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The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans 1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N1 2,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed the in vivo H7N9 mutations at the level of whole genomes and have compared with the genomes derived by in vitro cultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.

Absorption effects caused by the anelastic nature of the earth lead to the attenuation of amplitude and distortion of phase of seismic waves. The so-called quality factor “Q” accounting for this ab...

The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.

A comprehensive demonstration of Zika virus (ZIKV) molecular evolution is essential for understanding its adaptation and expansion in its recent pandemics. Despite several studies on mutations and codon usage in ZIKVs, the variations in codon usage patterns across individual genes and their biological implication remains unclear. Here, we performed a gene-by-gene comparison of the codon usage variation in ZIKVs of the African and Asian lineages. We found that besides the evidence of positive selection (Ka/Ks >1) in the Asian lineage of the ZIKV genome, codon usage patterns were gene-specific and codon usage variation of ZIKV genes, was possibly constrained by their individual functional features, such as transmembrane domains, or antigenicity. In particular, the NS2B and NS4A genes showed distinct codon usage patterns, clearly separating them from the clusters of other genes in the correspondence analysis (CA). In the Asian lineage, the NS2B and NS4A genes showed the highest codon usage bias (ENC values: 51.01 ± 0.72 and 48.89 ± 0.99 respectively), and were subjected to the highest translation selection (ENCobs/ENCexp ratio: 0.847 ± 0.0297 and 0.828 ± 0.0233 respectively) in comparison to the African lineages of ZIKV. The CpG frequency of the NS2B showed a gradual ascending trend in the Asian ZIKV lineages, while in NS4A it was constrained along with the expansion of the Asian lineage. Furthermore, between the African and Asian lineages, differentiated and specific over-represented codons were more prominent in the NS2B and NS4A. Together, our study implies that ZIKVs are in the process of evolutionary fine tuning their codon as seen in the recent pandemics, and NS2B and NS4A could have played a potential role in the molecular evolution of the Asian lineage and their establishment.

Several discoveries, such as Tupi, Bem-Te-Vi, Parati, and Guara, have been announced in Santos Basin off the coast of Brazil, mostly in presalt layers. These layers were well imaged by a salt-flood volume in 2003, but distortions in the base of salt (BOS) and presalt layers were still obvious. Therefore, a constant velocity model is not adequate to capture the velocity variation inside the salt bodies, which include mobile salt and evaporites. A depth migration with a complete salt model is necessary to correctly position the reservoir structures. In this paper, we discuss the challenges in building such a velocity model and share the lessons we learned while working on a data set from the deepwater Santos Basin.

Wide-azimuth towed streamer (WATS) acquisition improves the subsalt seismic image by suppressing multiples, improves the results of 3D surface-related-multiple elimination (SRME) processing, and provides more uniform seismic illumination of subsalt targets. A simple model shows that the additional suppression of multiples in the case of WATS acquisition is the result of a natural weighting of the traces going into the stack due to the areal nature of the acquisition. This simple model also shows that the extent of the additional multiple suppression is strongly dependent on the acquisition effort. A sparse acquisition effort will result in little additional multiple suppression. The use of 3D SRME processing is shown to be more accurate in predicting multiples, given input data with multiple azimuths, compared to making similar predictions from narrow-azimuth data. Three-dimensional SRME has the potential to reduce the residual multiples to the same extent as WATS acquisition with a higher acquisition effort. A complex model demonstrates that WATS acquisition does reduce the multiple-generated noise in subsalt images, but 3D SRME processing further reduces the residual multiple noise. The use of 3D SRME may reduce the multiples more than that achieved by increasing the cable half-aperture in the WATS acquisition effort. Finally, ray trace modeling is used to investigate the effect of WATS acquisition on subsurface illumination for subsalt imaging. We show that narrow-azimuth acquisition produces irregularities in subsalt illumination perpendicular to the acquisition direction which are a potential cause of migration noise. WATS acquisition results in higher and more uniform subsalt illumination and, hence, improves the subsalt image by reducing subsalt migration noise.

Variable-depth streamer acquisition is emerging as a key technique for providing wide-bandwidth seismic data. This technique allows us to obtain a usable bandwidth from 2.5 Hz up to the source notch. It has consistently produced high-quality images in terms of seismic resolution, layer stratigraphy and low-frequency penetration. Seismic interpretation and inversion becomes easier and more robust.

Summary Variable-depth streamer acquisition is emerging as a key technique for providing wide bandwidth seismic data. With several data sets acquired across the world, it has consistently produced high quality images in terms of seismic resolution, layer stratigraphy and low-frequency penetration. By varying receiver depth, variable-depth streamer acquisition introduces receiver ghost diversity over different offsets. Such diversity enables a joint deconvolution method to fully remove the receiver ghost. Variable-depth streamer data also tends to be less noisy due to the deep tow of cables. These two factors allow variabledepth streamer data to have a spectrum from 2.5 Hz up to the source notch. Challenges in processing include: how to maintain the full bandwidth in the data, how to effectively remove multiples, and how to robustly build a velocity model. This paper will discuss each of these challenges and their solutions.

Summary Variable-depth streamer acquisition is becoming a key technique for providing wide bandwidth seismic data. Varying the receiver depth creates wide receiver ghost diversity and produces a spectacular increase in the frequency bandwidth. However, compared to conventional data, this variable-depth streamer data implies a major challenge in processing: how to deal with various receiver ghosts. The ghosts have to be preserved up to the deghosting step. Here we present the implication for the following de-multiple methods: Shallow-Water Demultiple, Tau-P deconvolution and Surface-related multiples elimination in deep and shallow water environments.

In 2009, BP initiated a complete reprocessing of the Mad Dog WATS (wide-azimuth towed-streamer) dataset using TTI (tilted transverse isotropy) Pre-stack Depth Migration (PSDM) technology developed by CGGVeritas. This project would build upon the 2008 VTI (vertical transverse isotropy) model built by CGGVeritas by improving key areas that were imaged poorly. The TTI reprocessing was extremely successful. In fact, the uplift for the subsalt target area was qualitatively larger than the uplift observed between isotropic and VTI. Mad Dog TTI reprocessing further confirmed that by honoring the stratigraphic layering of the geologic structure, a TTI velocity model is a better approximation of the subsurface than both isotropic and VTI models. The Mad Dog WATS data combined with a previously recorded NATS (narrow azimuth towed streamer) dataset allowed the ability to detect and account for anisotropy in different azimuths, which is not possible with a single NATS survey. TTI reverse time migration (RTM) improved the ability to define salt geometry and thereby obtain a good subsalt image. TTI RTM should be considered for future imaging of fields with complex structures such as Mad Dog.

Summary Recent seismic acquisition and anisotropic velocity modeling has resulted in improved salt definition and sub-salt imaging at Puma and Mad Dog Fields in the Gulf of Mexico. For these fields, wide-azimuth towed-streamer (WATS) surveys, isotropic imaging, vertical transverse isotropy (VTI) imaging, and tilted transverse isotropy (TTI) imaging were carried out sequentially. This series offers a great opportunity to understand the impact of different levels of anisotropy approximation and why TTI reverse time migration (RTM) should be used for future WATS imaging.

Recent large pre-salt discoveries in deep water Santos Basin, Brazil, such as Tupi and Sugarloaf, prompt significant interest in better pre-salt imaging. In this paper, we present a pre-stack depth migration (PSDM) velocity model building flow that would produce a better velocity field. This allows us to obtain better pre-salt images through high-end imaging algorithms such as Controlled Beam Migration (CBM) and Reverse Time Migration (RTM). We also explore the benefits of tilted transverse isotropy (TTI) imaging in this area.

A030 Z-99 3D SRME Practice for Better Imaging Summary 1 DECHUN LIN JERRY YOUNG WEN-JACK LIN MALCOLM GRIFFITHS MONICA HARTMANN Veritas DGC 10300 Town Park Houston TX 77072 USA Proper parameter selection is key to the success of 3D SRME. The major parameters include surface grid size and crossline aperture. We show that SRME crossline gathers can be used to determine both parameters. We also use a data example from Gulf of Mexico (GOM) to demonstrate the benefits of 3D SRME. Introduction In a marine environment strong contamination from surface multiples is one of the major problems in imaging sub-surface

We review the space-and-time-dependent Monte Carlo code we have developed to simulate the relativistic radiation output from compact astrophysical objects. We also highlight some major recent results obtained with this code, which are most relevant to the observations of CGRO and other high energy astrophysics space missions.

While constrains on source and receiver sampling for convolution SRME are easily fulfilled in the 2D case, the problem become significantly more complex in 3D. By requiring ideally equal and coincident source and receiver sampling for performing the surface consistent data auto-convolution required by the method, it constrains the acquisition geometry toward the denser possible designs.