ALBERT

Description: As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C 〉 A/G 〉 T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.

Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.

Description: Fractured rocks are known to exhibit seismic anisotropy and shear wave splitting (SWS). SWS is commonly used for fractured rock characterization and has been shown to be sensitive to fluid type. The presence of partial liquid/gas saturation is also known to affect the elastic properties of rocks. The combined effect of both fractures and partial liquid/gas saturation is still unknown. Using synthetic, silica-cemented sandstones with aligned penny-shaped voids, we conducted laboratory ultrasonic experiments to investigate the effect fractures aligned at an oblique angle to wave propagation would have on SWS under partial liquid/gas saturation conditions. The result for the fractured rock shows a saturation dependence which can be explained by combining a fractured rock model and a partial saturation model. At high to full water saturation values, SWS decreases as a result of the fluid bulk modulus effect on the quasi-shear wave. This bulk modulus effect is frequency dependent as a result of wave-induced fluid flow mechanisms, which would in turn lead to frequency dependent SWS. This result suggests the possible use of SWS for discriminating between full liquid saturation and partial liquid/gas saturation.

Description: The effect of network density and geometric distribution on kinematic non-linear source inversion is investigated by inverting synthetic ground motions from a buried strike-slip fault ( M w 6.5), that have been generated by dynamic spontaneous rupture modelling. For the inversion, we use a physics-based regularized Yoffe function as slip velocity function. We test three different cases of station network geometry: (i) single station, varying azimuth and epicentral distance; (ii) multistation circular configurations, that is stations at similar distances from the fault, and regularly spaced around the fault; (iii) irregular multistation configurations using different numbers of stations. Our results show: (1) single station tests suggest that it may be possible to obtain a relatively good source model even using a single station. The best source model using a single station is obtained with stations at which amplitude ratios between three components are not large. We infer that both azimuthal angle and source-to-station distance play an important role in the design of optimal seismic network for source inversion. (2) Multistation tests show that the quality of the inverted source systematically correlates neither with the number of stations, nor with waveform misfit. (3) Waveform misfit has a direct correlation with the number of stations, resulting in overfitting the observed data without any systematic improvement of the source. It suggests that the best source model is not necessarily derived from the model with minimum waveform misfit. (4) A seismic network with a small number of well-spaced stations around the fault may be sufficient to obtain acceptable source inversion.

Description: Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present N orah D esk , the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. N orah D esk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with D ario and mir D eep 2 and found that N orah D esk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.

Description: Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of ‘deep sequencing’ technology (also known as ‘next generation sequencing’) to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories. We developed a software termed ‘RandA’ (which stands for ncRNA Read-and-Analyze) that performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data through a graphical user interface running on a local personal computer. Using RandA, we reveal the complexity of the ncRNA repertoire in a given cell population. We further demonstrate the relevance of such an extensive ncRNA analysis by elucidating a multitude of characterizing features in pathogen infected mammalian cells. RandA is available for download at http://ibis.tau.ac.il/RandA .

Description: Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3–5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae . We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.

Description: The Maule earthquake (2010 February 27, M w 8.8, Chile) broke the subduction megathrust along a previously locked segment. Based on an international aftershock deployment, catalogues of precisely located aftershocks have become available. Using 23 well-located aftershocks, we calibrate the classic teleseismic backprojection procedure to map the high-frequency seismic radiation emitted during the earthquake. The calibration corrects traveltimes in a standard earth model both with a static term specific to each station, and a ‘dynamic’ term specific to each combination of grid point and station. The second term has been interpolated over the whole slipping area by kriging, and is about an order of magnitude smaller than the static term. This procedure ensures that the teleseismic images of rupture development are properly located with respect to aftershocks recorded with local networks and does not depend on accurate hypocentre location of the main shock. We track a bilateral rupture propagation lasting ~160 s, with its dominant branch rupturing northeastwards at about 3 km s –1 . The area of maximum energy emission is offset from the maximum coseismic slip but matches the zone where most plate interface aftershocks occur. Along dip, energy is preferentially released from two disconnected interface belts, and a distinct jump from the shallower belt to the deeper one is visible after about 20 s from the onset. However, both belts keep on being active until the end of the rupture. These belts approximately match the position of the interface aftershocks, which are split into two clusters of events at different depths, thus suggesting the existence of a repeated transition from stick-slip to creeping frictional regime.

Description: Geophysical and geological data suggest that Tibetan middle crust is a partially molten, mechanically weak layer, but it is debated whether this low-viscosity layer is present beneath the entire plateau, what its properties are, how it deforms, and what role it has played in the plateau's evolution. Broad-band seismic surface waves yield resolution in the entire depth range of the Tibetan crust and can be used to constrain its shear-wave velocity structure (indicative of crustal composition, temperature and partial melting) and radial anisotropy (indicative of the patterns of deformation). We measured Love- and Rayleigh-wave phase-velocity curves in broad period ranges (up to 7–200 s) for a few tens of pairs and groups of stations across Tibet, combining, in each case, hundreds of interstation measurements, made with cross-correlation and waveform-inversion methods. Shear-velocity profiles were then determined by extensive series of non-linear inversions of the data, designed to constrain the depth-dependent ranges of isotropic-average shear speeds and radial anisotropy. Shear wave speeds within the Tibetan middle crust are anomalously low and, also, show strong lateral variations across the plateau. The lowest mid-crustal shear speeds are found in the north and west of the plateau (~3.1–3.2 km s –1 ), within a pronounced low-velocity zone. In southeastern Tibet, crustal shear wave speeds increase gradually towards southeast, whereas in the north, the change across the Kunlun Fault is relatively sharp. The lateral variations of shear speeds within the crust are indicative of those in temperature. A mid-crustal temperature of 800 °C, reported previously, can account for the low shear velocities across Lhasa. In the north, the temperature is higher and exceeds the solidus, resulting in partial melting that we estimate at 3–6 per cent. Strong radial anisotropy is required by the data in western-central Tibet (〉5 per cent) but not in northeastern Tibet. The amplitude of radial anisotropy in the crust does not correlate with isotropic-average shear speed (and, by inference, with crustal rock viscosity) or with surface elevation. Instead, radial anisotropy is related to the deformation pattern and is the strongest in regions experiencing extension (crustal flattening), as noted previously. The growth of Tibet by the addition of Indian crustal rocks into its crust from the south is reflected in the higher crustal seismic velocities (and, thus, lower temperatures) in the southern compared to northern parts of the plateau (more recently added rocks having had less time to undergo radioactive heating within the thickened Tibetan crust). Gravity-driven flattening—the basic cause of extension and normal faulting in the southern, western and central Tibet—is evidenced by pervasive radial anisotropy in the middle crust beneath the regions undergoing extension; the overall eastward flow of the crust is directed by the boundaries and motions of the lithospheric blocks that surround Tibet.

Description: The aseismic Murray ridge (MR) is a continuation of the Owen fracture zone which marks the boundary between the Indian and Arabian plates. Due to large variation in morphology and structure within this NE–SW trending ridge in the Arabian Sea a large variation of the bathymetry from few hundred metres to about 4000 m is seen. Observed seismicity on the ridge system is predominantly strike-slip. Tsunamis generated in the Makran subduction zone (MSZ) will propagate through the MR system due to its proximity. As the tsunami speed depends on the depth of the ocean, bathymetry plays a vital role on tsunami propagation. In this paper, the effect of tsunami propagation through the MR system is carried out with the existing bathymetry and comparing the results by removing the bathymetry. To study this phenomenon the 1945 Makran tsunami and worst possible tsunamigenic earthquakes form eastern and western MSZ are considered. The directivity of tsunami propagation with the ridge system is seen to change after crossing the MR towards the southeast direction for tsunamis generated in the eastern MSZ. For tsunami generated in the western MSZ there is no change in its directivity and is almost same as without the ridge with propagation being towards the open sea. Hence the MR not only affects the amplitude of the tsunamis but also the directionality and the arrival times.