Journal: The American Journal of Pathology

Article Title: Critical Role of the CXCL10/C-X-C Chemokine Receptor 3 Axis in Promoting Leukocyte Recruitment and Neuronal Injury during Traumatic Optic Neuropathy Induced by Optic Nerve Crush

doi: 10.1016/j.ajpath.2016.10.009

Figure Lengend Snippet: CXCL10/CXCR3 pathway is activated in TON. Wild-type mice were subjected to traumatic optic neuropathy (TON). A: Quantitative PCR analysis of CXCL10 mRNA expression in noninjured retinas [control (Con)] or injured retinas at 3, 6, 12, and 24 hours after TON. B: Normal and TON-performed eyes were collected at 6 hours after TON. CXCL10 mRNA localization was assessed in retinal frozen sections by fluorescence in situ hybridization with RNAscope Fluorescent Multiplex Kit. Green fluorescent signal reflects CXCL10 mRNA expression, and DAPI (blue) stains nuclei. Arrows indicate CXCL10-expressing retinal cells in the ganglion cell layer (GCL). C: Enzyme-linked immunosorbent assay analysis of CXCL10 protein in control or TON-performed retinas at 6 hours after TON. D: Quantitative PCR analysis of CXCR3 mRNA expression in control or injured retinas at 3, 6, 12, and 24 hours after TON. E: Representative images of CXCR3 immunostaining in retinal frozen sections from control and TON-performed eyes at 24 hours after TON. Fluorescent signal (red) reflects CXCR3 staining. n = 4 to 5 mice (E). ∗P < 0.05, ∗∗P < 0.01 versus control. Scale bars = 50 μm (B and E). INL, inner nuclear layer; ONL, outer nuclear layer.

Article Snippet: Fluorescence in Situ Hybridization Retinal frozen sections were fixed in 4% paraformaldehyde, incubated with mouse CXCL10 probe (Advanced Cell Diagnostics, Hayward, CA), and sequentially hybridized to a cascade of signal amplification reagents from RNAscope Fluorescent Multiplex detection kit (Advanced Cell Diagnostics), according to the manufacturer's instructions.

Techniques: Real-time Polymerase Chain Reaction, Expressing, Control, Fluorescence, In Situ Hybridization, RNAscope, Multiplex Assay, Enzyme-linked Immunosorbent Assay, Immunostaining, Staining

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Computationally identified mesenchymal clusters represent spatially distinct populations (A) Violin plots showing the expression of Hoxb6 or Ptn in each cluster. (B) Fluorescence in situ hybridization for Hoxb6 and Ptn in E 11.5 lungs. Scale bar shows 25 μm. (C) Violin plots showing the expression of Lef1 or Foxp1 in each cluster. (D) E 11.5 lungs immunostained for cluster 0 marker Lef1 or for cluster 1 marker Foxp1 and counterstained with Hoechst. Scale bars show 25 μm. (E) Quantifications of Lef1 and Foxp1 intensity profiles emanating from the epithelium (for Lef1) or from the mesothelium (for Foxp1). Schematics show lines and direction along which intensity profiles were measured. Mean and SD are plotted (n = 4). (F) Schematic depicting the sub-epithelial and sub-mesothelial compartments of the mesenchyme. (G) Heatmap showing the expression of genes specific to either mesenchymal compartment. Genes (rows) are clustered based on the dendrogram to the right. Cells (columns) are clustered based on the dendrogram above, and each column is color-coded according to the original cluster identity from Figure 1 B. (H) UMAP of mesenchymal and smooth muscle cells color-coded according to the sum of their expression of either sub-epithelial or sub-mesothelial mesenchyme marker genes. Dotted line indicates the location of smooth muscle cells

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing, Fluorescence, In Situ Hybridization, Marker

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Wnt signaling regulates cell identity in the embryonic pulmonary mesenchyme. (A) Bubble plot showing the enrichment percentage and adjusted p value of relevant GO terms identified based on genes upregulated in each mesenchymal cluster. (B) Heatmap showing the expression of Wnt-associated genes upregulated in either mesenchymal cluster. Activators and targets are colored in blue, inhibitors are colored in red. (C) Heatmap showing the expression of Wnt ligands, secreted inhibitors, and receptors detected in either mesenchymal cluster and in clusters containing cells from the mesothelium (meso), vascular endothelium (ve), epithelium (ep), and smooth muscle (sm). (D–G) Confocal sections and quantification of Lef1 and Foxp1 intensity profiles around branch L.L2 in lungs isolated at E 11.5 from CD1 embryos and immunostained for Lef1 or Foxp1 after treatment with either DMSO, LiCl (10 mM), or IWR1 (100 μM) for 24 h (n = 2–6). Yellow dashed lines indicate the border of the epithelium. Schematics show lines and direction along which intensity profiles were measured. Mean and SEM are plotted, and curves were compared using two-way ANOVA. (H–M) E 12.5 control and Tbx4-rtTA ; tet-O-Cre ; Ctnnb1 fl/fl lungs immunostained for Lef1 or Foxp1 and quantification of Lef1 and Foxp1 intensity profiles (n = 3). Low-magnification z-projections (H and I) and high-magnification confocal slices (J and K) are shown. Scale bars show 50 μm. ∗ indicates p<0.05, ∗∗ indicates p<0.001, and ∗∗∗ indicates p<0.0001

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing, Isolation, Control

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Regulators and features of smooth muscle differentiation (A) Sections of E 12.5 Dermo1-Cre/+; Yap fl/fl ; mTmG/+ lungs and littermate controls immunostained for GFP and either Yap1, Lef1, Foxp1, or αSMA. Insets show zoomed-in view of the mesenchyme to highlight the decrease in mesenchymal Yap1 levels in mutants. Yap1 + cells in the mesenchyme of mutants are vascular endothelial cells (ve, indicated by white arrowheads), which are not targeted by Dermo1-Cre . ep is epithelium. Scale bars show 50 μm. (B) Scaled expression of genes involved in cytoskeleton, cell adhesion, and extracellular matrix versus cell loadings along DC1 compared to the expression profiles of the smooth muscle markers Acta2 and Myocd (dotted lines). Pearson correlation coefficients and significance are indicated and lines represent smoothed data with SE shaded in gray. (C) Simplified pathway diagram depicting the steps of proliferative metabolism and showing relevant enzymes at each step. Enzymes that are significantly downregulated along DC1 are indicated in bold red font, with a significance of spline fit indicated by asterisks. ∗ indicates p < 0.05, ∗∗ indicates p < 0.001, and ∗∗∗ indicates p < 0.0001

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet:

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Recombinant, RNAscope, Multiplex Assay, Mutagenesis, Software, Sequencing

Journal: Cell

Article Title: Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation

doi: 10.1016/j.cell.2018.10.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: p-S6 ribosomal protein antibody , Cell Signaling , Cat# 2215S; RRID: AB_331682.

Techniques: Virus, Plasmid Preparation, Recombinant, Western Blot, Electron Microscopy, Clinical Proteomics, Modification, Enzyme-linked Immunosorbent Assay, Reverse Transcription, BIA-KA, RNAscope, Multiplex Assay, Fluorescence, Sample Prep, Software

Journal: Cell

Article Title: Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation

doi: 10.1016/j.cell.2018.10.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: p-p70 S6 kinase antibody , Cell Signaling , Cat# 9234; RRID: AB_2269803.

Techniques: Virus, Plasmid Preparation, Recombinant, Western Blot, Electron Microscopy, Clinical Proteomics, Modification, Enzyme-linked Immunosorbent Assay, Reverse Transcription, BIA-KA, RNAscope, Multiplex Assay, Fluorescence, Sample Prep, Software