ALBERT

Description: We report a target enrichment method to map nucleosomes of large genomes at unprecedented coverage and resolution by deeply sequencing locus-specific mononucleosomal DNA enriched via hybridization with bacterial artificial chromosomes. We achieved ~10 000-fold enrichment of specific loci, which enabled sequencing nucleosomes at up to ~500-fold higher coverage than has been reported in a mammalian genome. We demonstrate the advantages of generating high-sequencing coverage for mapping the center of discrete nucleosomes, and we show the use of the method by mapping nucleosomes during T cell differentiation using nuclei from effector T-cells differentiated from clonal, isogenic, naïve, primary murine CD4 and CD8 T lymphocytes. The analysis reveals that discrete nucleosomes exhibit cell type-specific occupancy and positioning depending on differentiation status and transcription. This method is widely applicable to mapping many features of chromatin and discerning its landscape in large genomes at unprecedented resolution.

Description: Using data from more than 2000 seismic stations from multiple networks arrayed throughout China (CEArray, China Array, NECESS, PASSCAL, GSN) and surrounding regions (Korean Seismic Network, F-Net, KNET), we perform ambient noise Rayleigh wave tomography across the entire region and earthquake tomography across parts of South China and Northeast China. We produce isotropic Rayleigh wave group and phase speed maps with uncertainty estimates from 8 to 50 s period across the entire region of study, and extend them to 70 s period where earthquake tomography is performed. Maps of azimuthal anisotropy are estimated simultaneously to minimize anisotropic bias in the isotropic maps, but are not discussed here. The 3D model is produced using a Bayesian Monte Carlo formalism covering all of China, extending eastwards through the Korean Peninsula, into the marginal seas, to Japan. We define the final model as the mean and standard deviation of the posterior distribution at each location on a 0.5° x 0.5° grid from the surface to 150 km depth. Surface wave dispersion data do not strongly constrain internal interfaces, but shear wave speeds between the discontinuities in the crystalline crust and uppermost mantle are well determined. We design the resulting model as a reference model, which is intended to be useful to other researchers as a starting model, to predict seismic wave fields and observables and to predict other types of data (e.g. topography, gravity). The model and the data on which it is based are available for download. In addition, the model displays a great variety and considerable richness of geological and tectonic features in the crust and in the uppermost mantle deserving of further focus and continued interpretation.

Description: We revisit the problem of coseismic rupture of the 2008 M w 7.9 Wenchuan earthquake. Precise determination of the fault structure and slip distribution provides critical information about the mechanical behaviour of the fault system and earthquake rupture. We use all the geodetic data available, craft a more realistic Earth structure and fault model compared to previous studies, and employ a nonlinear inversion scheme to optimally solve for the fault geometry and slip distribution. Compared to a homogeneous elastic half-space model and laterally uniform layered models, adopting separate layered elastic structure models on both sides of the Beichuan fault significantly improved data fitting. Our results reveal that: (1) The Beichuan fault is listric in shape, with near surface fault dip angles increasing from ~36° at the southwest end to ~83° at the northeast end of the rupture. (2) The fault rupture style changes from predominantly thrust at the southwest end to dextral at the northeast end of the fault rupture. (3) Fault slip peaks near the surface for most parts of the fault, with ~8.4 m thrust and ~5 m dextral slip near Hongkou and ~6 m thrust and ~8.4 m dextral slip near Beichuan, respectively. (4) The peak slips are located around fault geometric complexities, suggesting that earthquake style and rupture propagation were determined by fault zone geometric barriers. Such barriers exist primarily along restraining left stepping discontinuities of the dextral-compressional fault system. (5) The seismic moment released on the fault above 20 km depth is 8.2 x 10 21  N m, corresponding to an M w 7.9 event. The seismic moments released on the local slip concentrations are equivalent to events of M w 7.5 at Yingxiu-Hongkou, M w 7.3 at Beichuan-Pingtong, M w 7.2 near Qingping, M w 7.1 near Qingchuan, and M w 6.7 near Nanba, respectively. (6) The fault geometry and kinematics are consistent with a model in which crustal deformation at the eastern margin of the Tibetan plateau is decoupled by differential motion across a decollement in the mid crust, above which deformation is dominated by brittle reverse faulting and below which deformation occurs by viscous horizontal shortening and vertical thickening.

Description: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.

Description: An experimental system is built for the electrokinetic measurements with a small scaled seismoelectric detector and a high resolution digitizer (1 MS s –1 , 22 bits). The acoustic and seismoelectric experiments are carried out in different borehole models at the high frequency of 90 kHz in the laboratory. All the localized seismoelectric signals that accompany compressional wave, shear wave and Stoneley wave are first clearly observed with a monopole source in sandstone boreholes that are saturated by tap water. The amplitudes of these signals are measured in the range of 1–120 μV, which is useful for designing the seismoelectric logging instruments. Then the amplitude ratio of electric signal to acoustic pressure (REP) for each of the three waves is calculated and compared with the theoretical simulations. Based on the experimental data, we find that seismoelectric logging signals as well as REP become stronger at the more permeable borehole model. We also find that seismoelectric logging signals are more sensitive to permeability and porosity compared with acoustic logging signals. Therefore, this study verifies the feasibility of seismoelectric well logging, and further indicates that the seismoelectric logging technique might be a preferable method to estimate formation parameters in the field measurements.

Description: Seismoelectric logging has potential applications in exploring the porous formation characteristics. In this study, we theoretically address how the amplitudes of the Stoneley wave and its accompanying borehole seismoelectric field depend on the porous formation parameters such as porosity, permeability and tortuosity. We calculate the ratio of the electric field amplitude to the pressure amplitude (REP amplitude) for the low-frequency Stoneley wave of different formations and find that the REP amplitude is sensitive to porosity and tortuosity but insensitive to permeability. To confirm this conclusion, we derive the approximate expression of the REP amplitude in the wavenumber–frequency domain which shows that the REP amplitude is dependent on tortuosity but independent of permeability. This contradicts the result concluded by previous researchers from experiments that the REP amplitude is directly proportional to the permeability. The reason is probably attributed to the fact that the rock samples with different permeabilities typically have different tortuosities. Since the REP amplitude is sensitive to tortuosity, we propose a method of estimating formation tortuosity from seismoelectric logs. It is implemented by using the REP amplitude and the wavenumber of the Stoneley wave at a given frequency when the porosity and the pore fluid viscosity and salinity are known. We test the method by estimating the tortuosities from the synthetic seismoelectric waveforms in different formations. The result shows that the errors relative to the input tortuosities are lower than 5.0 per cent without considering the uncertainties of other input parameters.

Description: Using empirical matched field processing (MFP), we compare 4 yr of continuous seismic data to a set of 195 master templates from within an active geothermal field and identify over 140 per cent more events than were identified using traditional detection and location techniques alone. In managed underground reservoirs, a substantial fraction of seismic events can be excluded from the official catalogue due to an inability to clearly identify seismic-phase onsets. Empirical MFP can improve the effectiveness of current seismic detection and location methodologies by using conventionally located events with higher signal-to-noise ratios as master events to define wavefield templates that could then be used to map normally discarded indistinct seismicity. Since MFP does not require picking, it can be carried out automatically and rapidly once suitable templates are defined. In this application, we extend MFP by constructing local-distance empirical master templates using Southern California Earthquake Data Center archived waveform data of events originating within the Salton Sea Geothermal Field. We compare the empirical templates to continuous seismic data collected between 1 January 2008 and 31 December 2011. The empirical MFP method successfully identifies 6249 additional events, while the original catalogue reported 4352 events. The majority of these new events are lower-magnitude events with magnitudes between M0.2–M0.8. The increased spatial-temporal resolution of the microseismicity map within the geothermal field illustrates how empirical MFP, when combined with conventional methods, can significantly improve seismic network detection capabilities, which can aid in long-term sustainability and monitoring of managed underground reservoirs.