Advantageous shale lithofacies of Wufeng Formation-Longmaxi Formation in Fuling gas field of Sichuan Basin, SW China

The lithofacies types of Upper Ordovician Wufeng Formation-Lower Silurian Longmaxi Formation shale, the main producing layer in Fuling gas field, are classified in detail using the modified ternary diagram of siliceous minerals-carbonates minerals-clay minerals. There develop eight lithofacies in the Wufeng-Longmaxi shale: siliceous shale lithofacies (S), mixed siliceous shale lithofacies (S-2), clay-rich siliceous shale lithofacies (S-3), calcareous/siliceous mixed shale lithofacies (M-1), argillaceous/siliceous mixed shale lithofacies (M-2), mixed shale lithofacies (M), silica-rich argillaceous shale lithofacies (CM-1), and argillaceous/calcareous mixed shale lithofacies (M-3). The advantageous shale lithofacies is defined as lithofacies with gas content reaching a specific industrial standard. Based on the current development status of the study area, advantageous shale lithofacies is divided into two classes, namely, Class I with gas content of more than 4.0 m3/t (also known as extra superior), Class II with gas content of 2.0−4.0 m3/t (also known as superior). The correlation between the abundance of organic matter, the content of siliceous mineral, clay content and gas content has been analyzed to establish the classification criteria for advantageous shale lithofacies in the Wufeng-Longmaxi shale. The mixed siliceous shale lithofacies (S-2) and clay-rich siliceous shale lithofacies (S-3) have been identified as Class I advantageous shale lithofacies, and argillaceous/siliceous mixed shale lithofacies (M-2) as Class II. The classification criteria of advantageous shale lithofacies can provide reference for shale gas evaluation in other exploration areas Key words: shale, advantageous shale lithofacies, Ordovician Wufeng Formation, Silurian Longmaxi Formation, Fuling gas field, Sichuan Basi

Effects of volcanic activities in Ordovician Wufeng–Silurian Longmaxi period on organic-rich shale in the Upper Yangtze area, South China

Based on the corresponding relationship between the paleoproductivity, redox conditions and volcanism within a chronostratigraphic framework, the effects of volcanic events in the Wufeng–Longmaxi period on organic abundance of shale were examined. Bentonite layers were mostly developed in the transgressive systems tract 1 (TST1, Wufeng Formation) and transgressive systems tract 2 (TST2, Longmaxi Formation), and the two systems tracts corresponded to favorite shale lithofacies with high silica and total organic carbon (TOC) contents. According to the stratigraphic characteristics of bentonite rich interval, TST1 is classified as the interval with dense bentonite layers with the frequency of bentonite layer (bentonite layers/time) of more than 1.5 layers/Ma and the cumulative thickness ratio of bentonite layers (thickness of bentonite layers/thickness of shale) of more than 1%; TST2 is classified as the interval with sparse bentonite layers (frequency < 1.5 layers/Ma; cumulative thickness ratio < 1%). TST1 (dense interval) witnessed more intense and high-frequency volcanic activities than TST2 (sparse interval), so the TST1 has generally higher TOC than TST2. The intense and frequent volcanic activities had dual effects on organic-rich shale: on one hand, volcanic ash provided a sufficient supply of nutrients, which triggered high marine productivity; on the other hand, the extremely anoxic environment caused by volcanic activity enhanced the burial amount and preservation rate of organic matter. Key words: shale, organic abundance, volcanism, sequence stratigraphy, Ordovician Wufeng Formation, Silurian Longmaxi Formation, Upper Yangtze area, bentonit

Uncovering the potential molecular mechanism of liraglutide to alleviate the effects of high glucose on myoblasts based on high-throughput transcriptome sequencing technique

Abstract Background Myoblasts play an important role in muscle growth and repair, but the high glucose environment severely affects their function. The purpose of this study is to explore the potential molecular mechanism of liraglutide in alleviating the effects of high glucose environments on myoblasts. Methods MTT, western blot, and ELISA methods were used to investigate the role of liraglutide on C2C12 myoblasts induced by high glucose. The high-throughput transcriptome sequencing technique was used to sequence C2C12 myoblasts from different treated groups. The DESeq2 package was used to identify differentially expressed-mRNAs (DE-mRNAs). Then, functional annotations and alternative splicing (AS) were performed. The Cytoscape-CytoHubba plug-in was used to identify multicentric DE-mRNAs. Results The MTT assay results showed that liraglutide can alleviate the decrease of myoblasts viability caused by high glucose. Western blot and ELISA tests showed that liraglutide can promote the expression of AMPKα and inhibit the expression of MAFbx, MuRF1 and 3-MH in myoblasts. A total of 15 multicentric DE-mRNAs were identified based on the Cytoscape-CytoHubba plug-in. Among them, Top2a had A3SS type AS. Functional annotation identifies multiple signaling pathways such as metabolic pathways, cytokine-cytokine receptor interaction, cAMP signaling pathway and cell cycle. Conclusion Liraglutide can alleviate the decrease of cell viability and degradation of muscle protein caused by high glucose, and improves cell metabolism and mitochondrial activity. The molecular mechanism of liraglutide to alleviate the effect of high glucose on myoblasts is complex. This study provides a theoretical basis for the clinical effectiveness of liraglutide in the treatment of skeletal muscle lesions in diabetes

Additional file 1 of Uncovering the potential molecular mechanism of liraglutide to alleviate the effects of high glucose on myoblasts based on high-throughput transcriptome sequencing technique

Additional file 1: Table S1. All primers used for real time-PCR. Figure S1. Expression validation of Ccl2, Kif11, Cdc20 and Top2a by real-time PCR

Discrete Element Method for Simulation and Calibration of Cotton Stalk Contact Parameters

To improve the accuracy of the discrete element research, physical and simulation experiments were used to calibrate the cotton stalk contact parameters. Based on the stalk-stalk and stalk-steel contact mechanics, the parameters were measured in physical experiments, and the discrete element simulation software was used to build the stalk model. In the simulation process, the Plackett-Burman experiment was used to screen three significant factors from six initial factors. The steepest Plackett-Burman experiment was used to determine the optimal interval of the significant factors. A second-order regression model of the significant factors and the angle of repose was established according to the Central Composite design experiment. The best parameter combination of the significant factors was then obtained: the coefficient of static friction on stalk-steel contact was 0.31, the coefficient of static friction on stalk-stalk contact was 0.62, and the coefficient of rolling friction on stalk-stalk contact was 0.02. The relative error between the physical angle of repose and the simulated angle was 3.27%, indicating that it is feasible to apply the simulation experiment instead of the physical one. It offers insights into cotton stalk contact parameter settings and film-stalk separation in the simulation

Rational design of a structural and functional nitric oxide reductase

Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem Fe B centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico. © 2009 Macmillan Publishers Limited. All rights reserved

Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging.

During seed aging, there is a critical node (CN) where the population viability drops sharply. Exploring the specific locations of the CN in different species of plants is crucial for understanding the biological storage properties of seeds and refining seed life span management. Safflower, a bulk oil crop that relies on seeds for propagation, has a short seed life. However, at present, its biological characteristics during storage are not clear, especially the changes in metabolic capability and cell structures. Such knowledge is needed to improve the management of safflower seed life span and effective preservation in gene banks. Here, the seed survival curve of oilseed safflower under the controlled deterioration conditions of 60% relative humidity and 50°C was detected. The seed population showed an inverted S shape for the fall in germination. In the first 12 days of aging, germination remained above 86%. Prior to the CN at approximately day 10 (C10), when viability was in the “plateau” interval, seed vigor reduced at the same imbibition time point. Further analysis of the changes in sugar concentration found that the sucrose content decreased slowly with aging and the content of raffinose and two monosaccharides decreased abruptly at C10. Differentially metabolized lipids, namely lysophospholipids [lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamines (LPE)] and PMeOH, increased at day 3 of aging (C3). Fatty acid content increased by C6, and the content of phospholipids [phosphatidylcholines (PC), phosphatidylethanolamines (PE), and phosphatidylinositols (PI) and glycolipids [digalactosyl diacylglycerol, monogalactosyl diacylglycerol, and sulphoquinovosyl diglycerides (SQDG)] decreased significantly from C10. In addition, the activities of raffinose hydrolase alpha-galactosidase and the glyoxylate key enzyme isocitrate lyase decreased with seed aging. Confocal microscopy and transmission electron microscopy revealed shrinkage of the seed plasma membrane at C10 and the later fragmentation. Seedling phenotypic indicators and 2,3,5-triphenyltetrazolium chloride activity assays also verified that there were significant changes in seeds quality at the CN. In summary, the time point C10 is a CN during seed population aging. Before the CN, sugar and lipid metabolism, especially fatty acid metabolism into sugar, can make up for the energy consumed by aging. After this point, the seeds were irreversibly damaged, and their viability was greatly and rapidly reduced as the cell structure became increasingly destroyed