GEO dataset mining analysis reveals novel Staphylococcus aureus virulence gene regulatory networks and diagnostic targets in mice

Staphylococcus (S.) aureus infection is a serious, worldwide health concern, particularly in many communities and hospitals. Understanding the S. aureus pathogenetic regulatory network will provide significant insights into diagnostic target screening to improve clinical treatment of diseases caused by S. aureus. We screened differentially expressed genes between normal mice and S. aureus-infected mice. We used the Gene Expression Omnibus (GEO) DataSets database for functional analysis (GO-analysis) and the DAVID and KEGG databases for signaling pathway analyses. We next integrated the gene and pathway analyses with Transcriptional Regulatory Element Database (TRED) to build an antimicrobial resistance gene regulatory network of S. aureus. We performed association analysis of network genes and diseases using DAVID online annotation tools. We identified a total of 437 virulence genes and 15 transcription factors (TFs), as well as 444 corresponding target genes, in the S. aureus TF regulatory network. We screened seven key network nodes (Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl), four key transcription factors (Jun, C3, Spil, and Il6) and an important signaling pathway (TNF). We hypothesized that the cytokine activity and growth factor activity of S. aureus are combinatorically cross-regulated by Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl genes, the TFs Jun, C3, Spi1, and Il6, as well as the immune response, cellular response to lipopolysaccharide, and inflammatory response. Our study provides information and reference values for the molecular understanding of the S. aureus pathogenetic gene regulatory network

Quantitative analysis of endobronchial elastography combined with serum tumour markers of lung cancer in the diagnosis of benign and malignant mediastinal and hilar lymph nodes

Purpose: In malignant tumours, elastography and serum tumour markers have shown high diagnostic efficacy. Therefore, we aimed to quantitatively analyse the results of endobronchial elastography combined with serum tumour markers of lung cancer to accurately distinguish benign and malignant mediastinal and hilar lymph nodes.Methods: Data of patients who underwent endobronchial ultrasound-guided transbronchial needle aspiration for mediastinal lymph node enlargement in our hospital between January 2018 and August 2022 were retrospectively collected. The characteristics of quantitative elastography and serum tumour markers were evaluated.Results: We enrolled 197 patients (273 lymph nodes). In the differential diagnosis of benign and malignant mediastinal and hilar lymph nodes, the stiffness area ratio (SAR), strain ratio (SR), and strain rate in lymph nodes were significant, among which SAR had the highest diagnostic value (cut-off value, 0.409). The combination of the four tumour markers had a high diagnostic value (AUC, 0.886). Three types of quantitative elastography indices combined with serum tumour markers for lung cancer showed a higher diagnostic value (AUC, 0.930; sensitivity, 83.5%; specificity, 89.3%; positive predictive value, 88.1%; negative predictive value, 85%) (p < 0.05). In the differential diagnosis of pathological types of lung cancer, different quantitative elastography indicators and serum tumour markers for lung cancer have different diagnostic significance for the differential diagnosis of lung cancer pathological types.Conclusion: The quantitative analysis of endobronchial ultrasound elastography combined with tumour markers can improve the diagnosis rate of benign and malignant mediastinal and hilar lymph nodes, help guide the puncture of false negative lymph nodes, and reduce the misdiagnosis rate

Gate-dependent Pseudospin Mixing in Graphene/Boron Nitride Moire Superlattices

Electrons in graphene are described by relativistic Dirac-Weyl spinors with a two-component pseudospin1-12. The unique pseudospin structure of Dirac electrons leads to emerging phenomena such as the massless Dirac cone2, anomalous quantum Hall effect2, 3, and Klein tunneling4, 5 in graphene. The capability to manipulate electron pseudospin is highly desirable for novel graphene electronics, and it requires precise control to differentiate the two graphene sub-lattices at atomic level. Graphene/boron nitride (graphene/BN) Moire superlattice, where a fast sub-lattice oscillation due to B-N atoms is superimposed on the slow Moire period, provides an attractive approach to engineer the electron pseudospin in graphene13-18. This unusual Moire superlattice leads to a spinor potential with unusual hybridization of electron pseudospins, which can be probed directly through infrared spectroscopy because optical transitions are very sensitive to excited state wavefunctions. Here, we perform micro-infrared spectroscopy on graphene/BN heterostructure and demonstrate that the Moire superlattice potential is dominated by a pseudospin-mixing component analogous to a spatially varying pseudomagnetic field. In addition, we show that the spinor potential depends sensitively on the gate-induced carrier concentration in graphene, indicating a strong renormalization of the spinor potential from electron-electron interactions. Our study offers deeper understanding of graphene pseudospin structure under spinor Moire potential, as well as exciting opportunities to control pseudospin in two-dimensional heterostructures for novel electronic and photonic nanodevices

Layer-by-Layer Epitaxy of Multilayer MoS2 Wafers

Two-dimensional (2D) semiconductor of MoS2 has great potential for advanced electronics technologies beyond silicon1-9. So far, high-quality monolayer MoS2 wafers10-12 are already available and various demonstrations from individual transistors to integrated circuits have also been shown13-15. In addition to the monolayer, multilayers have narrower band gaps but improved carrier mobilities and current capacities over the monolayer5,16-18. However, achieving high-quality multilayer MoS2 wafers remains a challenge. Here we report the growth of high quality multilayer MoS2 4-inch wafers via the layer-by-layer epitaxy process. The epitaxy leads to well-defined stacking orders between adjacent epitaxial layers and offers a delicate control of layer numbers up to 6. Systematic evaluations on the atomic structures and electronic properties were carried out for achieved wafers with different layer numbers. Significant improvements on device performances were found in thicker-layer field effect transistors (FETs), as expected. For example, the average field-effect mobility ({\mu}FE) at room temperature (RT) can increase from ~80 cm2V-1s-1 for monolayer to ~110/145 cm2V-1s-1 for bilayer/trilayer devices. The highest RT {\mu}FE=234.7 cm2V-1s-1 and a record-high on-current densities of 1.704 mA{\mu}m-1 at Vds=2 V were also achieved in trilayer MoS2 FETs with a high on/off ratio exceeding 107. Our work hence moves a step closer to practical applications of 2D MoS2 in electronics.Comment: 13 pages,4 Figure

Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed

An alternative simulation approach for surface flashover in a vacuum using a 1D2V continuum and kinetic model

Surface flashover across an insulator in a vacuum is a destructive plasma discharge which undermines the behaviors of a range of applications in electrical engineering, particle physics and space engineering, etc. This phenomenon is widely modeled by the particle-in-cell (PIC) simulation, here the continuum and kinetic simulation method is first proposed and implemented as an alternative solution for flashover modeling, aiming for the prevention of unfavorable particle noises in PIC models. A one dimension in space, two dimensions in velocity kinetic simulation model is constructed. Modeling setup, physical assumptions, and simulation algorithm are presented in detail, and a comparison with the well-known secondary electron (SE) emission avalanche analytical expression and existing PIC simulation are made. The obtained kinetic simulation results are consistent with the analytical prediction, and feature noise-free data of surface charge density as well as fluxes of primary and SEs. Discrepancies between the two simulation models and analytical predictions are explained. The code is convenient for updating and to include additional physical processes. The possible implementations of outgassing and plasma species for the final breakdown stage are discussed. The proposed continuum and kinetic approach are expected to inspire future modeling studies for the flashover mechanism and mitigation

Structural insights into Ca2+-activated long-range allosteric channel gating of RyR1

Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR protein is folded into the cytoplasmic assembly and the remaining residues form the transmembrane domain, it has been hypothesized that the activation and regulation of RyR channels occur through an as yet uncharacterized long-range allosteric mechanism. Here we report the characterization of a Ca2+-activated open-state RyR1 structure by cryo-electron microscopy. The structure has an overall resolution of 4.9 angstrom and a resolution of 4.2 angstrom for the core region. In comparison with the previously determined apo/closed-state structure, we observed long-range allosteric gating of the channel upon Ca2+ activation. In-depth structural analyses elucidated a novel channel-gating mechanism and a novel ion selectivity mechanism of RyR1. Our work not only provides structural insights into the molecular mechanisms of channel gating and regulation of RyRs, but also sheds light on structural basis for channel-gating and ion selectivity mechanisms for the six-transmembrane-helix cation channel family.Strategic Priority Research Program of Chinese Academy of Sciences [XDB08030202]; National Basic Research Program (973 Program); Ministry of Science & Technology of China [2012CB917200, 2014CB910700]; National Natural Science Foundation of China [31270768]; Ministry of Education of China (111 Program China)SCI(E)PubMed中国科技核心期刊(ISTIC)[email protected]; [email protected]