Weighted gene co-expression network analysis reveals key biomarkers and immune infiltration characteristics for bronchial epithelial cells from asthmatic patients.

BACKGROUND: Asthma ranks among the most prevalent non-communicable diseases worldwide. Previous studies have elucidated the significant role of the immune system in its pathophysiology. Nevertheless, the immune-related mechanisms underlying asthma are complex and still inadequately understood. Thus, our objective was to investigate novel key biomarkers and immune infiltration characteristics associated with asthma by employing integrated bioinformatics tools. METHODS: In this study, we conducted a weighted gene co-expression network analysis (WGCNA) to identify key modules and genes potentially implicated in asthma. Functional annotation of these key modules and genes was carried out through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Additionally, we constructed a protein-protein interaction (PPI) network using the STRING database to identify 10 hub genes. Furthermore, we evaluated the relative proportion of immune cells in bronchial epithelial cell samples from 20 healthy individuals and 88 asthmatic patients using CIBERSORT. Finally, we validated the hub genes and explored their correlation with immune infiltration. RESULTS: Furthermore, 20 gene expression modules and 10 hub genes were identified herein. Among them, complement component 3 (C3), prostaglandin I2 receptor (PTGIR), parathyroid hormone-like hormone (PTHLH), and C-X3-C motif chemokine ligand 1 (CX3CL1) were closely correlated with the infiltration of immune cells. They may be novel candidate biomarkers or therapeutic targets for asthma. Furthermore, B cells memory, and plasma cells might play an important role in immune cell infiltration after asthma. CONCLUSIONS: C3, PTGIR, CX3CL1, and PTHLH have important clinical diagnostic values and are correlated with infiltration of multiple immune cell types in asthma. These hub genes, B cells memory, and plasma cells may become important biological targets for therapeutic asthma drug screening and drug design.

Upregulation of Long Noncoding RNA (lncRNA) X-Inactive Specific Transcript (XIST) is Associated with Cisplatin Resistance in Non-Small Cell Lung Cancer (NSCLC) by Downregulating MicroRNA-144-3p.

BACKGROUND Patients with advanced non-small cell lung cancer (NSCLC) treated with cisplatin, also termed cis-diamminedichloroplatinum (CDDP) or diamminedichloroplatinum (DDP), may develop chemoresistance. This study aimed to investigate the role of long non-coding RNA (lncRNA) X-inactive specific transcript (XIST) and multidrug resistance-1 (MDR1) in tumor tissue samples and the chemoresistant human NSCLC cell lines, H460/DDP and A549/DDP, and in a murine A549/DDP tumor xenograft. MATERIAL AND METHODS Tissue samples were from patients with NSCLC who responded cisplatin (DDP-sensitive) (n=24), patients with NSCLC unresponsive to cisplatin (DDP-resistant) (n=30), and normal lung tissue (n=25). In H460/DDP and A549/DDP cells, expression of XIST, microRNA (miR)-144-3p, MDR1, and multidrug resistance-associated protein 1 (MRP1) were detected by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot. The MTT assay measured cell survival and proliferation, a transwell assay evaluated cell migration, and flow cytometry measured apoptosis. Luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays examined the relationship between XIST and miR-144-3p. Tumor xenografts from A549/DDP cells were studied in BALB/c nude mice. RESULTS In tissue from patients with DDP-resistant NSCLC and the mouse A549/DDP tumor xenograft, lncRNA-XIST expression was upregulated and miR-144-3p expression was inhibited. In A549/DDP and H460/DDP cells, down-regulation of lncRNA-XIST and upregulation of miR-144-3p reduced cell survival, proliferation, migration, induced apoptosis and suppressed MDR1 and MRP1 expression. CONCLUSIONS Upregulation of lncRNA-XIST was associated with cisplatin resistance in NSCLC by downregulating miRNA-144-3p in H460/DDP and A549/DDP cells, a murine A549/DDP tumor xenograft, and human tumor tissues from patients with cisplatin-resistant NSCLC.

ABC Transporter CslAB, a Stabilizer of ComCDE Signal in Streptococcus mutans.

BACKGROUND: In Streptococcus mutans, ComCDE, a peptide-induced two-component signal transduction system, forms a closed signal transduction, and even if difunctional ComE closes this signal at its headstream to avoid its infinite amplification, it is not enough for ComE to work in a concentration-dependent manner. CslAB has a chance to regulate ComCDE by controlling extracellular competence-stimulating peptide (CSP) concentration through its processing and secretion. OBJECTIVES: To first confirm the binding properties of cslAB promoter (PcslAB) with ComE, then to uncover in vivo need of cslAB expression, and finally to unveil the role of CslAB. MATERIALS AND METHODS: Electrophoretic mobility shift assay was used to confirm the binding properties of PcslAB with ComE. In vivo cslAB transcription was detected by ß-galactosidase activity because its gene has been fused to cslAB operon, and finally the role of CslAB was reviewed. RESULTS: PcslAB is a weak promoter responding to ComE and its binding appears to be negative cooperative. Although PcslAB is partially controlled by ComCDE, it can respond to ComCDE regulation. Supported by the obtained molecular evidence, CslAB acts as a stabilizer of ComCDE signal on the patterns of its expression. CONCLUSIONS: PcslAB is partially controlled by ComCDE. CslAB is a stabilizer of ComCDE signal to ensure that ComE works in a concentration-dependent manner.

[Purification of Taq DNA polymerase expressed in Escherichia coli].

Taq DNA polymerase is one of the most commonly thermostable DNA polymerases in molecular biological researches, which shares its basic characters with others of the family, thereby its purifying strategy could be used not only in itself production but also in the extraction of the others as a reference. At present, the protocols reported for large scale preparation of Taq DNA are high cost, so a cheaper method was described here. In this protocol, by heat denaturation, ammonium sulfate precipitation and cation exchange chromatography of 724 resin, about 18 g powder of Na form resin could recover about 27.07 mg of Taq enzyme. The total activity and specific activity were approximately 2.2 × 105 U and 8131.98 U/mg. The total yield was about 48.92% with 59.35 of purification folds. Analysis of quality of purified enzyme indicated that only one protein 94 kDa was identified against SDS-PAGE and the remnant of DNA nuclease was not detected. For PCR reaction, The amplification ability of purified Taq polymerase was not different from that of the commercially avail-able ones. This method reported in the present study is effective and low cost, making it suitable for general purification in laboratories or business production.

Defect-pit-assisted growth of GaN nanostructures: nanowires, nanorods and nanobelts.

A new method using defect-pit-assisted growth technology to successfully synthesize the high-quality single crystalline GaN nanostructures by ammoniating Ga(2)O(3) films was proposed in this paper. During the ammoniating process, the amorphous middle buffer layer may unavoidably produce some defects and dislocations. Some defect pits come out, which have the lowest surface energy and can subsequently be used as a mask/template or act as potential nucleation sites to fabricate the GaN actinomorphic nanostructures. The as-prepared products are characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). The results indicate that all the reflections of the samples can be indexed to the hexagonal GaN phase and the clear lattice fringes in HRTEM further confirm the growth of high-quality single-crystal GaN nanostructures. The SEM images show that the nanostructures have been realized under different experimental conditions exhibiting different shapes: nanowires, nanorods, and nanobelts. No particles or other nanostructures are found in the SEM study, demonstrating that the product possesses pure nanostructures. These nanostructures show a very good emission peak at 366 nm, which will have a good advantage for applications in laser devices using one-dimensional structures. Finally, the growth mechanism is also briefly discussed.