alternative medicine sources for millennia and recently there has been a renewed interest in their known bioactive properties for anticancer agents, cosmetics and antibiotics. Although lichen-forming fungus-derived compounds are biologically and commercially valuable, few studies have been performed to determine their modes of action. This study used chemical-genetic and chemogenomic high-throughput analyses to gain insight into the modes of action of Caloplaca flavoruscens extracts. High-throughput screening of 575 lichen extracts was performed and 39 extracts were identified which inhibited yeast growth. A C. flavoruscens extract was selected as a promising antifungal and was subjected to genome-wide haploinsufficiency profiling and homozygous profiling assays. These screens revealed that yeast deletion strains lacking Rsc8, Pro1 and Toa2 were sensitive to three concentrations (IC 25.5 , IC 25 and IC 50 , respectively) of C. flavoruscens extract. Gene-enrichment analysis of the data showed that C. flavoruscens extracts appear to perturb transcription and chromatin remodeling.
    Keywords: Biotechnology & Synthetic Biology
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    Cytotoxic damage of soybean agglutinin on intestinal epithelial cells of broiler chicks: in vitro protection by Bifidobacterium infantis CRL1395 (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Plant lectins, which are proteins/glycoproteins present in a wide range of vegetables, fruits, cereals and beans, are resistant to digestive enzymes and food cooking temperatures. They bind reversibly to specific glycosidic residues expressed on the membrane of intestinal epithelial cells (IEC) and cause anti-nutritional effects in humans and animals. Soybean lectin (SBA) has been detected in poultry diets, and its ability to bind to the intestinal epithelium has been reported. The development of new methods for removing SBA from feeds or to prevent interaction with the intestinal mucosa is of interest. In this study, the in vitro cytotoxicity of SBA on IEC of chicks was demonstrated for the first time. The LD 50 , assessed after 2 h exposure of IEC to SBA, was 6.13 μg mL –1 . The ability of Bifidobacterium infantis CRL1395 to bind SBA on the bacterial envelope was confirmed, and prevention of IEC cytotoxicity by lectin removal was demonstrated. Safety of B. infantis CRL1395, resistance to gastrointestinal stress and adhesion were also determined. It was concluded that the early administration of B. infantis CRL1395 to chicks would effectively reduce the toxicity of SBA. Besides, it would favour the colonization of the gut with a beneficial microbiota.
    Keywords: Biotechnology & Synthetic Biology
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    Catalytic upgrading of butyric acid towards fine chemicals and biofuels (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: Fermentation-based production of butyric acid is robust and efficient. Modern catalytic technologies make it possible to convert butyric acid to important fine chemicals and biofuels. Here, current chemocatalytic and biocatalytic conversion methods are reviewed with a focus on upgrading butyric acid to 1-butanol or butyl-butyrate. Supported Ruthenium- and Platinum-based catalyst and lipase exhibit important activities which can pave the way for more sustainable process concepts for the production of green fuels and chemicals.
    Keywords: Biotechnology & Synthetic Biology
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    Passive seismic experiment and receiver functions analysis to determine crustal structure at the contact of the northern Dinarides and southwestern Pannonian Basin (2016)
    Oxford University Press
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    Publication Date: 2016-04-14
    Description: Passive seismic experiment was carried out at the SW contact of the Dinarides and Pannonian basin to determine the crustal structure and velocity discontinuities. The aim of the experiment was to define the relationship between the Adriatic microplate and the Pannonian segment as a part of the European plate. Most of the temporary seismic stations were deployed in Croatia along the Alp07 profile—a part of the active-source ALP 2002 project. About 300-km-long profile stretches from Istra peninsula to the Drava river, in a WSW–ESE direction. Teleseismic events recorded on 13 temporary seismic stations along the profile were analysed by P -receiver function method. Two types of characteristic receiver functions (RF) have been identified, belonging to Dinaridic and Pannonian crusts as defined on the Alp07 profile, while in transitional zone there are both types. Three major crustal discontinuities can be identified for the Dinaridic type: sedimentary basement, intracrustal discontinuity and Mohorovičić discontinuity, whereas the Pannonian type revealed only two discontinuities. The intracrustal discontinuity was not observed in the Pannonian type, thus pointing to a single-layered crust in the Pannonian basin. Two interpretation methods were applied: forward modelling of the receiver functions and H – stacking method, and the results were compared with the active-source seismic data at deep refraction profile Alp07. The receiver function modelling has given reliable results of the Moho depths that are in accordance with the seismic refraction results at the end of the Alp07 profile, that is in the area of Pannonian crust characterized by simple crustal structure and low seismic velocities ( Vp between 5.9 and 6.2 km s –1 ). In the Dinarides and its peripheral parts, receiver function modelling regularly gives greater Moho depths, up to +15 per cent, due to more complex crustal structure. The depths of the Moho calculated by the H – stacking method vary within wide limits (±13 km), due to band limited data of short-period stations. The results at five stations have to be rejected because of huge deviations in comparison with all previous results, while at the other seven stations the Moho depths vary within ±15 per cent around the Moho discontinuity of the Alp07 profile.
    Keywords: Geodynamics and Tectonics
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    Development of an inducible transposon system for efficient random mutagenesis in Clostridium acetobutylicum (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-15
    Description: Clostridium acetobutylicum is an industrially important Gram-positive organism, which is capable of producing economically important chemicals in the ABE (Acetone, Butanol and Ethanol) fermentation process. Renewed interests in the ABE process necessitate the availability of additional genetics tools to facilitate the derivation of a greater understanding of the underlying metabolic and regulatory control processes in operation through forward genetic strategies. In this study, a xylose inducible, mariner -based, transposon system was developed and shown to allow high-efficient random mutagenesis in the model strain ATCC 824. Of the thiamphenicol resistant colonies obtained, 91.9% were shown to be due to successful transposition of the catP- based mini-transposon element. Phenotypic screening of 200 transposon clones revealed a sporulation-defective clone with an insertion in spo0A , thereby demonstrating that this inducible transposon system can be used for forward genetic studies in C. acetobutylicum .
    Keywords: Biotechnology & Synthetic Biology
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    Keeping it simple: lessons from the golden era of antibiotic discovery (2016)
    Oxford University Press
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    Publication Date: 2016-04-15
    Description: Bacteria are becoming increasingly resistant to currently used antibiotics. At the same time, little progress has been made in discovering new antibacterial drugs to combat resistant organisms. History teaches us that ‘high tech’ target-based complex methods are not synonymous with success and a return to simple, systematic screening of natural products against bacteria from traditional and novel resources holds our greatest hope of success.
    Keywords: Biotechnology & Synthetic Biology
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    n-butanol: challenges and solutions for shifting natural metabolic pathways into a viable microbial production (2016)
    Oxford University Press
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    Publication Date: 2016-04-15
    Description: The economic upturn of the past 200 years would not have been conceivable without fossil resources such as coal and oil. However, the fossil-based economy increasingly reaches its limits and displays contradictions. Bioeconomy, strategically combining economy and ecology willing to make biobased and sustainable growth possible, is promising to make a significant contribution towards solving these issues. In this context, microbial bioconversions are promising to support partially the increasing need for materials and fuels starting from fresh, preferably waste, biomass. Butanol is a very attractive molecule finding applications both as a chemical platform and as a fuel. Today it principally derives from petroleum, but it also represents the final product of microbial catabolic pathways. Because of the need to maximize yield, titer and productivity to make the production competitive and viable, the challenge is to transform a robustly regulated metabolic network into the principal cellular activity. However, this goal can only be accomplished by a profound understanding of the cellular physiology, survival strategy and sensing/signalling cascades. Here, we shortly review on the natural cellular pathways and circumstances that lead to n -butanol accumulation, its physiological consequences that might not match industrial needs and on possible solutions for circumventing these natural constraints.
    Keywords: Biotechnology & Synthetic Biology
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    Afterslip and viscoelastic relaxation model inferred from the large-scale post-seismic deformation following the 2010 Mw 8.8 Maule earthquake (Chile) (2016)
    Oxford University Press
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    Publication Date: 2016-04-16
    Description: Megathrust earthquakes of magnitude close to 9 are followed by large-scale (thousands of km) and long-lasting (decades), significant crustal and mantle deformation. This deformation can be observed at the surface and quantified with GPS measurements. Here we report on deformation observed during the 5 yr time span after the 2010 M w 8.8 Maule Megathrust Earthquake (2010 February 27) over the whole South American continent. With the first 2 yr of those data, we use finite element modelling (FEM) to relate this deformation to slip on the plate interface and relaxation in the mantle, using a realistic layered Earth model and Burgers rheologies. Slip alone on the interface, even up to large depths, is unable to provide a satisfactory fit simultaneously to horizontal and vertical displacements. The horizontal deformation pattern requires relaxation both in the asthenosphere and in a low-viscosity channel along the deepest part of the plate interface and no additional low-viscosity wedge is required by the data. The vertical velocity pattern (intense and quick uplift over the Cordillera) is well fitted only when the channel extends deeper than 100 km. Additionally, viscoelastic relaxation alone cannot explain the characteristics and amplitude of displacements over the first 200 km from the trench and aseismic slip on the fault plane is needed. This aseismic slip on the interface generates stresses, which induce additional relaxation in the mantle. In the final model, all three components (relaxation due to the coseismic slip, aseismic slip on the fault plane and relaxation due to aseismic slip) are taken into account. Our best-fit model uses slip at shallow depths on the subduction interface decreasing as function of time and includes (i) an asthenosphere extending down to 200 km, with a steady-state Maxwell viscosity of 4.75 x 10 18 Pa s; and (ii) a low-viscosity channel along the plate interface extending from depths of 55–135 km with viscosities below 10 18 Pa s.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    The new release of the Italian contemporary stress map (2016)
    Oxford University Press
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    Publication Date: 2016-04-16
    Description: We provide an updated present-day stress map for the Italian territory. Following the World Stress Map (WSM) Project guidelines, we list the different stress indicators, explaining the criteria used to select data. We discuss the data, which will also be included in the 2016 release of the WSM, highlighting the areas for which we have added stress information. Our map displays the minimum horizontal stress orientations inferred from crustal stress indicators down to 40 km depth using data of A–C quality, updated for earthquakes until December 2015. We have completely reviewed all data, and the data set now contains 855 entries, in contrast to the previous 715. The number of data with A–C quality of 630 corresponds to an increase of 26 per cent relative to the previous data set. In particular, the new data set contains the results of the analysis of borehole breakouts, critically reviewed data from earthquake focal mechanisms, data concerning active faults, formal inversions of focal mechanisms of seismic sequences or of restricted areas and one stress determination from overcoring. The new data set defines the stress field in areas not well covered by the previous data: the region north to the Po Plain and the central Adriatic sea, both characterized by a thrust- and strike-faulting regime, the northern Sicilian belt with a prevailing normal-faulting regime, and the Ionian sea with a strike-slip regime.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Downstream process options for the ABE fermentation (2016)
    Oxford University Press
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    Publication Date: 2016-04-20
    Description: Butanol is a very interesting substance both for the chemical industry and as a biofuel. The classical distillation process for the removal of butanol is far too energy demanding, at a factor of 220% of the energy content of butanol. Alternative separation processes studied are hybrid processes of gas-stripping, liquid–liquid extraction and pervaporation with distillation and a novel adsorption/drying/desorption hybrid process. Compared with the energy content of butanol, the resulting energy demand for butanol separation and concentration of optimized hybrid processes is 11%–22% for pervaporation/distillation and 11%–17% for liquid–liquid extraction/distillation. For a novel adsorption/drying/desorption process, the energy demand is 9.4%. But all downstream process options need further proof of industrial applicability.
    Keywords: Biotechnology & Synthetic Biology
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    System-level modeling of acetone-butanol-ethanol fermentation (2016)
    Oxford University Press
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    Publication Date: 2016-04-20
    Description: Acetone–butanol–ethanol (ABE) fermentation is a metabolic process of clostridia that produces bio-based solvents including butanol. It is enabled by an underlying metabolic reaction network and modulated by cellular gene regulation and environmental cues. Mathematical modeling has served as a valuable strategy to facilitate the understanding, characterization and optimization of this process. In this review, we highlight recent advances in system-level, quantitative modeling of ABE fermentation. We begin with an overview of integrative processes underlying the fermentation. Next we survey modeling efforts including early simple models, models with a systematic metabolic description, and those incorporating metabolism through simple gene regulation. Particular focus is given to a recent system-level model that integrates the metabolic reactions, gene regulation and environmental cues. We conclude by discussing the remaining challenges and future directions towards predictive understanding of ABE fermentation.
    Keywords: Biotechnology & Synthetic Biology
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    Dynamics and excess temperature of a plume throughout its life cycle (2016)
    Oxford University Press
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    Publication Date: 2016-04-20
    Description: Measurements of the velocity field associated with plumes rising through a viscous fluid are performed using stereoscopic Particle-Image Velocimetry in the Rayleigh number range 4.4 x 10 5 –6.4 x 10 5 . The experimental model is analogous to a mantle plume rising from the core–mantle boundary to the base of the lithosphere. The behaviour of the plume is studied throughout its life cycle, which is broken up into four stages; the Formation Stage, when the plume forms; the Rising Stage, when the plume rises through the fluid; the Spreading Stage, when the plume reaches the surface and spreads; and finally the Declining Stage, when the heat source has been removed and the plume weakens. The latter three stages are examined in terms of the Finite-Time Lyapunov Exponent fields and the advection of passive tracers throughout the flow. The temperature at the heater and near the fluid surface are measured using thermocouples to infer how the presence of a mantle plume would produce excess temperature near the lithosphere throughout the various stages of its life cycle. In all experiments, a time lag is observed between the removal of the heat source and the decline in the excess temperature near the surface, which is proportional to the rise time. A simple analytical model is presented, which suggests that under mantle conditions (i.e. negligible thermal diffusion), the relationship between the time lag and the rise time is robust and independent of the Rayleigh number; however, the constant of proportionality is closer to unity in the absence of diffusion. Once the heat source is removed, the excess temperature near the surface declines exponentially at a rate that is inversely proportional to the rise time. The implications of this result are discussed in terms of the decline in volcanism in the Louisville hotspot chain over the past 20 Ma. The rise velocity of material in the plume is examined; the rise velocity is found to vary significantly with the plume height in a manner that is inconsistent with many of the common semi-analytical models of thermal plumes in the literature. It is also argued that this height dependency will cause estimates of the rise velocity based on the decay series of uranium isotopes to significantly underestimate the true value.
    Keywords: Geodynamics and Tectonics
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    Cry-like genes, in an uncommon gene configuration, produce a crystal that localizes within the exosporium when expressed in an acrystalliferous strain of Bacillus thuringiensis (2016)
    Oxford University Press
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    Publication Date: 2016-02-10
    Description: Cry proteins are pesticidal toxins produced by the bacterium Bacillus thuringiensis (Bt), which aggregate in sporulating cells to form a crystal. Except in a relatively few cases, these crystals are located outside the exosporium that surrounds the spore. Bt2-56 is a strain of Bt that has the relatively uncommon characteristic of locating its Cry protein-containing crystal within the exosporium, and in association with a long, multifiber filament. With the ultimate goal of both understanding and manipulating the localization of Cry proteins within the exosporium, we sought to identify the genes coding for the exosporium-localized Cry proteins in Bt2-56. Herein we show (i) that five cry-like genes are present in the genome of Bt2-56, (ii) that two pairs of these genes show organizational similarity to a relatively uncommon gene configuration that coexpress a cry gene along with a gene whose product aids crystal formation and (iii) that when one of these two gene pairs (cry21A-cdA) is expressed in an acrystalliferous strain of Bt, crystals are formed that localize within the exosporium. In Bt ssp. finitimus , the only other strain in which crystal localization has been studied, a Cry protein needed expression of two non-cry ORFs in order to localize within the exosporium, indicating that there are some mechanistic differences for crystal localization between Bt ssp. finitimus and Bt2-56.
    Keywords: Biotechnology & Synthetic Biology
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    GPS constraints on interplate locking within the Makran subduction zone (2016)
    Oxford University Press
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    Publication Date: 2016-02-10
    Description: The Makran subduction zone is one of the last convergent margins to be investigated using space-based geodesy. While there is a lack of historical and modern instrumentation in the region, a sparse sampling of continuous and campaign measurements over the past decade has allowed us to make the first estimates of convergence rates. We combine GPS measurements from 20 stations located in Iran, Pakistan and Oman along with hypocentral locations from the International Seismological Centre to create a preliminary 3-D estimate of the geometry of the megathrust, along with a preliminary fault-coupling model for the Makran subduction zone. Using a convergence rate which is strongly constrained by measurements from the incoming Arabia plate along with the backslip method of Savage, we find the Makran subduction zone appears to be locked to a depth of at least 38 km and accumulating strain.We also find evidence for a segmentation of plate coupling, with a 300 km long section of reduced plate coupling. The range of acceptable locking depths from our modelling and the 900 km along-strike length for the megathrust, makes the Makran subduction zone capable of earthquakes up to M w  = 8.8. In addition, we find evidence for slow-slip-like transient deformation events on two GPS stations. These observations are suggestive of transient deformation events observed in Cascadia, Japan and elsewhere.
    Keywords: Geodynamics and Tectonics
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    Production of biobutanol from cellulose hydrolysate by the Escherichia coli co-culture system (2016)
    Oxford University Press
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    Publication Date: 2016-02-12
    Description: The commercialization of the n -butanol bioprocess is largely dependent on the price of feedstocks. Renewable cellulose appears to be an appealing feedstock. The microbial production of n -butanol still remains challenging because of the limited availability of intracellular NADH. To address this issue, an Escherichia coli strain carrying the clostridial CoA-dependent pathway was supplied with heterologous formate dehydrogenase. With the cellulose hydrolysate of rice straw, this single strain produced cellulosic biobutanol with a production yield at 35% of the theoretical and a productivity of 0.093 g L –1  h –1 . In an alternative method, the production involved a co-culture system consisting of two separate strains provided with the full CoA-dependent pathway. This system achieved a production yield and productivity reaching 62.8% of the theoretical and 0.163 g L –1  h –1 , respectively. The result indicates that the E. coli co-culture system is technically promising for the production of cellulosic biobutanol.
    Keywords: Biotechnology & Synthetic Biology
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    Constraining mantle convection models with palaeomagnetic reversals record and numerical dynamos (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: We present numerical models of mantle dynamics forced by plate velocities history in the last 450 Ma. The lower-mantle rheology and the thickness of a dense basal layer are systematically varied and several initial procedures are considered for each case. For some cases, the dependence on the mantle convection vigour is also examined. The resulting evolution of the CMB heat flux is analysed in terms of criteria to promote or inhibit reversals inferred from numerical dynamos. Most models present a rather dynamic lower mantle with the emergence of two thermochemical piles towards present-day. Only a small minority of models present two stationary piles over the last 450 Myr. At present-day, the composition field obtained in our models is found to correlate better with tomography than the temperature field. In addition, the temperature field immediately at the CMB (and thus the heat flux pattern) slightly differs from the average temperature field over the 100-km thick mantle layer above it. The evolution of the mean CMB heat flux or of the amplitude of heterogeneity seldom presents the expected correlation with the evolution of the palaeomagnetic reversal frequency suggesting these effects cannot explain the observations. In contrast, our analysis favours ‘inertial control’ on the geodynamo associated with polar cooling and in some cases break of Taylor columns in the outer core as sources of increased reversal frequency. Overall, the most likely candidates among our mantle dynamics models involve a viscosity increase in the mantle equal or smaller than 30: models with a discontinuous viscosity increase at the transition zone tend to agree better at present-day with observations of seismic tomography, but models with a gradual viscosity increase agree better with some of the criteria proposed to affect reversal frequency.
    Keywords: Geodynamics and Tectonics
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    Dynamic topography, gravity and the role of lateral viscosity variations from inversion of global mantle flow (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: Lateral viscosity variations (LVVs) in the mantle influence geodynamic processes and their surface expressions. With the observed long-wavelength geoid, free-air anomaly, gravity gradient in three directions and discrete, high-accuracy residual topography, we invert for depth- and temperature-dependent and tectonically regionalized mantle viscosity with a mantle flow model. The inversions suggest that long-wavelength gravitational and topographic signals are mainly controlled by the radial viscosity profile; the pre-Cambrian lithosphere viscosity is slightly (~ one order of magnitude) higher than that of oceanic and Phanerozoic lithosphere; plate margins are substantially weaker than plate interiors; and viscosity has only a weak apparent, dependence on temperature, suggesting either a balancing between factors or a smoothing of actual higher amplitude, but short wavelength, LVVs. The predicted large-scale lithospheric stress regime (compression or extension) is consistent with the world stress map (thrust or normal faulting). Both recent compiled high-accuracy residual topography and the predicted dynamic topography yield ~1 km amplitude long-wavelength dynamic topography, inconsistent with recent studies suggesting amplitudes of ~100 to ~500 m. Such studies use a constant, positive admittance (transfer function between topography and gravity), in contrast to the evidence which shows that the earth has a spatially and wavelength-dependent admittance, with large, negative admittances between ~4000 and ~10 4 km wavelengths.
    Keywords: Geodynamics and Tectonics
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    Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach (2016)
    Oxford University Press
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    Publication Date: 2016-10-29
    Description: We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Crustal metamorphic fluid flux beneath the Dead Sea Basin: constraints from 2-D and 3-D magnetotelluric modelling (2016)
    Oxford University Press
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    Publication Date: 2016-10-27
    Description: We report on a study to explore the deep electrical conductivity structure of the Dead Sea Basin (DSB) using magnetotelluric (MT) data collected along a transect across the DSB where the left lateral strike-slip Dead Sea transform (DST) fault splits into two fault strands forming one of the largest pull-apart basins of the world. A very pronounced feature of our 2-D inversion model is a deep, subvertical conductive zone beneath the DSB. The conductor extends through the entire crust and is sandwiched between highly resistive structures associated with Precambrian rocks of the basin flanks. The high electrical conductivity could be attributed to fluids released by dehydration of the uppermost mantle beneath the DSB, possibly in combination with fluids released by mid- to low-grade metamorphism in the lower crust and generation of hydrous minerals in the middle crust through retrograde metamorphism. Similar high conductivity zones associated with fluids have been reported from other large fault systems. The presence of fluids and hydrous minerals in the middle and lower crust could explain the required low friction coefficient of the DST along the eastern boundary of the DSB and the high subsidence rate of basin sediments. 3-D inversion models confirm the existence of a subvertical high conductivity structure underneath the DSB but its expression is far less pronounced. Instead, the 3-D inversion model suggests a deepening of the conductive DSB sediments off-profile towards the south, reaching a maximum depth of approximately 12 km, which is consistent with other geophysical observations. At shallower levels, the 3-D inversion model reveals salt diapirism as an upwelling of highly resistive structures, localized underneath the Al-Lisan Peninsula. The 3-D model furthermore contains an E–W elongated conductive structure to the northeast of the DSB. More MT data with better spatial coverage are required, however, to fully constrain the robustness of the above-mentioned off-profile features.
    Keywords: Geodynamics and Tectonics
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    Preparation and evaluation of MS2 bacteriophage-like particles packaging hepatitis E virus RNA (2016)
    Oxford University Press
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    Publication Date: 2016-11-09
    Description: Hepatitis E virus (HEV) is the pathogen causing hepatitis E (HE). It arouses global public health concern since it is a zoonotic disease. The objective of this letter is to report a cost-effective internal control prepared for monitoring procedures of HEV reverse transcriptase (RT)-PCR detection. A selected conserved HEV RNA fragment was integrated into the downstream of the truncated MS2 bacteriophage genome based on Armored RNA technology. The resulting MS2-HEV gene harbored by the pET-28b-MS2-HEV plasmid was transformed into E. coli BL21(DE3) for expression analysis by SDS-PAGE. The expression products were purified and concentrated by ultrasonication and ultrafiltration separation. The morphology and stability properties of the virus-like particles (VLPs) were evaluated by electron microscopy scanning and nuclease challenges, respectively. SDS-PAGE results showed that the constructed MS2-HEV gene expressed efficiently and the purity of the VLPs was highly consistent with the result in electron microscopy. Stability evaluation results demonstrated that the prepared VLPs exhibited strong resistance to DNase I and RNase A attacks and also performed long-lasting protection of coated HEV RNA for at least 4 months at –20°C. These data revealed that the prepared VLPs meet the basic requirements of use as internal control material in the HEV RNA amplification assay.
    Keywords: Biotechnology & Synthetic Biology
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    A new approach to assess isostatic compensation of topography in continental domain from GOCE gravity gradients (2016)
    Oxford University Press
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    Publication Date: 2016-09-09
    Description: Estimating how topography is maintained provides insights into the different factors responsible for surface deformations and their relative roles. Here, we develop a new and simple approach to assess the degree of isostatic compensation of continental topography at regional scale from GOCE gravity gradients. We calculate the ratio between the radial gradient observed by GOCE and that calculated from topography only. From analytical and statistical formulations, simple relationships between this ratio and the degree of compensation are obtained under the Airy–Heiskanen isostasy hypothesis. Then, a value of degree of compensation at each point of study area can be easily deduced. We apply our method to the Alaska-Canada Cordillera and validate our results by comparison with a standard isostatic gravity anomaly model and additional geophysical information for this area. Both our GOCE-based results and the isostatic anomaly show that Airy–Heiskanen isostasy prevails for the Yukon Plateau whereas additional mechanisms are required to support topography below the Northwest Territories Craton and the Yakutat collision zone.
    Keywords: Geodynamics and Tectonics
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    Epigenetics knocks on synthetic biology's door (2016)
    Oxford University Press
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    Publication Date: 2016-09-08
    Description: Epigenetics is the study of heritable changes in gene expression without concomitant changes in DNA sequence. Due to its relevance in development, differentiation and human health, epigenetics has recently become an emerging area of science with regard to eukaryotic organisms and has shown enormous potential in synthetic biology. However, significant examples of epigenetic regulation in bacterial synthetic biology have not yet been reported. In the current study, we present the first model of such an epigenetic circuit. We termed the circuit the alternator circuit because parental cells carrying this circuit and their progeny alternate between distinct and heritable cellular fates without undergoing changes in genome sequence. Furthermore, we demonstrated that the alternator circuit exhibits hysteresis because its output depends not only on its present state but also on its previous states.
    Keywords: Biotechnology & Synthetic Biology
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    Appraisal of geodynamic inversion results: a data mining approach (2016)
    Oxford University Press
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    Publication Date: 2016-09-11
    Description: Bayesian sampling based inversions require many thousands or even millions of forward models, depending on how nonlinear or non-unique the inverse problem is, and how many unknowns are involved. The result of such a probabilistic inversion is not a single ‘best-fit’ model, but rather a probability distribution that is represented by the entire model ensemble. Often, a geophysical inverse problem is non-unique, and the corresponding posterior distribution is multimodal, meaning that the distribution consists of clusters with similar models that represent the observations equally well. In these cases, we would like to visualize the characteristic model properties within each of these clusters of models. However, even for a moderate number of inversion parameters, a manual appraisal for a large number of models is not feasible. This poses the question whether it is possible to extract end-member models that represent each of the best-fit regions including their uncertainties. Here, I show how a machine learning tool can be used to characterize end-member models, including their uncertainties, from a complete model ensemble that represents a posterior probability distribution. The model ensemble used here results from a nonlinear geodynamic inverse problem, where rheological properties of the lithosphere are constrained from multiple geophysical observations. It is demonstrated that by taking vertical cross-sections through the effective viscosity structure of each of the models, the entire model ensemble can be classified into four end-member model categories that have a similar effective viscosity structure. These classification results are helpful to explore the non-uniqueness of the inverse problem and can be used to compute representative data fits for each of the end-member models. Conversely, these insights also reveal how new observational constraints could reduce the non-uniqueness. The method is not limited to geodynamic applications and a generalized MATLAB code is provided to perform the appraisal analysis.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Inference of mantle viscosity for depth resolutions of GIA observations (2016)
    Oxford University Press
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    Publication Date: 2016-09-14
    Description: Inference of the mantle viscosity from observations for glacial isostatic adjustment (GIA) process has usually been conducted through the analyses based on the simple three-layer viscosity model characterized by lithospheric thickness, upper- and lower-mantle viscosities. Here, we examine the viscosity structures for the simple three-layer viscosity model and also for the two-layer lower-mantle viscosity model defined by viscosities of 670, D (670- D km depth) and D ,2891 ( D -2891 km depth) with D -values of 1191, 1691 and 2191 km. The upper-mantle rheological parameters for the two-layer lower-mantle viscosity model are the same as those for the simple three-layer one. For the simple three-layer viscosity model, rate of change of degree-two zonal harmonics of geopotential due to GIA process (GIA-induced 2 ) of –(6.0–6.5)  x  10 –11 yr –1 provides two permissible viscosity solutions for the lower mantle, (7–20)  x  10 21 and (5–9)  x  10 22  Pa s, and the analyses with observational constraints of the 2 and Last Glacial Maximum (LGM) sea levels at Barbados and Bonaparte Gulf indicate (5–9)  x  10 22  Pa s for the lower mantle. However, the analyses for the 2 based on the two-layer lower-mantle viscosity model only require a viscosity layer higher than (5–10)  x  10 21  Pa s for a depth above the core–mantle boundary (CMB), in which the value of (5–10)  x  10 21  Pa s corresponds to the solution of (7–20)  x  10 21  Pa s for the simple three-layer one. Moreover, the analyses with the 2 and LGM sea level constraints for the two-layer lower-mantle viscosity model indicate two viscosity solutions: 670,1191  〉 3  x  10 21 and 1191,2891  ~ (5–10)  x  10 22  Pa s, and 670,1691  〉 10 22 and 1691,2891  ~ (5–10)  x  10 22  Pa s. The inferred upper-mantle viscosity for such solutions is (1–4)  x  10 20  Pa s similar to the estimate for the simple three-layer viscosity model. That is, these analyses require a high viscosity layer of (5–10)  x  10 22  Pa s at least in the deep mantle, and suggest that the GIA-based lower-mantle viscosity structure should be treated carefully in discussing the mantle dynamics related to the viscosity jump at ~670 km depth. We also preliminarily put additional constraints on these viscosity solutions by examining typical relative sea level (RSL) changes used to infer the lower-mantle viscosity. The viscosity solution inferred from the far-field RSL changes in the Australian region is consistent with those for the 2 and LGM sea levels, and the analyses for RSL changes at Southport and Bermuda in the intermediate region for the North American ice sheets suggest the solution of 670, D  〉 10 22 , D ,2891  ~ (5–10)  x  10 22  Pa s ( D  = 1191 or 1691 km) and upper-mantle viscosity higher than 6  x  10 20  Pa s.
    Keywords: Geodynamics and Tectonics
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    The endolysin from the Enterococcus faecalis bacteriophage VD13 and conditions stimulating its lytic activity (2016)
    Oxford University Press
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    Publication Date: 2016-10-12
    Description: Bacteriophages produce endolysins (peptidoglycan hydrolases) to lyse the host cell from within and release nascent bacteriophage particles. Recombinant endolysins can lyse Gram-positive bacteria when added exogenously. As a potential alternative antimicrobial, we cloned and expressed the enterococcal VD13 bacteriophage endolysin. VD13 endolysin has a CHAP catalytic domain with 92% identity with the bacteriophage IME-EF1 endolysin. The predicted size of VD13 endolysin is ~27 kDa as verified by SDS-PAGE. The VD13 endolysin lyses Enterococcus faecalis strains, but not E. faecium or other non-enterococci. VD13 endolysin has activity from pH 4 to pH 8, with peak activity at pH 5, and exhibits greater activity in the presence of calcium. Optimum activity at pH 5 occurs in the absence of NaCl. VD13 endolysin, in ammonium acetate (C 2 H 3 O 2 NH 4 ) calcium chloride (CaCl 2 ) buffer pH 5, is stimulated to higher activity upon heating at temperatures up to 65°C for 30 min, whereas activity is lost upon heating to 42°C, in pH 7 buffer.
    Keywords: Biotechnology & Synthetic Biology
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    Topics: Biology
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  • 86
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    Resistivity distribution from mid-crustal conductor to near-surface across the 1200 km long Liquine-Ofqui Fault System, southern Chile (2016)
    Oxford University Press
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    Publication Date: 2016-10-16
    Description: Mid-crustal conductors are a common phenomenon in magnetotelluric studies. In the Andean Cordillera of southern Chile, they appear to concentrate along major fault zones. A high-resolution, broad-band magnetotelluric survey including 31 stations has been carried out along two profiles perpendicular to (1) the Liquiñe-Ofqui Fault Systems (LOFS) and (2) the Villarrica-Quetrupillán-Lanín volcanic lineament running parallel to the Mocha-Villarrica Fault Zone (MVFZ). The survey aimed at tracing one of the known conductors from mid-crustal depth to near-surface along these faults. Directionality and dimensionality were analysed using tensor decomposition. Phase tensors and induction arrows reveal two major geoelectric strike directions following the strike of LOFS and MVFZ. 2-D inversion shows low resistivity zones along both fault systems down to a depth of 〉10 km, where the brittle-ductile transition is expected. Along the LOFS, the two anomalies are linked to (1) Lake Caburgua, where the LOFS broadens to about 2 km of lateral extension and seems to represent a pull-apart structure, and (2) the intersection with the Villarrica-Quetrupillán-Lanín volcanic lineament, where seismic activity was observed during the latest eruption in March 2015. A connection of the mid-crustal conductor to the ESE-WNW-striking fault zones is indicated from the presented data.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor (2016)
    Oxford University Press
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    Publication Date: 2016-09-08
    Description: Cultivation in a bioreactor of immobilized deep-sea hydrothermal microbial community was tested in order to assess the stability and reactivity of this new system. A community composed of eight hydrothermal strains was entrapped in a polymer matrix that was used to inoculate a continuous culture in a gas-lift bioreactor. The continuous culture was performed for 41 days at successively 60°C, 55°C, 60°C, 85°C and 60°C, at pH 6.5, in anaerobic condition and constant dilution rate. Oxic stress and pH variations were tested at the beginning of the incubation. Despite these detrimental conditions, three strains including two strict anaerobes were maintained in the bioreactor. High cell concentrations (3 x 10 8 cells mL –1 ) and high ATP contents were measured in both liquid fractions and beads. Cloning-sequencing and qPCR revealed that Bacillus sp. dominated at the early stage, and was later replaced by Thermotoga maritima and Thermococcus sp. Acetate, formate and propionate concentrations varied simultaneously in the liquid fractions. These results demonstrate that these immobilized cells were reactive to culture conditions. They were protected inside the beads during the stress period and released in the liquid fraction when conditions were more favorable. This confirms the advantage of immobilization that highlights the resilience capacity of certain hydrothermal microorganisms after a stress period.
    Keywords: Biotechnology & Synthetic Biology
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    Topics: Biology
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  • 88
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    High-resolution reconstructions of Pacific-North America plate motion: 20 Ma to present (2016)
    Oxford University Press
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    Publication Date: 2016-09-14
    Description: We present new rotations that describe the relative positions and velocities of the Pacific and North America plates at 22 times during the past 19.7 Myr, offering 1-Myr temporal resolution for studies of the geotectonic evolution of western North America and other plate boundary locations. Derived from 18 000 magnetic reversal, fracture zone and transform fault identifications from the Pacific–Antarctic–Nubia–North America plate circuit and the velocities of 935 GPS sites on the Pacific and North America plates, the new rotations and GPS-derived angular velocity indicate that the rate of motion between the two plates increased by 70 per cent from 19.7 to 9±1 Ma, but changed by less than 2 per cent since 8 Ma and even less since 4.2 Ma. The rotations further suggest that the relative plate direction has rotated clockwise for most of the past 20 Myr, with a possible hiatus from 9 to 5 Ma. This conflicts with previously reported evidence for a significant clockwise change in the plate direction at 8–6 Ma. Our new rotations indicate that Pacific plate motion became obliquely convergent with respect to the San Andreas Fault of central California at 5.2–4.2 Ma, in agreement with geological evidence for a Pliocene onset of folding and faulting in central California. Our reconstruction of the northern Gulf of California at 6.3 Ma differs by only 15–30 km from structurally derived reconstructions after including 3–4 km Myr –1 of geodetically measured slip between the Baja California Peninsula and Pacific plate. This implies an approximate 15–30 km upper bound for plate non-rigidity integrated around the global circuit at 6.3 Ma. A much larger 200±54 km discrepancy between our reconstruction of the northern Gulf of California at 12 Ma and that estimated from structural and marine geophysical observations suggests that faults in northwestern Mexico or possibly west of the Baja California Peninsula accommodated large amounts of obliquely divergent dextral shear from 12–6.3 Ma. Pacific–North America plate motion since 16 Myr estimated with our new rotations agrees well with structurally summed deformation along two transects of western North America between the Colorado Plateau and western California, with a difference as small as 40 km out of 760 km of margin-parallel motion. A strong resemblance between a 20-Myr-to-present flow line reconstructed with our new rotations and the traces of the 700-km-long Queen Charlotte Fault and continental slope west of Canada suggests that the plate margin geometry was influenced by the passage of the Pacific plate and Yakutat block. The new rotations also suggest that (1) oblique convergence west of Canada initiated at 12–11 Ma, 5–8 Myr earlier than previously estimated, (2) no significant margin-normal shortening has occurred in areas of Canada located east of the Haida Gwaii archipelago since 20 Ma and (3) Pacific plate underthrusting of Haida Gwaii has accommodated the margin-normal component of plate motion since 12–11 Ma. Our rotations suggest an 70 per cent increase in the rate that the Pacific plate has been consumed by subduction beneath the Aleutian arc since 19.7 Ma, with still-unknown consequences for the rate of arc magmatism.
    Keywords: Geodynamics and Tectonics
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    Topics: Geosciences
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    A simple technique for suppressor detection in Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-10-12
    Description: To study the viability of a gyrA S83 stop mutation found in an Escherichia coli J53 ciprofloxacin-resistant strain (J53 CipR27), a pBR322 derivative was constructed with a TAG mutation in the bla gene knocking out ampicillin resistance. Ampicillin resistance was restored, suggesting that the strain contains tRNA suppressor activity able to suppress the UAG codon gyrA and allow viability. The method was applied to 22 unique clinical E. coli isolates, and all were found to have low-level suppressor activity.
    Keywords: Biotechnology & Synthetic Biology
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    Enterotoxigenic Escherichia coli heat-stable toxin and heat-labile toxin toxoid fusion 3xSTaN12S-dmLT induces neutralizing anti-STa antibodies in subcutaneously immunized mice (2016)
    Oxford University Press
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    Publication Date: 2016-11-17
    Description: Enterotoxigenic Escherichia coli (ETEC) bacteria producing heat-stable toxin (STa) and/or heat-labile toxin (LT) are among top causes of children's diarrhea and travelers’ diarrhea. Currently no vaccines are available for ETEC associated diarrhea. A major challenge in developing ETEC vaccines is the inability to stimulate protective antibodies against the key STa toxin that is potently toxic and also poorly immunogenic. A recent study suggested toxoid fusion 3xSTa N12S -dmLT, which consists of a monomer LT toxoid (LT R192G/L211A ) and three copies of STa toxoid STa N12S , may represent an optimal immunogen inducing neutralizing antibodies against STa toxin [IAI 2014, 82(5):1823-32]. In this study, we immunized mice with this fusion protein following a different parenteral route and using different adjuvants to further characterize immunogenicity of this toxoid fusion. Data from this study showed that 3xSTa N12S -dmLT toxoid fusion induced neutralizing anti-STa antibodies in the mice following subcutaneous immunization, as effectively as in the mice under intraperitoneal route. Data also indicated that double mutant LT (dmLT) can be an effective adjuvant for this toxoid fusion in mice subcutaneous immunization. Results from this study affirmed that toxoid fusion 3xSTa N12S -dmLT induces neutralizing antibodies against STa toxin, suggesting this toxoid fusion is potentially a promising immunogen for ETEC vaccine development.
    Keywords: Biotechnology & Synthetic Biology
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    A study of different fault slip modes governed by the gouge material composition in laboratory experiments (2016)
    Oxford University Press
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    Publication Date: 2016-12-04
    Description: Described are results of laboratory experiments which revealed regularities of gradual transition from stick-slip mode to aseismic creep. The behaviour of model gouge-filled fault was investigated with experimental setup of the spring-bock model. It was experimentally proven that small variations of a percentage of materials with velocity strengthening and velocity weakening properties in the fault principal slip zone may result in significant variation of the portion of seismic energy radiated during a fault slip event. The tests simulated different modes of interblock sliding whose characteristic values of scaled kinetic energy varied by several orders of magnitude, while differences in contact strength and shear stress drop remained relatively small. The obtained results led to the conclusion that the earthquake radiation efficiency and the fault slip mode are governed by the ratio of two parameters—maximum fault slip-weakening rate and shear stiffness of the enclosing massif. The ratio can be essentially changed by small variations of the material composition of the fault principal slip zone.
    Keywords: Geodynamics and Tectonics
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    Dynamics of intracontinental convergence between the western Tarim basin and central Tien Shan constrained by centroid moment tensors of regional earthquakes (2016)
    Oxford University Press
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    Publication Date: 2016-12-04
    Description: Among the outstanding tectonic questions regarding the convergence between the Tien Shan and Tarim basin in northwestern China are the manner in which deformation is accommodated within their lithospheres, and the extent that the Tarim lithosphere underthrusts the Tien Shan. In particular, the amount and type of deformation within the Tarim basin is poorly understood. It is also uncertain if the convergence between the Tarim and the Tien Shan takes place mainly along a discrete boundary, or if the Tarim lithosphere simply indents into the Kazach shield, forming the Tien Shan through crustal thickening accommodated by a distributed series of thrust faults. In this study we use hypocentres from published earthquake catalogues and waveforms recorded by regional seismic networks to determine earthquake source parameters through regional centroid moment tensor inversion. The entire dataset consists of 160 earthquakes that occurred between 1969 and 2009 and with moment magnitudes between 3.5 and 7 distributed throughout the central Tien Shan and northwestern Tarim Basin. The estimated focal depths of these earthquakes range from the near-surface to about 44 km. Focal mechanisms throughout much of the Tien Shan indicate active deformation accommodated by thrust faults from at least the upper crust to 30 km depth. South of the Tien Shan, the Jia-shi earthquake sequence within the Tarim basin suggests that both crustal shortening and localized flexure are part of a complicated process involving rotational convergence. Inside the Tarim basin, two earthquakes with thrust faulting mechanisms near the crust–mantle boundary beneath the Bachu uplift imply a brittle rheology of the lower crust. High-angle thrust events occur broadly across the Tien Shan, suggesting that the Tarim lithosphere as a whole is strong and indents into the Kazach shield to create the mountain range.
    Keywords: Geodynamics and Tectonics
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    The effect of a power-law mantle viscosity on trench retreat rate (2016)
    Oxford University Press
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    Publication Date: 2016-12-04
    Description: The subduction of lithospheric plates is partitioned between subducting plate motion and lateral slab migration (i.e. trench retreat and advance). We use 3-D, dynamic models of subduction to address the role of a power-law mantle viscosity on subduction dynamics and, in particular, rates of trench retreat. For all numerical models tested, we find that a power-law rheology results in reduced rates of trench retreat, and elevated slab dip angles, relative to the equivalent isoviscous mantle model. We analyse the asthenospheric pressure distribution and the style of mantle flow, which exhibits only limited variability as a function of mantle rheology, in order to compute estimates of the mantle forces associated with subduction. The inclusion of a power-law rheology reduces the mantle shear force (which resists subducting plate motion) to a greater degree than it reduces the dynamic pressure gradient across the slab (which resists trench retreat). Therefore, the inclusion of a power-law mantle rheology favours a shift towards a subduction mode with a reduced trench retreat component, typically a relative reduction of order 25 per cent in our 3-D models. We suggest that this mechanism may be of importance for reducing the high trench retreat rates observed in many previous models to levels more in line with the average subduction partitioning observed on Earth at present (i.e. trench velocity ≤ plate velocity), for most absolute plate motion reference frames.
    Keywords: Geodynamics and Tectonics
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    Insights into pulverized rock formation from dynamic rupture models of earthquakes (2016)
    Oxford University Press
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    Publication Date: 2016-12-18
    Description: Pulverized rocks (PR) are extremely incohesive and highly fractured rocks found within the damage zones of several large strike-slip faults around the world. They maintain their crystal structure, show little evidence of shearing or chemical alteration, and are believed to be produced by strong tensile forces. Several mechanisms for pulverization have been proposed based on simple qualitative analyses or laboratory experiments under simplified loading conditions. Numerical modelling, however, can offer new insights into what is needed to produce PR and likely conditions of formation. We perform dynamic rupture simulations of different earthquakes, varying the magnitude, the slip distribution, and the rupture speed (supershear and subshear), while measuring the stresses produced away from the fault. To contextualize our results, a basic threshold of 10 MPa is set as the tensile strength of the rock mass and recordings are made of where, when, and by how much this threshold is exceeded for each earthquake type. Guided by field observations, we discern that a large (〉 M w 7.1) subshear earthquake along a bimaterial fault produces a pulverized rock distribution most consistent with observations. The damage is asymmetric with the majority on the stiffer side of the fault extending out for several hundred metres. Within this zone there is a large and sudden volumetric expansion in all directions as the rupture passes. We propose that such an extreme tensile stress state, repeated for every earthquake, eventually produces the PR seen in the field.
    Keywords: Geodynamics and Tectonics
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    Current deformation in Central Afar and triple junction kinematics deduced from GPS and InSAR measurements (2016)
    Oxford University Press
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    Publication Date: 2016-12-22
    Description: Kinematics of divergent boundaries and Rift-Rift-Rift junctions are classically studied using long-term geodetic observations. Since significant magma-related displacements are expected, short-term deformation provides important constraints on the crustal mechanisms involved both in active rifting and in transfer of extensional deformation between spreading axes. Using InSAR and GPS data, we analyse the surface deformation in the whole Central Afar region in detail, focusing on both the extensional deformation across the Quaternary magmato-tectonic rift segments, and on the zones of deformation transfer between active segments and spreading axes. The largest deformation occurs across the two recently activated Asal-Ghoubbet (AG) and Manda Hararo-Dabbahu (MH-D) magmato-tectonic segments with very high strain rates, whereas the other Quaternary active segments do not concentrate any large strain, suggesting that these rifts are either sealed during interdyking periods or not mature enough to remain a plate boundary. Outside of these segments, the GPS horizontal velocity field shows a regular gradient following a clockwise rotation of the displacements from the Southeast to the East of Afar, with respect to Nubia. Very few shallow creeping structures can be identified as well in the InSAR data. However, using these data together with the strain rate tensor and the rotations rates deduced from GPS baselines, the present-day strain field over Central Afar is consistent with the main tectonic structures, and therefore with the long-term deformation. We investigate the current kinematics of the triple junction included in our GPS data set by building simple block models. The deformation in Central Afar can be described by adding a central microblock evolving separately from the three surrounding plates. In this model, the northern block boundary corresponds to a deep EW-trending trans-tensional dislocation, locked from the surface to 10–13 km and joining at depth the active spreading axes of the Red Sea and the Aden Ridge, from AG to MH-D rift segments. Over the long-term, this plate configuration could explain the presence of the en-échelon magmatic basins and subrifts. However, the transient behaviour of the spreading axes implies that the deformation in Central Afar evolves depending on the availability of magma supply within the well-established segments.
    Keywords: Geodynamics and Tectonics
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    Compound dislocation models (CDMs) for volcano deformation analyses (2016)
    Oxford University Press
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    Publication Date: 2016-12-22
    Description: Volcanic crises are often preceded and accompanied by volcano deformation caused by magmatic and hydrothermal processes. Fast and efficient model identification and parameter estimation techniques for various sources of deformation are crucial for process understanding, volcano hazard assessment and early warning purposes. As a simple model that can be a basis for rapid inversion techniques, we present a compound dislocation model (CDM) that is composed of three mutually orthogonal rectangular dislocations (RDs). We present new RD solutions, which are free of artefact singularities and that also possess full rotational degrees of freedom. The CDM can represent both planar intrusions in the near field and volumetric sources of inflation and deflation in the far field. Therefore, this source model can be applied to shallow dikes and sills, as well as to deep planar and equidimensional sources of any geometry, including oblate, prolate and other triaxial ellipsoidal shapes. In either case the sources may possess any arbitrary orientation in space. After systematically evaluating the CDM, we apply it to the co-eruptive displacements of the 2015 Calbuco eruption observed by the Sentinel-1A satellite in both ascending and descending orbits. The results show that the deformation source is a deflating vertical lens-shaped source at an approximate depth of 8 km centred beneath Calbuco volcano. The parameters of the optimal source model clearly show that it is significantly different from an isotropic point source or a single dislocation model. The Calbuco example reflects the convenience of using the CDM for a rapid interpretation of deformation data.
    Keywords: Geodynamics and Tectonics
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    OmpF of Pectobacterium carotovorum subsp. carotovorum Pcc3 is required for carocin D sensitivity (2016)
    Oxford University Press
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    Publication Date: 2016-12-23
    Description: Carocin D is a bacteriocin produced by Pectobacterium carotovorum subsp. carotovorum Pcc21. Carocin D inhibits the growth of P . carotovorum subsp. carotovorum and closely related strains. Pectobacterium carotovorum subsp. carotovorum is a causative bacterium for soft rot disease and leads to severe economic losses. Bacteriocins recognize and interact with a specific membrane protein of target bacteria as a receptor. To identify the receptor responsible for carocin D recognition, mutants that underwent a phenotypic change from carocin D sensitivity to carocin D insensitivity were screened. Based on Tn 5 insertions, carocin D sensitivity was dependent on expression of the outer membrane protein OmpF. The insensitivity of the mutant (Pcc3MR) to carocin D was complemented with ompF from carocin D-sensitive strains, not from carocin D-resistant strains. The selectivity between sensitive and resistant strains could be attributed to variation in OmpFs in the cell-surface-exposed regions. Based on sequence analysis and complementation assays, it appears that carocin D uses OmpF as a receptor and is translocated by the TonB system. According to previously reported translocation mechanisms of colicins, OmpF works along with the TolA system rather than the TonB system. Therefore, the current findings suggest that carocin D is imported by a unique colicin-like bacteriocin translocation system.
    Keywords: Biotechnology & Synthetic Biology
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    Active faulting within a megacity: the geometry and slip rate of the Pardisan thrust in central Tehran, Iran (2016)
    Oxford University Press
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    Publication Date: 2016-10-28
    Description: Tehran, the capital city of Iran with a population of over 12 million, is one of the largest urban centres within the seismically active Alpine–Himalayan orogenic belt. Although several historic earthquakes have affected Tehran, their relation to individual faults is ambiguous for most. This ambiguity is partly due to a lack of knowledge about the locations, geometries and seismic potential of structures that have been obscured by dramatic urban growth over the past three decades, and which have covered most of the young geomorphic markers and natural exposures. Here we use aerial photographs from 1956, combined with an ~1 m DEM derived from stereo Pleiades satellite imagery to investigate the geomorphology of a growing anticline above a thrust fault—the Pardisan thrust—within central Tehran. The topography across the ridge is consistent with a steep ramp extending from close to the surface to a depth of ~2 km, where it presumably connects with a shallow-dipping detachment. No primary fault is visible at the surface, and it is possible that the faulting dissipates in the near surface as distributed shearing. We use optically stimulated luminescence to date remnants of uplifted and warped alluvial deposits that are offset vertically across the Pardisan fault, providing minimum uplift and slip-rates of at least 1 mm yr –1 . Our study shows that the faults within the Tehran urban region have relatively rapid rates of slip, are important in the regional tectonics, and have a great impact on earthquake hazard assessment of the city and surrounding region.
    Keywords: Geodynamics and Tectonics
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    Compressible magma/mantle dynamics: 3-D, adaptive simulations in ASPECT (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-14
    Description: Melt generation and migration are an important link between surface processes and the thermal and chemical evolution of the Earth's interior. However, their vastly different timescales make it difficult to study mantle convection and melt migration in a unified framework, especially for 3-D global models. And although experiments suggest an increase in melt volume of up to 20 per cent from the depth of melt generation to the surface, previous computations have neglected the individual compressibilities of the solid and the fluid phase. Here, we describe our extension of the finite element mantle convection code ASPECT that adds melt generation and migration. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in areas where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high-resolution, 3-D, compressible, global mantle convection simulations coupled with melt migration. We evaluate the functionality and potential of this method using a series of benchmarks and model setups, compare results of the compressible and incompressible formulation, and show the effectiveness of adaptive mesh refinement when applied to melt migration. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modelling the generation of komatiites or other melts originating in greater depths. The implementation is available in the Open Source ASPECT repository.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Reconciling geodetic and geological estimates of recent plate motion across the Southwest Indian Ridge (2016)
    Oxford University Press
    Details
    Publication Date: 2016-11-10
    Description: We use recently published, high-resolution reconstructions of the Southwest Indian Ridge to test whether a previously described systematic difference between Global Positioning System (GPS) and 3.16-Myr-average estimates of seafloor spreading rates between Antarctica and Africa is evidence for a recent slowdown in Southwest Indian Ridge seafloor spreading rates. Along the Nubia-Antarctic segment of the ridge, seafloor opening rates that are estimated with the new, high-resolution reconstructions and corrected for outward displacement agree well with geodetic rate estimates and reduce previously reported, highly significant non-closure of the Nubia-Antarctic-Sur plate circuit. The observations are inconsistent with a slowdown in spreading rates and instead indicate that Nubia-Antarctic plate motion has been steady since at least 5.2 Ma. Lwandle-Antarctic seafloor spreading rates that are estimated from the new high-resolution reconstructions differ insignificantly from a GPS estimate, thereby implying steady Lwandle-Antarctic plate motion since 5.2 Ma. Between the Somalia and Antarctic plates, the new Southwest Indian Ridge reconstructions eliminate roughly half of the systematic difference between the GPS and MORVEL spreading rate estimates.We interpret the available observations as evidence that Somalia-Antarctic spreading rates have been steady since at least 5.2 Ma and postulate that the remaining difference is attributable to random and/or systematic errors in the plate kinematic estimates and the combined effects of insufficient geodetic sampling of undeforming areas of the Somalia plate, glacial isostatic adjustment in Antarctica and transient deformation triggered by the 1998 M w = 8.2 Antarctic earthquake, the 2004 M w = 9.3 Sumatra earthquake, or possibly other large historic earthquakes.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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