Journal: Nature Immunology

Article Title: Spatial patterning of fibroblast TGFβ signaling underlies treatment resistance in rheumatoid arthritis

doi: 10.1038/s41590-025-02386-2

Figure Lengend Snippet: a , b , ELISA quantification of POSTN ( a ) and COMP ( b ) production from fibroblasts and EC co-culture (1:1 ratio) treated with the indicated siRNAs (20 nM). P values are shown for the comparison between DLL4 siRNA and control siRNA conditions (cumulative POSTN P < 0.0001, cumulative COMP P = 0.0081). The bar plots to the right represent the area under the curve. c – n , RNAscope quantification of fibrogenic program in response to Notch perturbation. Representative images of siControl-treated and siRNA against DLL4 (siDLL4)-treated co-cultures with indicated fibrogenic ( a – f ), TGFB ( g – j ) and TGFBR ( k – n ) transcripts shown. PECAM and DLL4 transcripts denote endothelial cells. Scale bars, 200 μm. d , f , h , j , l , n , Boxen plots representing the distribution of MFIs of the corresponding genes in siControl and siDLL4 conditions on the indicated number of cells selected for quantification. d , f , l , n , Ribbon plots showing spatial gene expression patterns in relation to EC proximity for indicated genes between siRNA conditions. Solid line shows the mean intensity, and shaded regions show one standard deviation. d , f , Violin plots showing the distance to the nearest EC (in μm) for POSTN hi and COMP hi cells, defined as cells with the highest quantile of POSTN and COMP fluorescence intensity, respectively. P values for the comparisons between siCtrl and siDLL4 are P < 6 × 10 −51 and P < 2 × 10 −308 for TGFB3 ( j ) and TGFBR3 ( n ), respectively. The data in a and b are shown as means ± s.d., represent n = 3 biological replicates and are representative of at least two independent experiments. A two-tailed unpaired Student’s t -test was performed for a and b and two-tailed Wilcoxon tests for d , f , h , g , l and n . In the boxen plots, boxes show nested quantile ranges (median, 25–75%, 12.5–87.5%, 6.25–93.75%, and so on), the center line shows the median (50th percentile), the whiskers represent minimum and maximum values, and the outliers are shown as individual points outside the whiskers.

Article Snippet: After culture and treatment with siRNA for 5 days, cells were washed with PBS, fixed in 10% NBF and processed for staining and imaging according to the manufacturer’s protocol with the RNAScope multiplex fluorescent V2 assay (ACD Bio, SOP 45-009 A).

Techniques: Enzyme-linked Immunosorbent Assay, Co-Culture Assay, Comparison, Control, RNAscope, Gene Expression, Standard Deviation, Fluorescence, Two Tailed Test

Journal: Nature Communications

Article Title: Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors

doi: 10.1038/s41467-019-11266-x

Figure Lengend Snippet: TROP2 − foetal HHyPs are restricted to the ductal plate of foetal liver. a RNA- ISH for CDH6 and STAT1 on human second trimester (15–21 pcw) foetal liver ductal plate (DP) and bile duct (BD) regions. Scale bars represent 50 μm. b Immunofluorescence (IF) staining of CDH6 (yellow), CLDN3 (magenta) and STAT1 (grey) co-expression in human foetal liver slides. Slides counterstained in DAPI (cyan). DP and BD structures outlined in white. Scale bars represent 25 μm. c Immunohistochemistry (IHC) of EpCAM, CK19, CDH6 and STAT1 in BD and DP regions of human foetal liver. Scale bars represent 50 μm. d Duplex RNA-ISH for CDH6 (red)/ STAT1 (blue) and TROP-2 (red)/ STAT1 (blue) in foetal liver BD and DP structures. Scale bars represent 50 μm. Scale bars of zoomed in region represent 25 μm. e Phase contrast imaging and IF of foetal intra-hepatic organoids (f-IHOs) derived from EpCAM enriched foetal liver cells in liver expansion (LE) media. All structures are counterstained with DAPI (blue). All staining performed between passages 3 and 5. f Schematic and IF staining of f-IHOs cultured for 7 days in hepatic differentiation (HD media) and biliary differentiation (BD media). All staining performed between passages 3 and 5. Images representative of n = 3 foetal liver differentiation experiments

Article Snippet: After embedding, sections (5 μm) were processed for in situ RNA hybridisation RNA-ISH using the RNAscope 2.5 High Definition (Red, 322350 ACD Bio) according to the manufacturers instructions.

Techniques: Immunofluorescence, Staining, Expressing, Immunohistochemistry, Imaging, Derivative Assay, Cell Culture

Journal: Skeletal muscle

Article Title: Aminoguanidine hemisulfate improves mitochondrial autophagy, oxidative stress, and muscle force in Duchenne muscular dystrophy via the AKT/FOXO1 pathway in mdx mice.

doi: 10.1186/s13395-024-00371-1

Figure Lengend Snippet: Fig. 4 AGH improved glutathione metabolism and reduced apoptosis. TA muscles from WT, mdx, and AGH-treatment mdx mice were isolated at 8 weeks of age. The ratio of (A) oxidized glutathione (GSSG) to glutathione (GSH) (GSSG/GSH), (B) the concentration of total GSH, (C) GSSG, and (D) GSH were mea sured per assay kit instructions. The activities of (E) GSH reductase and (F) GSH peroxidase in TA muscle were measured per assay kit instructions. Gene expression of (G) Gpx2, Gpx3, Gpx4, and (J) caspase3 measured using real-time PCR. Values were normalized to 36B4 levels. (H–I) Representative images and quantification of TUNEL-positive nuclei on TA muscle (20× magnification, scale bar = 100 μm). Values are presented as the mean ± standard error of the mean for each experiment (n = 5). * p < 0.05 compared with WT control, # p < 0.05 compared with mdx

Article Snippet: For the apoptosis assay, sections were processed using a One Step TUNEL apoptosis assay kit (C1089, Beyotime) according to the manufacturer’s instructions.

Techniques: Muscles, Isolation, Concentration Assay, Gene Expression, Real-time Polymerase Chain Reaction, TUNEL Assay, Control

Journal: Skeletal muscle

Article Title: Aminoguanidine hemisulfate improves mitochondrial autophagy, oxidative stress, and muscle force in Duchenne muscular dystrophy via the AKT/FOXO1 pathway in mdx mice.

doi: 10.1186/s13395-024-00371-1

Figure Lengend Snippet: Fig. 8 Summary diagram of AGH treatment in mdx mice. AGH treatment reduced ROS and apoptosis by restoring mitochondrial autophagy, restored the composition of muscle fiber types, and improved muscle force through the AKT/FOXO1 signaling pathway

Article Snippet: For the apoptosis assay, sections were processed using a One Step TUNEL apoptosis assay kit (C1089, Beyotime) according to the manufacturer’s instructions.

Techniques:

Journal: PLoS ONE

Article Title: Maleic Acid – but Not Structurally Related Methylmalonic Acid – Interrupts Energy Metabolism by Impaired Calcium Homeostasis

doi: 10.1371/journal.pone.0128770

Figure Lengend Snippet: Increasing concentrations of MA led to more cell death and the activation of apoptosis pathways could be shown with annexin V–PI staining. Data are presented as percent of untreated control of n = 4 independent experiments.

Article Snippet: Human proximal tubule epithelial cells (hPTECs) were processed using an Annexin V apoptosis assay kit (BD Annexin V Apoptosis Detection Kit) according to the manufacturer’s protocol (BD Biosciences) and have been analyzed using flow cytometry.

Techniques: Activation Assay, Staining

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Article Title: Thermosensitive Hydrogel with Programmable, Self-Regulated HIF-1α Stabilizer Release for Myocardial Infarction Treatment.

doi: 10.1002/advs.202408013

Figure Lengend Snippet: Figure 1. The design, function and application of the injectable release-induced degradation thermosensitive hydrogel for HIF-1𝛼stabilization on my- ocardial infarction. Hydrogel formation is induced by hydrogen-bonding interactions between hydrophobic NIPAAm at 37 °C and 𝜋–𝜋interaction between DPCA. The pendant DPCAs on the polymer backbone enhanced gel formation by hydrophobic interaction. DPCA release can be initiated and controlled by the break of ester bonds. The released DPCA acts as an inhibitor of PHDs and maintains HIF-1𝛼stability to alleviate fibrosis and myocardial apoptosis, promote regeneration and angiogenesis.

Article Snippet: Besides similar preliminary processing, TUNEL staining (Colorimetric TUNEL Apoptosis Assay Kit, beyotime, C1091) and Masson’s trichrome staining (Masson’s Trichrome Staining Kit, beyotime, C0189S) were performed according to the instructions.

Techniques: Polymer