Journal: International Journal of Molecular Sciences

Article Title: Ribosomal Stress Couples with the Hypoxia Response in Dec1-Dependent Orthodontic Tooth Movement

doi: 10.3390/ijms24010618

Figure Lengend Snippet: Regulation of hypoxia-responsive genes, heat shock proteins, and ribosomal proteins in hPDL fibroblasts under compression force (CF). ( A ) Quantitative RT-PCR analysis reveals that the expression levels of HIF-1α, Dec1, HSP27, and HSP105 are induced at 4 and 6 h in the CF group. ( B ) CF treatment results in the induced expression of RPL4, RPL6, RPS7, and RPL9 in hPDL fibroblasts. ( C ) The expression levels of RPS12, RPS16, RPS24, and IL-1β were increased at 4 and 6 h in the CF group compared to the control group. The data shown represent means ± SD; * p < 0.05. All results are representative of experiments done in triplicate. CF, compression force.

Article Snippet: The membranes were incubated overnight with primary antibodies: from Abcam (Cambridge, UK) [(RPL4, ab174269, 1:1000), (RPL9, ab182556, 1:2000), (RPS12, ab167428, 1:1000), (RPS16, ab177951, 1:1000), (RPS24, ab196052, 1:1000), (HSP105, ab109624, 1:1000), (Bax ab32503, 1:1000), (HIF-1α, ab2185, 1:500)], from Thermo Fisher Scientific (Waltham, MA, USA) [(RPL6, PA5-30217, 1:1000), (RPS7, PA5-110326, 1:1000)], from Novus Biologicals (Centennial, CO, USA) [(Dec1, NB100-1800, 1:1000)] and from Cell Signaling Technology (Danvers, MA USA) [β-actin, 4970, 1:1000), (GAPDH, 2118, 1:1000) followed by incubation with horseradish peroxidase-conjugated anti-rabbit IgG (1:2000; Cell Signaling Technology, Danvers, MA, USA) at room temperature for 1 h. An ECL Plus Western Blotting Detection System (GE Healthcare, Tokyo, Japan) was used to visualize the immunoreactive bands, and images were captured using the Luminescent ImageQuant LAS 4000 Mini (GE Healthcare, Tokyo, Japan).

Techniques: Quantitative RT-PCR, Expressing, Control

Journal: bioRxiv

Article Title: RNA-protein interactome at the Hepatitis E virus internal ribosome entry site

doi: 10.1101/2022.04.11.487827

Figure Lengend Snippet: (A) The interaction between the HEV IRESI and RPS3A is shown in the cartoon and rendered in cyan and lime, respectively. The interacting nucleotides and amino acids are rendered in licorice and colored in atom-wise mode like C: cyan/white, O: red, N: blue and S: yellow. (B) The interaction between the HEV IRESI and RPS7 is shown in the cartoon and rendered in cyan and lime, respectively. The interacting nucleotides and amino acids are rendered as shown in (A). (C) The interaction between the HEV IRESI and RPL26 is shown in the cartoon and rendered in cyan and lime, respectively. The interacting nucleotides and amino acids are rendered as shown in (A). (D) The interaction between the HEV IRESI and RPL5 is shown in the cartoon and rendered in cyan and lime, respectively. The interacting nucleotides and amino acids are rendered as shown in (A). (E-H) The quantitative polar contacts between nucleotide and amino acids are measured for the indicated complexes and shown in bar-graph (Y-axis: hydrogen bond distance, X-axis interacting pair of nucleotides@aminoacids). (I) The binding free energy for the indicated complexes are plotted in the bar graph.

Article Snippet: Anti-RPL24 (Catalog No. ITT09128), anti- RPL41 (Catalog No.ITT09136) and anti-DHX9 (Catalog No. ITT12266) antibodies were from Geno Technology Inc. (St Louis, USA); anti-RPS3A (catalog No. STJ28158), anti- RPS7 (catalog No.STJ28814) and anti-PPIG (catalog No. STJ191133) antibodies were from St. John’s laboratory (London, UK).

Techniques: Binding Assay

Journal: Cancer Cell International

Article Title: Liquid biopsy-derived extracellular vesicle protein biomarkers for diagnosis and prognostic assessment of lung squamous cell carcinoma

doi: 10.1186/s12935-025-03792-0

Figure Lengend Snippet: Plasma EV protein biomarkers for the diagnosis of LUSC. ( A ) Proteins with the highest predictive values in classifying LUSC and BLD with XGBoost. ( B ) ROC curve and confusion matrix in the training set. ( C ) ROC curve and confusion matrix in the test set. ( D ) ROC curve and confusion matrix in the entire cohort. SEN (Sensitivity) and SPE (Specificity) refer to diagnostic performance metrics for distinguishing LUSC from BLD samples. ( E ) Levels of TUBB3 in total plasma from patients with LUSC and BLD. A total of 74 samples (38 BLD and 36 LUSC) were tested. ( F ) Levels of RPS7 in total plasma from patients with LUSC and BLD. A total of 149 samples (44 BLD and 105 LUSC) were tested

Article Snippet: Following the manufacturer’s instructions, commercial assay kits for RPS7 (MyBioSource, USA, Catalog Number: MBS7204349) and TUBB3 (CUSABIO, China, Catalog Number: CSB-E14121h) were used to determine the expression levels of these proteins in preoperative plasma samples.

Techniques: Clinical Proteomics, Biomarker Discovery, Diagnostic Assay

Journal: Viruses

Article Title: Screening of Duck Tembusu Virus NS3 Interacting Host Proteins and Identification of Its Specific Interplay Domains

doi: 10.3390/v11080740

Figure Lengend Snippet: The information of the gene products interacting with NS3 according to Y2H system screening.

Article Snippet: After high-stringency selection, positive alignment with the National Center for Biotechnology Information database revealed nine potential interactive proteins: MGST1, ERCC4, WIF1, WDR75, ACBD3, PRDX1, RPS7, ND5, and LDHA.

Techniques: Conjugation Assay, Membrane, Activity Assay

Journal: Genes & Diseases

Article Title: Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

doi: 10.1016/j.gendis.2022.07.002

Figure Lengend Snippet: BC-3 target proteins analyzed by mass spectrometry. ( A ) The binding of biotin- and FITC-labeled BC-3 to 5637 cells was measured by flow cytometry, with biotin- and FITC-labeled Library as a control. ( B ) SDS-PAGE with silver staining was used to identify the aptamer target. Lane library, protein captured with biotin-labeled library treated sample; Lane BC-3, protein captured with biotin-labeled BC-3 treated sample. ( C ) Western blot analysis of the concentrations of RPS7 and β-actin in the preparations captured via Library and BC-3. ( D ) After incubating the ER fluorescence probe ER-tracker (red) for 0.5 h and FITC-labeled BC-3 or Library (green) for 1 h, 5637 cells displayed the colocalization (yellow) of ER-tracker and FITC-labeled BC-3. ( E ) Enlarged view of intracellular fluorescence signals in colocalization. ( F ) Fluorescence intensity profile of yellow arrow regions in 5637 cells (scale bar = 40 μm).

Article Snippet: Firstly, the protein structure of RPS7 was downloaded from the RCSB PDB databank (PDB ID: 6YBW) with a resolution of 3.1 Å.

Techniques: Mass Spectrometry, Binding Assay, Labeling, Flow Cytometry, Control, SDS Page, Silver Staining, Western Blot, Fluorescence

Journal: Genes & Diseases

Article Title: Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

doi: 10.1016/j.gendis.2022.07.002

Figure Lengend Snippet: Computational analysis of the Binding Model between RPS7 and BC-3. ( A ) Interaction model between RPS7 and BC-3. Close view of the RPS7 and BC-3 interaction region in part α and part β with key amino acid residues marked. Promoter methylation ( B ) and the expression level ( C ) of RPS7 in bladder cancer and normal bladder samples from TCGA.

Article Snippet: Firstly, the protein structure of RPS7 was downloaded from the RCSB PDB databank (PDB ID: 6YBW) with a resolution of 3.1 Å.

Techniques: Binding Assay, Methylation, Expressing

Journal: Genes & Diseases

Article Title: Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

doi: 10.1016/j.gendis.2022.07.002

Figure Lengend Snippet: BC-3 target proteins analyzed by mass spectrometry. ( A ) The binding of biotin- and FITC-labeled BC-3 to 5637 cells was measured by flow cytometry, with biotin- and FITC-labeled Library as a control. ( B ) SDS-PAGE with silver staining was used to identify the aptamer target. Lane library, protein captured with biotin-labeled library treated sample; Lane BC-3, protein captured with biotin-labeled BC-3 treated sample. ( C ) Western blot analysis of the concentrations of RPS7 and β-actin in the preparations captured via Library and BC-3. ( D ) After incubating the ER fluorescence probe ER-tracker (red) for 0.5 h and FITC-labeled BC-3 or Library (green) for 1 h, 5637 cells displayed the colocalization (yellow) of ER-tracker and FITC-labeled BC-3. ( E ) Enlarged view of intracellular fluorescence signals in colocalization. ( F ) Fluorescence intensity profile of yellow arrow regions in 5637 cells (scale bar = 40 μm).

Article Snippet: PVDF membranes were then separately incubated with anti-RPS7 rabbit polyclonal antibody (D127523, Sangon Biotechnology Co., Ltd.) and anti-β-Actin antibody (MA5-11869, Thermo Fisher) at 4 °C overnight.

Techniques: Mass Spectrometry, Binding Assay, Labeling, Flow Cytometry, Control, SDS Page, Silver Staining, Western Blot, Fluorescence

Journal: Genes & Diseases

Article Title: Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

doi: 10.1016/j.gendis.2022.07.002

Figure Lengend Snippet: Computational analysis of the Binding Model between RPS7 and BC-3. ( A ) Interaction model between RPS7 and BC-3. Close view of the RPS7 and BC-3 interaction region in part α and part β with key amino acid residues marked. Promoter methylation ( B ) and the expression level ( C ) of RPS7 in bladder cancer and normal bladder samples from TCGA.

Article Snippet: PVDF membranes were then separately incubated with anti-RPS7 rabbit polyclonal antibody (D127523, Sangon Biotechnology Co., Ltd.) and anti-β-Actin antibody (MA5-11869, Thermo Fisher) at 4 °C overnight.

Techniques: Binding Assay, Methylation, Expressing