RNAa Is Conserved in Mammalian Cells

Background: RNA activation (RNAa) is a newly discovered mechanism of gene activation triggered by small doublestranded RNAs termed ‘small activating RNAs ’ (saRNAs). Thus far, RNAa has only been demonstrated in human cells and is unclear whether it is conserved in other mammals. Methodology/Principal Findings: In the present study, we evaluated RNAa in cells derived from four mammalian species including nonhuman primates (African green monkey and chimpanzee), mouse, and rat. Previously, we identified saRNAs leading to the activation of E-cadherin, p21, and VEGF in human cells. As the targeted sequences are highly conserved in primates, transfection of each human saRNA into African green monkey (COS1) and chimpanzee (WES) cells also resulted in induction of the intended gene. Additional saRNAs targeting clinically relevant genes including p53, PAR4, WT1, RB1, p27, NKX3-1, VDR, IL2, and pS2 were also designed and transfected into COS1 and WES cells. Of the nine genes, p53, PAR4, WT1, and NKX3-1 were induced by their corresponding saRNAs. We further extended our analysis of RNAa into rodent cell types. We identified two saRNAs that induced the expression of mouse Cyclin B1 in NIH/3T3 and TRAMP C1 cells, which led to increased phosphorylation of histone H3, a downstream marker for chromosome condensation and entry into mitosis. We also identified two saRNAs that activated the expression of CXCR4 in primary rat adipose–derived stem cells. Conclusions/Significance: This study demonstrates that RNAa exists in mammalian species other than human. Our finding

Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.)

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions

Fracture characterization using diffraction attributes in tight sandstone reservoirs: A case study from Keshen Gas Field, Tarim Basin

Reservoir characterization is indispensable in the development of the Cretaceous structural fractured Bashijiqike tight sandstone reservoir formation, which is the main production zone and known to exhibit high structural variability imparting on production at different scales. We performed an improved workflow based on diffraction extraction and analysis to characterize the fractures especially in locations proximal to the wellbore. Diffraction attributes significantly provide more details in the area, which are proven by three well FMI images and dipmeter logs. The results show that structural fractures in the study area are dominated by the upright shearing stress forming fractures with medium to high angles. The tending direction is also delineated to be similar despite the significant well offset, which is an indication of the underlying tectonic framework responsible for the overall architecture of this section of the basin. We opine due to our success that the proposed approach may be helpful to describe the distribution and direction of fractures in naturally fractured reservoirs tied by the well logs

Genetic Operators Design Using Division Algorithm in the Integer Solution Space

Genetic algorithm (GA) is a well known algorithm applied to a wide variety of optimization problems [4]. It combines selection, crossover, and mutation operators in order to find the best solution to a problem. The standard GA operates on chromosomes represented by binary code strings [1, 2]. This paper designs alternative operators in the GA process. The new operations reduce the binary decoding process of chromosomes when performing the computation. Variations of solutions with the implemented operations on chromosomes are studied. Computational examples show that the new methods save the computer time and enhance the efficiency when compared to the standard GA

An Efficient Finite-Difference Stencil with High-Order Temporal Accuracy for Scalar Wave Modeling

Solving a scalar wave equation by the finite-difference (FD) method is a key step for advanced seismic imaging, in which the numerical accuracy is significantly affected by the FD stencil. High-order spatial and temporal approximations of the FD stencil can effectively improve the numerical accuracy and mitigate dispersion error. However, the huge costs of high-order stenciling in computation and storage hinder the application of large-scale modeling. In this paper, we propose a new efficient FD stencil with high-order temporal accuracy for numerical seismic modeling. The new stencil has a radial shape, including a standard cross-stencil and a rotated cross-stencil with a (π/4) degree, and it can reach sixth-order accuracy in the time approximation. Compared with the well-known temporal high-order cross-rhombus stencil, the new stencil involves fewer grid nodes and thus has higher computational efficiency, especially in high-order cases. Dispersion and stability analyses show that the new stencil has great improvements in mitigating the dispersion error and stability problem compared with the conventional methods. Numerical accuracy and execution time analyses show that the new stencil is an economical and feasible method for large-scale modeling

End Late Paleozoic tectonic stress field in the southern edge of Junggar Basin

This paper presents the end Late Paleozoic tectonic stress field in the southern edge of Junggar Basin by interpreting stress-response structures (dykes, folds, faults with slickenside and conjugate joints). The direction of the maximum principal stress axes is interpreted to be NW–SE (about 325°), and the accommodated motion among plates is assigned as the driving force of this tectonic stress field. The average value of the stress index R′ is about 2.09, which indicates a variation from strike-slip to compressive tectonic stress regime in the study area during the end Late Paleozoic period. The reconstruction of the tectonic field in the southern edge of Junggar Basin provides insights into the tectonic deformation processes around the southern Junggar Basin and contributes to the further understanding of basin evolution and tectonic settings during the culmination of the Paleozoic

AVO-Friendly Velocity Analysis Based on the High-Resolution PCA-Weighted Semblance

Velocity analysis using the semblance spectrum can provide an effective velocity model for advanced seismic imaging technology, in which the picking accuracy of velocity analysis is significantly affected by the resolution of the semblance spectrum. However, the peak broadening of the conventional semblance spectrum leads to picking uncertainty, and it cannot deal with the amplitude-variation-with-offset (AVO) phenomenon. The well-known AB semblance can process the AVO anomalies, but it has a lower resolution compared with conventional semblance. To improve the resolution of the AB semblance spectrum, we propose a new weighted AB semblance based on principal component analysis (PCA). The principal components or eigenvalues of seismic events are highly sensitive to the components with spatial coherence. Thus, we utilized the principal components of the normal moveout (NMO)-corrected seismic events with different scanning velocities to construct a weighting function. The new function not only has a high resolution for velocity scanning, but it is also a friendly method for the AVO phenomenon. Numerical experiments with the synthetic and field seismic data sets proved that the new method significantly improves resolution and can provide more accurate picked velocities compared with conventional methods