Journal: Science Advances

Article Title: Phage-ICE tandems facilitate bacterial adaptation and antimicrobial resistance spread

doi: 10.1126/sciadv.aed3416

Figure Lengend Snippet: ( A ) Competitive fitness ( W ) of eight selected transconjugants/transformants obtained via HR or SR versus recipient P1/7RF. Data are mean ± SD ( n = 10). Abbreviations: HR, homologous recombination; SR, site-specific recombination. Statistical significance: ** P < 0.01, *** P < 0.001, and **** P < 0.0001; n.s., not significant. ( B ) H 2 O 2 sensitivity assayed by disk diffusion. Zones of growth inhibition are shown for the recipient strain S. suis P1/7RF and transconjugants/transformants. ( C ) Transcriptomic (RNA-seq) and qPCR validation of H 2 O 2 stress response in P1/7RF, cSS389_Phage2 (HR), and cAKJ18_Phage (SR) after 25-min exposure. Red: up-regulated (log 2 FC ≥ 1, P adj ≤ 0.05); blue: down-regulated (log 2 FC ≤ −1, P adj ≤ 0.05); yellow: nonchanging; white: not significant. ( D ) Intracellular H 2 O 2 levels after 25-min treatment with 25 mM H 2 O 2 . ( E ) Model of the H 2 O 2 stress response in HR-integrated recombinants versus recipient . Red and blue indicate up-regulated and down-regulated genes, respectively.

Article Snippet: qPCR reactions (20 μl) contained 20 ng of genomic DNA, 0.4 μM each primer, and 1X ChamQ SYBR qPCR Master Mix (Vazyme).

Techniques: Homologous Recombination, Sensitivity, Diffusion-based Assay, Inhibition, RNA Sequencing, Biomarker Discovery

Journal: Journal of Animal Science and Biotechnology

Article Title: ZBED6 deletion activates FNDC1 -mediated PI3K/AKT and MAPK/ERK1/2 signaling pathways to promote myogenesis in pigs

doi: 10.1186/s40104-026-01504-w

Figure Lengend Snippet: Primer and siRNA sequences used in this study

Article Snippet: qPCR was performed on a CFX96 Real-Time PCR Detection System (Bio-Rad) in 20 μL reactions containing 10 μL of ChamQ SYBR qPCR Master Mix (Vazyme, Q311-02), 1 μL of diluted cDNA, 0.6 μL of each primer, and 7.8 μL of nuclease-free water.

Techniques: Sequencing

Journal: Research

Article Title: A pH-Responsive Polysaccharide Hydrogel Modulates Oxygen Delivery and Immunometabolic Remodeling for Diabetic Bone Regeneration

doi: 10.34133/research.1428

Figure Lengend Snippet: The GOZ6 hydrogel regulates macrophage polarization and reprograms their metabolic phenotype. (A) Representative immunofluorescence images of CD86 and CD206 staining in macrophages from different groups, used to evaluate pro-inflammatory M1 polarization and anti-inflammatory/reparative M2 polarization, respectively. Scale bar, 100 μm. (B) Quantitative analysis of CD86 and CD206 fluorescence intensity. (C) Flow cytometry analysis of macrophages in different groups. (D) Western blot analysis of proteins associated with macrophage polarization. (E) ELISA detection of IL-10 and TNF-α expression levels. (F) RT-qPCR analysis of IL-10 , TNF-α , and TGF-β expression in RAW264.7 cells under different treatments. (G) GSEA enrichment analysis of pathways related to oxidative phosphorylation. (H) Detection of lactate levels in RAW264.7 cells under different treatments. (I) Detection of glucose levels in RAW264.7 cells under different treatments. (J) Detection of mtDNA levels in RAW264.7 cells under different treatments. (K) Detection of ATP levels in RAW264.7 cells under different treatments. Data are presented as the mean ± SD ( n = 5). Compared with the GO group: * P < 0.05, ** P < 0.01, *** P < 0.001, ns: not significant ( P > 0.05). Compared with the GOZ6 group: # P < 0.05, ## P < 0.01, ### P < 0.001, ns: not significant ( P > 0.05).

Article Snippet: Quantitative real-time PCR was performed using ChamQ Universal SYBR qPCR Master Mix (Vazyme, Q411) on a QuantStudio 6 Flex real-time PCR system (Applied Biosystems).

Techniques: Immunofluorescence, Staining, Analysis, Fluorescence, Flow Cytometry, Western Blot, Enzyme-linked Immunosorbent Assay, Expressing, Quantitative RT-PCR, Phospho-proteomics

Journal: Research

Article Title: A pH-Responsive Polysaccharide Hydrogel Modulates Oxygen Delivery and Immunometabolic Remodeling for Diabetic Bone Regeneration

doi: 10.34133/research.1428

Figure Lengend Snippet: GOZ6 improves mitochondrial function in BMSCs and promotes osteogenic differentiation. (A) Representative fluorescence images of JC-1 in BMSCs under different hydrogel treatments. Scale bar, 200 μm. (B) JC-1 flow cytometric analysis of BMSCs in different groups. (C) Representative fluorescence images of ROS staining in BMSCs under different hydrogel treatments. (D) Representative images of alkaline phosphatase (ALP) staining and Alizarin Red S (ARS) staining. Scale bar, 100 μm. (E) Quantitative analysis of ALP activity and mineralized nodule formation. (F) Immunofluorescent staining of BMSCs cultured for 3 d: green (COL1), red (phalloidin), and blue (DAPI). Scale bar, 200 μm. (G) Quantitative analysis of COL1 fluorescence intensity. (H to J) RT-qPCR analysis of osteogenesis-related gene expression ( Alpl, Runx2, and Col1a1 ) in BMSCs. Data are presented as the mean ± SD ( n = 5). Compared with the GO group: * P < 0.05, ** P < 0.01, *** P < 0.001, ns: not significant ( P > 0.05). Compared with the GOZ6 group: # P < 0.05, ## P < 0.01, ### P < 0.001, ns: not significant ( P > 0.05).

Article Snippet: Quantitative real-time PCR was performed using ChamQ Universal SYBR qPCR Master Mix (Vazyme, Q411) on a QuantStudio 6 Flex real-time PCR system (Applied Biosystems).

Techniques: Fluorescence, Analysis, Staining, Activity Assay, Cell Culture, Quantitative RT-PCR, Gene Expression

Journal: Genes to Cells

Article Title: A YAP – TEAD – CTCF Transcriptional Regulatory Axis Associated With the Elimination of Injured Hepatocytes From the Liver

doi: 10.1111/gtc.70150

Figure Lengend Snippet: Transcriptome analyses of livers and hepatocytes following YAP induction by AAV or HTVi. (a) Schematic overview of the RNA‐seq workflow for whole liver RNA‐seq (left) and sorted hepatocyte RNA‐seq (right). For sorted RNA‐seq, hepatocytes were isolated by collagenase perfusion and hepatocyte fractionation, followed by purification of live hepatocytes and FACS sorting of tdTomato‐positive hepatocytes. Liver tissues or sorted hepatocytes were collected 3 days after YAP induction and subjected to RNA‐seq analysis. (b) Unsupervised hierarchical clustering heatmap of whole liver RNA‐seq data using differentially expressed genes (DEGs) across the indicated groups (No treatment, HTVi‐empty, HTVi‐YAP, and AAV‐YAP). Red and blue indicate relatively high and low expression, respectively. (c) Venn diagram showing the overlap of significantly upregulated genes (fold change > 2, p < 0.05) in the AAV‐YAP and HTVi‐YAP groups compared with the no‐treatment control group in whole liver RNA‐seq. (d) Unsupervised hierarchical clustering heatmap of sorted hepatocyte RNA‐seq data using DEGs across the indicated groups (No treatment, HTVi‐empty, HTVi‐YAP, and AAV‐YAP). Red and blue indicate relatively high and low expression, respectively. (e) Venn diagram showing the overlap of significantly upregulated genes (fold change > 2, p < 0.05) in the AAV‐YAP and HTVi‐YAP groups compared with the no‐treatment control group in sorted hepatocyte RNA‐seq. (f) Venn diagram showing the overlap of HTVi‐specifically upregulated genes between whole RNA‐seq analysis and sort RNA‐seq analysis. (g) Reactome pathway analysis of genes commonly upregulated in the HTVi‐YAP group in both whole liver and sorted hepatocyte RNA‐seq datasets. The x ‐axis indicates −log10 (adjusted p value), dot size represents gene count, and color intensity indicates z‐score. (h–j) qPCR validation of representative genes associated with the indicated Reactome pathway terms: Cell cycle checkpoints (h), RHO GTPase effectors (i), and Immunoregulatory interactions between a lymphoid and a nonlymphoid cell (j). Relative mRNA expression was normalized to Gapdh . Data are shown as mean ± SD ( n = 3).

Article Snippet: cDNA was synthesized using ReverTra Ace qPCR RT Master Mix (Toyobo, Osaka, Japan).

Techniques: RNA Sequencing, Isolation, Fractionation, Purification, Analysis, Expressing, Control, Biomarker Discovery

Journal: Genes to Cells

Article Title: A YAP – TEAD – CTCF Transcriptional Regulatory Axis Associated With the Elimination of Injured Hepatocytes From the Liver

doi: 10.1111/gtc.70150

Figure Lengend Snippet: Transcriptome analyses of livers and hepatocytes following YAP induction by AAV or HTVi. (a) Schematic overview of the RNA‐seq workflow for whole liver RNA‐seq (left) and sorted hepatocyte RNA‐seq (right). For sorted RNA‐seq, hepatocytes were isolated by collagenase perfusion and hepatocyte fractionation, followed by purification of live hepatocytes and FACS sorting of tdTomato‐positive hepatocytes. Liver tissues or sorted hepatocytes were collected 3 days after YAP induction and subjected to RNA‐seq analysis. (b) Unsupervised hierarchical clustering heatmap of whole liver RNA‐seq data using differentially expressed genes (DEGs) across the indicated groups (No treatment, HTVi‐empty, HTVi‐YAP, and AAV‐YAP). Red and blue indicate relatively high and low expression, respectively. (c) Venn diagram showing the overlap of significantly upregulated genes (fold change > 2, p < 0.05) in the AAV‐YAP and HTVi‐YAP groups compared with the no‐treatment control group in whole liver RNA‐seq. (d) Unsupervised hierarchical clustering heatmap of sorted hepatocyte RNA‐seq data using DEGs across the indicated groups (No treatment, HTVi‐empty, HTVi‐YAP, and AAV‐YAP). Red and blue indicate relatively high and low expression, respectively. (e) Venn diagram showing the overlap of significantly upregulated genes (fold change > 2, p < 0.05) in the AAV‐YAP and HTVi‐YAP groups compared with the no‐treatment control group in sorted hepatocyte RNA‐seq. (f) Venn diagram showing the overlap of HTVi‐specifically upregulated genes between whole RNA‐seq analysis and sort RNA‐seq analysis. (g) Reactome pathway analysis of genes commonly upregulated in the HTVi‐YAP group in both whole liver and sorted hepatocyte RNA‐seq datasets. The x ‐axis indicates −log10 (adjusted p value), dot size represents gene count, and color intensity indicates z‐score. (h–j) qPCR validation of representative genes associated with the indicated Reactome pathway terms: Cell cycle checkpoints (h), RHO GTPase effectors (i), and Immunoregulatory interactions between a lymphoid and a nonlymphoid cell (j). Relative mRNA expression was normalized to Gapdh . Data are shown as mean ± SD ( n = 3).

Article Snippet: Quantitative real‐time PCR was performed using THUNDERBIRD SYBR qPCR Mix (Toyobo) on a CFX96 Real‐Time PCR System (Bio‐Rad, Hercules, California, USA).

Techniques: RNA Sequencing, Isolation, Fractionation, Purification, Analysis, Expressing, Control, Biomarker Discovery