Density functional theory study of the NO₂-sensing mechanism on a WO₃ (0 0 1) surface: the role of surface oxygen vacancies in the formation of NO and NO₃

<p>The trapping and detection of nitrogen oxide with tungsten trioxide has become a popular research topic in recent years. Knowledge of the complete reaction mechanism for nitrogen oxide adsorption is necessary to improve detector performance. In this work, we used density functional theory (DFT) calculations to study the adsorption characteristics and electron transfer of nitrogen dioxide on an oxygen-deficient monoclinic WO₃ (0 0 1) surface. We observed different reactions of NO₂ on slabs with different O- and WO-terminated WO₃ (0 0 1) surfaces with oxygen vacancies. Our calculations show that the bridging oxygen atom on an oxygen defect on an O-terminated WO₃ (0 0 1) surface is the active site where an NO₂ molecule is oxidised into nitrate and is adsorbed onto the surface. On a WO-terminated (0 0 1) surface, one of the oxygen atoms from the NO₂ molecule fills the oxygen vacancy, and the resulting NO fragment is adsorbed onto a W atom. Both of these adsorption models can cause an increase in the electrical resistance of WO₃. We also calculated the adsorption energies of NO₂ on slabs with different oxygen-deficient WO₃ surfaces.</p

Additional file 1: Figure S1A–E. of Tuning Tribological Performance of Layered Zirconium Phosphate Nanoplatelets in Oil by Surface and Interlayer Modifications

Surface roughness of five metal balls examined by a 3D profiler. The average surface roughness is 155.0 ± 14.8 nm. Figure S2. FTIR of various surface modified-ZrP samples. The strong characteristic bands associated with the asymmetric and symmetric stretching of the C−H, between 2900 and 3000cm−1, and bending at ca. 1450 cm−1 are an indication of the attachments of alkyl chains from various silanes on ZrP nanoplatelets. Figure S3. SEM and EDS results for the original metal surface before testing. Figure S4. SEM and EDS results for the worn metal surface after testing with the C16-ZrP-N6 oil sample. Figure S5. SEM and EDS results for the worn metal surface after testing with the C16-ZrP oil sample. (DOCX 3672 kb

Image1_The new ceRNA crosstalk between mRNAs and miRNAs in intervertebral disc degeneration.TIFF

Degeneration of the intervertebral disc has been linked to lower back pain. To date, pathophysiological mechanisms of intervertebral disc degeneration (IDD) remain unclear; it is meaningful to find effective diagnostic biomarkers and new therapeutic strategies for IDD. This study aimed to reveal the molecular mechanism of IDD pathogenesis from the multidimensional transcriptomics perspective. Here, we acquired IDD bulk omics datasets (GSE67567 and GSE167199) including mRNA, microRNA expression profiles, and single-cell RNA sequencing (GSE199866) from the public Gene Expression Omnibus (GEO) database. Through principal component analysis and Venn analysis, we found different expression patterns in the IDD transcription level and identified 156 common DEGs in both bulk datasets. GO and KEGG functional analyses showed these dysregulators were mostly enriched in the collagen-containing extracellular matrix, cartilage development, chondrocyte differentiation, and immune response pathways. We also constructed a potentially dysregulated competing endogenous RNA (ceRNA) network between mRNAs and miRNAs related to IDD based on microRNA target information and co-expression analysis of RNA profiles and identified 36 ceRNA axes including ZFP36/miR-155-5p/FOS, BTG2/hsa-miR-185-5p/SOCS3, and COL9A2/hsa-miR-664a-5p/IBA57. Finally, in integrating bulk and single-cell transcriptome data analyses, a total of three marker genes, COL2A1, PAX1, and ZFP36L2, were identified. In conclusion, the key genes and the new ceRNA crosstalk we identified in intervertebral disc degeneration may provide new targets for the treatment of IDD.</p

Image2_The new ceRNA crosstalk between mRNAs and miRNAs in intervertebral disc degeneration.TIFF

Degeneration of the intervertebral disc has been linked to lower back pain. To date, pathophysiological mechanisms of intervertebral disc degeneration (IDD) remain unclear; it is meaningful to find effective diagnostic biomarkers and new therapeutic strategies for IDD. This study aimed to reveal the molecular mechanism of IDD pathogenesis from the multidimensional transcriptomics perspective. Here, we acquired IDD bulk omics datasets (GSE67567 and GSE167199) including mRNA, microRNA expression profiles, and single-cell RNA sequencing (GSE199866) from the public Gene Expression Omnibus (GEO) database. Through principal component analysis and Venn analysis, we found different expression patterns in the IDD transcription level and identified 156 common DEGs in both bulk datasets. GO and KEGG functional analyses showed these dysregulators were mostly enriched in the collagen-containing extracellular matrix, cartilage development, chondrocyte differentiation, and immune response pathways. We also constructed a potentially dysregulated competing endogenous RNA (ceRNA) network between mRNAs and miRNAs related to IDD based on microRNA target information and co-expression analysis of RNA profiles and identified 36 ceRNA axes including ZFP36/miR-155-5p/FOS, BTG2/hsa-miR-185-5p/SOCS3, and COL9A2/hsa-miR-664a-5p/IBA57. Finally, in integrating bulk and single-cell transcriptome data analyses, a total of three marker genes, COL2A1, PAX1, and ZFP36L2, were identified. In conclusion, the key genes and the new ceRNA crosstalk we identified in intervertebral disc degeneration may provide new targets for the treatment of IDD.</p

Table1_The new ceRNA crosstalk between mRNAs and miRNAs in intervertebral disc degeneration.XLS

Degeneration of the intervertebral disc has been linked to lower back pain. To date, pathophysiological mechanisms of intervertebral disc degeneration (IDD) remain unclear; it is meaningful to find effective diagnostic biomarkers and new therapeutic strategies for IDD. This study aimed to reveal the molecular mechanism of IDD pathogenesis from the multidimensional transcriptomics perspective. Here, we acquired IDD bulk omics datasets (GSE67567 and GSE167199) including mRNA, microRNA expression profiles, and single-cell RNA sequencing (GSE199866) from the public Gene Expression Omnibus (GEO) database. Through principal component analysis and Venn analysis, we found different expression patterns in the IDD transcription level and identified 156 common DEGs in both bulk datasets. GO and KEGG functional analyses showed these dysregulators were mostly enriched in the collagen-containing extracellular matrix, cartilage development, chondrocyte differentiation, and immune response pathways. We also constructed a potentially dysregulated competing endogenous RNA (ceRNA) network between mRNAs and miRNAs related to IDD based on microRNA target information and co-expression analysis of RNA profiles and identified 36 ceRNA axes including ZFP36/miR-155-5p/FOS, BTG2/hsa-miR-185-5p/SOCS3, and COL9A2/hsa-miR-664a-5p/IBA57. Finally, in integrating bulk and single-cell transcriptome data analyses, a total of three marker genes, COL2A1, PAX1, and ZFP36L2, were identified. In conclusion, the key genes and the new ceRNA crosstalk we identified in intervertebral disc degeneration may provide new targets for the treatment of IDD.</p

A Novel Vector-Based Method for Exclusive Overexpression of Star-Form MicroRNAs

<div><p>The roles of microRNAs (miRNAs) as important regulators of gene expression have been studied intensively. Although most of these investigations have involved the highly expressed form of the two mature miRNA species, increasing evidence points to essential roles for star-form microRNAs (miRNA*), which are usually expressed at much lower levels. Owing to the nature of miRNA biogenesis, it is challenging to use plasmids containing miRNA coding sequences for gain-of-function experiments concerning the roles of microRNA* species. Synthetic microRNA mimics could introduce specific miRNA* species into cells, but this transient overexpression system has many shortcomings. Here, we report that specific miRNA* species can be overexpressed by introducing artificially designed stem-loop sequences into short hairpin RNA (shRNA) overexpression vectors. By our prototypic plasmid, designed to overexpress hsa-miR-146b-3p, we successfully expressed high levels of hsa-miR-146b-3p without detectable change of hsa-miR-146b-5p. Functional analysis involving luciferase reporter assays showed that, like natural miRNAs, the overexpressed hsa-miR-146b-3p inhibited target gene expression by 3′UTR seed pairing. Our demonstration that this method could overexpress two other miRNAs suggests that the approach should be broadly applicable. Our novel strategy opens the way for exclusively stable overexpression of miRNA* species and analyzing their unique functions both <em>in vitro</em> and <em>in vivo</em>.</p> </div

Figure S2 from Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in <i>Streptococcus pneumoniae</i>

Residue Tyr84 in Spr1654 allows enough space for accommodating the N-acetyl group of the sugar substrate. Residues Y84 in Spr1654, W89 in ArnB and F84 in PseC are colored in cyan, orange and violet, respectively. PseC binds to PMP-UDP-4-amino-4, 6-dideoxy-L-AltNAc (PMP-UDP-L-AltNAc) and ArnB binds to UDP- 4-amino-4-deoxy-L-Arabinose (UDP- Ara4N)

Successful overexpression of hsa-miR-146b-3p by plvx-hs-146b-3p with no detectable increase of hsa-miR-146b-5p.

<p>HeLa cells were transfected with the indicated plasmids (400 ng per well) and RNA was collected and extracted 24 h later. The expression of hsa-miR-146b-3p (A) and hsa-miR-146b-5p (B) was detected using qRT–PCR. The same experiments were done in Hep G2 cells (C) for hsa-miR-146b-3p; (D) for hsa-miR-146b-5p and HEK 293T cells (E) for hsa-miR-146b-3p; (F) for hsa-miR-146b-5p. Each graph shows the mean of three independent experiments that measured the relative expression levels (2^−deltaCT) of the two miRNAs to the reference gene RNU48. Error bars represent SEMs. * means p value ≤0.05; ** means p value ≤0.01; *** means p value ≤0.001; ns means no significance.</p

plvx-hs-146b-3p overexpressed functional hsa-miR-146b-3p with no detectable activity change of hsa-miR-146b-5p.

<p>(A) Transcription products from plvx-hs-146b-3p had hsa-miR-146b-3p activities, without changing the activity of hsa-miR-146b-5p. HeLa cells were transfected with psicheck-ctrl (20 ng per well), psicheck-146b-3psensor (20 ng per well), or psicheck-146b-5psensor (20 ng per well), in combination with either plvx-ctrl (100 ng per well) or plvx-hs-146b-3p (100 ng per well), as indicated in the graph. (B) The repression of psicheck-146b-3psensor activity could be rescued using hsa-miR-146b-3p inhibitors. HeLa cells were transfected with psicheck-146b-3psensor (20 ng per well) in combination of plvx-ctrl (100 ng per well) or plvx-hs-146b-3p (100 ng per well) under the presentation of hsa-miR-146b-3p inhibitors (100 nM) or inhibitor negative controls (100 nM), as indicated in the graph. (C) Designed modified complementary sequences (designed anti-hsa-miR-146b-3p) could not repress psicheck-146b-3psensor activity as effectively as hsa-miR-146b-3p. HeLa cells were transfected with psicheck-146b-3psensor (20 ng per well) in combination with single stranded RNA mimics of negative control sequences (100 nM), designed anti-hsa-miR-146b-3p (100 nM), hsa-miR-146b-3p (100 nM), and hsa-miR-410 (100 nM), as indicated in the graph. The miRNA hsa-miR-410, which had no ability to repress psicheck-146b-3psensor activity, was used as a negative control miRNA. (D) The miRNA hsa-miR-146b-3p overexpressed by plvx-hs-146b-3p could repress the activity of bulged sensor of hsa-miR-146b-3p (pMIR-hs-146b-3p) and this repression was abolished by mutation of the seed sequences of the bulged sensor. HeLa cells were transfected with pMIR-hs-146b-3p (2 ng per well) or pMIR-hs-146b-3p-mut (2 ng per well), together with plvx-ctrl (400 ng per well) or plvx-hs-146b-3p (400 ng per well), as indicated in the graph. Renilla luciferase vector (5 ng per well) was delivered simultaneously as a transfection control. For all assays, protein was collected 24 h after transfection. Luciferase activity was quantified and expressed as relative luciferase activity. The data represent one of at least three independent experiments, each of which involved four replicates. Error bars represent SEMs. ** means p value ≤0.01; *** means p value ≤0.001; ns means no significance.</p

Figure S1 from Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in <i>Streptococcus pneumoniae</i>

Absorption spectrum of Spr1654 and Spr1654-PLP. (a) Analysis of recombinant Spr1654-his (MW 47.7 kDa) by SDS-gel electrophoresis. The protein was separated by SDS-12% PAGE, followed by staining with Coomassie blue. Lane 1, Spr1654-his; M, molecular mass marker. (b) The absorption spectra of Spr1654 with (red line) and without PLP (blue line) were collected between 300 and 500 nm. The appearance of a 420nm peak indicates PLP binding to Spr1654