Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction–modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range of biochemical assays on purified enzymes and single molecule real-time sequencing on genomic DNA to determine these target sequences and their patterns of methylation. Knowledge of the main target sequences for Sau1 will facilitate the synthesis of new vectors for transformation of the most prevalent lineages of this ‘untransformable’ bacterium.
Conventional methods of prestack depth imaging aim at producing a structural image that delineates the interfaces of the geologic variations or the reflectivity of the earth. However, it is the underlying impedance and velocity changes that generate this reflectivity that are of more interest for characterizing the reservoir. Indeed, the need to generate a better product for geologic interpretation leads to the subsequent application of traditional seismic-inversion techniques to the reflectivity sections that come from typical depth-imaging processes. The drawback here is that these seismic-inversion techniques use additional information, e.g., from well logs or velocity models, to fill the low frequencies missing in traditional seismic data due to the free-surface ghost in marine acquisition. We found that with the help of broadband acquisition and processing techniques, the bandwidth gap between the depth-imaging world and seismic inversion world is reducing. We outlined a theory that shows how angle-domain common-image gathers produced by an amplitude-preserving reverse time migration can estimate impedance and velocity perturbations. The near-angle stacked image provides the impedance perturbation estimate whereas the far-angle image can be used to estimate the velocity perturbation. In the context of marine acquisition and exploration, our method can, together with a ghost compensation technique, be a useful tool for seismic inversion, and it is also adaptable to a full-waveform inversion framework. We developed synthetic and real data examples to test that the method is reliable and provides additional information for interpreting geologic structures and rock properties.
The estimation of the source signature is often one of the necessary first steps in the processing of seismic reflection data, especially if the processing chain includes prestack multiple removal. However, most methods for source estimation are based on poststack data or assume that the earth is 1-D. In this work, a new source estimation method for prestack data is presented. It consists of finding the source signature that permits the removal of events attributable to the first-order free-surface reflections (i.e., first-order multiples). The method exploits the formulation of the relationship between the free-surface reflections and the source signature as a scattering Born series. In this formulation, the order of the scattering series coincides with that of the free-surface reflections, and the series is constructed exclusively with seismic data Manuscript
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