ALBERT

Description: Existing economic analysis of corn stover as an energy feedstock has not considered potential changes in land use associated with different stover prices. We estimate the response of corn stover supply density to its price driven by changes in land use and examine its implications for a processing plant's pricing strategy and marginal cost, as well as associated changes in soil erosion. We find that plants will exploit the intensive margin as well as the extensive margin to secure additional amounts of stover. Our results show, counterintuitively, that a market for stover may result in lower soil erosion due to reallocations of land to continuous corn with removal, which, combined with no-till farming, results in lower soil erosion than the baseline without stover removal. Also contrary to expectations, using cover crops with stover removal may result in higher soil erosion due to land use changes within the fuel shed associated with optimal pricing.

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: 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 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: Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data ( 3DBG ), and a 3D genome browser to visualize and explore 3D genome structures ( 3DGB ). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/ .

Description: Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets. Among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available at https://code.google.com/p/seqtu/ . We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.

Description: Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. Current state-of-the-art variant calling approaches avoid such regions, arguing that it is necessary to sacrifice detection sensitivity to limit false discovery. We developed a method that links candidate variant positions within repetitive genomic regions into clusters. The technique relies on a resource, a thesaurus of genetic variation, that enumerates genomic regions with similar sequence. The resource is computationally intensive to generate, but once compiled can be applied efficiently to annotate and prioritize variants in repetitive regions. We show that thesaurus annotation can reduce the rate of false variant calls due to mappability by up to three orders of magnitude. We apply the technique to whole genome datasets and establish that called variants in low mappability regions annotated using the thesaurus can be experimentally validated. We then extend the analysis to a large panel of exomes to show that the annotation technique opens possibilities to study variation in hereto hidden and under-studied parts of the genome.

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 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: We explore thermal convection of a fluid with a temperature-dependent viscosity in a basally heated 3-D spherical shell using linear stability analyses and numerical experiments, while considering the application of our results to terrestrial planets. The inner to outer radius ratio of the shell f assumed in the linear stability analyses is in the range of 0.11–0.88. The critical Rayleigh number R c for the onset of thermal convection decreases by two orders of magnitude as f increases from 0.11 to 0.88, when the viscosity depends sensitively on the temperature, as is the case for real mantle materials. Numerical simulations carried out in the range of f  = 0.11–0.55 show that a thermal boundary layer (TBL) develops both along the surface and bottom boundaries to induce cold and hot plumes, respectively, when f is 0.33 or larger. However, for smaller f values, a TBL develops only on the bottom boundary. Convection occurs in the stagnant-lid regime where the root mean square velocity on the surface boundary is less than 1 per cent of its maximum at depth, when the ratio of the viscosity at the surface boundary to that at the bottom boundary exceeds a threshold that depends on f . The threshold decreases from 10 6.5 at f  = 0.11 to 10 4 at f  = 0.55. If the viscosity at the base of the convecting mantle is 10 20 –10 21  Pa s, the Rayleigh number exceeds R c for Mars, Venus and the Earth, but does not for the Moon and Mercury; convection is unlikely to occur in the latter planets unless the mantle viscosity is much lower than 10 20  Pa s and/or the mantle contains a strong internal heat source.

Description: Subducting oceanic lithosphere is an example of a thin sheet-like object whose characteristic lateral dimension greatly exceeds its thickness. Here we exploit this property to derive a new hybrid boundary-integral/thin sheet (BITS) representation of subduction that combines in a single equation all the forces acting on the sheet: gravity, internal resistance to bending and stretching, and the tractions exerted by the ambient mantle. For simplicity, we limit ourselves to 2-D. We solve the BITS equations using a discrete Lagrangian approach in which the sheet is represented by a set of vertices connected by edges. Instantaneous solutions for the sinking speed of a slab attached to a trailing flat sheet obey a scaling law of the form V / V Stokes  = fct(St), where V Stokes is a characteristic Stokes sinking speed and St is the sheet's flexural stiffness. Time-dependent solutions for the evolution of the sheet's shape and thickness show that these are controlled by the viscosity ratio between the sheet and its surroundings. An important advantage of the BITS approach is the possibility of generalizing the sheet's rheology, either to a viscosity that varies along the sheet or to a non-Newtonian shear-thinning rheology.

Description: The aftershock distribution of the 1933 Sanriku-oki outer trench earthquake is estimated by using modern relocation methods and a newly developed velocity structure to examine the spatial extent of the source-fault and the possibility of a triggered interplate seismicity. In this study, we first examined the regional data quality of the 1933 earthquake based on smoked-paper records and then relocated the earthquakes by using the 3-D velocity structure and double-difference method. The improvements of hypocentre locations using these methods were confirmed by the examination of recent earthquakes that are accurately located based on ocean bottom seismometer data. The results show that the 1933 aftershocks occurred under both the outer- and inner-trench-slope regions. In the outer-trench-slope region, aftershocks are distributed in a ~280-km-long area and their depths are shallower than 50 km. Although we could not constrain the fault geometry from the hypocentre distribution, the depth distribution suggests the whole lithosphere is probably not under deviatoric tension at the time of the 1933 earthquake. The occurrence of aftershocks under the inner trench slope was also confirmed by an investigation of waveform frequency difference between outer and inner trench earthquakes as recorded at Mizusawa. The earthquakes under the inner trench slope were shallow (depth less double equals30 km) and the waveforms show a low-frequency character similar to the waveforms of recent, precisely located earthquakes in the same area. They are also located where recent activity of interplate thrust earthquakes is high. These suggest that the 1933 outer-trench-slope main shock triggered interplate earthquakes, which is an unusual case in the order of occurrence in contrast with the more common pairing of a large initial interplate shock with subsequent outer-slope earthquakes. The off-trench earthquakes are distributed about 80 km width in the trench perpendicular direction. This wide width cannot be explained from a single high-angle fault confined at a shallow depth (depth less double equals50 km). The upward motion of the 1933 tsunami waveform records observed at Sanriku coast also cannot be explained from a single high-angle west-dipping normal fault. If we consider additional fault, involvement of high-angle, east-dipping normal faults can better explain the tsunami first motion and triggering of the aftershock in a wide area under the outer trench slope. Therefore multiple off-trench normal faults may have activated during the 1933 earthquake. We also relocated recent (2001–2012) seismicity by the same method. The results show that the present seismicity in the outer-trench-slope region can be divided into several groups along the trench. Comparison of the 1933 rupture dimensions based on our aftershock relocations with the morphologies of fault scarps in the outer trench slope suggest that the rupture was limited to the region where fault scarps are largely trench parallel and cross cut the seafloor spreading fabric. These findings imply that bending geometry and structural segmentation of the incoming plate largely controls the spatial extent of the 1933 seismogenic faulting. In this shallow rupture model for this largest outer trench earthquake, triggered seismicity in the forearc and structural control of faulting represent an important deformation styles for off-trench and shallow megathrust zones.

Description: The 16S rRNA gene (16S rDNA) codes for RNA that plays a fundamental role during translation in the ribosome and is used extensively as a marker gene to establish relationships among bacteria. However, the complementary non-coding 16S rDNA (nc16S rDNA) has been ignored. An idea emerged in the course of analyzing bacterial 16S rDNA sequences in search for nucleotide composition and substitution patterns: Does the nc16S rDNA code? If so, what does it code for? More importantly: Does 16S rDNA evolution reflect its own evolution or the evolution of its counterpart nc16S rDNA? The objective of this minireview is to discuss these thoughts. nc strands often encode small RNAs (sRNAs), ancient components of gene regulation. nc16S rDNA sequences from different bacterial groups were used to search for possible matches in the Bacterial Small Regulatory RNA Database. Intriguingly, the sequence of one published sRNA obtained from Legionella pneumophila (GenBank: AE017354.1) showed high non-random similarity with nc16S rDNA corresponding in part to the V5 region especially from Legionella and relatives. While the target(s) of this sRNA is unclear at the moment, its mere existence might open up a new chapter in the use of the 16S rDNA to study relationships among bacteria.

Description: Thermotolerance of the fungus Fomes sp. EUM1 was evaluated in solid state fermentation (SSF). This thermotolerant strain improved both hyphal invasiveness (38%) and length (17%) in adverse thermal conditions exceeding 30°C and to a maximum of 40°C. In contrast, hyphal branching decreased by 46% at 45°C. The production of cellulases over corn stover increased 1.6-fold in 30°C culture conditions, xylanases increased 2.8-fold at 40°C, while laccase production improved 2.7-fold at 35°C. Maximum production of lignocellulolytic enzymes was obtained at elevated temperatures in shorter fermentation times (8–6 days), although the proteases appeared as a thermal stress response associated with a drop in lignocellulolytic activities. Novel and multiple isoenzymes of xylanase (four bands) and cellulase (six bands) were secreted in the range of 20–150 kDa during growth in adverse temperature conditions. However, only a single laccase isoenzyme (46 kDa) was detected. This is the first report describing the advantages of a thermotolerant white-rot fungus in SSF. These results have important implications for large-scale SSF, where effects of metabolic heat are detrimental to growth and enzyme production, which are severely affected by the formation of high temperature gradients.

Description: Geodetic, geologic and palaeomagnetic data reveal that Oregon (western USA) rotates clockwise at 0.3 to 1.0° Ma –1 (relative to North America) about an axis near the Idaho–Oregon–Washington border, while northeast Washington is relatively fixed. This rotation has been going on for at least 15 Ma. The Yakima fold and thrust belt (YFTB) forms the boundary between northern Oregon and central Washington where convergence of the clockwise-rotating Oregon block is apparently accommodated. North–south shortening across the YFTB has been thought to occur in a fan-like manner, increasing in rate to the west. We obtained high-accuracy, high-density geodetic GPS measurements in 2012–2014 that are used with earlier GPS measurements from the 1990s to characterize YFTB kinematics. The new results show that the deformation associated with the YFTB starts at the Blue Mountains Anticline in northern Oregon and extends north beyond the Frenchman Hills in Washington, past the epicentre of the 1872 M w 7.0 Entiat earthquake to 49°N. The north–south strain rate across the region is 2 to 3 x 10 –9 yr –1 between the volcanic arc and the eastern edge of the YFTB (241.0°E); east of there it drops to about 10 –9 yr –1 . At the eastern boundary of the YFTB, faults and earthquake activity are truncated by a north-trending, narrow zone of deformation that runs along the Pasco Basin and Moses Lake regions near 240.9°E. This zone, abutting the Department of Energy Hanford Nuclear Reservation, accommodates about 0.5 mm yr –1 of east to northeast shortening. A similar zone of N-trending transpression is seen along 239.9°E where there is a change in the strike of the Yakima folds. The modern deformation of the YFTB is about 600 km wide from south to north and internally may be controlled by pre-existing crustal structure.

Description: The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of ‘dynamic topography’. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N–S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ~1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.

Description: In many geological systems, inversion of density stratification sets in Rayleigh–Taylor (RT) instabilities, leading to an ascent of relatively low-density materials through the high-density overburden in the form of diapirs. These diapirs often originate from dipping low-density layers. This study aims to show how the initial tilt of such source layers can control the ascent behaviour of diapirs initiated by RT instabilities. Using two-layer viscous models we produced RT instabilities in physical experiments, and investigated the effects of source-layer tilts ( β ). Our experiments suggest that these diapirs ascend with contrasting lateral spreading rates in the up and down slope directions, resulting in their axi-asymmetric geometry. However, their heads retain a circular outline on the horizontal top surface, where the upwelling axis is located away from their geometric centre in the upslope direction. In this paper, we present a series of experimental models to demonstrate the spectrum of axi-symmetric to -asymmetric geometrical transitions with increasing β . Our experiments also reveal that when β is large (〉4°) the diapirs become unstable, resulting in a continuous migration of their stems in the upslope direction. Using the volume of fluid method we ran computational fluid dynamic (CFD) simulations to study the underlying hydrodynamics of axi-asymmetric diapiric growth. The CFD simulations show that β 〉 0° conditions develop stronger flow vortices on the downslope side of an ascending diapir, leading to a pressure difference between the up- and downslope flanks. Such a differential pressure causes the diapir head to spread at a faster rate in the tilt direction. An estimate of the asymmetric spreading rates is given as a function of β . Our present study provides a fundamental understanding of the hydrodynamic flow structure responsible for the asymmetric growth of RT instabilities on tilted source layers, as applicable to a wide range of large-scale geological settings, such as sedimentary basins and subduction zones.

Description: The geomechanical analysis of a highly compartmentalized reservoir is performed to simulate the seafloor subsidence due to gas production. The available observations over the hydrocarbon reservoir consist of bathymetric surveys carried out before and at the end of a 10-yr production life. The main goal is the calibration of the reservoir compressibility c M , that is, the main geomechanical parameter controlling the surface response. Two conceptual models are considered: in one (i) c M varies only with the depth and the vertical effective stress (heterogeneity due to lithostratigraphic variability); in another (ii) c M varies also in the horizontal plane, that is, it is spatially distributed within the reservoir stratigraphic units. The latter hypothesis accounts for a possible partitioning of the reservoir due to the presence of sealing faults and thrusts that suggests the idea of a block heterogeneous system with the number of reservoir blocks equal to the number of uncertain parameters. The method applied here relies on an ensemble-based data assimilation (DA) algorithm (i.e. the ensemble smoother, ES), which incorporates the information from the bathymetric measurements into the geomechanical model response to infer and reduce the uncertainty of the parameter c M . The outcome from conceptual model (i) indicates that DA is effective in reducing the c M uncertainty. However, the maximum settlement still remains underestimated, while the areal extent of the subsidence bowl is overestimated. We demonstrate that the selection of the heterogeneous conceptual model (ii) allows to reproduce much better the observations thus removing a clear bias of the model structure. DA allows significantly reducing the c M uncertainty in the five blocks (out of the seven) characterized by large volume and large pressure decline. Conversely, the assimilation of land displacements only partially constrains the prior c M uncertainty in the reservoir blocks marginally contributing to the cumulative seafloor subsidence, that is, blocks with low pressure.

Description: This work aims to explore the ongoing tectonic activity of structures in the outermost sector of the Northern Apennines, which represents the active leading edge of the thrust belt and is dominated by compressive deformation. We have applied the Persistent Scatterer Interferometry (PSI) technique to obtain new insights into the present-day deformation pattern of the frontal area of the Northern Apennine. PSI has proved to be effective in detecting surface deformation of wide regions involved in low tectonic movements. We used 34 Envisat images in descending geometry over the period of time between 2004 and 2010, performing about 300 interferometric pairs. The analysis of the velocity maps and of the PSI time-series has allowed to observe ground deformation over the sector of the Po Plain between Piacenza and Reggio Emilia. The time-series of permanent GPS stations located in the study area, validated the results of the PSI technique, showing a good correlation with the PS time-series. The PS analysis reveals the occurrence of a well-known subsidence area on the rear of the Ferrara arc, mostly connected to the exploitation of water resources. In some instances, the PS velocity pattern reveals ground uplift (with mean velocities ranging from 1 to 2.8 mm yr –1 ) above active thrust-related anticlines of the Emilia and Ferrara folds, and part of the Pede-Apennine margin. We hypothesize a correlation between the observed uplift deformation pattern and the growth of the thrust-related anticlines. As the uplift pattern corresponds to known geological features, it can be used to constrain the seismo-tectonic setting, and a working hypothesis may involve that the active Emilia and Ferrara thrust folds would be characterized by interseismic periods possibly dominated by aseismic creep.

Description: Assigning cancer patients to the most effective treatments requires an understanding of the molecular basis of their disease. While DNA-based molecular profiling approaches have flourished over the past several years to transform our understanding of driver pathways across a broad range of tumors, a systematic characterization of key driver pathways based on RNA data has not been undertaken. Here we introduce a new approach for predicting the status of driver cancer pathways based on signature functions derived from RNA sequencing data. To identify the driver cancer pathways of interest, we mined DNA variant data from TCGA and nominated driver alterations in seven major cancer pathways in breast, ovarian and colon cancer tumors. The activation status of these driver pathways were then characterized using RNA sequencing data by constructing classification signature functions in training datasets and then testing the accuracy of the signatures in test datasets. The signature functions differentiate well tumors with nominated pathway activation from tumors with no signs of activation: average AUC equals to 0.83. Our results confirm that driver genomic alterations are distinctively displayed at the transcriptional level and that the transcriptional signatures can generally provide an alternative to DNA sequencing methods in detecting specific driver pathways.

Description: The rhizobacterium Serratia plymuthica 4Rx13 emits the novel and unique volatile sodorifen (C 16 H 26 ), which has a polymethylated bicyclic structure. Transcriptome analysis revealed that gene SOD_c20750 (annotated as terpene cyclase) is involved in the biosynthesis of sodorifen. Here we show that this gene is located in a small cluster of four genes ( SOD_c20750 – SOD_c20780 ), and the analysis of the knockout mutants demonstrated that SOD_c20760 (annotated as methyltransferase) and SOD_c20780 (annotated as isopentenyl pyrophosphate (IPP) isomerase) are needed for the biosynthesis of sodorifen, while a sodorifen-negative phenotype was not achieved with the SOD_c20770 (annotated as deoxy-xylulose-5-phosphate (DOXP) synthase) mutant. Altogether, the function of this new gene cluster was assigned to the biosynthesis of this structurally unusual volatile compound sodorifen.

Description: Among staphylococci Staphylococcus saprophyticus is the only species that is typically uropathogenic and an important cause of urinary tract infections in young women. The amino acid D-serine occurs in relatively high concentrations in human urine and has a bacteriostatic or toxic effect on many bacteria. In uropathogenic Escherichia coli and S. saprophyticus , the amino acid regulates the expression of virulence factors and can be used as a nutrient. The ability of uropathogens to respond to or to metabolize D-serine has been suggested as a factor that enables colonization of the urinary tract. Until now nothing is known about D-serine transport in S.   saprophyticus . We generated mutants of putative transporter genes in S.   saprophyticus 7108 that show homology to the D-serine transporter cyc A of E. coli and tested them in a D-serine depletion assay to analyze the D-serine uptake rate of the cells. The mutant of SPP1070 showed a strong decrease in D-serine uptake. Therefore, SSP1070 was identified as a major D-serine transporter in S. saprophyticus 7108 and was named D-serine transporter A (DstA). D-serine caused a prolonged lag phase of S. saprophyticus in a chemically defined medium. This negative effect was dependent on the presence of DstA.

Description: Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of function. A powerful predictive model for the function of non-coding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is non-coding and 93% of disease-associated variants lie in these regions. To address this need, we propose DanQ, a novel hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer captures regulatory motifs, while the recurrent layer captures long-term dependencies between the motifs in order to learn a regulatory ‘grammar’ to improve predictions. DanQ improves considerably upon other models across several metrics. For some regulatory markers, DanQ can achieve over a 50% relative improvement in the area under the precision-recall curve metric compared to related models. We have made the source code available at the github repository http://github.com/uci-cbcl/DanQ .

Description: Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (‘mislabels’) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa .

Description: DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with ( n = 9) or without ( n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (~90%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95%, n = 22). Importantly, iGEMS identified a variety of AEU events, including 3'UTR extension, as well as exon inclusion/exclusion impacting on protein kinase and extracellular matrix domains. In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5–10 times more prevalent than reported by the Genotype-Tissue Expression consortium using RNA sequencing.

Description: In Europe, common input data types for seismic hazard evaluation include earthquake catalogues, seismic zonation models and ground motion models, all with well-constrained epistemic uncertainties. In contrast, neotectonic deformation models and their related uncertainties are rarely considered in earthquake forecasting and seismic hazard studies. In this study, for the first time in Europe, we developed a seismic hazard model based exclusively on active fault and geodynamic deformation models. We applied it to the External Dinarides, a slow-deforming fold-and-thrust belt in the Central Mediterranean. The two deformation models furnish consistent long-term earthquake rates above the M w 4.7 threshold on a latitude/longitude grid with 0.2° spacing. Results suggest that the use of deformation models is a valid alternative to empirical-statistical approaches in earthquake forecasting in slow-deforming regions of Europe. Furthermore, we show that the variability of different deformation models has a comparable effect on the peak ground motion acceleration uncertainty as do the ground motion prediction equations.

Description: The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.

Description: Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle.

Description: An important real world application of doublet flow occurs in well design of both geothermal and hydrocarbon reservoirs. A guiding principle for fluid management of injection and extraction wells is that mass balance is commonly assumed between the injected and produced fluid. Because the doublets are considered closed loops, the injection fluid is assumed to eventually reach the producer well and all the produced fluid ideally comes from stream tubes connected to the injector of the well pair making up the doublet. We show that when an aquifer background flow occurs, doublets will rarely retain closed loops of fluid recirculation. When the far-field flow rate increases relative to the doublet's strength, the area occupied by the doublet will diminish and eventually vanishes. Alternatively, rather than using a single injector (source) and single producer (sink), a linear array of multiple injectors separated by some distance from a parallel array of producers can be used in geothermal energy projects as well as in waterflooding of hydrocarbon reservoirs. Fluid flow in such an arrangement of parallel source-sink arrays is shown to be macroscopically equivalent to that of a line doublet. Again, any far-field flow that is strong enough will breach through the line doublet, which then splits into two vortices. Apart from fundamental insight into elementary flow dynamics, our new results provide practical clues that may contribute to improve the planning and design of doublets and direct line drives commonly used for flow management of groundwater, geothermal and hydrocarbon reservoirs.

Description: Genes encoding fluoride transporters have been identified in bacterial and archaeal species. The genome sequence of the cariogenic  Streptococcus mutans  bacteria suggests the presence of a putative fluoride transporter, which is referred to as a chloride channel permease. Two homologues of this gene (GenBank locus tags SMU_1290c and SMU_1289c) reside in tandem in the genome of  S. mutans . The aim of this study was to determine whether the chloride channel permeases contribute to fluoride resistance. We constructed SMU_1290c- and SMU_1289c-knockout  S. mutans  UA159 strains. We also constructed a double-knockout strain lacking both genes. SMU_1290c or SMU_1289c was transformed into a fluoride transporter- disrupted  Escherichia coli strain. All bacterial strains were cultured under appropriate conditions with or without sodium fluoride, and fluoride resistance was evaluated. All three gene-knockout  S. mutans  strains showed lower resistance to sodium fluoride than did the wild-type strain. No significant changes in resistance to other sodium halides were recognized between the wild-type and double-knockout strains. Both SMU_1290c and SMU_1289c transformation rescued fluoride transporter-disrupted  E. coli  cell from fluoride toxicity. We conclude that the chloride channel permeases contribute to fluoride resistance in  S. mutans .

Description: Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are bacteria under investigation for production of biofuels from plant biomass. Thermoanaerobacterium saccharolyticum has been engineered to produce ethanol at high yield (〉90% of theoretical) and titer (〉70 g/l). Efforts to engineer C. thermocellum have not, to date, been as successful, and efforts are underway to transfer the ethanol production pathway from T. saccharolyticum to C. thermocellum . One potential challenge in transferring metabolic pathways is the possibility of incompatible levels of nicotinamide cofactors. These cofactors (NAD + , NADH, NADP + and NADPH) and their oxidation state are important in the context of microbial redox metabolism. In this study we directly measured the concentrations and reduced oxidized ratios of these cofactors in a number of strains of C. thermocellum and T. saccharolyticum by using acid/base extraction and enzymatic assays. We found that cofactor ratios are maintained in a fairly narrow range, regardless of the metabolic network modifications considered. We have found that the ratios are similar in both organisms, which is a relevant observation in the context of transferring the T. saccharolyticum ethanol production pathway to C. thermocellum .

Description: The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats, sometimes inheriting from them suboptimal design choices; this hinders flexible and effective data sharing. Here, we present CARGO (Compressed ARchiving for GenOmics), a high-level framework to automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of our approach to FASTQ and SAM archives require a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors and scale well to multi-TB datasets. All CARGO software components can be freely downloaded for academic and non-commercial use from http://bio-cargo.sourceforge.net .

Description: Phasing of single nucleotide (SNV), and structural variations into chromosome-wide haplotypes in humans has been challenging, and required either trio sequencing or restricting phasing to population-based haplotypes. Selvaraj et al . demonstrated single individual SNV phasing is possible with proximity ligated (HiC) sequencing. Here, we demonstrate HiC can phase structural variants into phased scaffolds of SNVs. Since HiC data is noisy, and SV calling is challenging, we applied a range of supervised classification techniques, including Support Vector Machines and Random Forest, to phase deletions. Our approach was demonstrated on deletion calls and phasings on the NA12878 human genome. We used three NA12878 chromosomes and simulated chromosomes to train model parameters. The remaining NA12878 chromosomes withheld from training were used to evaluate phasing accuracy. Random Forest had the highest accuracy and correctly phased 86% of the deletions with allele-specific read evidence. Allele-specific read evidence was found for 76% of the deletions. HiC provides significant read evidence for accurately phasing 33% of the deletions. Also, eight of eight top ranked deletions phased by only HiC were validated using long range polymerase chain reaction and Sanger. Thus, deletions from a single individual can be accurately phased using a combination of shotgun and proximity ligation sequencing. InPhaDel software is available at: http://l337x911.github.io/inphadel/.

Description: Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous genomes from short sequencing reads is a challenging task because it is difficult to accurately recover the different haplotypes. When confronted with highly heterozygous genomes, the standard assembly process tends to collapse homozygous regions and reports heterozygous regions in alternative contigs. The boundaries between homozygous and heterozygous regions result in multiple assembly paths that are hard to resolve, which leads to highly fragmented assemblies with a total size larger than expected. This, in turn, causes numerous problems in downstream analyses such as fragmented gene models, wrong gene copy number, or broken synteny. To circumvent these caveats we have developed a pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. We tested our pipeline on simulated and naturally-occurring heterozygous genomes and compared its accuracy to other existing tools. Our method is freely available at https://github.com/Gabaldonlab/redundans .

Description: Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.

Description: The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander , implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander , users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander .

Description: We estimate fluid sources around a subducted seamount along the northern Hikurangi subduction margin of New Zealand, using thermomechanical numerical modelling informed by wedge structure and porosities from multichannel seismic data. Calculated fluid sources are input into an independent fluid-flow model to explore the key controls on overpressure generation to depths of 12 km. In the thermomechanical models, sediment transport through and beneath the wedge is calculated assuming a pressure-sensitive frictional rheology. The change in porosity, pressure and temperature with calculated rock advection is used to compute fluid release from compaction and dehydration. Our calculations yield more precise information about source locations in time and space than previous averaged estimates for the Hikurangi margin. The volume of fluid release in the wedge is smaller than previously estimated from margin-averaged calculations (~14 m 3  yr –1  m –1 ), and is exceeded by fluid release from underlying (subducting) sediment (~16 m 3  yr –1  m –1 ). Clay dehydration contributes only a small quantity of fluid by volume (~2 m 3  yr –1  m –1 from subducted sediment), but the integrated effect is still significant landward of the seamount. Fluid source terms are used to estimate fluid pressures around a subducting seamount in the fluid-flow models, using subducted sediment permeability derived from porosity, and testing two end-members for décollement permeability. Models in which the décollement acts as a fluid conduit predict only moderate fluid overpressure in the wedge and subducting sediment. However, if the subduction interface becomes impermeable with depth, significant fluid overpressure develops in subducting sediment landward of the seamount. The location of predicted fluid overpressure and associated dehydration reactions is consistent with the idea that short duration, shallow, slow slip events (SSEs) landward of the seamount are caused by anomalous fluid pressures; alternatively, it may result from frictional effects of changing clay content along the subduction interface.

Description: A method is outlined by means of which it is possible to estimate high-resolution vertical displacements due to an earthquake even in the case where high-resolution topography is lacking before the earthquake. This result can be achieved by combining a highly accurate, post-event digital elevation model (DEM), for example lidar, with archived satellite imagery. The method is illustrated by calculating vertical displacements for the 2010 El Mayor-Cucapah earthquake. For this earthquake, there are both pre- and post-event lidar DEMs from which vertical displacements may also be estimated after correcting for the lateral advection of topography due to horizontal displacements. A comparison between the two means of deriving vertical displacements shows generally good agreement, with the displacements obtained using satellite imagery performing better in high relief areas. As a result of this property, we are able to trace the vertical offsets due to the El Mayor-Cucapah earthquake as the rupture jumped from the Pescadores fault to the Borrego fault in propagating through the high relief of the Sierra Cucapah.

Description: Inversion polymorphisms have important phenotypic and evolutionary consequences in humans. Two different methodologies have been used to infer inversions from SNP dense data, enabling the use of large cohorts for their study. One approach relies on the differences in linkage disequilibrium across breakpoints; the other one captures the internal haplotype groups that tag the inversion status of chromosomes. In this article, we assessed the convergence of the two methods in the detection of 20 human inversions that have been reported in the literature. The methods converged in four inversions including inv-8p23, for which we studied its association with low-BMI in American children. Using a novel haplotype tagging method with control on inversion ancestry, we computed the frequency of inv-8p23 in two American cohorts and observed inversion haplotype admixture. Accounting for haplotype ancestry, we found that the European inverted allele in children carries a recessive risk of underweight, validated in an independent Spanish cohort (combined: OR= 2.00, P = 0.001). While the footprints of inversions on SNP data are complex, we show that systematic analyses, such as convergence of different methods and controlling for ancestry, can reveal the contribution of inversions to the ancestral composition of populations and to the heritability of human disease.

Description: The Metabolic Models Reconstruction Using Genome-Scale Information ( merlin ) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin .

Description: For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen .

Description: Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ~200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.

Description: A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/ .

Description: We present high-resolution tomographic images in source areas of 26 large crustal earthquakes ( M 6.0–7.2) which occurred in Northeast Japan (Tohoku) during the past 120 yr from 1894 to 2014. Prominent low-velocity (low- V ) and high Poisson's ratio (high- ) anomalies are revealed in the crust and mantle wedge under the source areas. Beneath the volcanic front and backarc areas, the low- V and high- zones reflect arc-magma related high-temperature anomalies which are produced by joint effects of corner flow in the mantle wedge and fluids from dehydration of the subducting Pacific slab. The hot anomalies cause locally thinning and weakening of the brittle seismogenic layer above them. Low-frequency micro-earthquakes are observed in the lower crust and uppermost mantle in or around the low- V zones, which reflect ascending of arc magma and fluids from the mantle wedge to the crust. No volcano and magma exist in the forearc area due to low temperature there, hence the low- V zones in the forearc reflect fluids from the slab dehydration. The ascending fluids may have produced a ‘water wall’ in the mantle wedge and crust beneath the forearc area. When the water enters active faults in the crust, the fault-zone friction is reduced and so large earthquakes can be induced. These results indicate that the nucleation of a large earthquake is not entirely a mechanical process, but is closely associated with subduction dynamics and physical and chemical properties of rocks in the crust and upper mantle. In particular, arc magma and fluids play an important role in the seismogenesis.

Description: We present observations and models of the Sulaiman Range of western Pakistan that shed new light on the evolution and deformation of fold-thrust belts. Earthquake source inversions show that the seismic deformation in the range is concentrated in the thick pile of sediments overlying the underthrusting lithosphere of the Indian subcontinent. The slip vectors of the earthquakes vary in strike around the margin of the range, in tandem with the shape of the topography, suggesting that gravitational driving forces arising from the topography play an important role in governing the deformation of the region. Numerical models suggest that the active deformation, and the extreme plan-view curvature of the range, are governed by the presence of weak sediments in a pre-existing basin on the underthrusting Indian Plate. These sediments affect the stress-state in the over-riding mountain range and allow for the rapid propagation of the nose of the range and the development of extreme curvature and laterally varying surface gradients.

Description: The mechanical damage characteristics of sandstone subjected to cyclic loading is very significant to evaluate the stability and safety of deep excavation damage zones. However to date, there are very few triaxial experimental studies of sandstone under cyclic loading. Moreover, few X-ray micro-computed tomography (micro-CT) observations have been adopted to reveal the damage mechanism of sandstone under triaxial cyclic loading. Therefore, in this research, a series of triaxial cyclic loading tests and X-ray micro-CT observations were conducted to analyse the mechanical damage characteristics of sandstone with respect to different confining pressures. The results indicated that at lower confining pressures, the triaxial strength of sandstone specimens under cyclic loading is higher than that under monotonic loading; whereas at confining pressures above 20 MPa, the triaxial strength of sandstone under cyclic loading is approximately equal to that under monotonic loading. With the increase of cycle number, the crack damage threshold of sandstone first increases, and then significantly decreases and finally remains constant. Based on the damage evolution of irreversible deformation, it appears that the axial damage value of sandstone is all higher than the radial damage value before the peak strength; whereas the radial damage value is higher than the axial damage value after the peak strength. The evolution of Young's modulus and Poisson's ratio of sandstone can be characterized as having four stages: (i) Stage I: material strengthening; (ii) Stage II: material degradation; (iii) Stage III: material failure and (iv) Stage IV: structure slippage. X-ray micro-CT observations demonstrated that the CT scanning surface images of sandstone specimens are consistent with actual surface crack photographs. The analysis of the cross-sections of sandstone supports that the system of crack planes under triaxial cyclic loading is much more complicated than that under triaxial monotonic loading. More axial and lateral tensile cracks were observed in the specimens under cyclic loading than under monotonic loading.

Description: We determine the deep structure of the eastern Algerian basin and its southern margin in the Annaba region (easternmost Algeria), to better constrain the plate kinematic reconstruction in this region. This study is based on new geophysical data collected during the SPIRAL cruise in 2009, which included a wide-angle, 240-km-long, onshore–offshore seismic profile, multichannel seismic reflection lines and gravity and magnetic data, complemented by the available geophysical data for the study area. The analysis and modelling of the wide-angle seismic data including refracted and reflected arrival travel times, and integrated with the multichannel seismic reflection lines, reveal the detailed structure of an ocean-to-continent transition. In the deep basin, there is an ~5.5-km-thick oceanic crust that is composed of two layers. The upper layer of the crust is defined by a high velocity gradient and P -wave velocities between 4.8 and 6.0 km s –1 , from the top to the bottom. The lower crust is defined by a lower velocity gradient and P -wave velocity between 6.0 and 7.1 km s –1 . The Poisson ratio in the lower crust deduced from S -wave modelling is 0.28, which indicates that the lower crust is composed mainly of gabbros. Below the continental edge, a typical continental crust with P -wave velocities between 5.2 and 7.0 km s –1 , from the top to the bottom, shows a gradual seaward thinning of ~15 km over an ~35-km distance. This thinning is regularly distributed between the upper and lower crusts, and it characterizes a rifted margin, which has resulted from backarc extension at the rear of the Kabylian block, here represented by the Edough Massif at the shoreline. Above the continental basement, an ~2-km-thick, pre-Messinian sediment layer with a complex internal structure is interpreted as allochthonous nappes of flysch backthrusted on the margin during the collision of Kabylia with the African margin. The crustal structure, moreover, provides evidence for Miocene emplacement of magmatic intrusions in both the deep basin and the continental margin. Based on the crustal structure, we propose that the eastern Algerian basin opened during the southeastward migration of the European forearc before the collision, along a NW–SE elongated spreading centre that ran perpendicular to the subduction trend. Such an atypical geometry is explained by the diverging directions of the subduction rollback during the backarc opening: eastward for the Corsica–Sardinia block, and southward for the Kabylian blocks. This geometry of the forearc can be interpreted as the surface expression of a slab tear at depth, which is responsible for atypical magmatism in the overlying backarc oceanic basin.

Description: In November 2010, intense seismic activity including 29 events with a magnitude above 5.0, started in the western part of the Gulf of Aden, where the structure of the oceanic spreading ridge is characterized by a series of N115°-trending slow-spreading segments set within an EW-trending rift. Using signals recorded by permanent and temporary networks in Djibouti and Yemen, we located 1122 earthquakes, with a magnitude ranging from 2.1 to 5.6 from 2010 November 1 to 2011 March 31. By looking in detail at the space–time distribution of the overall seismicity, and both the frequency and the moment tensor of large earthquakes, we re-examine the chronology of this episode. In addition, we also interpret the origin of the activity using high-resolution bathymetric data, as well as from observations of seafloor cable damage caused by high temperatures and lava flows. The analysis allows us to identify distinct active areas. First, we interpret that this episode is mainly related to a diking event along a specific ridge segment, located at E044°. In light of previous diking episodes in nearby subaerial rift segments, for which field constraints and both seismic and geodetic data exist, we interpret the space–time evolution of the seismicity of the first few days. Migration of earthquakes suggests initial magma ascent below the segment centre. This is followed by a southeastward dike propagation below the rift immediately followed by a northwestward dike propagation below the rift ending below the northern ridge wall. The cumulative seismic moment associated with this sequence reaches 9.1 x 10 17 Nm, and taking into account a very low seismic versus geodetic moment, we estimate a horizontal opening of ~0.58–2.9 m. The seismic activity that followed occurred through several bursts of earthquakes aligned along the segment axis, which are interpreted as short dike intrusions implying fast replenishment of the crustal magma reservoir feeding the dikes. Over the whole period, the opening is estimated to be ~1.76–8.8 m across the segment. A striking feature of this episode is that the seismicity remained confined within one individual segment, whereas the adjacent en-echelon segments were totally quiescent, suggesting that the magma supply system of one segment is disconnected from those of the neighbouring segments. Second, we identify activity induced by the first intrusion with epicentres aligned along an N035°E-trending, ~30 km long at the northwestern end of the active opening segment. This group encompasses more than seven earthquakes with magnitude larger than 5.0, and with strike-slip focal mechanisms consistent with the faults identified in the bathymetry and the structural pattern of the area. We propose that a transform fault is currently in formation which indicates an early stage of the ridge segmentation, at the locus of the trend change of the spreading ridge, which also corresponds to the boundary between a clear oceanic lithosphere and the zone of transform between continental and oceanic crust.

Description: We challenge the perspective that seismicity could contribute to polar motion by arguing quantitatively that, in first approximation and on the average, interseismic deformations can compensate for it. This point is important because what we must simulate and observe in Earth Orientation Parameter time-series over intermediate timescales of decades or centuries is the residual polar motion resulting from the two opposing processes of coseismic and interseismic deformations. In this framework, we first simulate the polar motion caused by only coseismic deformations during the longest period available of instrumental seismicity, from 1900 to present, using both the CMT and ISC-GEM catalogues. The instrumental seismicity covering a little longer than one century does not represent yet the average seismicity that we should expect on the long term. Indeed, although the simulation shows a tendency to move the Earth rotation pole towards 133°E at the average rate of 16.5 mm yr –1 , this trend is still sensitive to individual megathrust earthquakes, particularly to the 1960 Chile and 1964 Alaska earthquakes. In order to further investigate this issue, we develop a global seismicity model (GSM) that is independent from any earthquake catalogue and that describes the average seismicity along plate boundaries on the long term by combining information about present-day plate kinematics with the Anderson theory of faulting, the seismic moment conservation principle and a few other assumptions. Within this framework, we obtain a secular polar motion of 8 mm yr –1 towards 112.5°E that is comparable with that estimated from 1900 to present using the earthquake catalogues, although smaller by a factor of 2 in amplitude and different by 20° in direction. Afterwards, in order to reconcile the idea of a secular polar motion caused by earthquakes with our simplest understanding of the seismic cycle, we adapt the GSM in order to account for interseismic deformations and we use it to quantify, for the first time ever, their contribution to polar motion. Taken together, coseismic and interseismic deformations make the rotation pole wander around the north pole with maximum polar excursions of about 1 m. In particular, the rotation pole moves towards about Newfoundland when the interseismic contribution dominates over the coseismic ones (i.e. during phases of low seismicity or, equivalently, when most of the fault system associated with plate boundaries is locked). When megathrust earthquakes occur, instead, the rotation pole is suddenly shifted in an almost opposite direction, towards about 133°E.

Description: This article applies the concept of a term structure to agricultural land rental prices. Based on theoretical considerations, we develop a hedonic pricing model that allows for different shapes of the term structure curve while controlling for other price-relevant characteristics. We apply this model to land lease contracts in Saxony-Anhalt. We find an upward-sloping term structure during the agricultural price boom in 2007 and 2008, where market participants expected increasing rental prices. For the subsequent years, however, we detect a single-humped term structure. Hence, market participants revised their expectations and assumed a decline of land rental prices in the long term.

Description: Cadmium is a widespread environmental pollutant and poses some potential risks to human health. However, the signaling events controlling cadmium toxicity are not fully understood. In this study, we examined the effect of cadmium chloride on cell viability and the intracellular nitric oxide (NO) level in yeast cells. The results showed that exposure of yeast cells to cadmium (0–100 μM) could induce cell killing with significantly increased intracellular NO levels. Morphological analysis of the nuclei with 4 ' ,6-diamidino-2-phenylindole staining and DNA strand breaks analysis showed that cadmium at 50 μM can induce cell apoptosis in yeast cells. Treatment of yeast cells with cadmium (50 μM) and the nitric oxide scavenger c-PTIO [2-(4-carboxyphenyl)-4,4,5,5-teramethylimidazoline-1-oxyl-3-oxide; 0.2 mM] showed that c-PTIO attenuated the cadmium-induced cell killing. Our findings indicated that cadmium-induced yeast cell killing is mediated by a directly increased intracellular NO level.

Description: While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U x L . When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U x L favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.

Description: This article uses the 2007 Farm and Ranch Irrigation Survey database developed by the U.S. Department of Agriculture to assess the impact of water scarcity and climate on irrigation decisions for producers of specialty crops, wheat, and forage crops. We estimate an irrigation management model for major crops in the West Coast (California, Oregon, and Washington), which includes a farm-level equation of irrigated share and crop-specific equations of technology adoption and water application rate (orchard/vineyard, vegetable, wheat, alfalfa, hay, and pasture). We find that economic and physical water scarcity, climate, and extreme weather, such as frost, extreme heat, and drought, significantly impact producers’ irrigation decisions. Producers use sprinkler technologies or additional water applications to mitigate risk of crop damage from extreme weather. Water application rates are least responsive to surface water cost or groundwater well depth for producers of orchard/vineyard. Water supply institutions influence producers’ irrigation decisions. Producers who receive water from federal agencies use higher water application rates and are less likely to adopt water-saving irrigation technologies for some crops. Institutional arrangements, including access to distinct water sources (surface or ground) and whether surface water cost is fee based, also affect the responsiveness of water application rates to changes in surface water cost. The analysis provides valuable information about how producers in irrigated agricultural production systems would respond and adapt to water pricing policies and climate change.

Description: Steady plate subduction elastically brings about permanent lithospheric deformation in island arcs, though this effect has been neglected in most studies based on elastic dislocation theory. We investigate the characteristics of the permanent lithospheric deformation using a kinematic model, in which steady slip motion is given along a plate interface in the elastic lithosphere overlying the viscoelastic asthenosphere under gravity. As a rule of thumb, long-term lithospheric deformation can be understood as a bending of an elastic plate floating on non-viscous fluid, because the asthenosphere behaves like water on the long term. The steady slip below the lithosphere–asthenosphere boundary does not contribute to long-term lithospheric deformation. Hence, the key parameters that control the lithospheric deformation are only the thickness of the lithosphere and the geometry of the plate interface. Slip on a plate interface generally causes substantial vertical displacement, and gravity always tries to retrieve the original gravitational equilibrium. For a curved plate interface gravity causes convex upward bending of the island-arc lithosphere, while for a planar plate interface gravity causes convex downward bending. Larger curvature and thicker lithosphere generally results in larger deformation. When the curvature changes along the plate interface, internal deformation is also involved intrinsically, which modifies the deformation field due to gravity. Because the plate interface generally has some curvature, at least near the trench, convex upward bending of the island-arc lithosphere, which involves uplift of island-arc and subsidence around the trench, is always realized. On the other hand, the deformation field of the island-arc lithosphere sensitively depends on lithospheric thickness and plate interface geometry. These characteristics obtained by the numerical simulation are consistent with observed topography and free-air gravity anomalies in subduction zones: a pair of topography and gravity anomalies, high in the arc and low around the trench, is observed without exceptions all over the world, while there are large variety in the amplitude and horizontal scale of the topography and gravity anomalies.

Description: Effective uptake of fermentable substrates is a fundamentally important aspect of any fermentation process. The solventogenic bacterium Clostridium beijerinckii is noted for its ability to ferment a wide range of carbohydrates, yet few of its sugar transport systems have been characterized. In common with other anaerobes, C. beijerinckii shows a marked dependence on the PEP-dependent phosphotransferase system (PTS) for sugar accumulation. In this study, the gene cbe0751 encoding the sugar-specific domains of a phosphotransferase belonging to the glucose family was cloned into an Escherichia coli strain lacking the ability to take up and phosphorylate glucose. Transformants gained ability to ferment glucose, and also mannose, and further analysis of a selected transformant demonstrated that it could take up and phosphorylate glucose, confirming that cbe0751 encodes a glucose PTS which also recognizes mannose as a substrate. RT-PCR analysis showed that cbe0751 was expressed in cultures grown on both substrates, but also to varying extents during growth on some other carbon sources. Although analogue inhibition studies suggested that Cbe0751 is not the only glucose PTS in C. beijerinckii , this system should nevertheless be regarded as a potential target for metabolic engineering to generate a strain showing improved sugar fermentation properties.

Description: We investigate the influence of the glacial isostatic adjustment (GIA) on the deformation at the surface and at seismogenic depths in Fennoscandia. The surface strain rate field, derived from geodetic data, is controlled by GIA which causes NW–SE extension of up to 4  x  10 –9  yr –1 in most of mainland Fennoscandia, surrounded by regions of radial shortening towards the centre of uplift. The seismic deformation field, derived from a new compilation of focal mechanisms, shows consistent NW–SE compression on the Norwegian continental margin and a tendency towards tension in mainland Fennoscandia. The seismic moment rate is at least two orders of magnitude smaller than the geodetic moment rate. We propose that the low level of seismicity and the tendency towards tensional focal mechanisms in mainland Fennoscandia may be explained by the destructive interference of the regional stress from ridge push with the flexural stress due to GIA.

Description: New Guinea is a region characterized by rapid oblique convergence between the Pacific and Australian tectonic plates. The detailed tectonics of the region, including the partitioning of relative block motions and fault slip rates within this complex boundary plate boundary zone are still not well understood. In this study, we quantify the distribution of the deformation throughout the central and western parts of Papua New Guinea (PNG) using 20 yr of GPS data (1993–2014). We use an elastic block model to invert the regional GPS velocities as well as earthquake slip vectors for the location and rotation rates of microplate Euler poles as well as fault slip parameters in the region. Convergence between the Pacific and the Australian plates is accommodated in northwestern PNG largely by the New Guinea Trench with rates exceeding 90 mm yr –1 , indicating that this is the major active interplate boundary. However, some convergent deformation is partitioned into a shear component with ~12 per cent accommodated by the Bewani-Torricelli fault zone and the southern Highlands Fold-and-Thrust Belt. New GPS velocities in the eastern New Guinea Highlands region have led to the identification of the New Guinea Highlands and the Papuan Peninsula being distinctly different blocks, separated by a boundary through the Aure Fold-and-Thrust Belt complex which accommodates an estimated 4–5 mm yr –1 of left-lateral and 2–3 mm yr –1 of convergent motion. This implies that the Highlands Block is rotating in a clockwise direction relative to the rigid Australian Plate, consistent with the observed transition to left-lateral strike-slip regime observed in western New Guinea Highlands. We find a better fit of our block model to the observed velocities when assigning the current active boundary between the Papuan Peninsula and the South Bismark Block to be to the north of the city of Lae on the Gain Thrust, rather than on the more southerly Ramu-Markham fault as previously thought. This may indicate a temporary shift of activity onto out of sequence thrusts like the Gain Thrust as opposed to the main frontal thrust (the Ramu-Markham fault). In addition, we show that the southern Highlands Fold-and-Thrust Belt is the major boundary between the rigid Australian Plate and the New Guinea Highlands Block, with convergence occurring at rates between ~6 and 13 mm yr –1 .

Description: We examine the geodetically derived rotational variations for the rate of change of degree-two harmonics of Earth's geopotential, $\skew5\dot J_2$ , and true polar wander, combining a recent melting model of glaciers and the Greenland and Antarctic ice sheets taken from the IPCC 2013 Report (AR5) with two representative GIA ice models describing the last deglaciation, ICE5G and the ANU model developed at the Australian National University. Geodetically derived observations of $\skew4\dot J_2$ are characterized by temporal changes of –(3.7 ± 0.1)  x 10 –11 yr –1 for the period 1976–1990 and –(0.3 ± 0.1)  x 10 –11 yr –1 after ~2000. The AR5 results make it possible to evaluate the recent melting of the major ice sheets and glaciers for three periods, 1900–1990, 1991–2001 and after 2002. The observed $\skew4\dot J_2$ and the component of $\skew4\dot J_2$ due to recent melting for different periods indicate a long-term change in $\skew4\dot J_2$ —attributed to the Earth's response to the last glacial cycle—of –(6.0–6.5)  x 10 –11 yr –1 , significantly different from the values adopted to infer the viscosity structure of the mantle in most previous studies. This is a main conclusion of this study. We next compare this estimate with the values of $\skew4\dot J_2$ predicted by GIA ice models to infer the viscosity structure of the mantle, and consequently obtain two permissible solutions for the lower mantle viscosity ( lm ), ~10 22 and (5–10)  x 10 22 Pa s, for both adopted ice models. These two solutions are largely insensitive to the lithospheric thickness and upper mantle viscosity as indicated by previous studies and relatively insensitive to the viscosity structure of the D '' layer. The ESL contributions from the Antarctic ice sheet since the last glacial maximum (LGM) for ICE5G and ANU are about 20 and 30 m, respectively, but glaciological reconstructions of the Antarctic LGM ice sheet have suggested that its ESL contribution may have been less than ~10 m. The GIA-induced $\skew4\dot J_2$ for GIA ice models with an Antarctic ESL component of ~10 m suggests two permissible lower mantle viscosity solutions of lm ~ 2  x 10 22 and ~5  x 10 22 Pa s or one solution with (2–5)  x 10 22 Pa s. These results suggest that the effective lower mantle viscosity is larger than ~10 22 Pa s regardless of the uncertainties for an Antarctic ESL component. We also examine the polar wander due to recent melting and GIA processes, suggesting that the observed polar wander may be significantly attributed to convection motions in the mantle and/or another cause, particularly for permissible lower mantle viscosity solution of (5–10)  x 10 22 Pa s.

Description: Much of the inter-individual variation in gene expression is triggered via perturbations of signaling networks by DNA variants. We present a novel probabilistic approach for identifying the particular pathways by which DNA variants perturb the signaling network. Our procedure, called PINE, relies on a systematic integration of established biological knowledge of signaling networks with data on transcriptional responses to various experimental conditions. Unlike previous approaches, PINE provides statistical aspects that are critical for prioritizing hypotheses for followup experiments. Using simulated data, we show that higher accuracy is attained with PINE than with existing methods. We used PINE to analyze transcriptional responses of immune dendritic cells to several pathogenic stimulations. PINE identified statistically significant genetic perturbations in the pathogen-sensing signaling network, suggesting previously uncharacterized regulatory mechanisms for functional DNA variants.

Description: In this work, we test the analysis of anisotropy of magnetic susceptibility (AMS) for the study of diapirs in the Naval salt wall that is located in the western end of the South Pyrenean Central Unit. Two hundred eighty-six specimens from 30 sites were sampled in the mobilized Middle-Upper Triassic evaporites and shales that constitute the core of this diapir. Resulting magnetic ellipsoids are mostly oblate and scalar parameters are similar to those found in weakly deformed, sedimentary rocks. From the observation of samples and thin sections, magnetic fabrics can be related to petrofabric: magnetic foliation corresponds to flattening or shear planes and magnetic lineation to flow/shear direction, elongation of grains or tight microfolds. The magnetic foliation shows a roughly circular pattern with shallow dips and some deflections due to Pyrenean structures. Magnetic lineations show a slightly dominant NE–SW trend and shallow plunges. Magnetic lineations and foliations are consistent with the theoretical pattern expected at the roof of a vertically grown salt wall, thus supporting that magnetic fabrics registered evaporitic flow at late stages of diapiric growth. We demonstrate that AMS is an efficient and promising tool to define diapiric flow where tectonic fabric cannot be directly measured. Knowledge of the geometry and internal deformation of the diapiric body helps to minimize ambiguities in the interpretation of magnetic fabrics in terms of internal deformation.

Description: Several large earthquakes in the Hellenic subduction zone have been documented in historical records from around the eastern Mediterranean, but the relative seismic quiescence of the region over the period of instrumental observation means that the exact locations of these earthquakes and their tectonic significance are not known. We present AMS radiocarbon dates from uplifted late Holocene palæoshorelines from the island of Rhodes, showing that uplift is most consistent with a single large ( M W  ≥ 7.7) reverse-faulting earthquake between about 2000 BC and 200 BC. Analysis of the uplift treating the earthquake as a dislocation in an elastic half-space shows a predominantly reverse-faulting event with a slip vector oblique to the direction of convergence between Rhodes and Nubia. We suggest that the fault responsible for the uplift dips at an angle of 30–60° above the more gently dipping oblique subduction interface. The highly oblique convergence across the eastern Hellenic plate boundary zone appears to be partitioned into reverse slip on faults that strike parallel to the boundary and strike-parallel or oblique slip on the subduction interface. Hydrodynamical simulation of tsunami propagation from a range of tectonically plausible sources suggests that earthquakes on the fault uplifting Rhodes represent a significant tsunami hazard for Rhodes and SW Turkey, and also possibly for Cyprus and the Nile Delta.

Description: Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean–variance relationship of the log-counts-per-million using ‘voom’. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source ‘limma’ package.

Description: Most mammalian genes have mRNA variants due to alternative promoter usage, alternative splicing, and alternative cleavage and polyadenylation. Expression of alternative RNA isoforms has been found to be associated with tumorigenesis, proliferation and differentiation. Detection of condition-associated transcription variation requires association methods. Traditional association methods such as Pearson chi-square test and Fisher Exact test are single test methods and do not work on count data with replicates. Although the Cochran Mantel Haenszel (CMH) approach can handle replicated count data, our simulations showed that multiple CMH tests still had very low power. To identify condition-associated variation of transcription, we here proposed a ranking analysis of chi-squares (RAX2) for large-scale association analysis. RAX2 is a nonparametric method and has accurate and conservative estimation of FDR profile. Simulations demonstrated that RAX2 performs well in finding condition-associated transcription variants. We applied RAX2 to primary T-cell transcriptomic data and identified 1610 (16.3%) tags associated in transcription with immune stimulation at FDR 〈 0.05. Most of these tags also had differential expression. Analysis of two and three tags within genes revealed that under immune stimulation short RNA isoforms were preferably used.

Description: Reconstructions of the history of convergence between the Nubia and Eurasia plates constitute an important part of a broader framework for understanding deformation in the Mediterranean region and the closing of the Mediterranean Basin. Herein, we combine high-resolution reconstructions of Eurasia-North America and Nubia-North America Plate motions to determine rotations that describe Nubia-Eurasia Plate motion at ~1 Myr intervals for the past 20 Myr. We apply trans-dimensional hierarchical Bayesian inference to the Eurasia-North America and Nubia-North America rotation sequences in order to reduce noise in the newly estimated Nubia-Eurasia rotations. The noise-reduced rotation sequences for the Eurasia-North America and Nubia-North America Plate pairs describe remarkably similar kinematic histories since 20 Ma, consisting of relatively steady seafloor spreading from 20 to 8 Ma, ~20 per cent opening-rate slowdowns at 8–6.5 Ma, and steady plate motion from ~7 Ma to the present. Our newly estimated Nubia-Eurasia rotations predict that convergence across the central Mediterranean Sea slowed by ~50 per cent and rotated anticlockwise after ~25 Ma until 13 Ma. Motion since 13 Ma has remained relatively steady. An absence of evidence for a significant change in motion immediately before or during the Messinian Salinity Crisis at 6.3–5.6 Ma argues against a change in plate motion as its causative factor. The detachment of the Arabian Peninsula from Africa at 30–24 Ma may have triggered the convergence rate slowdown before 13 Ma; however, published reconstructions of Nubia-Eurasia motion for times before 20 Ma are too widely spaced to determine with confidence whether the two are correlated. A significant discrepancy between our new estimates of Nubia-Eurasia motion during the past few Myr and geodetic estimates calls for further investigation.

Description: The Yellowstone–East Snake River Plain hotspot track has been intensely studied since several decades and is widely considered to result from the interaction of a mantle plume with the North American plate. An integrated conclusive geodynamic interpretation of this extensive data set is however presently still lacking, and our knowledge of the dynamical processes beneath Yellowstone is patchy. It has been argued that the Yellowstone plume has delaminated the lower part of the thick Wyoming cratonic lithosphere. We derive an original dynamic model to quantify delamination processes related to mantle plume–lithosphere interactions. We show that fast (~300 ka) lithospheric delamination is consistent with the observed timing of formation of successive volcanic centres along the Yellowstone hotspot track and requires (i) a tensile stress regime within the whole lithosphere exceeding its failure threshold, (ii) a purely plastic rheology in the lithosphere when stresses reach this yield limit, (iii) a dense lower part of the 200 km thick Wyoming lithosphere and (iv) a decoupling melt horizon inside the median part of the lithosphere. We demonstrate that all these conditions are verified and that ~150 km large and ~100 km thick lithospheric blocks delaminate within 300 ka when the Yellowstone plume ponded below the 200 km thick Wyoming cratonic lithosphere. Furthermore, we take advantage of the available extensive regional geophysical and geological observation data sets to design a numerical 3-D upper-mantle convective model. We propose a map of the ascending convective sheets contouring the Yellowstone plume. The model further evidences the development of a counter-flow within the lower part of the lithosphere centred just above the Yellowstone mantle plume axis. This counter-flow controls the local lithospheric stress field, and as a result the trajectories of feeder dykes linking the partial melting source within the core of the mantle plume with the crust by crosscutting the lithospheric mantle. This counter-flow further explains the 50 km NE shift observed between the mantle plume axis and the present-day Yellowstone Caldera as well as the peculiar shaped crustal magma chambers.

Description: We present source models for the August 2014 Murmuri (Dehloran) earthquake sequence in the Zagros Mountains of Iran. An M w 6.2 mainshock was followed by an aftershock sequence containing five events of M w ≥ 5.4. Models of P and SH waveforms show that all events had dominantly thrust-faulting mechanisms, and had centroid depths that place them within the thick sedimentary sequence, above the crystalline basement. The combination of our estimated focal mechanisms, relative relocations of the event hypocentres and the surface displacement patterns observed using InSAR imply that the mainshock and largest aftershock ruptured different fault planes and both contributed to the surface deformation. The fault planes both slipped in horizontally elongated patches, possibly due to rheological layering limiting the updip and downdip extent of rupture. The slip vector of the Murmuri mainshock implies that the decollement beneath the Lorestan Arc is weaker than any such feature beneath the Dezful Embayment, providing an explanation for the plan-view sinuosity of the range-front of the Zagros Mountains.

Description: Analyses of the costs of regulating greenhouse gas emissions from dairy production, which could be used to assess the effectiveness of alternative policy measures, is a missing link in the literature. This article addresses this gap by establishing the economic impact associated with a hypothetical greenhouse gas environmental regulatory regime across major dairy producing counties in the United States. In doing so, the article makes three important contributions to the literature. First, it develops a comprehensive pollution index based on Environmental Protection Agency methodologies, which contrasts with previous studies that rely on partial measures based only on surplus nitrogen stemming from the over-application of fertilizer. Second, the article uses a directional output distance function, an approach that has not been employed previously to evaluate polluting technologies in the U.S. dairy sector. Third, the article incorporates a four-way error approach that accounts for unobserved county heterogeneity, time-invariant persistent technical efficiency, time-varying transient technical efficiency, and a random error. The results indicate that regulating greenhouse gas emissions from dairy farming would induce a 5-percentage point increase in average technical efficiency. In addition, the economic costs of implementing this hypothetical regulatory framework exhibit significant spatial variation across counties in the United States.

Description: Displacements and stress-field changes associated with earthquakes, volcanoes, landslides and human activity are often simulated using numerical models in an attempt to understand the underlying processes and their governing physics. The application of elastic dislocation theory to these problems, however, may be biased because of numerical instabilities in the calculations. Here, we present a new method that is free of artefact singularities and numerical instabilities in analytical solutions for triangular dislocations (TDs) in both full-space and half-space. We apply the method to both the displacement and the stress fields. The entire 3-D Euclidean space $\mathbb {R}^{3}$ is divided into two complementary subspaces, in the sense that in each one, a particular analytical formulation fulfils the requirements for the ideal, artefact-free solution for a TD. The primary advantage of the presented method is that the development of our solutions involves neither numerical approximations nor series expansion methods. As a result, the final outputs are independent of the scale of the input parameters, including the size and position of the dislocation as well as its corresponding slip vector components. Our solutions are therefore well suited for application at various scales in geoscience, physics and engineering. We validate the solutions through comparison to other well-known analytical methods and provide the MATLAB codes.

Description: Using dynamic rupture models of a right-lateral fault embedded in an elastic or elastoplastic 3-D medium, we investigate elastic and inelastic responses of compliant fault zones to nearby earthquake ruptures. We particularly examine effects of fault zone depth, width, shape and rigidity reduction on the surface displacement field. Our results from elastic models show that deeper and wider fault zones generally result in larger residual displacements. However, for shallow fault zones, the vertical residual displacement is insensitive to or even decreases with fault zone width. The width of horizontal displacement anomalies across a fault zone is only indicative of the fault zone width near the Earth's surface. There are trade-off effects among fault zone depth, width, shape and rigidity reduction on the amplitude of surface residual displacements. Our elastoplastic models show that plastic strain can occur along the entire fault zone near the Earth's surface and in the extensional quadrant at depth, if fault zone rocks are close to failure before a nearby earthquake happens. Compared with results from elastic models, plastic strain near the Earth's surface generally enhances surface displacements of a fault zone and does not change the trend of effects of fault zone depth and width, while plastic strain at depth can result in reduced retrograde motion or sympathetic motion across the fault zone, and introduce complexities in effects of fault zone depth and width. Sympathetic horizontal motion more likely occurs across a narrow fault zone with inelastic response at depth. Vertical motion in the extensional quadrant may actually decrease with fault zone width in elastoplastic models. Sympathetic horizontal motion, or small retrograde horizontal motion in conjunction with large vertical motion above a fault zone is indicative of inelastic response of a fault zone at depth.

Description: Models of the glacial isostatic adjustment process, which is dominated by the influence of the Late Pleistocene cycle of glaciation and deglaciation, depend on two fundamental inputs: a history of ice-sheet loading and a model of the radial variation of mantle viscosity. These models may be tested and refined by comparing their local predictions of relative sea level history to geological inferences based upon appropriate sea level indicators. The U.S. Atlantic coast is a region of particular interest in this regard, due to the fact that data from the length of this coast provides a transect of the forebulge associated with the former Laurentide ice sheet. High-quality relative sea level histories from this region are employed herein to explore the ability of current models of mantle viscosity to explain the inferred evolution of relative sea level that have accompanied forebulge collapse following deglaciation. Existing misfits are characterized, and alternatives are explored for their reconciliation. It is demonstrated that a new model of mantle viscosity, referred to herein as VM6, when coupled with the latest model of deglaciation history ICE-6G_C, is able to eliminate the majority of these misfits, while continuing to reconcile a wide range of other important geophysical observables, as well as additional relative sea level data from the North American. West coast which also record the collapse of the forebulge but which have not been employed in tuning the viscosity profile to enable ICE-6G_C (VM6) to fit the East coast data set.

Description: Heavy metals are dense chemicals with dual biological role as micronutrients and intoxicants. A few hypersaline environmental systems are naturally enriched with heavy metals, while most metal-contaminated sites are a consequence of human activities. Numerous halotolerant and moderately halophilic Bacteria possess metal tolerance, whereas a few archaeal counterparts share similar features. The main mechanisms underlying heavy metal resistance in halophilic Bacteria and Archaea include extracellular metal sequestration by biopolymers, metal efflux mediated by specific transporters and enzymatic detoxification. Biotransformation of metals by halophiles has implications both for trace metal turnover in natural saline ecosystems and for development of novel bioremediation strategies.

Description: We screened for a gene that inhibits streptomycin production in Streptomyces griseus when it is introduced on a high-copy-number plasmid pIJ702, and obtained a plasmid pKM545. The introduction of pKM545 abolished streptomycin production on all media tested including YMP-sugar and Nutrient broth. S1 protection analysis demonstrated that the introduction of this plasmid downregulated the transcriptional activity of the promoter preceding strR , the pathway-specific transcriptional regulator for streptomycin biosynthesis. The 2.8-kb Bam HI fragment cloned onto pKM545 contained two coding sequences SGR_5442 and 5443. These coding sequences and the two downstream ones (SGR_5444 and 5445) constituted a possible operon structure designated to be rspABCD (regulation of streptomycin production). RspB and RspC exhibited a marked similarity with an ATP-binding domain and a membrane-associating domain of an ABC-2 type transporter, respectively, suggesting that the Rsp proteins comprise a membrane exporter. The gene cluster consisting of the rsp operon and the upstream divergent small coding sequence (SGR_5441) was widely distributed to Streptomyces genome. An rspB mutant of S. griseus produced 3-fold streptomycin of the parental strain in YMP liquid medium. The evidence implies that the Rsp translocator is involved in the export of a substance that specifies the expression level of streptomycin biosynthesis genes in S. griseus .

Description: We previously demonstrated that in Streptomyces coelicolor two-component system AfsQ1/Q2 activates the production of the yellow-colored coelimycin P2 (also named as yCPK) on glutamate-supplemented minimal medium, and the response regulator AfsQ1 could specifically bind to the intergenic region between two structural genes, cpkA and cpkD . Here, a more in-depth investigation was performed to elucidate the mechanism underlying the role of AfsQ1/Q2 in regulating coelimycin P2 biosynthesis. Deletion of afsQ1/Q2 resulted in markedly decreased expression of the whole coelimycin P2 biosynthetic gene cluster. Electrophoretic mobility shift assays revealed that AfsQ1 bound only to the target site identified previously, but not to any other promoters in the gene cluster. Mutations of AfsQ1-binding motif only resulted in drastically reduced transcription of the cpkA/B/C operon (encoding three type I polyketide synthases) and intriguingly, led to enhanced expression of some coelimcyin P2 genes, particularly accA1 and scF . These results suggested the direct role of AfsQ1/Q2 in regulating coelimycin production, which is directly mediated by the structural genes, but not the cluster-situated regulatory genes, and also implied that other unknown mechanisms may be involved in AfsQ1/Q2-mediated regulation of coelimycin P2 biosynthesis.

Description: Sulfate-reducing bacteria (SRBs) gain their energy by coupling the oxidation of organic substrate to the reduction of sulfate to sulfide. Several SRBs are able to use alternative terminal electron acceptors to sulfate such as nitrate. Nitrate-reducing SRBs have been isolated from a diverse range of environments. In order to be able to understand the significance of nitrate reduction in SRBs, we need to examine the ecology and physiology of the nitrate-reducing SRB isolates.

Description: The ADP-ribosylating enzymes are encoded in many pathogenic bacteria in order to affect essential functions of the host. In this study, we show that Neisseria gonorrhoeae possess a locus that corresponds to the ADP-ribosyltransferase NarE, a previously characterized enzyme in N. meningitidis . The 291 bp coding sequence of gonococcal narE shares 100% identity with part of the coding sequence of the meningococcal narE gene due to a frameshift previously described, thus leading to a 49-amino-acid deletion at the N-terminus of gonococcal NarE protein. However, we found a promoter region and a GTG start codon, which allowed expression of the protein as demonstrated by RT-PCR and western blot analyses. Using a gonococcal NarE–6xHis fusion protein, we demonstrated that the gonococcal enzyme underwent auto-ADP-ribosylation but to a lower extent than meningococcal NarE. We also observed that gonoccocal NarE exhibited ADP-ribosyltransferase activity using agmatine and cell-free host proteins as ADP-ribose acceptors, but its activity was inhibited by human β-defensins. Taken together, our results showed that NarE of Neisseria gonorrhoeae is a functional enzyme that possesses key features of bacterial ADP-ribosylating enzymes.

Description: The effect of fructose 1,6-bisphosphate (Fru 1,6-P 2 ) on the regulatory enzymes of pentose phosphate pathway of Escherichia coli was examined. Fru 1,6-P 2 inhibited E. coli transaldolase (EC 2.2.1.2) competitively against fructose 6-phosphate and uncompetitively against erythrose 4-phosphate, whereas Fru 1,6-P 2 did not affect glucose 6-phosphate dehydrogenase (EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (EC 1.1.1.44). Kinetic results can be explained by assuming that transaldolase has two kinds of binding sites for Fru 1,6-P 2 : a competitive binding site for fructose 6-phosphate and a second binding site on the enzyme-erythrose 4-phosphate complex. Fru 1,6-P 2 increased resulting from the stimulation of glycolysis, can inhibit transaldolase and further participates in the elevation of the concentration of ribose 5-phosphate that can be preferentially utilized for anabolic reaction in exponential phase of E. coli .

Description: In the context of the 2014 realization of the International Terrestrial Reference Frame, the International DORIS (Doppler Orbitography Radiopositioning Integrated by Satellite) Service (IDS) has delivered to the IERS a set of 1140 weekly SINEX files including station coordinates and Earth orientation parameters, covering the time period from 1993.0 to 2015.0. From this set of weekly SINEX files, the IDS combination centre estimated a cumulative DORIS position and velocity solution to obtain mean horizontal and vertical motion of 160 stations at 71 DORIS sites. The main objective of this study is to validate the velocities of the DORIS sites by comparison with external models or time-series. Horizontal velocities are compared with two recent global plate models (GEODVEL 2010 and NNR-MORVEL56). Prior to the comparisons, DORIS horizontal velocities were corrected for Global Isostatic Adjustment from the ICE-6G (VM5a) model. For more than half of the sites, the DORIS horizontal velocities differ from the global plate models by less than 2–3 mm yr –1 . For five of the sites (Arequipa, Dionysos/Gavdos, Manila and Santiago) with horizontal velocity differences with respect to these models larger than 10 mm yr –1 , comparisons with GNSS estimates show the veracity of the DORIS motions. Vertical motions from the DORIS cumulative solution are compared with the vertical velocities derived from the latest GPS cumulative solution over the time span 1995.0–2014.0 from the University of La Rochelle solution at 31 co-located DORIS-GPS sites. These two sets of vertical velocities show a correlation coefficient of 0.83. Vertical differences are larger than 2 mm yr –1 at 23 percent of the sites. At Thule, the disagreement is explained by fine-tuned DORIS discontinuities in line with the mass variations of outlet glaciers. Furthermore, the time evolution of the vertical time-series from the DORIS station in Thule show similar trends to the GRACE equivalent water height.

Description: We have used ensemble averages of satellite-derived free-air gravity anomaly data, together with inverse modelling techniques, to determine the effective elastic thickness, T e , of circum-Pacific subducting oceanic lithosphere and its relationship to plate age. Synthetic modelling tests show that T e can be recovered best using gravity anomaly, rather than bathymetry, data and profiles that are at least 750 km long. Inverse modelling based on a uniform T e elastic plate suggests that T e increases with age of the subducting oceanic lithosphere and is given approximately by the depth to the 390 ± 10 °C oceanic isotherm based on a cooling plate model. Misfits between the observed and calculated gravity anomalies are significantly improved if a mechanically weak zone is included between the trench axis and the outer rise. This weak zone is coincident with observations of bend-faulting and seismicity. Inverse modelling shows that T e landward of the outer rise is generally 40–65 per cent less than the T e seaward of the outer rise. Both landward and seaward T e increases with age of the lithosphere and are given by the depth to the 342–349 °C and 671–714 °C oceanic isotherm, respectively. A dependence of T e on age is consistent with models for the cooling of oceanic lithosphere as it moves away from a mid-ocean ridge and the temperature-dependent ductile creep of oceanic lithospheric minerals such as olivine. By comparing the observed T e to the predicted T e based on laboratory-derived yield strength envelopes and an assumption of elastic-perfectly plastic deformation, we have attempted to constrain the rheology of oceanic lithosphere. Regardless of the assumed friction coefficient, the dry-olivine low-temperature plasticity flow laws of Goetze, Evans & Goetze, Raterron et al . and Mei et al . all provide quite a good fit to the observed T e at circum-Pacific subduction zones. This result contrasts with the Hawaiian Islands, where these flow laws are generally too strong to fit the observations. The discrepancy in rheology within Pacific plate may be caused by differences in the timescale of loading and therefore the amount of viscoelastic stress relaxation that has occurred. Other possibilities include thermal rejuvenation and magma-assisted flexure at the Hawaiian Islands.

Description: Large gaps and inconsistencies remain in published estimates of Nubia–Somalia plate motion based on reconstructions of seafloor spreading data around Africa. Herein, we use newly available reconstructions of the Southwest Indian Ridge at ~1-Myr intervals since 20 Ma to estimate Nubia–Somalia plate motion farther back in time than previously achieved and with an unprecedented degree of temporal resolution. At the northern end of the East African rift, our new estimates of Nubia–Somalia motion for six times from 0.78 Ma to 5.2 Ma differ by only 2 per cent from the rift-normal component of motion that is extrapolated from a recently estimated GPS angular velocity. The rate of rift-normal extension thus appears to have remained steady since at least 5.2 Ma. Our new rotations indicate that the two plates have moved relative to each other since at least 16 Ma and possibly longer. Motion has either been steady since at least 16 Ma or accelerated modestly between 6 and 5.2 Ma. Our Nubia–Somalia rotations predict 42.5 ± 3.8 km of rift-normal extension since 10.6 Ma across the well-studied, northern segment of the Main Ethiopian Rift, consistent with 40–50 km estimates for extension since 10.6 Myr based on seismological surveys of this narrow part of the plate boundary. Nubia–Somalia rotations are also derived by combining newly estimated Somalia–Arabia rotations that reconstruct the post-20-Ma opening of the Gulf of Aden with Nubia–Arabia rotations estimated via a probabilistic analysis of plausible opening scenarios for the Red Sea. These rotations predict Nubia–Somalia motion since 5.2 Myr that is consistent with that determined from Southwest Indian Ridge data and also predict 40 ± 3 km of rift-normal extension since 10.6 Ma across the Main Ethiopian Rift, consistent with our 42.5 ± 3.8 km Southwest Indian Ridge estimate. Our new rotations exclude at high confidence level previous estimates of 12 ± 13 and 123 ± 14 km for rift-normal extensions across the Main Ethiopian Rift since 10.6 Ma based on reconstructions of Chron 5n.2 along the Southwest Indian Ridge. Sparse coverage of magnetic reversals older than 16 Ma along the western third of the Southwest Indian Ridge precludes reliable determinations of Nubia–Somalia plate motion before 16 Ma, leaving unanswered the key question of when the motion between the two plates began.

Description: The TAMMAR segment of the Mid-Atlantic Ridge forms a classic propagating system centred about two degrees south of the Kane Fracture Zone. The segment is propagating to the south at a rate of 14 mm yr –1 , 15 per cent faster than the half-spreading rate. Here, we use seismic refraction data across the propagating rift, sheared zone and failed rift to investigate the crustal structure of the system. Inversion of the seismic data agrees remarkably well with crustal thicknesses determined from gravity modelling. We show that the crust is thickened beneath the highly magmatic propagating rift, reaching a maximum thickness of almost 8 km along the seismic line and an inferred (from gravity) thickness of about 9 km at its centre. In contrast, the crust in the sheared zone is mostly 4.5–6.5 km thick, averaging over 1 km thinner than normal oceanic crust, and reaching a minimum thickness of only 3.5 km in its NW corner. Along the seismic line, it reaches a minimum thickness of under 5 km. The PmP reflection beneath the sheared zone and failed rift is very weak or absent, suggesting serpentinisation beneath the Moho, and thus effective transport of water through the sheared zone crust. We ascribe this increased porosity in the sheared zone to extensive fracturing and faulting during deformation. We show that a bookshelf-faulting kinematic model predicts significantly more crustal thinning than is observed, suggesting that an additional mechanism of deformation is required. We therefore propose that deformation is partitioned between bookshelf faulting and simple shear, with no more than 60 per cent taken up by bookshelf faulting.

Description: The Hdr (heterodisulfide reductase)-like enzyme is predicted, from gene transcript profiling experiments previously published, to be essential in oxidative sulfur metabolism in a number of bacteria and archaea. Nevertheless, no biochemical and physicochemical data are available so far about this enzyme. Genes coding for it were identified in Aquifex aeolicus , a Gram-negative, hyperthermophilic, chemolithoautotrophic and microaerophilic bacterium that uses inorganic sulfur compounds as electron donor to grow. We provide biochemical evidence that this Hdr-like enzyme is present in this sulfur-oxidizing prokaryote (cultivated with thiosulfate or elemental sulfur). We demonstrate, by immunolocalization and cell fractionation, that Hdr-like enzyme is associated, presumably monotopically, with the membrane fraction. We show by co-immunoprecipitation assay or partial purification, that the Hdr proteins form a stable complex composed of at least five subunits, HdrA, HdrB1, HdrB2, HdrC1 and HdrC2, present in two forms of high molecular mass on native gel (~240 and 450 kDa). These studies allow us to propose a revised model for dissimilatory sulfur oxidation pathways in A. aeolicus , with Hdr predicted to generate sulfite.

Description: Geobacter sulfurreducens is an anaerobic soil bacterium that is involved in biogeochemical cycles of elements such as Fe and Mn. Although significant progress has been made in the understanding of the electron transfer processes in G. sulfurreducens , little is known about the regulatory mechanisms involved in their control. To expand the study of gene regulation in G. sulfurreducens , we carried out a genome-wide identification of transcription start sites (TSS) by 5'RACE and by deep RNA sequencing of primary mRNAs in two growth conditions. TSSs were identified along G. sulfurreducens genome and over 50% of them were located in the upstream region of the associated gene, and in some cases we detected genes with more than one TSS. Our global mapping of TSSs contributes with valuable information, which is needed for the study of transcript structure and transcription regulation signals and can ultimately contribute to the understanding of transcription initiation phenomena in G. sulfurreducens .

Description: A multi-year drought has taken a severe toll on the agricultural economy of California’s Central Valley. Index insurance is an instrument with the potential to protect water users from economic losses due to periodic water shortages. An index insurance product based on the Sacramento Index and adapted to the Central Valley Project water supply is proposed. To address the potential for intertemporal adverse selection, three product designs are suggested: (1) "early bird" insurance; (2) variable premium insurance; and (3) variable deductible insurance. The performance of the designs are assessed using loss functions from the Westlands Water District in the San Joaquin Valley.

Description: DnpA, a putative de- N -acetylase of the PIG-L superfamily, is required for antibiotic tolerance in Pseudomonas aeruginosa . Exactly how dnpA (gene locus PA5002) directs the formation of antibiotic-tolerant persister cells is currently unknown. Previous research provided evidence for a role in surface-associated process(es), possibly in lipopolysaccharide biosynthesis. In silico sequence analysis of DnpA predicts a single transmembrane domain and N in /C out orientation of DnpA. In contrast, we here show that DnpA is an integral inner membrane protein containing two transmembrane domains, with the major C-terminal part located at the cytoplasmic face. Correct insertion into the inner membrane is necessary for DnpA to promote fluoroquinolone tolerance. The membrane localization of DnpA further supports its role in cell envelope-associated process(es). In addition to shedding light on the biological role of DnpA, this study highlights the risks of overreliance on the predictive value of bioinformatics tools and the importance of rigorous experimental validation of in silico predictions.

Description: Knowledge and understanding of the ocean–continent transition (OCT) structure, continent–ocean boundary (COB) location and crustal type are of critical importance in evaluating rifted continental margin formation and evolution. OCT structure, COB location and magmatic type also have important implications for the understanding of the geodynamics of continental breakup and in the evaluation of petroleum systems in deep-water frontier oil and gas exploration at rifted continental margins. Mapping the distribution of thinned continental crust and lithosphere, its distal extent and the start of unequivocal oceanic crust and hence determining the OCT structure and COB location at rifted continental margins is therefore a generic global problem. In order to assist in the determination of the OCT structure and COB location, we present methodologies using gravity anomaly inversion, residual depth anomaly (RDA) analysis and subsidence analysis, which we apply to the west Iberian rifted continental margin. The west Iberian margin has one of the most complete data sets available for deep magma-poor rifted margins, so there is abundant data to which the results can be calibrated. Gravity anomaly inversion has been used to determine Moho depth, crustal basement thickness and continental lithosphere thinning; subsidence analysis has been used to determine the distribution of continental lithosphere thinning; and RDAs have been used to investigate the OCT bathymetric anomalies with respect to expected oceanic bathymetries at rifted continental margins. These quantitative analytical techniques have been applied to the west Iberian rifted continental margin along profiles IAM9, Lusigal 12 (with the TGS-extension) and ISE-01. Our predictions of OCT structure, COB location and magmatic type (i.e. the volume of magmatic addition, whether the margin is ‘normal’ magmatic, magma-starved or magma-rich) have been tested and validated using ODP wells (Legs 103, 149 and 173), which provide observational constraints on the west Iberian margin.

Description: The large-scale geological evolution of the North Atlantic Realm during the past 450 Myr is largely understood, but crucial elements remain uncertain. These involve the Caledonian orogeny, the formation of the North Atlantic and accompanying igneous activity, and the present-day high topography surrounding the North Atlantic. Teleseismic receiver function interpretation in the Central Fjord Region of East Greenland recently suggested the presence of a fossil Caledonian subduction complex, including a slab of eclogitised mafic crust and an overlying wedge of serpentinised mantle peridotite. Here we further investigate this topic using inverse receiver functions modelling. The obtained velocity models are tested with regard to their consistency with the regional gravity field and topography. We find that the obtained receiver function model is generally consistent with gravity and isostasy. The western part of the section, with topography of 〉1000 m, is clearly supported by the 40-km-thick crust. The eastern part requires additional buoyancy as provided by the hydrated mantle wedge. The geometry, velocities and densities are consistent with interpretation of the lithospheric structure as a fossil subduction zone complex. The spatial relations with Caledonian structures suggest a Caledonian origin. The results indicate that topography is isostatically compensated by density variations within the lithosphere, and that significant dynamic topography is not required at the present-day.

Description: We present a high-resolution shear wave tomography of the Japan subduction zone down to a depth of 700 km, which is determined by inverting a large number of high-quality S -wave arrival-time data from local earthquakes and teleseismic events. The subducting Pacific and Philippine Sea (PHS) slabs are revealed clearly as high-velocity (high- V ) zones, whereas low-velocity (low- V ) anomalies are revealed in the mantle wedge above the two slabs. The PHS slab has subducted aseismically down to a depth of 480 km under the Japan Sea and to a depth of 540 km under the Tsushima Strait. A window is revealed within the aseismic PHS slab, being consistent with P -wave tomography. Prominent low- V and high-Poisson's ratio ( ) anomalies exist below the PHS slab and above the Pacific slab, which reflect hot and wet mantle upwelling caused by the joint effect of deep dehydration of the Pacific slab and convective circulation process in the mantle wedge above the Pacific slab. The hot and wet mantle upwelling has caused the complex geometry and structure of the PHS slab in SW Japan, and contributed to the Quaternary volcanism along the Japan Sea coast. In eastern Japan, low- V zones are revealed at depths of 200–700 km below the Pacific slab, which may reflect hot upwelling from the lower mantle or even the core–mantle boundary.

Description: The Piano di Pezza fault is the central section of the 35 km long L'Aquila-Celano active normal fault-system in the central Apennines of Italy. Although palaeoseismic data document high Holocene vertical slip rates (~1 mm yr –1 ) and a remarkable seismogenic potential of this fault, its subsurface setting and Pleistocene cumulative displacement are still poorly known. We investigated for the first time the shallow subsurface of a key section of the main Piano di Pezza fault splay by means of high-resolution seismic and electrical resistivity tomography coupled with time-domain electromagnetic soundings (TDEM). Our surveys cross a ~5-m-high fault scarp that was generated by repeated surface-rupturing earthquakes displacing Holocene alluvial fans. We provide 2-D Vp and resistivity images, which show significant details of the fault structure and the geometry of the shallow basin infill material down to 50 m depth. Our data indicate that the upper fault termination has a sub-vertical attitude, in agreement with palaeoseismological trench evidence, whereas it dips ~50° to the southwest in the deeper part. We recognize some low-velocity/low-resistivity regions in the fault hangingwall that we relate to packages of colluvial wedges derived from scarp degradation, which may represent the record of some Holocene palaeo-earthquakes. We estimate a ~13–15 m throw of this fault splay since the end of the Last Glacial Maximum (~18 ka), leading to a 0.7–0.8 mm yr –1 throw rate that is quite in accordance with previous palaeoseismic estimation of Holocene vertical slip rates. The 1-D resistivity models from TDEM soundings collected along the trace of the electrical profile significantly match with 2-D resistivity images. Moreover, they indicate that in the fault hangingwall, ~200 m away from the surface fault trace, the pre-Quaternary carbonate basement is at ~90–100 m depth. We therefore provide a minimal ~150–160 m estimate of the cumulative throw of the Piano di Pezza fault system in the investigated section. We further hypothesize that the onset of the Piano di Pezza fault activity may date back to the Middle Pleistocene (~0.5 Ma), so this is a quite young active normal fault if compared to other mature normal fault systems active since 2–3 Ma in this portion of the central Apennines.

Description: To investigate the coupling relationship between great earthquake and ionosphere, the GPS-derived total electron contents (TECs) by the Center for Orbit Determination in Europe and the foF2 data from the Space Weather Prediction Center were used to analyse the impending ionospheric anomalies before the Iquique Mw8.2 earthquake in Chile on 2014 April 1. Eliminating effects of the solar and geomagnetic activities on ionosphere by the sliding interquartile range with the 27-day window, the TEC analysis results represent that there were negative anomalies occurred on 15th day prior to the earthquake, and positive anomalies appeared in 5th day before the earthquake. The foF2 analysis results of ionosonde stations Jicamarca, Concepcion and Ramey show that the foF2 increased by 40, 50 and 45 per cent, respectively, on 5th day before the earthquake. The TEC anomalous distribution indicates that there was a widely TEC decrement over the epicentre with the duration of 6 hr on 15th day before the earthquake. On 5th day before the earthquake, the TEC over the epicentre increased with the amplitude of 15 TECu, and the duration exceeded 6 hr. The anomalies occurred on the side away from the equator. All TEC anomalies in these days were within the bounds of equatorial anomaly zone where should be the focal area to monitor ionospheric anomaly before strong earthquakes. The relationship between ionospheric anomalies and geomagnetic activity was detected by the cross wavelet analysis, which implied that the foF2 was not affected by the magnetic activities on 15th day and 5th day prior to the earthquake, but the TECs were partially affected by anomalous magnetic activity during some periods of 5th day prior to the earthquake.

Description: We present the first estimates of Southwest Indian Ridge (SWIR) plate motions at high temporal resolution during the Quaternary and Neogene based on nearly 5000 crossings of 21 magnetic reversals out to C6no (19.72 Ma) and the digitized traces of 17 fracture zones and transform faults. Our reconstructions of this slow-spreading mid-ocean ridge reveal several unexpected results with notable implications for regional and global plate reconstructions since 20 Ma. Extrapolations of seafloor opening distances to zero-age seafloor based on reconstructions of reversals C1n (0.78 Ma) through C3n.4 (5.2 Ma) reveal evidence for surprisingly large outward displacement of 5 ± 1 km west of 32°E, where motion between the Nubia and Antarctic plates occurs, but 2 ± 1 km east of 32°E, more typical of most mid-ocean ridges. Newly estimated SWIR seafloor spreading rates are up to 15 per cent slower everywhere along the ridge than previous estimates. Reconstructions of the numerous observations for times back to 11 Ma confirm the existence of the hypothesized Lwandle plate at high confidence level and indicate that the Lwandle plate's western and eastern boundaries respectively intersect the ridge near the Andrew Bain transform fault complex at 32°E and between ~45°E and 52°E, in accord with previous results. The Nubia–Antarctic, Lwandle–Antarctic and Somalia–Antarctic rotation sequences that best fit many magnetic reversal, fracture zone and transform fault crossings define previously unknown changes in the Neogene motions of all three plate pairs, consisting of ~20 per cent slowdowns in their spreading rates at 7.2 $^{+0.9 }_{ -1.4}$ Ma if we enforce a simultaneous change in motion everywhere along the SWIR and gradual 3°–7° anticlockwise rotations of the relative slip directions. We apply trans-dimensional Bayesian analysis to our noisy, best-fitting rotation sequences in order to estimate less-noisy rotation sequences suitable for use in future global plate reconstructions and geodynamic studies. Notably, our new Nubia–Antarctic reconstruction of C5n.2 (11.0 Ma) predicts 20 per cent less opening than do two previous estimates, with important implications for motion that is estimated between the Nubia and Somalia plates. A Nubia–Somalia rotation determined from our Nubia–Antarctic and Somalia–Antarctic plate rotations for C5n.2 (11.0 Ma) predicts cumulative opening of 45 ± 4 km (95 per cent uncertainty) across the northernmost East Africa rift since 11.0 Ma, 70 per cent less than a recent 129 ± 62 km opening estimate based on a now-superseded interpretation of Anomaly 5 along the western portion of the SWIR.

Description: To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of 〉300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, 〉500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (〈25%) of transposon families comprise the majority (〉70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.

Description: Geodynamic models predict that rifting of thick, ancient continental lithosphere should not occur unless it is weakened by heating and magmatic intrusion. Therefore, the processes occurring along sections of the western branch of the East African Rift, where ~150 km thick, Palaeoproterozoic lithosphere is rifting with no surface expression of magmatism, are a significant challenge to understand. In an attempt to understand the apparently amagmatic extension we probed the regional uppermost mantle for signatures of thermal alteration using compressional ( Vp ) and shear ( Vs ) wave speeds derived from Pn and Sn tomography. Pervasive thermal alteration of the uppermost mantle and possibly the presence of melt can be inferred beneath the Rungwe volcanic centre, but no signatures on a similar scale were discerned beneath amagmatic portions of the western rift branch encompassing the southern half of the Lake Tanganyika rift and much of the Rukwa rift. In this region, Vp and Vs wave speeds indicate little, if any, heating of the uppermost mantle and no studies have reported dyking. Vp / Vs ratios are consistent with typical, melt-free, olivine-dominated upper mantle. Although our resolution limit precludes us from imaging potential localised magmatic intrusions with dimensions of tens of kilometres, the absence of surface volcanism, the amagmatic upper crustal rupture known to have occurred at disparate locations on the western branch, the presence of lower crustal seismicity and the low temperatures implied by the fast seismic wave speeds in the lower crust and uppermost mantle in this region suggests possible amagmatic extension. Most dynamic models predict that this should not happen. Indeed even with magmatic intrusion, rifting of continental lithosphere 〉100 km thick is considered improbable under conditions found on Earth. Yield strength envelopes confirm that currently modelled stresses are insufficient to produce the observed deformation along these portions of the rift system. Stresses arising from the gravitational force related to the uplift of the East African Plateau provide only one-eighth of the minimum stress necessary to produce observed lower crustal earthquakes in the western branch. We expect that some of this disparity may be accounted for by considering smaller scale bending stresses and dynamic feedbacks between brittle and elastic deformation and between faulting, topography and weathering that are not currently included in models of the East African Rift.

Description: Cell wall impermeability and active efflux of drugs are among the primary reasons for drug resistance in mycobacteria. Efflux pumps are tripartite membrane localized transport proteins that expel drug molecules outside the cells. Several of such efflux pumps are annotated in mycobacteria, but few have been characterized, like MSMEG_2991, a putative efflux pump permease of Mycobacterium smegmatis . To substantiate this, we overexpressed MSMEG_2991 protein in Escherichia coli 2443. Expression of MSMEG_2991 elevated the resistance towards structurally unrelated groups of antibiotics. An active antibiotic efflux pump nature of MSMEG_2991 was revealed by assessing the acquisition of ciprofloxacin in the absence and presence of the efflux pump inhibitor, carbonyl cyanide m-chlorophenyl hydrazone, indicating the involvement of proton-motive force (pmf) during the efflux activity. MSMEG_2991 expression elevated biofilm formation in E. coli by 4-fold, keeping parity to some of the earlier reported efflux pumps. In silico analysis suggested the presence of 12 transmembrane helices in MSMEG_2991 resembling EmrD efflux pump of E. coli . Based on in vivo and in silico analyses, MSMEG_2991 may be designated as a pmf-mediated multidrug efflux pump protein that expels diverse groups of antibiotics and might as well be involved in the biofilm enhancement.

Description: Bacterial small RNAs (sRNAs) play essential roles in the post-transcriptional control of gene expression. To improve their detection by conventional microarrays, we designed a custom microarray containing a group of probes targeting known and some putative Escherichia coli sRNAs. To assess its potential in detection of sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells exponentially grown in rich (Luria–Bertani) and minimal (M9/glucose) media. We found that many sRNAs could yield reasonably strong and statistically significant signals corresponding to nearly all sRNAs annotated in the EcoCyc database. Besides differential expression of two sRNAs (GcvB and RydB), expression of other sRNAs was less affected by the composition of the growth media. Other examples of the differentially expressed sRNAs were revealed by comparing gene expression of the wild-type strain and its isogenic mutant lacking functional poly(A) polymerase I ( pcnB ). Further, northern blot analysis was employed to validate these data and to assess the existence of new putative sRNAs. Our results suggest that the use of custom microarrays with improved capacities for detection of sRNAs can offer an attractive opportunity for efficient gene expression profiling of sRNAs and their target mRNAs at the whole transcriptome level.

Description: Escherichia coli DedA/Tvp38 family proteins YghB and YqjA are putative membrane transporters with 62% amino acid identity and overlapping functions. An E. coli strain (BC202) with nonpolar yghB and yqjA mutations displays cell-division defects and temperature sensitivity and is sensitive to antibiotics and alkaline pH. In this study, we performed site-directed mutagenesis on conserved, charged amino acids of YqjA and YghB. We discovered two conserved predicted membrane-embedded arginines (R130 and R136) that are critical for function in both proteins as defined by their ability to complement BC202 phenotypes, when expressed from a plasmid. Lysine can substitute for arginine at position R130 indicating a charge dependence at this position, but could not substitute at R136. In light of the established role that arginine plays in the translocation mechanism of numerous membrane transporters, we hypothesize that these amino acids play a role in the transport mechanism of these DedA/Tvp38 family proteins.

Description: Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations . The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.

Description: The impact of gene mutations on the growth of the cells can be studied using pure cultures. However, the importance of certain proteins and pathways can be also examined via co-culturing wild type and its mutant derivative. Here, the relative fitness of a mutant strain that lacks the global nitrogen regulator, CodY, was examined in Bacillus cereus , a food poisoning Gram-positive bacterium. Fitness measurements revealed that the codY strain was outcompeted when cocultured with the wild-type ATCC 14579 under various rich laboratory medium, and also when inoculated in certain beverages. In nutrient-poor minimal medium, the codY mutant had comparable fitness to the wild-type strain. Interestingly, the relative fitness of the codY strain was antagonistic when it was cultivated in apple or orange juices due to unknown properties of these beverages, highlighting the importance of chemical composition of the test medium during the bacterial fitness measurements.

Description: Out of 8000 candidates from a genetic screening for Pseudomonas putida KT2442 mutants showing defects in biofilm formation, 40 independent mutants with diminished levels of biofilm were analyzed. Most of these mutants carried insertions in genes of the lap cluster, whose products are responsible for synthesis, export and degradation of the adhesin LapA. All mutants in this class were strongly defective in biofilm formation. Mutants in the flagellar regulatory genes fleQ and flhF showed similar defects to that of the lap mutants . On the contrary, transposon insertions in the flagellar structural genes fliP and flgG , that also impair flagellar motility, had a modest defect in biofilm formation. A mutation in gacS , encoding the sensor element of the GacS/GacA two-component system, also had a moderate effect on biofilm formation. Additional insertions targeted genes involved in cell envelope function: PP3222, encoding the permease element of an ABC-type transporter and tolB , encoding the periplasmic component of the Tol-OprL system required for outer membrane stability. Our results underscore the central role of LapA, suggest cross-regulation between motility and adhesion functions and provide insights on the role of cell envelope trafficking and maintenance for biofilm development in P. putida .

Description: Horizontal gene transfer plays a significant role in bacterial evolution and has major clinical importance. Thus, it is vital to understand the mechanisms and kinetics of genetic transformations. Natural transformation is the driving mechanism for horizontal gene transfer in diverse genera of bacteria. Our study introduces a simple and rapid method for the investigation of natural transformation. This highly sensitive system allows the detection of a transformation event directly from a bacterial population without any separation step or selection of cells. The system is based on the bacterial luciferase operon from Photorhabdus luminescens . The studied molecular tools consist of the functional modules luxCDE and luxAB , which involve a replicative plasmid and an integrative gene cassette. A well-established host for bacterial genetic investigations, Acinetobacter baylyi ADP1, is used as the model bacterium. We show that natural transformation followed by homologous recombination or plasmid recircularization can be readily detected in both actively growing and static biofilm-like cultures, including very rare transformation events. The system allows the detection of natural transformation within 1 h of introducing sample DNA into the culture. The introduced method provides a convenient means to study the kinetics of natural transformation under variable conditions and perturbations.

Description: The legume–rhizobial interaction results in the formation of symbiotic nodules in which rhizobia fix nitrogen. During the process of symbiosis, reactive oxygen species (ROS) are generated. Thus, the response of rhizobia to ROS is important for successful nodulation and nitrogen fixation. In this study, we investigated how Azorhizobium caulinodans , a rhizobium that forms both root and stem nodules on its host plant, regulates ROS resistance. We found that in-frame deletions of a gene encoding the putative catalase-peroxidase katG or a gene encoding a LysR-family regulatory protein, oxyR , exhibited increased sensitivity to H 2 O 2 . We then showed that OxyR positively regulated katG expression in an H 2 O 2 -independent fashion. Furthermore, we found that deletion of katG or oxyR led to significant reduction in the number of stem nodules and decrease of nitrogen fixation capacities in symbiosis. Our results revealed that KatG and OxyR are not only critical for antioxidant defense in vitro , but also important for nodule formation and nitrogen fixation during interaction with plant hosts.