Journal: Investigative Ophthalmology & Visual Science

Article Title: Ly93 Inhibits Sphingomyelin Synthesis and Attenuates Inflammation and Injury in Dry Eye Conjunctival Organoids

doi: 10.1167/iovs.67.2.58

Figure Lengend Snippet: Establishment of human conjunctival organoids. ( A ) Schematic workflow for the generation of human conjunctival organoids from primary conjunctival tissue. ( B ) Representative images of organoids after 10 days of culture at passages 0, 1, and 2 ( scale bar , 200 µm). ( C ) PAS staining in the conjunctival organoids ( scale bar , 50 µm). ( D ) Immunofluorescence staining showing expression of K19, K13, p63, Ki67, ZO-1, MUC1, and MUC5AC in passage day 10 organoids ( scale bar , 50 µm).

Article Snippet: Immunofluorescence staining was performed to evaluate the expression of K19 (1:200, Cell Signaling Technology, Danvers, MA, USA), K13 (1:200, Cell Signaling Technology), IL-1β (1:200, Abcam, Cambridge, UK), STAT1 (1:200, Proteintech, Rosemont, IL, USA), p63 (1:250, Abcam), Ki67 (1:200, Abcam), NF-κB p65 (1:200, Abcam), MUC1 (1:200, Abcam), MUC5AC(1:250, Abcam), caspase-9 (1:200, Cell Signaling Technology), ZO-1 (1:200, Abcam), and 4-hydroxynonenal (4-HNE) (1:100, Invitrogen, Carlsbad, CA, USA) in frozen sections of the conjunctival organoids.

Techniques: Staining, Immunofluorescence, Expressing

Journal: Investigative Ophthalmology & Visual Science

Article Title: Ly93 Inhibits Sphingomyelin Synthesis and Attenuates Inflammation and Injury in Dry Eye Conjunctival Organoids

doi: 10.1167/iovs.67.2.58

Figure Lengend Snippet: Exogenous SM induced inflammation and injury of conjunctival organoids. ( A ) Effects of SM treatment on the viability of conjunctival cells and morphology of organoids ( scale bar , 100 µm for cells and 200 µm for organoids). ( B , C ) Western blotting analysis of inflammatory markers (phospho-STAT1, STAT1, IL-1β, and iNOS) in SM-treated organoids. ( D – F ) Relative mRNA expression of IL-1β, IL-6, and STAT1 after SM treatment. ( G ) Immunofluorescence staining of K13, K19, Ki67, MUC1, and MUC5AC in SM-treated organoids ( scale bar , 50 µm). ( H – L ) Comparative analysis of immunofluorescent results: K13 ( H ), K19 ( I ), Ki67 ( J ), MUC1 ( K ), and MUC5AC ( L ). * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant.

Article Snippet: Immunofluorescence staining was performed to evaluate the expression of K19 (1:200, Cell Signaling Technology, Danvers, MA, USA), K13 (1:200, Cell Signaling Technology), IL-1β (1:200, Abcam, Cambridge, UK), STAT1 (1:200, Proteintech, Rosemont, IL, USA), p63 (1:250, Abcam), Ki67 (1:200, Abcam), NF-κB p65 (1:200, Abcam), MUC1 (1:200, Abcam), MUC5AC(1:250, Abcam), caspase-9 (1:200, Cell Signaling Technology), ZO-1 (1:200, Abcam), and 4-hydroxynonenal (4-HNE) (1:100, Invitrogen, Carlsbad, CA, USA) in frozen sections of the conjunctival organoids.

Techniques: Western Blot, Expressing, Immunofluorescence, Staining

Journal: Nature Communications

Article Title: Actomyosin forces trigger a conformational change in desmoplakin within desmosomes

doi: 10.1038/s41467-025-64124-4

Figure Lengend Snippet: A Schematic of desmosome structure. Extracellular regions of desmoglein-2 (Dsg2) interact to mediate adhesion, while their cytoplasmic tails bind to the plaque protein, plakoglobin (PG), plakophilin (PKP), and desmoplakin (DP). B Representative confocal image of desmosome puncta along cell-cell borders in WT cells. The desmosomes were immunolabeled for DPC (green) and Dsg2 (red). Scale bar: 50 μm. Images were taken across three biological replicates. C Representative STED image of desmosomes showing a characteristic ‘railroad track’ pattern. Scale bar: 10 μm. Images were taken across three biological replicates. Representative close-up STED images of desmosomes exhibiting the signature ‘railroad track’ pattern in D MCF7 WT cells, E MCF7 K19-KO cells, and F MCF7 K19-GFP cells. Scale bar: 500 nm. G The boxed area from the representative STED images of WT cells shows a closer look at an individual DP railroad track with Dsg2 between the two parallel DP plaques. Scale bar: 200 nm. H Line-scan analysis of DPC and Dsg2 fluorescence intensity (indicated by the dashed line in G ). I Quantification of DPC-DPC distance from WT, K19-GFP, and K19-KO cells shows that desmosomes in WT and K19-GFP cells are wider than in K19-KO cells. Number of data points ( n ) = 630 (WT), 505 (K19-KO), 716 (K19-GFP); Number of replicates ( N ) = 3. Group differences were assessed with a two-sided Kruskal–Wallis test. Post-hoc pairwise comparisons used Dunn’s test with Holm adjustment for multiple comparisons; adjusted P = 1.03E-12 (WT vs. KO), P = 1.55E-09 (K19-Rescue vs. KO), P = 0.158 (WT vs. K19-Rescue); *** P < 0.001; ns, P > 0.05. Boxplots show median, 25th and 75th percentile with whiskers reaching the last data point within 1.5× interquartile range. Data points outside this range are plotted individually as outliers. The number of data points n represents the number of line scans across the desmosomes.

Article Snippet: MCF7 WT cells (ATCC), MCF7 K19-KO cells, and MCF7 K19-GFP rescued cells were maintained in low-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) (Life Technologies) and 1% penicillin-streptomycin (Sigma-Aldrich) in 5% CO 2 at 37 °C.

Techniques: Immunolabeling, Fluorescence

Journal: Nature Communications

Article Title: Actomyosin forces trigger a conformational change in desmoplakin within desmosomes

doi: 10.1038/s41467-025-64124-4

Figure Lengend Snippet: A Representative confocal overlay image of XY maximum intensity projection of DP (red) and F-actin (cyan) in MCF7 cells. Scale bar: 10 μm. Images were taken across three biological replicates. B Magnified view of the boxed area in ( A ) illustrates the selected ROI at a specific cell-cell junction. C XZ plane of cross-sectional view of the ROI demonstrates the distribution of DP (red) and F-actin (cyan) signals along the X - and Z- axes. D Fluorescence intensity profile of DP and F-actin reveals peak intensities and corresponding Z positions at the junction. E Scatter plot of actin peak intensities along the Z -axis in WT and K19-KO cells shows generally higher actin peak intensities in WT compared to K19-KO cells. F Quantification of actin peak intensities along the Z -axis from WT and K19-KO cells. n = 197 (WT), 331 (K19-KO); N = 3. Two-sided Mann–Whitney’s U test; P = 4.287E-44, *** P < 0.001. Actin peak intensities along the junction are significantly higher in the WT compared to the K19-KO cells. G A scatter plot of DP peak intensities along the Z -axis in WT and K19-KO cells shows overlapping distributions between WT and K19-KO cells. H Quantification of DP peak intensities along the Z -axis from WT and K19-KO cells. n = 197 (WT), 331 (K19-KO); N = 3. Two-sided Mann–Whitney’s U test; P = 1.32E–4, *** P < 0.001. The DP peak intensities along the junction are slightly greater in the K19-KO compared to the WT cells. I A scatter plot of actin/DP peak intensity ratios along the Z -axis from WT and K19-KO cells shows a clear separation between the WT and K19-KO cells. J Quantification of actin/DP peak intensity ratios along the Z -axis from WT and K19-KO cells. n = 197 (WT), 331 (K19-KO); N = 3. Two-sided Mann–Whitney’s U test; P = 8.435E–64, *** P < 0.001. The actin/DP peak intensity ratio along the junction is significantly greater in the WT compared to the K19-KO cells. All boxplots show median, 25th and 75th percentile with whiskers reaching the last data point within 1.5× interquartile range. Data points outside this range are plotted individually as outliers. The number of data points n represents the number of peak intensities for the corresponding Z -axes.

Article Snippet: MCF7 WT cells (ATCC), MCF7 K19-KO cells, and MCF7 K19-GFP rescued cells were maintained in low-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) (Life Technologies) and 1% penicillin-streptomycin (Sigma-Aldrich) in 5% CO 2 at 37 °C.

Techniques: Fluorescence

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A ) Venn diagram shows a comparison of matrisome proteins differentially enriched in Total CCl 4 and DDC proteomes. Color coding indicates identified matrisome categories. ( B–D ) Representative IF images of collagen type I (B), fibronectin (C), and collagen type IV (D), all in green in liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at time points of fibrosis development (T2) and resolution (T4). Bile ducts were visualized with antibodies to keratin 19 (K19; red); nuclei were stained with DAPI (blue). CV, central vein; PV, portal vein. Scale bar = 100 μm. Line plots show time-dependent change in respective mass spectrometry (MS) intensities in Total (solid line) and E-fraction (broken line) proteomes in CCl 4 and DDC models; n=4–6.

Article Snippet: The following primary antibodies were used: rat mAb to K19 (Troma III; Developmental Studies Hybridoma Bank, University of Iowa, Iowa City, IA, USA); mouse mAbs to αSMA (DAKO, Glostrup, Denmark) and ECM1 (Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal antibodies to clusterin (R&D Systems, Minneapolis, MN, USA), rabbit polyclonal antibodies to fibronectin, collagen type I, collagen type IV, and monoclonal to integrin αV (all from Abcam, Cambridge, UK).

Techniques: Comparison, Staining, Mass Spectrometry

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A–D ) Box plots show mean z -scored mass spectrometry (MS) intensities of the indicated cell-type-specific protein signatures in time. Hepatocytes (A; n=18), hepatic stellate cells (HSCs), and activated portal fibroblasts (PFs) (B; n=3 and 4), Kupffer cells (C; n=6), granulocytes, and macrophages (D; n=16 and 33). One-way ANOVA with Bonferroni’s post-test; *p<0.05; **p<0.01; † p<0.001. ( E ) The line plots show the time-dependent change in MS intensities of indicated selected integrins in Total (solid line) and E-fraction (broken line) proteomes in carbon tetrachloride (CCl 4 ) and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) models; n=4–6. ( F ) Representative immunofluorescence images of liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at time points of fibrosis development (T2) and resolution (T3) immunolabeled for integrin αv (green), K19 (red), and αSMA (blue). Arrowheads, integrin αv-positive injured hepatocytes; arrows, integrin αv-positive biliary epithelial cells of reactive ductuli. CV, central vein; PV, portal vein. Boxed areas, ×2 images. Scale bar = 50 μm.

Article Snippet: The following primary antibodies were used: rat mAb to K19 (Troma III; Developmental Studies Hybridoma Bank, University of Iowa, Iowa City, IA, USA); mouse mAbs to αSMA (DAKO, Glostrup, Denmark) and ECM1 (Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal antibodies to clusterin (R&D Systems, Minneapolis, MN, USA), rabbit polyclonal antibodies to fibronectin, collagen type I, collagen type IV, and monoclonal to integrin αV (all from Abcam, Cambridge, UK).

Techniques: Mass Spectrometry, Immunofluorescence, Immunolabeling

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A, B ) Representative immunofluorescence (IF) images of liver sections from untreated controls (Ctrl), carbon tetrachloride (CCl 4 )-, and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-treated mice at time points of fibrosis development (T1, T2) and resolution (T3, T4) immunolabeled for indicated cell-type-specific markers. (A) HNF4α (yellow; detecting changes in hepatocyte abundance), αSMA (cyan; detecting activated hepatic stellate cells [HSCs] and portal fibroblasts), and K19 (magenta; detecting cholangiocytes). (B) B-cell marker (B220, yellow) and macrophage/monocyte/Kupffer cell marker (F4/80; magenta) together with αSMA (cyan) antibody show the role of the inflammation component in the context of fibrosis development and resolution in both models. Arrowheads, B cells recruited to the sites of injury. CV, central vein; PV, portal vein. Scale bar = 50 μm.

Article Snippet: The following primary antibodies were used: rat mAb to K19 (Troma III; Developmental Studies Hybridoma Bank, University of Iowa, Iowa City, IA, USA); mouse mAbs to αSMA (DAKO, Glostrup, Denmark) and ECM1 (Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal antibodies to clusterin (R&D Systems, Minneapolis, MN, USA), rabbit polyclonal antibodies to fibronectin, collagen type I, collagen type IV, and monoclonal to integrin αV (all from Abcam, Cambridge, UK).

Techniques: Immunofluorescence, Immunolabeling, Marker

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A ) Schematic illustrates the correlation of protein abundance changes with changes in sirius red-positive (SR + ) areas of fibrous extracellular matrix (ECM) deposits in carbon tetrachloride (CCl 4 )-treated animals at the indicated time points. ( B ) The regulator of the actin cytoskeleton, coronin 1a (CORO1A), serves as an example of a protein with a positive slope of the correlation fit. The methionine cycle enzyme, adenosylhomocysteinase (AHCY), serves as an example of a protein with a negative slope of the correlation fit. ( C, D ) The scatter plots show the linear regression slope and the Pearson correlation coefficient for proteins of CCl 4 Total (C), and E-fraction (D) proteomes. Statistical significance of the correlation is color-coded as indicated. The line plots show time-dependent change in mass spectrometry (MS) intensities of indicated representative proteins with significant correlation in Total (solid line) and E-fraction (broken line) proteomes in CCl 4 and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) models; n=4–6. ( E ) Representative immunofluorescence (IF) images of liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at indicated time points of fibrosis development (T2) and resolution (T3 and T4) immunolabeled for clusterin (Clu, green), keratin 19 (K19, red), and collagen type I (Col1, blue). Arrowheads, clusterin staining signal delineating collagen deposits; arrows, clusterin-positive injured hepatocytes; yellow arrows, clusterin-positive biliary epithelial cells. CV, central vein; PV, portal vein. Boxed areas, ×2 images. Scale bar = 50 μm. ( F ) Representative IF images of human liver sections from different stages of chronic liver diseases of various etiologies (biliary-type, steatotic liver disease, and chronic hepatitis C [HCV] infection) immunolabeled for clusterin (Clu, green) and collagen type I (Col1, magenta). Nuclei were stained with DAPI (blue). Top row shows increase in clusterin expression along collagen fibrils in biliary-type and metabolic syndrome-related cirrhosis compared to the stage of mild fibrosis. Bottom row documents change in clusterin staining pattern with chronic HCV progression from fibrosis stage F1 to stage F4 (METAVIR grading system: F1, portal fibrosis; F2, periportal fibrosis; F3, bridging septal fibrosis; F4, cirrhosis). Arrowheads, clusterin staining delineating collagen deposits; arrows, clusterin-positive capillarized sinusoids; yellow arrows, clusterin-positive bile canaliculi (stage F1 only). PV, portal vein. Boxed areas, ×4 images. Scale bar = 50 μm.

Article Snippet: The following primary antibodies were used: rat mAb to K19 (Troma III; Developmental Studies Hybridoma Bank, University of Iowa, Iowa City, IA, USA); mouse mAbs to αSMA (DAKO, Glostrup, Denmark) and ECM1 (Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal antibodies to clusterin (R&D Systems, Minneapolis, MN, USA), rabbit polyclonal antibodies to fibronectin, collagen type I, collagen type IV, and monoclonal to integrin αV (all from Abcam, Cambridge, UK).

Techniques: Quantitative Proteomics, Mass Spectrometry, Immunofluorescence, Immunolabeling, Staining, Infection, Expressing

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet:

Article Snippet: The following primary antibodies were used: rat mAb to K19 (Troma III; Developmental Studies Hybridoma Bank, University of Iowa, Iowa City, IA, USA); mouse mAbs to αSMA (DAKO, Glostrup, Denmark) and ECM1 (Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal antibodies to clusterin (R&D Systems, Minneapolis, MN, USA), rabbit polyclonal antibodies to fibronectin, collagen type I, collagen type IV, and monoclonal to integrin αV (all from Abcam, Cambridge, UK).

Techniques: Software, Staining

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A ) Venn diagram shows a comparison of matrisome proteins differentially enriched in Total CCl 4 and DDC proteomes. Color coding indicates identified matrisome categories. ( B–D ) Representative IF images of collagen type I (B), fibronectin (C), and collagen type IV (D), all in green in liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at time points of fibrosis development (T2) and resolution (T4). Bile ducts were visualized with antibodies to keratin 19 (K19; red); nuclei were stained with DAPI (blue). CV, central vein; PV, portal vein. Scale bar = 100 μm. Line plots show time-dependent change in respective mass spectrometry (MS) intensities in Total (solid line) and E-fraction (broken line) proteomes in CCl 4 and DDC models; n=4–6.

Article Snippet: Antibody , Anti- K19 (TROMA III; Rat monoclonal) , DSHB , TROMA III RRID: AB_2133570 , IHCP (1:250).

Techniques: Comparison, Staining, Mass Spectrometry

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A–D ) Box plots show mean z -scored mass spectrometry (MS) intensities of the indicated cell-type-specific protein signatures in time. Hepatocytes (A; n=18), hepatic stellate cells (HSCs), and activated portal fibroblasts (PFs) (B; n=3 and 4), Kupffer cells (C; n=6), granulocytes, and macrophages (D; n=16 and 33). One-way ANOVA with Bonferroni’s post-test; *p<0.05; **p<0.01; † p<0.001. ( E ) The line plots show the time-dependent change in MS intensities of indicated selected integrins in Total (solid line) and E-fraction (broken line) proteomes in carbon tetrachloride (CCl 4 ) and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) models; n=4–6. ( F ) Representative immunofluorescence images of liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at time points of fibrosis development (T2) and resolution (T3) immunolabeled for integrin αv (green), K19 (red), and αSMA (blue). Arrowheads, integrin αv-positive injured hepatocytes; arrows, integrin αv-positive biliary epithelial cells of reactive ductuli. CV, central vein; PV, portal vein. Boxed areas, ×2 images. Scale bar = 50 μm.

Article Snippet: Antibody , Anti- K19 (TROMA III; Rat monoclonal) , DSHB , TROMA III RRID: AB_2133570 , IHCP (1:250).

Techniques: Mass Spectrometry, Immunofluorescence, Immunolabeling

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A, B ) Representative immunofluorescence (IF) images of liver sections from untreated controls (Ctrl), carbon tetrachloride (CCl 4 )-, and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-treated mice at time points of fibrosis development (T1, T2) and resolution (T3, T4) immunolabeled for indicated cell-type-specific markers. (A) HNF4α (yellow; detecting changes in hepatocyte abundance), αSMA (cyan; detecting activated hepatic stellate cells [HSCs] and portal fibroblasts), and K19 (magenta; detecting cholangiocytes). (B) B-cell marker (B220, yellow) and macrophage/monocyte/Kupffer cell marker (F4/80; magenta) together with αSMA (cyan) antibody show the role of the inflammation component in the context of fibrosis development and resolution in both models. Arrowheads, B cells recruited to the sites of injury. CV, central vein; PV, portal vein. Scale bar = 50 μm.

Article Snippet: Antibody , Anti- K19 (TROMA III; Rat monoclonal) , DSHB , TROMA III RRID: AB_2133570 , IHCP (1:250).

Techniques: Immunofluorescence, Immunolabeling, Marker

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet: ( A ) Schematic illustrates the correlation of protein abundance changes with changes in sirius red-positive (SR + ) areas of fibrous extracellular matrix (ECM) deposits in carbon tetrachloride (CCl 4 )-treated animals at the indicated time points. ( B ) The regulator of the actin cytoskeleton, coronin 1a (CORO1A), serves as an example of a protein with a positive slope of the correlation fit. The methionine cycle enzyme, adenosylhomocysteinase (AHCY), serves as an example of a protein with a negative slope of the correlation fit. ( C, D ) The scatter plots show the linear regression slope and the Pearson correlation coefficient for proteins of CCl 4 Total (C), and E-fraction (D) proteomes. Statistical significance of the correlation is color-coded as indicated. The line plots show time-dependent change in mass spectrometry (MS) intensities of indicated representative proteins with significant correlation in Total (solid line) and E-fraction (broken line) proteomes in CCl 4 and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) models; n=4–6. ( E ) Representative immunofluorescence (IF) images of liver sections from untreated controls (Ctrl), CCl 4 -, and DDC-treated mice at indicated time points of fibrosis development (T2) and resolution (T3 and T4) immunolabeled for clusterin (Clu, green), keratin 19 (K19, red), and collagen type I (Col1, blue). Arrowheads, clusterin staining signal delineating collagen deposits; arrows, clusterin-positive injured hepatocytes; yellow arrows, clusterin-positive biliary epithelial cells. CV, central vein; PV, portal vein. Boxed areas, ×2 images. Scale bar = 50 μm. ( F ) Representative IF images of human liver sections from different stages of chronic liver diseases of various etiologies (biliary-type, steatotic liver disease, and chronic hepatitis C [HCV] infection) immunolabeled for clusterin (Clu, green) and collagen type I (Col1, magenta). Nuclei were stained with DAPI (blue). Top row shows increase in clusterin expression along collagen fibrils in biliary-type and metabolic syndrome-related cirrhosis compared to the stage of mild fibrosis. Bottom row documents change in clusterin staining pattern with chronic HCV progression from fibrosis stage F1 to stage F4 (METAVIR grading system: F1, portal fibrosis; F2, periportal fibrosis; F3, bridging septal fibrosis; F4, cirrhosis). Arrowheads, clusterin staining delineating collagen deposits; arrows, clusterin-positive capillarized sinusoids; yellow arrows, clusterin-positive bile canaliculi (stage F1 only). PV, portal vein. Boxed areas, ×4 images. Scale bar = 50 μm.

Article Snippet: Antibody , Anti- K19 (TROMA III; Rat monoclonal) , DSHB , TROMA III RRID: AB_2133570 , IHCP (1:250).

Techniques: Quantitative Proteomics, Mass Spectrometry, Immunofluorescence, Immunolabeling, Staining, Infection, Expressing

Journal: eLife

Article Title: Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

doi: 10.7554/eLife.98023

Figure Lengend Snippet:

Article Snippet: Antibody , Anti- K19 (TROMA III; Rat monoclonal) , DSHB , TROMA III RRID: AB_2133570 , IHCP (1:250).

Techniques: Software, Staining

Journal: Disease Models & Mechanisms

Article Title: A new effLuc/Kate dual reporter allele for tumor imaging in mice

doi: 10.1242/dmm.052130

Figure Lengend Snippet: Assessment of the LSL-effLuc-Kate dual reporter in a genetically engineered mouse model of pancreas cancer. (A) Representative images of bioluminescence detection in male Kras LSL-G12D ; Trp53 LSL-R172H ; p48-Cre + mice carrying the Col1a1 LSL-effLuc-Kate dual reporter. Images were taken at age 5, 9 and 13 weeks (late PDAC stage) as indicated. For each time point, the same two mice are shown. (B) Immunofluorescence images of primary pancreatic tumors (top) and liver sections with micrometastases (bottom) stained for luciferase (Luc, green) and keratin 19 (K19, red). Images were taken using a representative Kras LSL-G12D ; Trp53 LSL-R172H ; Col1a1 LSL-effLuc-Kate ; p48-Cre + PDAC female mouse aged 15 weeks. Nuclei are counterstained with DAPI (blue). Scale bars: 100 µm. (C,D) Flow cytometric quantification of CD45-negative, mKate-positive cells in pancreas (C) and liver (D) of Kras LSL-G12D ; Trp53 LSL-R172H ; Col1a1 LSL-effLuc-Kate ; p48-Cre + mice at end stage (mutant: 13-15 weeks, male and female, n =8). Sex- and age-matched values from wild-type mice are shown for comparison (control, n =3). (E) Quantitative qRT-PCR analysis of Krt19 mRNA expression in mKate-positive cells FACS-sorted from the pancreas, liver or blood of Kras LSL-G12D ; Trp53 LSL-R172H ; Col1a1 LSL-effLuc-Kate ; p48-Cre + mice at end stage (13-15 weeks), compared to bulk (pre-sorting) single cell suspensions of pancreas and liver. Data in C−E are shown as box-and-whisker plots around the median, * P <0.05, ** P <0.01 (two-tailed unpaired Mann–Whitney test).

Article Snippet: For immunofluorescence, 10-mm-thick methanol-fixed sections were stained with antibodies against luciferase (Novus Biologicals cat. no.: NB100-1677, dilution 1:200) or keratin 19 (K19) (Troma III, Developmental Studies Hybridoma Bank, University of Iowa, cat. no.: AB 2133570; dilution: 1:1000), and counterstained with suitable fluorescence labeled secondary antibodies or DAPI (Roche, cat. no.: 10236276001).

Techniques: Immunofluorescence, Staining, Luciferase, Mutagenesis, Comparison, Control, Quantitative RT-PCR, Expressing, Whisker Assay, Two Tailed Test, MANN-WHITNEY