ALBERT

Description: While the kinematics of Anatolia plate and the North Anatolian Fault System (NAFS) has been studied extensively, the slip rate and locking depth along the NAFS are usually assumed constant in the analyses due to the lack of sufficient data. This is also partly due to the reasonably good fit of Euler small circle and partly due to the lack of spatial resolution of observations to determine slip rates independently from locking depths. On the other hand, recent geodetic studies show a contrast for locking depth between Marmara and other parts of the NAFS, implying a non-uniform locking depth across the NAFS. In this study, we analyse new GPS data and homogenously combine available data sets covering the eastern part of the NAFS to form the most complete data set. In particular, we incorporate the first results of Turkish Real-Time Kinematic GPS Network (CORS-TR) into our data set. A detailed analysis of three profiles within the NAFS reveals an increase of locking depth in the middle profile to 19.1 ± 3.4 km from 11.9 ± 3.5 km in the easternmost profile while the slip rate is nearly constant (20–22 mm yr –1 ), which implies a variation of strain rate of ~100 nanostrain yr –1 . Assuming a constant locking depth throughout whole NAFS gives an average locking depth of 14.3 ± 1.7 km. Our best estimates of slip rates in block modelling which takes the variation of locking depths into account are in the range between 22.5 and 22.8 mm yr –1 over eastern part of the NAFS.

Description: Seismic waves sensitive to the outermost part of the Earth's liquid core seem to be affected by a stably stratified layer at the core–mantle boundary. Such a layer could have an observable signature in both long-term and short-term variations of the magnetic field of the Earth, which are used to probe the flow at the top of the core. Indeed, with the recent SWARM mission, it seems reasonable to be able to identify waves propagating in the core with period of several months, which may play an important role in the large-scale dynamics. In this paper, we characterize the influence of a stratified layer at the top of the core on deep quasi-geostrophic (Rossby) waves. We compute numerically the quasi-geostrophic eigenmodes of a rapidly rotating spherical shell, with a stably stratified layer near the outer boundary. Two simple models of stratification are taken into account, which are scaled with commonly adopted values of the Brunt–Väisälä frequency in the Earth's core. In the absence of magnetic field, we find that both azimuthal wavelength and frequency of the eigenmodes control their penetration into the stratified layer: the higher the phase speed, the higher the permeability of the stratified layer to the wave motion. We also show that the theory developed by Takehiro & Lister for thermal convection extends to the whole family of Rossby waves in the core. Adding a magnetic field, the penetrative behaviour of the quasi-geostrophic modes (the so-called fast branch) is insensitive to the imposed magnetic field and only weakly sensitive to the precise shape of the stratification. Based on these results, the large-scale and high-frequency modes (1–2 month periods) may be detectable in the geomagnetic data measured at the Earth's surface, especially in the equatorial area where the modes can be trapped.

Description: The attenuation and velocity dispersion of sonic waves contain valuable information on the mechanical and hydraulic properties of the probed medium. An inherent complication arising in the interpretation of corresponding measurements is, however, that there are multiple physical mechanisms contributing to the energy dissipation and that the relative importance of the various contributions is difficult to unravel. To address this problem for the practically relevant case of terrestrial alluvial sediments, we analyse the attenuation and velocity dispersion characteristics of broad-band multifrequency sonic logs with dominant source frequencies ranging between 1 and 30 kHz. To adequately compensate for the effects of geometrical spreading, which is critical for reliable attenuation estimates, we simulate our experimental setup using a correspondingly targeted numerical solution of the poroelastic equations. After having applied the thus inferred corrections, the broad-band sonic log data set, in conjunction with a comprehensive suite of complementary logging data, allows for assessing the relative importance of a range of pertinent attenuation mechanisms. In doing so, we focus on the effects of wave-induced fluid flow over a wide range of scales. Our results indicate that the levels of attenuation due to the presence of mesoscopic heterogeneities in unconsolidated clastic sediments fully saturated with water are expected to be largely negligible. Conversely, Monte-Carlo-type inversions indicate that Biot's classical model permits to explain most of the considered data. Refinements with regard to the fitting of the observed attenuation and velocity dispersion characteristics are locally provided by accounting for energy dissipation at the microscopic scale, although the nature of the underlying physical mechanism remains speculative.

Description: Hydrocarbon reservoir pressure depletion leads to stress changes inside the reservoir and ground deformation which is registered at the surface as subsidence. As reservoirs are often overlain by layers of rocksalt (or other evaporites), which are materials that flow so as to relax stresses inside them, there is the potential for time-varying surface subsidence. This work focuses on understanding the macroscopic mechanisms that lead to rocksalt flow-induced ground displacements. A Finite Element Model is used for this purpose in which the rocksalt layer is represented by a viscoelastic Maxwell material. Two distinct mechanisms that lead to displacement are observed. These are active during different stages of the deformation and have different timescales associated with them. An important observation is that the timescale for deformation that is measured at the ground surface is not equal to the timescale for deformation of a viscoelastic material element, but can be many times larger than that. The sensitivity of the response to the thickness and location of the rocksalt layer is also presented. Conclusions are drawn which allow for the relative importance of the presence of the rocksalt layer to be assessed and for a framework for understanding time-dependent subsidence above producing hydrocarbon reservoirs to be developed. Finally the changes in stress distribution around a producing reservoir are also briefly discussed.

Description: We investigate spatiotemporal variations of the crustal stress field orientation along the rupture zones of the 1999 August Izmit M w 7.4 and November Düzce M w 7.1 earthquakes at the North Anatolian Fault zone (NAFZ) in NW Turkey. Our primary focus is to elaborate on the relation between the state of the crustal stress field and distinct seismotectonic features as well as variations of coseismic slip within the seismogenic layer of the crust. To achieve this, we compile an extensive data base of hypocentres and first-motion polarities including a newly derived local hypocentre catalogue extending from 2 yr prior (1997) to 2 yr after (2001) the Izmit and Düzce main shocks. This combined data set allows studying spatial and temporal variations of stress field orientation along distinct fault segments for the pre- and post-seimic phase of the two large earthquakes in detail. Furthermore, the occurrence of two M  〉 7 earthquakes in rapid succession gives the unique opportunity to analyse the 87-d-long ‘inter-seismic phase’ between them. We use the MOTSI (first MOTion polarity Stress Inversion) procedure directly inverting first-motion polarities to study the stress field evolution of nine distinct segments. In particular, this allows to determine the stress tensor also for the pre- and post-seismic phases when no stable single-event focal mechanisms can be determined. We observe significantly different stress field orientations along the combined 200-km-long rupture in accordance with lateral variations of coseismic slip and seismotectonic setting. Distinct vertical linear segments of the NAFZ show either pure-strike slip behaviour or transtensional and normal faulting if located near pull-apart basins. Pull-apart structures such as the Akyazi and Düzce basins show a predominant normal faulting behaviour along the NAFZ and reflect clearly different characteristic from neighbouring strike-slip segments. Substantial lateral stress field heterogeneity following the two main shocks is observed that declines with time towards the post-seismic period that rather reflects the regional right-lateral strike-slip stress field.

Description: The Taupo Volcanic Zone (TVZ) is one of the world's most productive regions of rhyolitic volcanism and contains the highly active Okataina Volcanic Centre (OVC). Within the TVZ, intra-arc extension is expressed as normal faulting within a zone known as the Taupo Rift. The OVC is located within a complex part of the rift, where volcanism and deformation is considered influenced by rift structure and kinematics. There has been significant research on the structural, volcanic and geophysical properties of the rift and OVC, but less focus on deformation using geodetic data. The limited studies that have utilized geodetic data do not clearly resolve the distribution of deformation and strain rates within the rift and OVC. This is essential to ensure that deformation signals from volcanic processes at the OVC are correctly identified and distinguished from those related to regional tectonic or local hydrothermal processes within the rift. In this paper, we present a picture of contemporary deformation at the OVC and within the surrounding rift in detail, using existing and new GPS campaign and continuous GPS (cGPS) data collected between 1998 and 2011. The results show a highly heterogeneous deformation and strain rate field (both extension and shortening) through the study area, partitioned into different parts of the rift. Our results agree well with earlier geodetic studies, as well as identify new features, but some deformation patterns conflict with long-term geological observations. In the OVC, we observe a locally rotated horizontal velocity field, significant vertical deformation and variable strain rates across the caldera. In the Tarawera Rift, we identify elevated extension and shear rates, which may have significant implications for volcanism there. A shortening pattern is identified through the central rift, which is unexpected in an intra-arc rifting environment. We attempt to explain the source/s of shortening and extension and discuss their implications for geodetic monitoring efforts in the OVC.

Description: The Piton de la Fournaise basaltic volcano, on La Réunion Island in the western Indian Ocean, is one of the most active volcanoes in the world. This volcano is classically considered as the surface expression of an upwelling mantle plume and its activity is continuously monitored, providing detailed information on its superficial dynamics and on the edifice structure. Deeper crustal and upper mantle structure under La Réunion Island is surprisingly poorly constrained, motivating this study. We used receiver function techniques to determine a shear wave velocity profile through the crust and uppermost mantle beneath La Réunion, but also at other seismic stations located on the hotspot track, to investigate the plume and lithosphere interaction and its evolution through time. Receiver functions (RFs) were computed at permanent broad-band seismic stations from the GEOSCOPE network (on La Réunion and Rodrigues), at IRIS stations MRIV and DGAR installed on Mauritius and Diego Garcia islands, and at the GEOFON stations KAAM and HMDM on the Maldives. We performed non-linear inversions of RFs through modelling of P -to- S conversions at various crustal and upper mantle interfaces. Joint inversion of RF and surface wave dispersion data suggests a much deeper Mohorovičić discontinuity (Moho) beneath Mauritius (~21 km) compared to La Réunion (~12 km). A magmatic underplated body may be present under La Réunion as a thin layer (≤3 km thick), as suggested by a previous seismic refraction study, and as a much thicker layer beneath other stations located on the hotspot track, suggesting that underplating is an important process resulting from the plume–lithosphere interaction. We find evidence for a strikingly low velocity layer starting at about 33 km depth beneath La Réunion that we interpret as a zone of partial melt beneath the active volcano. We finally observe low velocities below 70 km beneath La Réunion and below 50 km beneath Mauritius that could represent the base of the oceanic lithosphere.

Description: We describe a multihomogeneity theory for source-parameter estimation of potential fields. Similar to what happens for random source models, where the monofractal scaling-law has been generalized into a multifractal law, we propose to generalize the homogeneity law into a multihomogeneity law. This allows a theoretically correct approach to study real-world potential fields, which are inhomogeneous and so do not show scale invariance, except in the asymptotic regions (very near to or very far from their sources). Since the scaling properties of inhomogeneous fields change with the scale of observation, we show that they may be better studied at a set of scales than at a single scale and that a multihomogeneous model is needed to explain its complex scaling behaviour. In order to perform this task, we first introduce fractional-degree homogeneous fields, to show that: (i) homogeneous potential fields may have fractional or integer degree; (ii) the source-distributions for a fractional-degree are not confined in a bounded region, similarly to some integer-degree models, such as the infinite line mass and (iii) differently from the integer-degree case, the fractional-degree source distributions are no longer uniform density functions. Using this enlarged set of homogeneous fields, real-world anomaly fields are studied at different scales, by a simple search, at any local window W , for the best homogeneous field of either integer or fractional-degree, this yielding a multiscale set of local homogeneity-degrees and depth estimations which we call multihomogeneous model. It is so defined a new technique of source parameter estimation (Multi-HOmogeneity Depth Estimation, MHODE), permitting retrieval of the source parameters of complex sources. We test the method with inhomogeneous fields of finite sources, such as faults or cylinders, and show its effectiveness also in a real-case example. These applications show the usefulness of the new concepts, multihomogeneity and fractional homogeneity-degree, to obtain valid estimates of the source parameters in a consistent theoretical framework, so overcoming the limitations imposed by global-homogeneity to widespread methods, such as Euler deconvolution.

Description: In this paper, two separate but related goals are tackled. The first one is to demonstrate that in some saturated rock textures the non-linear behaviour of induced polarization (IP) and the violation of Ohm's law not only are real phenomena, but they can also be satisfactorily predicted by a suitable physical-mathematical model, which is our second goal. This model is based on Fick's second law. As the model links the specific dependence of resistivity and chargeability of a laboratory sample to the injected current and this in turn to its pore size distribution, it is able to predict pore size distribution from laboratory measurements, in good agreement with mercury injection capillary pressure test results. This fact opens up the possibility for hydrogeophysical applications on a macro scale. Mathematical modelling shows that the chargeability acquired in the field under normal conditions, that is at low current, will always be very small and approximately proportional to the applied current. A suitable field test site for demonstrating the possible reliance of both resistivity and chargeability on current was selected and a specific measuring strategy was established. Two data sets were acquired using different injected current strengths, while keeping the charging time constant. Observed variations of resistivity and chargeability are in agreement with those predicted by the mathematical model. These field test data should however be considered preliminary. If confirmed by further evidence, these facts may lead to changing the procedure of acquiring field measurements in future, and perhaps may encourage the design and building of a new specific geo-resistivity meter. This paper also shows that the well-known Marshall and Madden's equations based on Fick's law cannot be solved without specific boundary conditions.

Description: Successful implementation of Ecosystem-Based Fisheries Management (EBFM) requires appropriate action as informed by reference points in an ecosystem context. Thresholds in the response of ecological indicators to system drivers have been suggested as reference points for EBFM, though the management performance of these indicators and possible values for their reference points have not been widely evaluated. We used Management Strategy Evaluation to test the performance of control rules that used ecological indicators to adjust the advice from single-species stock assessments, using the Georges Bank finfish fishery as a case study. We compare the performance of control rules that used ecological indicators to that of single-species F MSY control rules when the system dynamics were governed by the same multispecies population model. Control rules that used indicator-based reference points were able to perform better against catch and biodiversity objectives than when harvests were based on single-species advice alone. Indicators and values for reference points associated with good performance varied depending on the management objective. We quantified tradeoffs between total catch, biodiversity, and interannual variability in catch, noting that it was possible in some instances to achieve higher than average biodiversity while maintaining high catches using indicator-based control rules. While improved performance was noted using ecological indicators, outcomes were variable, and the gains in performance obtained may be similar to alternative methods of implementing precaution in single-species fishery control rules.

Description: Climate change and fishing can have major impacts on the distribution of natural marine resources. Climate change alters the distribution of suitable habitat, forcing organisms to shift their range or attempt to survive under suboptimal conditions. Fishing reduces the abundance of marine populations and truncates their age structure leading to range contractions or shifts. Along the east coast of the United States, there have been major changes in fish populations due to the impacts of fishing and subsequent regulations, as well as changes in the climate. Black sea bass, scup, summer flounder, and winter flounder are important commercial and recreational species, which utilize inshore and offshore waters on the northeast shelf. We examined the distributions of the four species with the Northeast Fisheries Science Center trawl surveys to determine if the along-shelf centres of biomass had changed over time and if the changes were attributed to changes in temperature or fishing pressure through changes in abundance and length structure. Black sea bass, scup, and summer flounder exhibited significant poleward shifts in distributions in at least one season while the Southern New England/Mid-Atlantic Bight stock of winter flounder did not shift. Generalized additive modelling indicated that the changes in the centres of biomass for black sea bass and scup in spring were related to climate, while the change in the distribution of summer flounder was largely attributed to a decrease in fishing pressure and an expansion of the length–age structure. While the changes in ocean temperatures will have major impacts on the distribution of marine taxa, the effects of fishing can be of equivalent magnitude and on a more immediate time scale. It is important for management to take all factors into consideration when developing regulations for natural marine resources.

Description: Many snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5–22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0 + crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2 + , while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0 + crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns.

Description: Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called "latent states"), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.

Description: While the impact of environmental forcing on recruitment variability in marine populations remains largely elusive, studies spanning large spatial areas and many stocks are able to identify patterns common to different regions and species. In this study, we investigate the effects of the environment on the residuals of a Ricker stock–recruitment (SR) model, used as a proxy of prerecruits' survival, of 18 assessed stocks in the Baltic and North Seas. A probabilistic principal components (PCs) analysis permits the identification of groups of stocks with shared variability in the prerecruits' survival, most notably a group of pelagics in the Baltic Sea and a group composed of gadoids and herring in the North Sea. The first two PCs generally grouped the stocks according to their localizations: the North Sea, the Kattegat–Western Baltic, and the Baltic Sea. This suggests the importance of the local environmental variability on the recruitment strength. Hence, the prerecruits' survival variability is studied according to geographically disaggregated and potentially impacting abiotic or biotic variables. Time series (1990–2009) of nine environmental variables consistent with the spawning locations and season for each stock were extracted from a physical–biogeochemical model to evaluate their ability to explain the survival of prerecruits. Environmental variables explained 〉70% of the survival variability for eight stocks. The variables water current, salinity, temperature, and biomass of other fish stocks are regularly significant in the models. This study shows the importance of the local environment on the dynamics of SR. The results provide evidence of the necessity of including environmental variables in stock assessment for a realistic and efficient management of fisheries.

Description: Ecosystem-based fisheries management seeks to consider trade-offs among management objectives for interacting species, such as those that arise through predator–prey linkages. In particular, fisheries-targeting forage fish (small and abundant pelagic fish) might have a detrimental effect on fisheries-targeting predators that consume them. However, complexities in ecological interactions might dampen, negate, or even reverse this trade-off, because small pelagic fish can be important predators on egg stages of piscivorous fish. Further, the strength of this trade-off might depend on the extent to which piscivorous fish targeted by fisheries regulate forage species productivity. Here, we developed a novel delay-differential bioeconomic model of predator–prey and fishing dynamics to quantify how much egg predation or weak top-town control affects the strength of trade-off between forage and piscivore fisheries, and to measure how ecological interactions dictate policies that maximize steady-state profits. We parameterized the model based on ecological and economic data from the North Sea Atlantic cod ( Gadus morhua ) and Atlantic herring ( Clupea harengus ). The optimal policy was very sensitive to the ecological interactions (either egg predation or weak top-down control of forage by predators) at relatively low forage prices but was less sensitive at high forage fish prices. However, the optimal equilibrium harvest rates on forage and piscivores were not substantially different from what might be derived through analyses that did not consider species interactions. Applying the optimal multispecies policy would produce substantial losses (〉25%) in profits in the piscivore fishery, and the extent of loss was sensitive to ecological scenarios. While our equilibrium analysis is informative, a dynamic analysis under similar ecological scenarios is necessary to reveal the full economic and ecological benefits of applying ecosystem-based fishery management policies to predator–prey fishery systems.

Description: Leptocephali, the larvae of eels, grow to large sizes and are widely distributed in tropical and subtropical oceans. Their role in oceanic food webs is poorly known because they are rarely reported as food items in fish stomach content studies. Data from 13 years of research on the trophic dynamics of Pacific Ocean predatory fish indicate that among 8746 fish of 76 species/taxa (33 families) that had been feeding, only 16 fish of 6 species had remains of 34 leptocephali in their stomachs. Only 0.013% of the 256 308 total prey items were leptocephalus larvae, and 0.03% of the total prey items were juvenile or adult eels (mostly snipe eels: Nemichthyidae). There were 10 fish of 2 species of lancetfish ( Alepisaurus spp., n = 152), 2 rainbow runners ( Elagatis bipinnulata , n = 222), and 2 yellowfin tuna ( Thunnus albacares , n = 3103) that had leptocephali in their stomach contents, but all except one T. albacares (contained 15 leptocephali) had each eaten ≤3 leptocephali. A swallower, Pseudoscopelus sp., and a frigate tuna, Auxis thazard , had eaten single leptocephali. Twenty-eight bigeye tuna, Thunnus obesus , had eaten 76 juvenile/adult nemichthyid or serrivomerid eels. A literature survey found that only 15 out of 75 examined publications listed leptocephali in the stomach contents of a total of 6 species out of ~ 42 300 predatory fish of 40 species. The transparency of leptocephali and their apparent mimicry of gelatinous zooplankton could contribute to lower rates of predation. Their soft bodies likely digest rapidly, so although this study and existing literature indicate that leptocephali sometimes contribute to predatory fish diets, particularly for fish that do not exclude gelatinous prey types, and fish with low digestion rates in their stomachs such as lancetfish, their levels of contribution to fish diets and the impacts of predators on eel recruitment remain uncertain.

Description: Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.

Description: Jellyfish disruption of fisheries has been described in some coastal systems, but few thorough investigations have been conducted. To ascertain the economic impact and trend of jellyfish blooms in the Northern California Current (NCC), we mailed surveys to resident commercial shrimpers, salmon trollers, rockfish (blue, black), and groundfish fishers ( n = 872). We asked fishers to estimate the damages caused by jellyfish—including costs of relocating to avoid blooms, lost fishing time, time lost to bycatch sorting, fish depreciation, and gear damage. Of the total respondents ( n = 111), 67% reported that jellyfish reduce their seasonal revenue, but the degree of impact ranged considerably by fishery and location. Highest jellyfish nuisance corresponded to regions with the most salmon trolling effort. Using the mean revenue losses provided by respondents, we estimate that the combined economic impact of jellyfish on Oregon's salmon and pink shrimp fishers was over $650 000 in peak jellyfish season (June–September) in 2012. Fishers reported that jellyfish biomass varies annually, but most respondents (51%) reported observing no appreciable change in jellyfish populations in the last 5 years. Since economic impact analyses have been conducted primarily in areas with anomalous, high-density blooms, data from the NCC, which is not known to be experiencing increases in jellyfish abundance, provides baseline information on the socio-economic impact of jellyfish blooms in this region. In addition, the finding that jellyfish impact hook and line fisheries—not solely net fisheries—has implications for many other regions where fishers employ this gear type.

Description: Odontocete depredation on longlines involves socioeconomic and conservation issues with significant losses for fisheries and potential impacts on wild populations of depredating species. As technical solutions to this conflict are limited and difficult to implement, this study aimed to identify fishing practices that could reduce odontocete depredation, with a focus on killer whales (Orcinus orca) interacting with Patagonian toothfish (Dissostichus eleginoides) longliners off the Crozet islands. Data collected by fishery observers from 6013 longline sets between 2003 and 2013 allowed us to statistically detect the significant influence of five operational variables using GLMMs. The probability of interactions between vessels and killer whales was decreased by (i) the number of vessels operating simultaneously in the area: the limited number of depredating killer whales may induce a dilution effect with increased fleet size, and (ii) depth of longline sets: vessels operating in shallow waters may be more accessible to whales that are initially distributed on peri-insular shelves. The cpue was negatively influenced by (iii) length of longlines: longer sets may provide killer whales access to a greater proportion of hooked fish per set, and positively influenced by (iv) hauling speed: increased speed may shorten the time during which toothfish are accessible to whales during hauling. The time it takes for killer whales to reach vessels was positively correlated to (v) the distance travelled between longline sets with an estimated threshold of 100 km beyond which whales seem to temporarily lose track of vessels. These findings provide insightful guidelines about what fishing strategy to adopt given these variables to reduce killer whale depredation here and in similar situations elsewhere. To a greater extent, this study is illustrative of how collaborative work with fishermen in a fully controlled fishery framework may lead to the definition of cost-limited and easy-to-implement mitigation solutions when facing such human-wildlife conflict.

Description: In Alaskan waters, depredation on sablefish longline gear by sperm whales increases harvesting cost, negatively biases stock assessments, and presents a risk of entanglement for whales. The Southeast Alaska Sperm Whale Avoidance Project (SEASWAP), a collaborative effort involving industry, scientists, and managers, since 2003 has undertaken research to evaluate depredation with a goal of recommending measures to reduce interactions. Prior to 2003, little was known about sperm whale distribution and behaviour in the Gulf of Alaska (GOA). Although fishers were reporting increasing interactions, the level of depredation varied with no apparent predictor of occurrence across vessels. Between 2003 and 2007, fishers were provided with fishery logbooks and recorded information on whale behaviour, whale presence and absence, during the set, soak, and haul for 319 sets in the GOA. Data were evaluated for a vessel, area, and seasonal (month) effect in the presence and absence of sperm whales. Using catch per unit effort ( cpue ) as a metric, in kg/100 hooks, results indicated that depredation depended on both the vessel and the area. More whales associated with vessels from April to August. Sperm whales were also likely to be present when cpue was high, revealing that whales and fishers both knew the most productive fishing areas, but confounding the use of cpue as a metric for depredation. Using a Bayesian mark-recapture analysis and the sightings histories of photo-identified whales, an estimated $$\hat{N}=135$$ (95% CI 124, 153) sperm whales were associating with vessels in 2014. A spatial model was fitted to 319 longline sets and quantified a 3% loss in cpue , comparable to other global studies on sperm whale depredation. Through all phases of SEASWAP, our understanding of depredation has gained significantly. This successful collaboration should be considered as a model to create partnerships and build collaborations between researchers and fisherpeople encountering marine mammal interactions with fishing gear.

Description: This paper provides a synthesis of results obtained as part of a long-term collaborative study involving biologists, fishers, and resource managers—centring on the occurrence of killer whales in the Crozet Archipelago before and after the implementation of a demersal longline fishery for Patagonian toothfish. Depredation behaviour was reported as soon as the fishery was initiated, with dramatic effects on both the demographic trajectories of the killer whales and on the amount of fish lost by the fishers. Killer whales interacting with the fishery exhibited very high mortality rates when illegal fishing took place, while killer whales not interacting were unaffected. However, after illegal fishing ended, killer whales interacting with the fishery exhibited both higher fecundity and survival rates compared with killer whales not interacting. Since whales typically removed fish entirely from the hooks, an adapted methodology that did not rely on determining the number of damaged fish was developed to estimate depredation rates. In the Crozet EEZ over a 10-year period, 33.9% of the total amount of Patagonian toothfish caught, representing a total of 28 million , was estimated to be lost due to the combined effects of killer whale and sperm whale depredation. In an effort to reduce depredation losses, modifications to fishing methods, such as changing the fishing season, changing fishing areas when exposed to depredation and changing longline length and hauling speed were successfully tested. Acoustic deterrent devices were ineffective in deterring killer whales from depredating longlines. Alternative fishing gears, such as fish pots, were also tested. However, while providing encouraging results regarding the suppression of depredation and seabird bycatch, fish pots were not efficient enough to sustain an economically viable fishery. In conclusion, we discuss how the findings of this comprehensive study can be used elsewhere in fisheries confronted with depredation.

Description: The scattering of seismic waves travelling in the Earth is not only caused by random velocity heterogeneity but also by surface topography. Both factors are known to strongly affect ground-motion complexity even at relatively short distance from the source. In this study, we simulate ground motion with a 3-D finite-difference wave propagation solver in the 0–5 Hz frequency band using three topography models representative of the Swiss alpine region and realistic heterogeneous media characterized by the Von Karman correlation functions. Subsequently, we analyse and quantify the characteristics of the scattered wavefield in the near-source region. Our study shows that both topography and velocity heterogeneity scattering may excite large coda waves of comparable relative amplitude, especially at around 1 Hz, although large variability in space may occur. Using the single scattering model, we estimate average Q C values in the range 20–30 at 1 Hz, 36–54 at 1.5 Hz and 62–109 at 3 Hz for constant background velocity models with no intrinsic attenuation. In principle, envelopes of topography-scattered seismic waves can be qualitatively predicted by theoretical back-scattering models, while forward- or hybrid-scattering models better reproduce the effects of random velocity heterogeneity on the wavefield. This is because continuous multiple scattering caused by small-scale velocity perturbations leads to more gentle coda decay and envelope broadening, while topography abruptly scatters the wavefield once it impinges the free surface. The large impedance contrast also results in more efficient mode mixing. However, the introduction of realistic low-velocity layers near the free surface increases the complexity of ground motion dramatically and indicates that the role of topography in elastic waves scattering can be relevant especially in proximity of the source. Long-period surface waves can form most of the late coda, especially when intrinsic attenuation is taken into account. Our simulations indicate that both topography and velocity heterogeneity scattering may result in large ground-motion variability, characterized by standard deviation values in the range 0.2–0.5 also at short distance from the source. We conclude that both topography and velocity heterogeneity should be considered to correctly assess the ground-motion variability in earthquake scenario studies even at intermediate frequency.

Description: In this study, we have systematically investigated the influence of the parameters of the slip-weakening law and the size of nucleation asperity on dynamic rupture of a planar fault in full-space and half-space using the boundary integral equation method, in particular, the occurrence conditions for subshear (or sub-Rayleigh for strike-slip rupture) and supershear ruptures. Besides the well-known rupture styles of subshear (or sub-Rayleigh) and supershear, we defined a new kind of rupture style in this study, termed the ‘self-arresting rupture’, for which the rupture process can be autonomously arrested by itself without any outside interference (e.g. a high strength barrier). Based on the vast number of simulations, we obtained rupture phase diagrams for strike-slip and dip-slip ruptures vertically and obliquely embedded in half-space and full-space with different buried depths. The rupture phase diagram clearly illustrates the occurrence conditions of three kinds of rupture styles and the transitions between them. In full-space, the supershear transition is sensitive with the fault width. Owing to the influence of the free surface, the rupture in half-space becomes much more complicated comparing to the one in full-space. For a strike-slip fault with zero buried depth, all ruptures that occur within the parameter range for sub-Rayleigh ruptures in full-space case become supershear ruptures. This means that as long as a rupture is able to grow incessantly, it will always evolve into a supershear rupture. For dip-slip faults, however, ruptures will always propagate with subshear speed, although slip rate could be almost twice that of a strike-slip fault. Although the influence of the free surface is strong, it is limited to very shallow ruptures (i.e. buried depth 〈1 km). The rupture phase diagram discussed in this study could provide a new insight on earthquake rupture mechanics.

Description: Mainland Portugal, on the southwestern edge of the European continent, is located directly north of the boundary between the Eurasian and Nubian plates. It lies in a region of slow lithospheric deformation (〈5 mm yr –1 ), which has generated some of the largest earthquakes in Europe, both intraplate (mainland) and interplate (offshore). Some offshore earthquakes are nucleated on old and cold lithospheric mantle, at depths down to 60 km. The seismicity of mainland Portugal and its adjacent offshore has been repeatedly classified as diffuse. In this paper, we analyse the instrumental earthquake catalogue for western Iberia, which covers the period between 1961 and 2013. Between 2010 and 2012, the catalogue was enriched with data from dense broad-band deployments. We show that although the plate boundary south of Portugal is diffuse, in that deformation is accommodated along several distributed faults rather than along one long linear plate boundary, the seismicity itself is not diffuse. Rather, when located using high-quality data, earthquakes collapse into well-defined clusters and lineations. We identify and characterize the most outstanding clusters and lineations of epicentres and correlate them with geophysical and tectonic features (historical seismicity, topography, geologically mapped faults, Moho depth, free-air gravity, magnetic anomalies and geotectonic units). Both onshore and offshore, clusters and lineations of earthquakes are aligned preferentially NNE–SSW and WNW–ESE. Cumulative seismic moment and epicentre density decrease from south to north, with increasing distance from the plate boundary. Only few earthquake lineations coincide with geologically mapped faults. Clusters and lineations that do not match geologically mapped faults may correspond to previously unmapped faults (e.g. blind faults), rheological boundaries or distributed fracturing inside blocks that are more brittle and therefore break more easily than neighbour blocks. The seismicity map of western Iberia presented in this article opens important questions concerning the regional seismotectonics. This work shows that the study of low-magnitude earthquakes using dense seismic deployments is a powerful tool to study lithospheric deformation in slowly deforming regions, such as western Iberia, where high-magnitude earthquakes occur with long recurrence intervals.

Description: We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (~90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

Description: The accurate estimation of dispersion curves has been a key issue for ensuring high quality in geophysical surface wave exploration. Many studies have been carried out on the generation of a high-resolution dispersion image from array measurements. In this study, the sparse signal representation and reconstruction techniques are employed to obtain the high resolution Rayleigh-wave dispersion image from seismic wave data. First, a sparse representation of the seismic wave data is introduced, in which the signal is assumed to be sparse in terms of wave speed. Then, the sparse signal is reconstructed by optimization using l 1 -norm regularization, which gives the signal amplitude spectrum as a function of wave speed. A dispersion image in the f – v domain is generated by arranging the sparse spectra for all frequency slices in the frequency range. Finally, to show the efficiency of the proposed approach, the Surfbar-2 field test data, acquired by B. Luke and colleagues at the University of Nevada Las Vegas, are analysed. By comparing the real-field dispersion image with the results from other methods, the high mode-resolving ability of the proposed approach is demonstrated, particularly for a case with strongly coherent modes.

Description: Many applications of seismology require the calculation of wave speed and attenuation in rocks saturated with multiple fluids. Squirt flow is known to be an important effect in fully saturated rocks but the extension to the multifluid case is unclear. Neglecting capillary effects, we generalize previous work on squirt flow to the case where two fluids are present. We derive expressions for the effective fluid properties, but the results depend on the spatial distributions, and not only volume fractions, of the two fluids. Our results demonstrate that such multifluid squirt flow may be responsible for hysteresis effects in elastic properties during imbibition and drainage.

Description: Iterative substitution of the coupled Marchenko equations is a novel methodology to retrieve the Green's functions from a source or receiver array at an acquisition surface to an arbitrary location in an acoustic medium. The methodology requires as input the single-sided reflection response at the acquisition surface and an initial focusing function, being the time-reversed direct wavefield from the acquisition surface to a specified location in the subsurface. We express the iterative scheme that is applied by this methodology explicitly as the successive actions of various linear operators, acting on an initial focusing function. These operators involve multidimensional crosscorrelations with the reflection data and truncations in time. We offer physical interpretations of the multidimensional crosscorrelations by subtracting traveltimes along common ray paths at the stationary points of the underlying integrals. This provides a clear understanding of how individual events are retrieved by the scheme. Our interpretation also exposes some of the scheme's limitations in terms of what can be retrieved in case of a finite recording aperture. Green's function retrieval is only successful if the relevant stationary points are sampled. As a consequence, internal multiples can only be retrieved at a subsurface location with a particular ray parameter if this location is illuminated by the direct wavefield with this specific ray parameter. Several assumptions are required to solve the Marchenko equations. We show that these assumptions are not always satisfied in arbitrary heterogeneous media, which can result in incomplete Green's function retrieval and the emergence of artefacts. Despite these limitations, accurate Green's functions can often be retrieved by the iterative scheme, which is highly relevant for seismic imaging and inversion of internal multiple reflections.

Description: The pre- and current collision of the Juan Fernández Ridge with the central Chilean margin at 31°–33°S is characterized by large-scale crustal thinning and long-term subsidence of the submarine forearc caused by subduction erosion processes. Here, we study the structure of the central Chilean margin in the ridge–trench collision zone by using wide-angle and multichannel seismic data. The transition from the upper to middle continental slope is defined by a trenchward dipping normal scarp with variable offsets of 500–2000 m height. Beneath the scarp, the 2-D velocity–depth models show a prominent lateral velocity contrast of 〉1 s –1 that propagates deep into the continental crust defining a major lateral seismic discontinuity. The discontinuity is interpreted as the lithological contact between the subsided/collapsed outermost forearc (composed of eroded and highly fractured volcanic rocks) and the seaward part of the uplifted Coastal Cordillera (made of less fractured metamorphic/igneous rocks). Extensional faults are abundant in the collapsed outermost forearc, however, landward of the continental slope scarp, both extensional and compressional structures are observed along the uplifted continental shelf that forms part of the Coastal Cordillera. Particularly, at the landward flank of the Valparaíso Forearc Basin (32°–33.5°S), shallow crustal seismicity has been recorded in 2008–2009 forming a dense cluster of thrust events of M w 4–5. The estimated hypocentres spatially correlate with the location of the fault scarp, and they highlight the upper part of the seismic crustal discontinuity.

Description: Employing dynamic reciprocity can be an effective tool to simplify the calculation of elastic wavefields for borehole problems and to check the results. We analytically obtain the reciprocity relations for the elastodynamic fields generated by multipole sources in a fluid–solid configuration: if the multipole sources are located in the fluid, the particle displacement due to a dipole source is reciprocal to the particle acceleration due to a single force; the fluid pressure due to a dipole source is reciprocal to the particle acceleration due to a monopole source; the particle displacement due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a single force; the fluid pressure due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a monopole source. These relations are tested by numerical experiments for different borehole problems, including acoustic logging, single-well imaging and vertical seismic profiling. A reciprocity test can be used as a quick check of a finite-difference algorithm and the implementation of the sources, although it cannot detect errors due to improper discretization of the interfaces.

Description: Sheila Peacock reports on a meeting that explored the UK's contribution to seismology in the past, present and future.

Description: Jenny Collier , marine geophysicist and President of the BGA, explains why she is addicted to science.

Description: The Matachewan Large Igneous Province (LIP) is interpreted to have formed during the early stages of mantle plume-induced continental break-up in the early Proterozoic. When the Matachewan LIP is reconstructed to its original configuration with units from the Superior Craton and other formerly adjacent blocks (Karelia, Kola, Wyoming and Hearne), the dyke swarms, layered intrusions and flood basalts, emplaced over the lifetime of the province, form one of the most extensive magmatic provinces recognized in the geological record. New geochemical data allow, for the first time, the Matachewan LIP to be considered as a single, coherent entity and show that Matachewan LIP rocks share a common tholeiitic composition and trace element geochemistry, characterized by enrichment in the most incompatible elements and depletion in the less incompatible elements. This signature, ubiquitous in early Proterozoic continental magmatic rocks, may indicate that the Matachewan LIP formed through contamination of the primary magmas with lithospheric material or that the early Proterozoic mantle had a fundamentally different composition from the modern mantle. In addition to the radiating geometry of the dyke swarms, a plume origin for the Matachewan LIP is consistent with the geochemistry of some of the suites; these suites are used to constrain a source mantle potential temperature of c. 1500–1550°C. Comparison of these mantle potential temperatures with estimated temperatures for the early Proterozoic upper mantle indicates that they are consistent with a hot mantle plume source for the magmatism. Geochemical data from coeval intrusions suggest that the plume head was compositionally heterogeneous and sampled material from both depleted and enriched mantle. As has been documented with less ancient but similarly vast LIPs, the emplacement of the Matachewan LIP probably had a significant impact on the early Proterozoic global environment. Compilation of the best age estimates for various suites shows that the emplacement of the Matachewan LIP occurred synchronously with the Great Oxidation Event. We explore the potential for the eruption of this LIP and the emission of its associated volcanic gases to have been a driver of the irreversible oxygenation of the Earth.

Description: Olivine major and trace element compositions from 12 basalts from the southern Payenia volcanic province in Argentina have been analyzed by electron microprobe and laser ablation inductively coupled plasma mass spectrometry. The olivines have high Fe/Mn and low Ca/Fe and many fall at the end of the global olivine array, indicating that they were formed from a pyroxene-rich source distinct from typical mantle peridotite. The olivines with the highest Fe/Mn have higher Zn/Fe, Zn and Co and lower Co/Fe than the olivines with lower Fe/Mn, also suggesting contributions from a pyroxene-rich source. Together with whole-rock radiogenic isotopes and elemental concentrations, the samples indicate mixing between two mantle sources: (1) a pyroxene-rich source with EM-1 ocean island basalt type trace element and isotope characteristics; (2) a peridotitic source with more radiogenic Pb that was metasomatized by subduction-zone fluids and/or melts. The increasing contributions from the pyroxene-rich source in the southern Payenia basalts are correlated with an increasing Fe-enrichment, which caused the olivines to have lower forsterite contents at a given Ni content. Al-in-olivine crystallization temperatures measured on olivine–spinel pairs are between 1155 and 1243°C and indicate that the magmas formed at normal upper mantle (asthenospheric) temperatures of ~1350°C. The pyroxene-rich material is interpreted to have been brought up from the deeper parts of the upper mantle by vigorous asthenospheric upwelling caused by break-off of the Nazca slab south of Payenia during the Pliocene and roll-back of the subducting slab beneath Payenia. The pyroxene-rich mantle mixed with peridotitic metasomatized South Atlantic mantle in the mantle wedge beneath Payenia.

Description: To reconstruct the magmatic–hydrothermal processes leading to porphyry Mo ore formation at the Climax Mo mine, Colorado, four magma units that were emplaced before, during and shortly after the mineralization events were investigated: (1) a pre-mineralization white dike of the Alma district; (2) the syn-mineralization Chalk Mountain Rhyolite; (3) a late- to post-mineralization rhyolite porphyry dyke; (4) a mafic enclave within the productive Bartlett stock. Melt inclusions, mineral inclusions and fluid inclusions in quartz phenocrysts were investigated by means of laser ablation inductively coupled plasma mass spectrometry, electron microprobe and microthermometry. Based on melt inclusion data both the Chalk Mountain Rhyolite and the rhyolite porphyry were ~10 times more fractionated than average granite and show geochemical characteristics of topaz rhyolites. They were saturated in magnetite, Mn-rich ilmenite, fluorite, aeschynite, monazite, pyrrhotite and thorite, and crystallized predominantly at 710–730°C, 1·2–2·6 kbar and log f O 2 FMQ + 2·2 (where FMQ is fayalite–magnetite–quartz). The silicate melt of the Chalk Mountain Rhyolite contained 3·5 ± 0·4 wt % F, 0·09 ± 0·03 wt % Cl, ≥ 3·0 wt % H 2 O, 15–90 µg g –1 Cs, 500–1500 µg g –1 Rb and 5–7 µg g –1 Mo, whereas that of the rhyolite porphyry contained 1·1 ± 0·3 wt % F and 4·9 ± 1·2 wt % H 2 O, but otherwise had a virtually identical major and trace element composition. The fluid exsolving from the latter melt had a bulk salinity of 10 ± 2 wt % NaCl equiv and contained of the order of 100 µg g –1 Mo. After emplacement of the Chalk Mountain Rhyolite magma at subvolcanic levels, extremely fractionated silicate melts coexisting with hypersaline brines (salt melts) and low-density vapor percolated at near-solidus conditions through the rock. These silicate melts contained 6·6 ± 0·4 wt % F, ≥ 7·5 ± 0·6 wt % H 2 O, 0·51 ± 0·05 wt % Cl, and up to 0·5 wt % Cs and 100 µg g –1 Mo, whereas the hypersaline brines contained 1–2 wt % Cs and 0·3–0·6 wt % Mo. However, owing to their negligible masses these liquids are unlikely to have played a major role in the mineralization process. The majority of Mo in the Climax deposit appears to have been derived from melts containing 5–7 µg g –1 Mo and bulk fluids containing ~100 µg g –1 Mo. These concentrations are similar to those found in similarly fractionated melts and fluids in barren and sub-economically mineralized intrusions. However, whereas in the latter intrusions fractionated melts occurred in a rather dispersed state, they seem to have been present as large, coherent masses in the apical parts of Climax-type porphyry Mo-forming magma systems. Efficient segregation of fractionated melts and fluids into the top of mineralizing magma chambers appears to have been promoted by high fluorine concentrations in the silicate melt, which was partly a primary feature, and partly an indirect consequence of other characteristics of within-plate magmatism.

Description: The Skaergaard intrusion, Greenland, is the type locality for Skaergaard-type mineralizations. Mineralization levels are perfectly concordant with igneous layering, up to 5 m thick, internally fractionated, and contain crystallized sulphide droplets and precious metal alloys, sulphides, arsenides and telluride. Immiscible Cu-rich sulphide droplets, formed in a mush zone below the roof, scavenged precious metals. They were subsequently dissolved and transported to the floor in late-formed, immiscible, Fe-rich mush melts. Mineralized stratigraphic intervals of floor gabbro formed in ‘proto-macrolayers‘, owing to local sulphide saturation in melt concentrated between floating plagioclase and sinking clinopyroxene. The floor mineralization is divided into four stratigraphic sections. Formation of the Lower Platinum Group Element Mineralization (LPGEM) involved: (1) crystallization of the bulk liquid liquidus paragenesis and in situ fractionation; (2) sulphide saturation and formation of sulphide droplets in melt in the upper part of ‘proto-macrolayers‘. After further in situ fractionation, the following steps occurred: (3) the onset of silicate–silicate immiscibility and the consequent loss of buoyant and immiscible Si-rich melt; (4) dissolution of unprotected droplets of sulphide melt present in the Fe-rich mush melt; (5) compaction-driven upwards loss of residual mush melt enriched in, for example, Au. The LPGEM preserves upward increasing bulk Pd/Pt (~6–13) owing to a continued supply of PGE and Au, with high Pd/Pt. The further development of the LPGEM ceased as the supply of precious metals to the floor waned. The Upper PGE Mineralization (UPGEM) subsequently formed from precious metals recycled in the floor. The UPGEM is characterized by increasing Au substitution in PGE phases, and a decrease in total PGE and Pd/Pt owing to upward fractionation in migrating mush melts and exhaustion of Pd and Pt. An upper Au-rich mineralization level (UAuM) was caused by late remobilization of Au and deposition on grain boundaries in fully crystallized gabbro. Cu concentrations (~150 ppm) are not correlated with PGE and Au. Repeated Cu mineralization levels (CuM), attaining 〉1000 ppm, occur above the Au levels, caused by local mush layer sulphide saturation. PGE, Au and Cu distributions in the floor mineralization reflect sub-liquidus, but supra-solidus, processes and reactions in mushes at the roof, wall and floor. Constraints provided by a new model for the mineralization provide the basis for re-evaluation of the solidification processes in the Skaergaard intrusion. We have identified the importance of extensive in situ fractionation and intrusion-wide elemental redistributions in immiscible Fe- and Si-rich silicate melts. Our model characterizes the floor cumulates as bulk liquid orthocumulates containing an upwards-increasing proportion crystallized from Fe-rich, immiscible mush melt. The roof-rocks are complementary to the floor, with downwards increasing proportions crystallized from the conjugate Si-rich melt. Petrographic observations and the relative timing of crystallization support the hypothesis that crystallization was restricted to marginal mush zones. Bulk melt remaining in the magma chamber evolved not, as generally assumed, as a result of loss of crystals grown from the bulk melt, but as the consequence of mixing with recycled and evolved melt expelled from the mush by compaction. Redistribution of Fe in immiscible melts may be common to mafic intrusions and puts into question the validity of petrogenetic modelling of bulk liquids in mafic intrusions based only on consideration of floor cumulates.

Description: We have determined experimentally the hydrous phase relations and trace element partitioning behaviour of ocean floor basalt protoliths at pressures and temperatures (3 GPa, 750–1000°C) relevant to melting in subduction zones. To avoid potential complexities associated with trace element doping of starting materials we have used natural, pristine mid-ocean ridge basalt (MORB from Kolbeinsey Ridge) and altered oceanic crust (AOC from Deep Sea Drilling Project leg 46, ~20°N Atlantic). Approximately 15 wt % water was added to starting materials to simulate fluid fluxing from dehydrating serpentinite underlying the oceanic crust. The vapour-saturated solidus is sensitive to basalt K 2 O content, decreasing from 825 ± 25°C in MORB (~0·04 wt % K 2 O) to 750°C in AOC (~0·25 wt % K 2 O). Textural evidence indicates that near-solidus fluids are sub-critical in nature. The residual solid assemblage in both MORB and AOC experiments is dominated by garnet and clinopyroxene, with accessory kyanite, epidote, Fe–Ti oxide and rutile (plus quartz–coesite, phengite and apatite below the solidus). Trace element analyses of quenched silica-rich melts show a strong temperature dependence of key trace elements. In contrast to the trace element-doped starting materials of previous studies, we do not observe residual allanite. Instead, abundant residual epidote provides the host for thorium and light rare earth elements (LREE), preventing LREE from being released (LREE 〈3 ppm at 750–900°C). Elevated Ba/Th ratios, characteristic of many arc basalts, are found to be generated within a narrow temperature field above the breakdown temperature of phengite, but below exhaustion of epidote. Melts with Ba/Th 〉1500 and La/Sm PUM (where PUM indicates primitive upper mantle) ~1, most closely matching the geochemical signal of arc lavas worldwide, were generated from AOC at 800–850°C.

Description: We constrain the physical nature of the magma reservoir and the mechanisms of rhyolite generation at Yellowstone caldera via detailed characterization of zircon and sanidine crystals hosted in three rhyolites erupted during the ( c . 170–70 ka) Central Plateau Member eruptive episode—the most recent post-caldera magmatism at Yellowstone. We present 238 U– 230 Th crystallization ages and trace-element compositions of the interiors and surfaces (i.e. unpolished rims) of single zircon crystals from each rhyolite. We compare these zircon data with 238 U– 230 Th crystallization ages of bulk sanidine separates coupled with chemical and isotopic data from single sanidine crystals. Zircon age and trace-element data demonstrate that the magma reservoir that sourced the Central Plateau Member rhyolites was long-lived (150–250 kyr) and genetically related to the preceding episode of magmatism, which occurred c . 256 ka. The interiors of most zircons in each rhyolite were inherited from unerupted material related to older stages of Central Plateau Member magmatism or the preceding late Upper Basin Member magmatism (i.e. are antecrysts). Conversely, most zircon surfaces crystallized near the time of eruption from their host liquids (i.e. are autocrystic). The repeated recycling of zircon interiors from older stages of magmatism demonstrates that sequentially erupted Central Plateau Member rhyolites are genetically related. Sanidine separates from each rhyolite yield 238 U– 230 Th crystallization ages at or near the eruption age of their host magmas, coeval with the coexisting zircon surfaces, but are younger than the coexisting zircon interiors. Chemical and isotopic data from single sanidine crystals demonstrate that the sanidines in each rhyolite are in equilibrium with their host melts, which considered along with their near-eruption crystallization ages suggests that nearly all Central Plateau Member sanidines are autocrystic. The paucity of antecrystic sanidine crystals relative to antecrystic zircons requires a model in which eruptible rhyolites are generated by extracting melt and zircons from a long-lived mush of immobile crystal-rich magma. In this process the larger sanidine crystals remain trapped in the locked crystal network. The extracted melts (plus antecrystic zircon) amalgamate into a liquid-dominated (i.e. eruptible) magma body that is maintained as a physically distinct entity relative to the bulk of the long-lived crystal mush. Zircon surfaces and sanidines in each rhyolite crystallize after melt extraction and amalgamation, and their ages constrain the residence time of eruptible magmas at Yellowstone. Residence times of the large-volume rhyolites (~40–70 km 3 ) are ≤1 kyr (conservatively 〈6 kyr), which suggests that large volumes of rhyolite can be generated rapidly by extracting melt from a crystal mush. Because the lifespan of the crystal mush that sourced the Central Plateau Member rhyolites is two orders of magnitude longer than the residence time of eruptible magma bodies within the reservoir, it is apparent that the Yellowstone magma reservoir spends most of its time in a largely crystalline (i.e. uneruptible) state, similar to the present-day magma reservoir, and that eruptible magma bodies are ephemeral features.

Description: We report and interpret new geochemical and Pb–Sr–Nd isotopic data from 325 samples of shield, late-shield, postshield, and rejuvenated stage lavas from Kauai and Niihau, the two most northwesterly islands in the Hawaiian island chain. Kauai is unique in the Hawaiian chain in that it exhibits a near-continuous geochemical transition from shield to postshield to rejuvenated stage volcanism between 4·4 and 3·6 Ma and has been continuously active over ~6 Myr. From c . 5·7 to 4·3 Ma, the shield stage of both islands produced tholeiitic basalts typical of other Hawaiian shield volcanoes. The Niihau basalts are more evolved and have high Gd/Yb compared with Kauai, indicating a higher residual garnet content in the source. Both Kauai and Niihau shield basalts have Kea-like trace element ratios, but isotopic ratios are transitional between Kea- and Loa-like compositions. The geochemical similarity of the two shields indicates that mantle sources in different regions of the plume source were similar, and that the 〈2 Ma Loa and Kea trends of the southeastern Hawaiian volcanoes are not observed. More Loa-like compositions are evident in shield lavas from eastern Kauai, where the enhanced Loa composition may reflect melting of low-melting temperature plume components as the island migrates off the hotter, more Kea-like, center of the Hawaiian plume. Postshield lavas and intrusive rocks on both islands are rare: Kauai includes alkalic basalts, hawaiites and mugearites that are isotopically homogeneous and include a significant depleted mantle component compared with the shield basalts, whereas the Niihau late-shield and postshield rocks consist of highly contrasting transitional tholeiites or basanites with variable but shield-like isotopic compositions. The Niihau postshield rocks represent variable, but lower degrees of melting of the shield mantle source. Large volumes of rejuvenated stage lavas cover both islands and also form submarine cone fields, but lava compositions are different. On Kauai, rejuvenated lavas range from melilitite to alkalic basalt with trace element, Nd isotope, and Pb isotope ratios that vary as a function of Th and SiO 2 content. Low-degree (high-Th) melts are dominated by a mixed Kea–Loihi component and high-degree (low-Th) melts include more of a depleted rejuvenated component (DRC) typified by rejuvenated stage lavas and xenoliths from nearby Kaula Island. With the exception of a single basanite, the Niihau rejuvenated stage lavas are uniformly alkalic basalt, with Sr and Ba excesses combined with depleted Th and Nb abundances relative to the light rare earth elements. Rejuvenated stage alkalic basalts from both islands are dominated by contributions from the DRC, which have high Sr/Ce and 87 Sr/ 86 Sr but low 206 Pb/ 204 Pb. The Sr-rich, possibly carbonate-bearing, DRC component may be distributed patchily in the rejuvenated stage mantle source such that, where present, the degree of partial melting was enhanced compared with the degree of partial melting of the Sr-poor, mixed Kea–Loihi component. Given the lack of a hiatus between postshield and rejuvenated stages on Kauai, the rejuvenated mantle source is already able to melt at the tail end of shield stage activity and no secondary melting mechanism is required to explain the rejuvenated stage.

Description: Previous formalisms for determining the static perturbation of spherically symmetric self-gravitating elastic Earth models due to displacement dislocations deal with each infinitesimal element of the fault system in its epicentral reference frame. In this work, we overcome this restriction and present novel and compact formulas for obtaining the perturbation due to the whole fault system in an arbitrary and common reference frame. Furthermore, we show that, even in an arbitrary reference frame, it is still possible to discriminate the contributions associated with the polar, bipolar and quadrupolar patterns of the seismic source response, as well as their relation with the along strike, along dip and tensile components of the displacement dislocation. These results allow a better understanding of the relation between the static perturbation and the whole fault system, and find direct applications in geodetic problems, like the modelling of long-wavelength geoid or gravity data from GRACE and GOCE space missions and of the perturbation of the deviatoric inertia tensor of the Earth.

Description: We analyse daily cross-correlation computed from continuous records by permanent stations operating in vicinity of the Klyuchevskoy group of volcanoes (Kamchatka). Seismic waves generated by volcanic tremors are clearly seen on the cross-correlations between some pairs of stations as strong signals at frequencies between 0.2 and 2 Hz and with traveltimes typically shorter than those corresponding to interstation propagation. First, we develop a 2-D source-scanning algorithm based on summation of the envelops of cross-correlations to detect seismic tremors and to determine locations from which the strong seismic energy is continuously emitted. In an alternative approach, we explore the distinctive character of the cross-correlation waveforms corresponding to tremors emitted by different volcanoes and develop a phase-matching method for detecting volcanic tremors. Application of these methods allows us to detect and to distinguish tremors generated by the Klyuchevskoy and the Tolbachik, volcanoes and to monitor evolution of their intensity in time.

Description: In geophysical inversion, inferences of Earth's properties from sparse data involve a trade-off between model complexity and the spatial resolving power. A recent Markov chain Monte Carlo (McMC) technique formalized by Green, the so-called trans-dimensional samplers, allows us to sample between these trade-offs and to parsimoniously arbitrate between the varying complexity of candidate models. Here we present a novel framework using trans-dimensional sampling over tree structures. This new class of McMC sampler can be applied to 1-D, 2-D and 3-D Cartesian and spherical geometries. In addition, the basis functions used by the algorithm are flexible and can include more advanced parametrizations such as wavelets, both in Cartesian and Spherical geometries, to permit Bayesian multiscale analysis. This new framework offers greater flexibility, performance and efficiency for geophysical imaging problems than previous sampling algorithms. Thereby increasing the range of applications and in particular allowing extension to trans-dimensional imaging in 3-D. Examples are presented of its application to 2-D seismic and 3-D teleseismic tomography including estimation of uncertainty.

Description: The area of the 9.1-km-deep Continental Deep Drillhole (KTB) in Germany is used as a case study for a geothermal reservoir situated in folded and faulted metamorphic crystalline crust. The presented approach is based on the analysis of 3-D seismic reflection data combined with borehole data and hydrothermal numerical modelling. The KTB location exemplarily contains all elements that make seismic prospecting in crystalline environment often more difficult than in sedimentary units, basically complicated tectonics and fracturing and low-coherent strata. In a first step major rock units including two known nearly parallel fault zones are identified down to a depth of 12 km. These units form the basis of a gridded 3-D numerical model for investigating temperature and fluid flow. Conductive and advective heat transport takes place mainly in a metamorphic block composed of gneisses and metabasites that show considerable differences in thermal conductivity and heat production. Therefore, in a second step, the structure of this unit is investigated by seismic waveform modelling. The third step of interpretation consists of applying wavenumber filtering and log-Gabor-filtering for locating fractures. Since fracture networks are the major fluid pathways in the crystalline, we associate the fracture density distribution with distributions of relative porosity and permeability that can be calibrated by logging data and forward modelling of the temperature field. The resulting permeability distribution shows values between 10 –16 and 10 –19 m 2 and does not correlate with particular rock units. Once thermohydraulic rock properties are attributed to the numerical model, the differential equations for heat and fluid transport in porous media are solved numerically based on a finite difference approach. The hydraulic potential caused by topography and a heat flux of 54 mW m –2 were applied as boundary conditions at the top and bottom of the model. Fluid flow is generally slow and mainly occurring within the two fault zones. Thus, our model confirms the previous finding that diffusive heat transport is the dominant process at the KTB site. Fitting the observed temperature–depth profile requires a correction for palaeoclimate of about 4 K at 1 km depth. Modelled and observed temperature data fit well within 0.2 °C bounds. Whereas thermal conditions are suitable for geothermal energy production, hydraulic conditions are unfavourable without engineered stimulation.

Description: Sensitive instruments like strainmeters and tiltmeters are necessary for measuring slowly varying low amplitude Earth deformations. Nonetheless, laser and fibre interferometers are particularly suitable for interrogating such instruments due to their extreme precision and accuracy. In this paper, a practical design of a simple pendulum borehole tiltmeter based on laser fibre interferometric displacement sensors is presented. A prototype instrument has been constructed using welded borosilicate with a pendulum length of 0.85 m resulting in a main resonance frequency of 0.6 Hz. By implementing three coplanar extrinsic fibre Fabry-Perot interferometric probes and appropriate signal filtering, our instrument provides tilt measurements that are insensitive to parasitic deformations caused by temperature and pressure variations. This prototype has been installed in an underground facility (Rustrel, France) where results show accurate measurements of Earth strains derived from Earth and ocean tides, local hydrologic effects, as well as local and remote earthquakes. The large dynamic range and the high sensitivity of this tiltmeter render it an invaluable tool for numerous geophysical applications such as transient fault motion, volcanic strain and reservoir monitoring.

Description: Rupture properties, such as rupture direction, length, propagation speed and source duration, provide important insights into earthquake mechanisms. One approach to estimate these properties is to investigate the body-wave duration that depends upon the relative location of the station with respect to the rupture direction. Under the assumption that the propagation is unilateral, the duration can be expressed as a function of the dip and azimuth of the rupture. Examination of duration measurements with respect to both the take-off angle and the azimuth is crucial to obtain robust estimates of rupture parameters, especially for nearly vertical rupture propagation. Moreover, limited data coverage, such as using only teleseismic data, can bias the source duration estimate for dipping ruptures, and this bias can map into estimates of other source properties such as rupture extent and rupture speed. Based upon this framework, we introduce an inversion scheme that uses the duration measurements to obtain four parameters: the source duration, a measure of the rupture extent and speed, and dip and azimuth of the rupture propagation. The method is applied to two deep-focus events in the Sea of Okhotsk region, an M w 7.7 event that occurred on 2012 August 14 and an M w 8.3 event from 2013 May 24. The source durations are 26 ± 1 and 37 ± 1 s, and rupture speeds are 49 ± 4 per cent and 26 ± 3 per cent of shear wave speed for the M w 7.7 and 8.3 events, respectively. The azimuths of the two ruptures are parallel to the trench, but are in opposite directions. The dips of the M w 7.7 and 8.3 events are constrained to be 48° ± 8° downdip and 19° ± 8° updip, respectively. The fit to the data is significantly poorer for the M w 8.3 event than the M w 7.7 event, suggesting that the unilateral rupture may not be a good assumption. The analysis is expanded into a multi-episode model, and a secondary episode is determined for the M w 8.3 event in the southeast direction. The two-episode model gives a better fit to the data than the unilateral model and is compatible with the back-projection analysis, demonstrating that the rupture propagation of the M w 8.3 event is complex.

Description: Simon Mitton summarizes the RAS Specialist Discussion Meeting that examined from a historical perspective Hoyle's remarkable career and the impact of his science, in the first of two articles on his scientific legacy.

Description: Fred Hoyle's interest in geophysics has been largely forgotten; Helge Kragh takes another look.

Description: Assessments of the risk posed by near-Earth objects ignore the possibility of a giant comet entering the inner solar system. Bill Napier, David Asher, Mark Bailey and Duncan Steel examine the likelihood and potential consequences of the appearance of such a centaur.

Description: Toby Samuels and Natasha Nicholson report on a debate over the pros and cons of turning humans into martians.

Description: Nevil Maskelyne became the fifth Astronomer Royal 250 years ago, at a time when science and politics were intertwined. Paul Edwards maps his career.

Description: Space physicist Mike Lockwood , who was awarded the RAS Gold Medal in 2015, was inspired by his school physics teacher, JFK and Feynman.

Description: Ferritins and other cage proteins have been utilized as models to understand the fundamentals of protein folding and self-assembly. The bacterioferritin (BFR) from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for a mutagenesis study to investigate the role of electrostatic intermolecular interactions mediated through charged amino acids. Through structural and computational analyses, three charged amino acids R30, D56 and E60 which involved in an electrostatic interaction network were mutated to the opposite charge. Four mutants, R30D, D56R, E60H and D56R-E60H, were expressed, purified and characterized. All of the mutants fold into α-helical structures. Consistent with the computational prediction, they all show a lowered thermostability; double mutant D56R-E60H was found to be 16°C less stable than the wild type. Except for the mutant E60H, all the other mutations completely shut down the formation of protein cages to favour the dimer state in solution. The mutants, however, retain their ability to form cage-like nanostructures in the dried, surface immobilized conditions of transmission electron microscopy. Our findings confirm that even a single charge-inversion mutation at the 2-fold interface of BFR can affect the quaternary structure of its dimers and their ability to self-assemble into cage structures.

Description: Most of bacteria can swim by rotating flagella bidirectionally. The C ring, located at the bottom of the flagellum and in the cytoplasmic space, consists of FliG, FliM and FliN, and has an important function in flagellar protein secretion, torque generation and rotational switch of the motor. FliG is the most important part of the C ring that interacts directly with a stator subunit. Here, we introduced a three-amino acids in-frame deletion mutation (PSA) into FliG from Vibrio alginolyticus , whose corresponding mutation in Salmonella confers a switch-locked phenotype, and examined its phenotype. We found that this FliG mutant could not produce flagellar filaments in a fliG null strain but the FliG(PSA) protein could localize at the cell pole as does the wild-type protein. Unexpectedly, when this mutant was expressed in a wild-type strain, cells formed flagella efficiently but the motor could not rotate. We propose that this different phenotype in Vibrio and Salmonella might be due to distinct interactions between FliG mutant and FliM in the C ring between the bacterial species.

Description: Sulphation is known to be critically involved in the metabolism of acetaminophen in vivo . This study aimed to systematically identify the major human cytosolic sulfotransferase (SULT) enzyme(s) responsible for the sulphation of acetaminophen. A systematic analysis showed that three of the twelve human SULTs, SULT1A1, SULT1A3 and SULT1C4, displayed the strongest sulphating activity towards acetaminophen. The pH dependence of the sulphation of acetaminophen by each of these three SULTs was examined. Kinetic parameters of these three SULTs in catalysing acetaminophen sulphation were determined. Moreover, sulphation of acetaminophen was shown to occur in HepG2 human hepatoma cells and Caco-2 human intestinal epithelial cells under the metabolic setting. Of the four human organ samples tested, liver and intestine cytosols displayed considerably higher acetaminophen-sulphating activity than those of lung and kidney. Collectively, these results provided useful information concerning the biochemical basis underlying the metabolism of acetaminophen in vivo previously reported.

Description: In this study, the physicochemical and enzymatic properties of recombinant human ubiquitin (Ub)-specific protease (USP) 47, a novel member of the C19 family of de-ubiquitinating enzymes (DUB), were characterized for the first time. Recombinant human USP47 was expressed in a baculovirus expression system and purified to homogeneity. The purified protein was shown to be a monomeric protein with a molecular mass of ~146 kDa on sodium dodecyl sulphate—polyacrylamide gel electrophoresis. USP47 released Ub from Ub-aminoacyl-4-metheylcoumaryl-7-amide and Ub-tagged granzyme B. The substitution of the potential nucleophile Cys109 with Ser severely abrogated the Ub-releasing activity of USP47, indicating that USP47 is indeed a cysteine DUB. An assay using Ub dimer substrates showed that the enzyme cleaved a variety of isopeptide bonds between 2 Ub molecules, including the Lys48- and Lys63-linked isopeptide bonds. USP47 also released a Ub moiety from Lys48- and Lys63-linked polyUb chains. Of the inhibitors tested, N -ethylmaleimide, Zn ion and Ub aldehyde revealed a dose-dependent inhibition of USP47. In this study, clear differences in the enzymatic properties between USP47 and USP7 (the most closely related proteins among DUBs) were also found. Therefore, our results suggest that USP47 may play distinct roles in Ub-mediated cellular processes via DUB activity.

Description: P24 antigen is the main structural protein of HIV-1, its detection provide a means to aid the early diagnosis of HIV-1 infection. The aim of this study was to improve the selectivity and sensitivity of the HIV P24 diagnostic assay by developing a cohort of 9E8 affinity-matured antibodies through in vitro phage affinity maturation which was performed by complementarity determining region (CDR)-hot spot mutagenesis strategy. Antibody 9E8-491 had an affinity constant of 5.64 x 10 –11 M, which was 5.7-fold higher than that of the parent antibody (9E8). Furthermore, the affinity, sensitivity and specificity of 9E8-491 were higher than those of 9E8, which indicate that 9E8-491 is a good candidate detection antibody for HIV P24 assay. Structure analysis of matured variants revealed that most hydrogen bonds resided in HCDR3. Among the antibody–antigen predicted binding residues, Tyr 100A/100B was the original conserved residue that was commonly present in HCDR3 of 9E8 and variants. Arg 100 /Asp 100C was the major variant substitution that most likely influenced the binding differences among variants and 9E8 monoclonal antibody. Both efficient library panning and predicted structural data were in agreement that the binding residues were mostly located in HCDR3 and enabled identification of key residues that influence antibody affinity.

Description: Many skeletal diseases have common pathological phenotype of defective osteogenesis of bone marrow stromal cells (BMSCs), in which histone modifications play an important role. However, few studies have examined the dynamics of distinct histone modifications during osteogenesis. In this study, we examined the dynamics of H3K9/K14 and H4K12 acetylation; H3K4 mono-, di- and tri-methylation; H3K9 di-methylation and H3K27 tri-methylation in osteogenic genes, runt-related transcription factor 2 (Runx2), osterix (Osx), alkaline phosphatase, bone sialoprotein and osteocalcin, during C3H10T1/2 osteogenesis. H3 and H4 acetylation and H3K4 di-methylation were elevated, and H3K9 di-methylation and H3K27 tri-methylation were reduced in osteogenic genes during C3H10T1/2 osteogenesis. C3H10T1/2 osteogenesis could be modulated by altering the patterns of H3 and H4 acetylation and H3K27 tri-methylation. In a glucocorticoid-induced osteoporosis mouse model, we observed the attenuation of osteogenic potential of osteoporotic BMSCs in parallel with H3 and H4 hypo-acetylation and H3K27 hyper-tri-methylation in Runx2 and Osx genes. When H3 and H4 acetylation was elevated, and H3K27 tri-methylation was reduced, the attenuated osteogenic potential of osteoporotic BMSCs was rescued effectively. These observations provide a deeper insight into the mechanisms of osteogenic differentiation and the pathophysiology of osteoporosis and can be used to design new drugs and develop new therapeutic methods to treat skeletal diseases.

Description: Dihydrouridine (D) is formed by tRNA dihydrouridine synthases (Dus). In mesophiles, multiple Dus enzymes bring about D modifications at several positions in tRNA. The extreme-thermophilic eubacterium Thermus thermophilus , in contrast, has only one dus gene in its genome and only two D modifications (D20 and D20a) in tRNA have been identified. Until now, an in vitro assay system for eubacterial Dus has not been reported. In this study, therefore, we constructed an in vitro assay system using purified Dus. Recombinant T. thermophilus Dus lacking bound tRNA was successfully purified. The in vitro assay revealed that no other factors in living cells were required for D formation. A dus gene disruptant ( dus ) strain of T. thermophilus verified that the two D20 and D20a modifications in tRNA were derived from one Dus protein. The dus strain did not show growth retardation at any temperature. The assay system showed that Dus modified tRNA Phe transcript at 60°C, demonstrating that other modifications in tRNA are not essential for Dus activity. However, a comparison of the formation of D in native tRNA Phe purified from the dus strain and tRNA Phe transcript revealed that other tRNA modifications are required for D formation at high temperatures.

Description: Human lactate dehydrogenase (LDH) has attracted attention as a potential target for cancer therapy and contraception. In this study, we reconstituted human lactic acid fermentation in Saccharomyces cerevisiae , with the goal of constructing a yeast cell-based LDH assay system. pdc null mutant yeast (mutated in the endogenous pyruvate decarboxylase genes) are unable to perform alcoholic fermentation; when grown in the presence of an electron transport chain inhibitor, pdc null strains exhibit a growth defect. We found that introduction of the human gene encoding LDHA complemented the pdc growth defect; this complementation depended on LDHA catalytic activity. Similarly, introduction of the human LDHC complemented the pdc growth defect, even though LDHC did not generate lactate at the levels seen with LDHA. In contrast, the human LDHB did not complement the yeast pdc null mutant, although LDHB did generate lactate in yeast cells. Expression of LDHB as a red fluorescent protein (RFP) fusion yielded blebs in yeast, whereas LDHA-RFP and LDHC-RFP fusion proteins exhibited cytosolic distribution. Thus, LDHB exhibits several unique features when expressed in yeast cells. Because yeast cells are amenable to genetic analysis and cell-based high-throughput screening, our pdc /LDH strains are expected to be of use for versatile analyses of human LDH.

Description: RelB is activated by the non-canonical NF-B pathway, which is crucial for immunity by establishing lymphoid organogenesis and B-cell and dendritic cell (DC) maturation. To elucidate the mechanism of the RelB-mediated immune cell maturation, a precise understanding of the relationship between cell maturation and RelB expression and activation at the single-cell level is required. Therefore, we generated knock-in mice expressing a fusion protein between RelB and fluorescent protein (RelB-Venus) from the Relb locus. The Relb Venus / Venus mice developed without any abnormalities observed in the Relb –/– mice, allowing us to monitor RelB-Venus expression and nuclear localization as RelB expression and activation. Relb Venus / Venus DC analyses revealed that DCs consist of RelB – , RelB low and RelB high populations. The RelB high population, which included mature DCs with projections, displayed RelB nuclear localization, whereas RelB in the RelB low population was in the cytoplasm. Although both the RelB low and RelB – populations barely showed projections, MHC II and co-stimulatory molecule expression were higher in the RelB low than in the RelB – splenic conventional DCs. Taken together, our results identify the RelB low population as a possible novel intermediate maturation stage of cDCs and the Relb Venus / Venus mice as a useful tool to analyse the dynamic regulation of the non-canonical NF-B pathway.

Description: Hyperthermophilic bacteria Thermotoga maritima and Thermotoga hypogea produce ethanol as a metabolic end product, which is resulted from acetaldehyde reduction catalysed by an alcohol dehydrogenase (ADH). However, the enzyme that is involved in the production of acetaldehyde from pyruvate is not well characterized. An oxygen sensitive and coenzyme A-dependent pyruvate decarboxylase (PDC) activity was found to be present in cell free extracts of T. maritima and T. hypogea . Both enzymes were purified and found to have pyruvate ferredoxin oxidoreductase (POR) activity, indicating their bifunctionality. Both PDC and POR activities from each of the purified enzymes were characterized in regards to their optimal assay conditions including pH dependency, oxygen sensitivity, thermal stability, temperature dependency and kinetic parameters. The close relatedness of the PORs that was shown by sequence analysis could be an indication of the presence of such bifunctionality in other hyperthermophilic bacteria. This is the first report of a bifunctional PDC/POR enzyme in hyperthermophilic bacteria. The PDC and the previously reported ADHs are most likely the key enzymes catalysing the production of ethanol from pyruvate in bacterial hyperthermophiles.

Description: Alexander Russell , Anthony Yeates and Jonathan Eastwood review the state of the art and interesting future directions in this developing field, drawing on the RAS discussion meeting held on 12 December 2014.

Description: We take account of the effect of Earth's surface topography in quasi-dynamic earthquake cycle simulations using a boundary integral equation method. While we have so far assumed a homogeneous elastic half-space medium with a flat free surface, Earth's actual surface topography is complicated. Here, we constructed new slip response functions in half-space with an arbitrarily shaped surface topography in which we used slip response functions in full-space by introducing imaginary free surface cells in addition to embedded fault ones. By comparing analytical slip response functions in the case of a flat surface overlying half-space with the new ones, we developed a computationally efficient method for setting the Earth's surface region, which was divided into cells with the appropriate sizes depending on the fault source cell depth to maintain the computational accuracy. With these new slip response functions, we simulated simple interplate earthquake cycles in the region close to the Japan Trench, off Miyagi, Tohoku, in northeast Japan, which has the amplitude of 7 km in depth. Compared with the case where the flat surface level was set at the trench depth, the slip response functions for the case where actual seafloor topography was used had smaller amplitudes. Hence, the actual topography produces smaller recurrence times for earthquake cycles than that for the flat surface case. These effects of the actual Earth's surface topography mainly come from changes in the distance between the surface and the fault compared with the flat surface case. Changes in the slip response function also represent changes in the fault stiffness of the system. Considering the actual topography of the Earth's surface to be convex upwards as opposed to the flat, the fault stiffness becomes larger compared to the case of the flat Earth's surface. This leads to a change in the frictional instability, and sometime leads to the change in the way of rupture.

Description: The scaffolding protein Salvador (Sav) plays a key role in the Hippo (Hpo) signalling pathway, which controls tissue growth by inhibiting cell proliferation and promoting apoptosis. Dysregulation of the Hippo pathway contributes to cancer development. Since the identification of the first Sav gene in 2002, very little is known regarding the molecular basis of Sav-SARAH mediating interactions due to its insolubility. In this study, refolding of the first Sav (known as WW45)-SARAH provided insight into the biochemical and biophysical properties, indicating that WW45-SARAH exhibits properties of a disordered protein, when the domain was refolded at a neutral pH. Interestingly, WW45-SARAH shows folded and rigid conformations relative to the decrease in pH. Further, diffracting crystals were obtained from protein refolded under acidic pH, suggesting that the refolded WW45 protein at low pH has a homogeneous and stable conformation. A comparative analysis of molecular properties found that the acidic-stable fold of WW45-SARAH enhances a heterotypic interaction with Mst2-SARAH. In addition, using an Mst2 mutation that disrupts homotypic dimerization, we showed that the monomeric Mst2-SARAH domain could form a stable complex of 1:1 stoichiometric ratio with WW45 refolded under acidic pH.

Description: Hypercholesterolemia is one of the factors contributing to cardiovascular problems. Erythrocytes are known to contribute its cholesterol to atherosclerotic plaque. Our earlier study showed that erythrocytes overexpress chondroitin sulphate/dermatan sulphate (CS/DS), a linear co-polymer, during diabetes which resulted in increased cytoadherence to extracellular matrix (ECM) components. This study was carried out to determine whether diet-induced hypercholesterolemia had any effect on erythrocyte CS/DS and impacted cytoadherence to ECM components. Unlike in diabetes, diet-induced hypercholesterolemia did not show quantitative changes in erythrocyte CS/DS but showed difference in proportion of un-sulphated and 4- O -sulphated disaccharides. Erythrocytes from hypercholesterolemic rats showed increased adhesion to ECM components which was abrogated to various extents when subjected to chondroitinase ABC digestion. However, isolated CS/DS chains showed a different pattern of binding to ECM components indicating that orientation of CS/DS chains could be playing a role in binding.

Description: The antigen-binding domain of camelid dimeric heavy chain antibodies, known as VHH or Nanobody, has much potential in pharmaceutical and industrial applications. To establish the isolation process of antigen-specific VHH, a VHH phage library was constructed with a diversity of 8.4 x 10 7 from cDNA of peripheral blood mononuclear cells of an alpaca ( Lama pacos ) immunized with a fragment of IZUMO1 (IZUMO1 PFF ) as a model antigen. By conventional biopanning, 13 antigen-specific VHHs were isolated. The amino acid sequences of these VHHs, designated as N-group VHHs, were very similar to each other (〉93% identity). To find more diverse antibodies, we performed high-throughput sequencing (HTS) of VHH genes. By comparing the frequencies of each sequence between before and after biopanning, we found the sequences whose frequencies were increased by biopanning. The top 100 sequences of them were supplied for phylogenic tree analysis. In total 75% of them belonged to N-group VHHs, but the other were phylogenically apart from N-group VHHs (Non N-group). Two of three VHHs selected from non N-group VHHs showed sufficient antigen binding ability. These results suggested that biopanning followed by HTS provided a useful method for finding minor and diverse antigen-specific clones that could not be identified by conventional biopanning.

Description: The autophosphorylation of specific tyrosine residues occurs in the cytoplasmic region of the insulin receptor (IR) upon insulin binding, and this in turn initiates signal transduction. The R3 subfamily (Ptprb, Ptprh, Ptprj and Ptpro) of receptor-like protein tyrosine phosphatases (RPTPs) is characterized by an extracellular region with 6–17 fibronectin type III-like repeats and a cytoplasmic region with a single phosphatase domain. We herein identified the IR as a substrate for R3 RPTPs by using the substrate-trapping mutants of R3 RPTPs. The co-expression of R3 RPTPs with the IR in HEK293T cells suppressed insulin-induced tyrosine phosphorylation of the IR. In vitro assays using synthetic phosphopeptides revealed that R3 RPTPs preferentially dephosphorylated a particular phosphorylation site of the IR: Y960 in the juxtamembrane region and Y1146 in the activation loop. Among four R3 members, only Ptprj was co-expressed with the IR in major insulin target tissues, such as the skeletal muscle, liver and adipose tissue. Importantly, the activation of IR and Akt by insulin was enhanced, and glucose and insulin tolerance was improved in Ptprj -deficient mice. These results demonstrated Ptprj as a physiological enzyme that attenuates insulin signalling in vivo , and indicate that an inhibitor of Ptprj may be an insulin-sensitizing agent.

Description: The diazotrophic cyanobacterium Anabaena sp. strain PCC 7120 (A.7120) differentiates into specialized heterocyst cells that fix nitrogen under nitrogen starvation conditions. Although reducing equivalents are essential for nitrogen fixation, little is known about redox systems in heterocyst cells. In this study, we investigated thioredoxin (Trx) networks in Anabaena using TrxM, and identified 16 and 38 candidate target proteins in heterocysts and vegetative cells, respectively, by Trx affinity chromatography (Motohashi et al. (Comprehensive survey of proteins targeted by chloroplast thioredoxin. Proc Natl Acad Sci USA , 2001; 98 , 11224–11229)). Among these, the Fe–S cluster scaffold protein NifU that facilitates functional expression of nitrogenase in heterocysts was found to be a potential TrxM target. Subsequently, we observed that the scaffold activity of N-terminal catalytic domain of NifU is enhanced in the presence of Trx-system, suggesting that TrxM is involved in the Fe–S cluster biogenesis.

Description: The fate of subducted slabs is enigmatic, yet intriguing. We analyse seismic arrivals at ~20–50 s after the direct P wave in an array in northeast China (NECESSArray) recordings of four deep earthquakes occurring beneath the west-central Pacific subduction zones (from the eastern Indonesia to Tonga region). We employ the array analysing techniques of fourth root vespagram and beam-forming analysis to constrain the slowness and backazimuth of later arrivals. Our analyses reveal that these arrivals have a slightly lower slowness value than the direct P wave and the backazimuth deviates slightly from the great circle direction. Along with calculation of 1-D synthetic seismograms, we conclude that the later arrival is corresponding to an energy of S -to- P converted at a scatterer below the sources. Total five scatterers are detected at depths varying from ~700 to 1110 km in the study region. The past subducted oceanic crust most likely accounts for the seismic scatterers trapped in the mid-mantle beneath the west-central subduction zones. Our observation in turn reflects that oceanic crust at least partly separated from subducted oceanic lithosphere and may be trapped substantially in the mid-mantle surrounding subduction zones, in particular in the western Pacific subduction zones.

Description: Geodetic observations of interseismic deformation in the Western United States provide constraints on microplate rotations, earthquake cycle processes, and slip partitioning across the Pacific–North America Plate boundary. These measurements may be interpreted using block models, in which the upper crust is divided into microplates bounded by faults that accumulate strain in a first-order approximation of earthquake cycle processes. The number and geometry of microplates are typically defined with boundaries representing a limited subset of the large number of potentially seismogenic faults. An alternative approach is to include a large number of potentially active faults bounding a dense array of microplates, and then algorithmically estimate the boundaries at which strain is localized. This approach is possible through the application of a total variation regularization (TVR) optimization algorithm, which simultaneously minimizes the L 2 norm of data residuals and the L 1 norm of the variation in the differential block motions. Applied to 3-D spherical block models, the TVR algorithm can be used to reduce the total variation between estimated rotation vectors, effectively grouping microplates that rotate together as larger blocks, and localizing fault slip on the boundaries of these larger block clusters. Here we develop a block model comprised of 137 microplates derived from published fault maps, and apply the TVR algorithm to identify the kinematically most important faults in the western United States. This approach reveals that of the 137 microplates considered, only 30 unique blocks are required to approximate deformation in the western United States at a residual level of 〈2 mm yr –1 .

Description: We examine spatio-temporal patterns of microseismicity recorded during one month in an underground mine by addressing three key questions: (1) where does the seismicity occur? (2) Why does it occur in these locations? and (3) what triggers it? To obtain accurate locations, we perform a multiplet analysis and use a modified version of the double-difference (DD) relocation method. This approach leads to highly accurate relative event locations and requires groups of multiplets only. Most of the 281 relocated events are close to the main shaft and tunnels; thus we postulate seismicity is facilitated by stresses associated with the potential for subsidence in addition to the hoop stresses acting on the two vertical shafts. Most events occurred during certain hours of the day and there is a 68 per cent correlation with reported rock removal; therefore, it is likely they were triggered by static and dynamic stress perturbations caused by the transportation of debris along tunnels instead of our initial guess that blasting was the principal causative mechanism. Given that seismicity is present around the main shaft but absent close to the second one, we conclude that for seismicity to occur both a favourable stress state and additional external perturbing forces must exist, thus leading to dynamic event triggering in an initially stable stress situation. This analysis provides more insight into anthropogenic processes that might trigger seismicity, thereby facilitating identification of hazardous and potential damage areas in mine settings.

Description: This paper presents the results from the Deflo-hydroacoustic experiment in the Southern Indian Ocean using three autonomous underwater hydrophones, complemented by two permanent hydroacoustic stations. The array monitored for 14 months, from November 2006 to December 2007, a 3000 x 3000 km wide area, encompassing large segments of the three Indian spreading ridges that meet at the Indian Triple Junction. A catalogue of 11 105 acoustic events is derived from the recorded data, of which 55 per cent are located from three hydrophones, 38 per cent from 4, 6 per cent from five and less than 1 per cent by six hydrophones. From a comparison with land-based seismic catalogues, the smallest detected earthquakes are m b 2.6 in size, the range of recorded magnitudes is about twice that of land-based networks and the number of detected events is 5–16 times larger. Seismicity patterns vary between the three spreading ridges, with activity mainly focused on transform faults along the fast spreading Southeast Indian Ridge and more evenly distributed along spreading segments and transforms on the slow spreading Central and ultra-slow spreading Southwest Indian ridges; the Central Indian Ridge is the most active of the three with an average of 1.9 events/100 km/month. Along the Sunda Trench, acoustic events mostly radiate from the inner wall of the trench and show a 200-km-long seismic gap between 2 °S and the Equator. The array also detected more than 3600 cryogenic events, with different seasonal trends observed for events from the Antarctic margin, compared to those from drifting icebergs at lower (up to 50°S) latitudes. Vocalizations of five species and subspecies of large baleen whales were also observed and exhibit clear seasonal variability. On the three autonomous hydrophones, whale vocalizations dominate sound levels in the 20–30 and 100 Hz frequency bands, whereas earthquakes and ice tremor are a dominant source of ambient sound at frequencies 〈20 Hz.

Description: Geodetic vertical velocities derived from data as short as 3 yr are often assumed to be representative of linear deformation over past decades to millennia. We use two decades of surface loading deformation predictions due to variations of atmospheric, oceanic and continental water mass to assess the effect on secular velocities estimated from short time-series. The interannual deformation is time-correlated at most locations over the globe, with the level of correlation depending mostly on the chosen continental water model. Using the most conservative loading model and 5-yr-long time-series, we found median vertical velocity errors of 0.5 mm yr –1 over the continents (0.3 mm yr –1 globally), exceeding 1 mm yr –1 in regions around the southern Tropic. Horizontal velocity errors were seven times smaller. Unless an accurate loading model is available, a decade of continuous data is required in these regions to mitigate the impact of the interannual loading deformation on secular velocities.

Description: We develop and validate a systematic approach to infer plate boundary strength and rheological parameters in models of mantle flow from surface velocity observations. Based on a realistic rheological model that includes yielding and strain rate weakening from dislocation creep, we formulate the inverse problem in a Bayesian inference framework. To study the distribution of parameters that are consistent with the observations, we compute the maximum a posteriori (MAP) point, Gaussian approximations of the parameter distribution around that MAP point, and employ Markov Chain Monte Carlo (MCMC) sampling methods. The computation of the MAP point and the Gaussian approximation require first and second derivatives of an objective function subject to non-linear Stokes equations; these derivatives are computed efficiently using adjoint Stokes equations. We set up 2-D numerical experiments with many of the elements expected in a global geophysical inversion. This setup incorporates three subduction zones with slab and weak zone (interplate fault) geometry consistent with average seismic characteristics. With these experiments, we demonstrate that when the temperature field is known, we can recover the strength of plate boundaries, the yield stress and strain rate exponent in the upper mantle. When the number of uncertain parameters increases, there are trade-offs between the inferred parameters. These trade-offs depend on how well the observational data represents the surface velocities, and on the weakness of plate boundaries. As the plate boundary coupling drops below a threshold, the uncertainty of the inferred parameters increases due to insensitivity of plate motion to plate coupling. Comparing the trade-offs between inferred rheological parameters found from the Gaussian approximation of the parameter distribution and from MCMC sampling, we conclude that the Gaussian approximation—which is significantly cheaper to compute—is often a good approximation, in particular locally around the MAP point. Thus, the method can be applied to the global problem of inferring non-linear constitutive parameters and plate coupling factors for each subduction zone in a global geophysical inversion with known slab structure.

Description: Seismic reflections from the oceanic water column contain information about ocean temperature and salinity. Even though seismic waveform inversion is effective for studying oceanic structure, its application is limited in the absence of sufficient direct temperature/velocity measurements. Here, two methods are developed to invert pre-stack seismic waveform data for temperature and salinity when independent temperature/velocity data are sparse or unavailable, allowing estimation of water-column temperature/salinity from any marine seismic reflection data set. The first method combines a genetic algorithm (GA) with non-linear least squares inversion, and the second method is a parallel implementation of a GA. Both methods produce results to an accuracy between 0 and 0.1 °C in estimating temperature when applied to a field data set from the South China Sea. Although the second approach is superior, it is computationally demanding and requires large parallel computers. The first approach runs extremely fast on parallel computers and can even be run on much smaller machines to provide results in a reasonable runtime. While both methods are viable choices for estimating temperature and salinity, the choice of one over the other will largely depend upon the available computational resources and the time frame within which the inversion needs to be completed.

Description: A 3-D magnetotelluric (MT) inversion code using unstructured tetrahedral elements has been developed in order to correct the topographic effect by directly incorporating it into computational grids. The electromagnetic field and response functions get distorted at the observation sites of MT surveys because of the undulating surface topography, and without correcting this distortion, the subsurface structure can be misinterpreted. Of the two methods proposed to correct the topographic effect, the method incorporating topography explicitly in the inversion is applicable to a wider range of surveys. For forward problems, it has been shown that the finite element method using unstructured tetrahedral elements is useful for the incorporation of topography. Therefore, this paper shows the applicability of unstructured tetrahedral elements in MT inversion using the newly developed code. The inversion code is capable of using the impedance tensor, the vertical magnetic transfer function (VMTF), and the phase tensor as observational data, and it estimates the subsurface resistivity values and the distortion tensor of each observation site. The forward part of the code was verified using two test models, one incorporating topographic effect and one without, and the verifications showed that the results were almost the same as those of previous works. The developed inversion code was then applied to synthetic data from a MT survey, and was verified as being able to recover the resistivity structure as well as other inversion codes. Finally, to confirm its applicability to the data affected by topography, inversion was performed using the synthetic data of the model that included two overlapping mountains. In each of the cases using the impedance tensor, the VMTF and the phase tensor, by including the topography in the mesh, the subsurface resistivity was determined more proficiently than in the case using the flat-surface mesh. Although the locations of the anomalies were not accurately estimated by the inversion using distorted impedance tensors due to the slightly undervalued gain, these locations were correctly estimated by using undistorted impedance tensors or adding VMTFs in the data. Therefore, it can be concluded that the inversion using the unstructured tetrahedral element effectively prevents the misinterpretation of subsurface resistivity and recovers subsurface resistivity proficiently by representing the topography in the computational mesh.

Description: We present synthetic tests of 2-D adjoint tomography of surface wave traveltimes obtained by the ambient noise cross-correlation analysis across the Czech Republic. The data coverage may be considered perfect for tomography due to the density of the station distribution. Nevertheless, artefacts in the inferred velocity models arising from the data noise may be still observed when weak regularization (Gaussian smoothing of the misfit gradient) or too many iterations are considered. To examine the effect of the regularization and iteration number on the performance of the tomography in more detail we performed extensive synthetic tests. Instead of the typically used (although criticized) checkerboard test, we propose to carry out the tests with two different target models—simple smooth and complex realistic models. The first test reveals the sensitivity of the result on the data noise, while the second helps to analyse the resolving power of the data set. For various noise and Gaussian smoothing levels, we analysed the convergence towards (or divergence from) the target model with increasing number of iterations. Based on the tests we identified the optimal regularization, which we then employed in the inversion of 16 and 20 s Love-wave group traveltimes.

Description: Least-squares migration (LSM) is a linearized inversion technique for subsurface reflectivity estimation. Compared to conventional migration algorithms, it can improve spatial resolution significantly with a few iterative calculations. There are three key steps in LSM, (1) calculate data residuals between observed data and demigrated data using the inverted reflectivity model; (2) migrate data residuals to form reflectivity gradient and (3) update reflectivity model using optimization methods. In order to obtain an accurate and high-resolution inversion result, the good estimation of inverse Hessian matrix plays a crucial role. However, due to the large size of Hessian matrix, the inverse matrix calculation is always a tough task. The limited-memory BFGS (L-BFGS) method can evaluate the Hessian matrix indirectly using a limited amount of computer memory which only maintains a history of the past m gradients (often m 〈 10). We combine the L-BFGS method with least-squares pre-stack Kirchhoff depth migration. Then, we validate the introduced approach by the 2-D Marmousi synthetic data set and a 2-D marine data set. The results show that the introduced method can effectively obtain reflectivity model and has a faster convergence rate with two comparison gradient methods. It might be significant for general complex subsurface imaging.