Computational studies of the self-cleavage mechanism in the glmS ribozyme

Ribozymes are catalytically functional RNA molecules. To overcome the lack of structural and chemical diversity, ribozymes employ several interesting strategies for catalysis. The glmS ribozyme regulates the level of glucosamine-6-phosphate (GlcN6P) in bacteria by catalyzing a self-cleavage reaction. Namely, the GlcN6P bonds to the glmS ribozyme and triggers a cleavage of a phosphodiester bond at a certain position via a general acid-base mechanism. This work explored the following aspects of its self-cleavage mechanism: general acid-base species, multiple roles of the cofactor GlcN6P, as well as the beneficial and deleterious effects of metal ions. Computational approaches including classical molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and free energy simulations were employed to study the cleavage mechanisms and explain experimental observations such as the thio effects and metal ion rescue effects. A concerted yet asynchronous cleavage mechanism with an active site guanine as the general base and the cofactor as the general acid was elucidated. The calculated free energy barrier associated with this mechanism was consistent with experimental measurements. Additional catalytic roles of the cofactor such as disrupting an inhibitory hydrogen bond were revealed by simulations together with the large thio effect found in the ribozyme-cofactor complex and the inverse thio effect found in the apo ribozyme. Metal ion rescue experiments indicated the direct participation of an active site Mg2+ ion in the catalysis in the apo ribozyme but not in the ribozyme-cofactor complex. Therefore, the beneficial and deleterious effects of the active site Mg2+ ion were examined by computational approaches. The findings in this work have provided insights for general ribozyme catalysis. All of these findings have implications for general ribozyme catalysis

Effects of HIF-1α on ERRα/γ protein expression in mouse skeletal muscle

Aims: HIF-1α plays an important role in the adaptive responses to hypoxia. The ERRα and γ are crucial regulators of energy metabolism in skeletal muscle. The aim of the present study was to generate the inducible HIF-1α transgenic mice and examine the effects of different HIF-1α protein expression levels on ERRα/γ in mouse skeletal muscle. Methods: We generated the HIF-1α high-expression transgenic mice (HT)and HIF-1α low-expression transgenic mice (LT),and then compared the expressions of ERRα/γ and its target genes in skeletal muscles of three kinds of mice: HT, LT, and non-transgenic mice (NT).Results: The results showed that (1) the double positive mice from the founder of 3# and 68# showed an obvious expression of HIF- 1α induced by tamoxifen and both of them were maintained to the further research as HT and LT mice, respectively; and (2) the nucleoprotein expressions of ERRα/γ and the mRNA levels of the ERRα/γ target genes: MCAD, PPARα, NRF1 and PDK4 were higher in the LT mice than the values in the NT, but only the mRNA levels of MCAD and PPARα were significantly higher. The HT mice showed significantly lower ERRα protein content than that of the NT mice. Conclusion: Our study was the first to report the generation of the inducible HIF-1α transgenic mice and effects of HIF-1α on ERRα/γ protein expression in mouse skeletal muscle in vivo. These data demonstrate that the low HIF-1α protein expression may associate with an up-regulation of ERRα/γ and their target genes in skeletal muscles, while the aggravated HIF-1α protein expression would reduce the effects

MSGNet: multi-source guidance network for fish segmentation in underwater videos

Fish segmentation in underwater videos provides basic data for fish measurements, which is vital information that supports fish habitat monitoring and fishery resources survey. However, because of water turbidity and insufficient lighting, fish segmentation in underwater videos has low accuracy and poor robustness. Most previous work has utilized static fish appearance information while ignoring fish motion in underwater videos. Considering that motion contains more detail, this paper proposes a method that simultaneously combines appearance and motion information to guide fish segmentation in underwater videos. First, underwater videos are preprocessed to highlight fish in motion, and obtain high-quality underwater optical flow. Then, a multi-source guidance network (MSGNet) is presented to segment fish in complex underwater videos with degraded visual features. To enhance both fish appearance and motion information, a non-local-based multiple co-attention guidance module (M-CAGM) is applied in the encoder stage, in which the appearance and motion features from the intra-frame salient fish and the moving fish in video sequences are reciprocally enhanced. In addition, a feature adaptive fusion module (FAFM) is introduced in the decoder stage to avoid errors accumulated in the video sequences due to blurred fish or inaccurate optical flow. Experiments based on three publicly available datasets were designed to test the performance of the proposed model. The mean pixel accuracy (mPA) and mean intersection over union (mIoU) of MSGNet were 91.89% and 88.91% respectively with the mixed dataset. Compared with those of the advanced underwater fish segmentation and video object segmentation models, the mPA and mIoU of the proposed model significantly improved. The results showed that MSGNet achieves excellent segmentation performance in complex underwater videos and can provide an effective segmentation solution for fisheries resource assessment and ocean observation. The proposed model and code are exposed via Github1

Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet

Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience

Correction:Structural and Functional Insights into an Archaeal Lipid Synthase

(Cell Reports 33, 108294-1–9.e1–e4; October 20, 2020) In the originally published version of this article, the supplemental information file containing Figures S1–S7 and Table S1 was inadvertently removed. The complete supplemental information file is now included with the paper online. The production team regrets this error

Structural and Functional Insights into an Archaeal Lipid Synthase

The UbiA superfamily of intramembrane prenyltransferases catalyzes an isoprenyl transfer reaction in the biosynthesis of lipophilic compounds involved in cellular physiological processes. Digeranylgeranylglyceryl phosphate (DGGGP) synthase (DGGGPase) generates unique membrane core lipids for the formation of the ether bond between the glycerol moiety and the alkyl chains in archaea and has been confirmed to be a member of the UbiA superfamily. Here, the crystal structure is reported to exhibit nine transmembrane helices along with a large lateral opening covered by a cytosolic cap domain and a unique substrate-binding central cavity. Notably, the lipid-bound states of this enzyme demonstrate that the putative substrate-binding pocket is occupied by the lipidic molecules used for crystallization, indicating the binding mode of hydrophobic substrates. Collectively, these structural and functional studies provide not only an understanding of lipid biosynthesis by substrate-specific lipid-modifying enzymes but also insights into the mechanisms of lipid membrane remodeling and adaptation

Research on the Influence of Marketing Information Quality on Consumer Behavior — Taking Wechat Marketing as an Example

With the continuous prosperity and development of Internet technology, the amount of information generated is increasing day by day, which inevitably leads to a series of problems such as marketing information surplus and user perception disorder. How to improve the quality of information and reduce the information disturbance to users has become an urgent problem for social media. This paper takes wechat marketing as an example, through literature research, questionnaire collection, SPSS statistical analysis and Amos structural equation fitting, based on previous research and the development status at home and abroad, summarizes various dimensions of marketing information quality, and combines drive theory and relationship marketing theory to identify three levels that affect user satisfaction and behavior: information content, utility and carrier quality. After reliability and validity test and structural equation fitting analysis, it is found that in three levels, there are five dimensions (authenticity, integrity, incentive, security, system performance) with user satisfaction as the intermediary variable, which positively affect user consumer behavior, and the influence coefficients of each dimension on user satisfaction are obtained. Among them, the influence coefficient of incentive on user satisfaction is the largest Suggestions on strengthening users' interest perception, improving the richness of media, optimizing the system layout and improving the information security mechanism

Metabolomics of Early Stage Plant Cell–Microbe Interaction Using Stable Isotope Labeling

Metabolomics has been used in unraveling metabolites that play essential roles in plant–microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms

Protein Phosphorylation and Redox Modification in Stomatal Guard Cells

Post-translational modification (PTM) is recognized as a major process accounting for protein structural variation, functional diversity, and the dynamics and complexity of the proteome. Since PTMs can change the structure and function of proteins, they are essential to coordinate signaling networks and to regulate important physiological processes in eukaryotes. Plants are constantly challenged by both biotic and abiotic stresses that reduce productivity, causing economic losses in crops. The plant responses involve complex physiological, cellular, and molecular processes, with stomatal movement as one of the earliest responses. In order to activate such a rapid response, stomatal guard cells employ cellular PTMs of key protein players in the signaling pathways to regulate the opening and closure of the stomatal pores. Here we discuss two major types of PTMs, protein phosphorylation and redox modification that play essential roles in stomatal movement under stress conditions. We present an overview of PTMs that occur in stomatal guard cells, especially the methods and technologies, and their applications in PTM identification and quantification. Our focus is on PTMs that modify molecular components in guard cell signaling at the stages of signal perception, second messenger production, as well as downstream signaling events and output. Improved understanding of guard cell signaling will enable generation of crops with enhanced stress tolerance, and increased yield and bioenergy through biotechnology and molecular breeding

Relationship between the Coloration Mechanism and Gemological Properties of Purple Scapolite

Purple scapolite is a precious gemstone. In this paper, we compared the crystal structure and spectral characteristics of purple scapolite before and after heat treatment with conventional gemological tests, EPMA, XRF, LA-ICP-MS, infrared spectroscopy, Raman spectroscopy, UV–vis spectrophotometer, EPR, and other tests. The XRD results showed that the structure of purple scapolite fits perfectly with that of marialite. Compositional analyses indicate that purple scapolite has an average Me value of 16.85 and belongs to the subspecies marialite, and thus its specific gravity and refractive index are low. The absorption peak at 1045 cm−1 in the infrared spectra has a direct relationship with the Me value, which is blue-shifted with increasing Me value. After heating at 400 °C for 2 h, the purple scapolite changed to colorless, and no phase transformation or significant structural changes occurred during this process. But this process is accompanied by the disappearance of the signal at g = 2.011 in the EPR spectra, which indicates the presence of oxygen hole centers, thus proving that the color of purple scapolite is caused by oxygen hole centers rather than Fe3+. The chlorine in the marialite structure occupies the structural center, which provides for the appearance of oxygen hole centers, and thus purple scapolite always has a high marialite content. This further leads to the refractive index and specific gravity always being lower. That is a new explanation for the relationship between scapolite coloration mechanism, specific gravity, and refractive index