Journal: The Journal of Cell Biology

Article Title: Mesenchymal–epithelial interactions in the skin

doi: 10.1083/jcb.200311122

Figure Lengend Snippet: Differential expression of leupaxin, DKK1, and DKK3 by palmoplantar (PP) and by nonpalmoplantar (NP) fibroblasts. Representative differences in gene expression patterns of leupaxin, DKK1, and DKK3 between palmoplantar fibroblasts and nonpalmoplantar fibroblasts as measured by microarray (top; quantitative results are summarized in and ). (middle) RT-PCR confirms the expression patterns of leupaxin, DKK1, and DKK3 in palmoplantar and in nonpalmoplantar fibroblasts. These data are representative of five independent experiments. (bottom) Real-time PCR to quantitate the expression of leupaxin, DKK1, and DKK3 after normalization of the target gene to GAPDH. Data are reported as means ± SD.

Article Snippet: Scanning of the two fluorescent intensities of the cDNA chip was performed by a standard two-color microarray scanner (model GenePix 4000A DNA; Axon Instruments, Inc.).

Techniques: Quantitative Proteomics, Gene Expression, Microarray, Reverse Transcription Polymerase Chain Reaction, Expressing, Real-time Polymerase Chain Reaction

Journal: BMC Molecular and Cell Biology

Article Title: Role of tumor cell senescence in non-professional phagocytosis and cell-in-cell structure formation

doi: 10.1186/s12860-020-00326-6

Figure Lengend Snippet: a Immunofluorescence staining of the senescence markers HMGA2 and H3K9me3 in red without and after 6 days treatment with camptothecin (CPT) 120 nM and 200 nM for senescence induction in pancreas carcinoma cells BxPC-3. The cell nuclei were stained with DAPI (blue). Scale bar 10 μm. b Cell nucleus length and width of BxPC-3 cells after 6 days CPT treatment. c C 12 FDG β-galactosidase activity in untreated and 120 nM treated BxPC-3 cells on day 6. d Activity of the acidic β-galactosidase in pancreas carcinoma cells after CPT treatment on days 5, 6 and 7 using flow cytometry. The graphs represent the mean values from three independent experiments ± standard deviation, p -values: * < 0.05, ** < 0.01, *** < 0.001. e C 12 FDG β-galactosidase activity in 120 nM treated BxPC-3, SBLF-7 and SBLF-4 cells on day 6. f Flow cytometric determination of the amount of Annexin V−/7AAD- (living cells) compared to all others (dead cells) 7 days after 120 nM camptothecin treatment. p-values were determined from a two-tailed unpaired Mann Whitney U test: ** < 0.01, *** < 0.001

Article Snippet: Senescent cells were detected by anti-H3K9me3 antibodies and a fast-blue color reaction (Sigma-Aldrich, Deisenhofen, Germany).

Techniques: Immunofluorescence, Staining, Activity Assay, Flow Cytometry, Standard Deviation, Two Tailed Test, MANN-WHITNEY

Journal: BMC Molecular and Cell Biology

Article Title: Role of tumor cell senescence in non-professional phagocytosis and cell-in-cell structure formation

doi: 10.1186/s12860-020-00326-6

Figure Lengend Snippet: Representative microscopic images of typical cell-in-cell structures in phagocytosis experiments with ( a , d ) pancreas carcinoma cell line (BxPC-3) and fibroblast cell lines ( b , e ) (SBLF-7) and ( c , f ) (SBLF-4). Viable CTOG-stained (green) cell, which completely encloses a hyperthermia-damaged, CTFR-stained (red) cell ( a - c ). Senescent H3K9me3-stained (red) cells that completely enclose a hyperthermia-damaged CTOG-stained (green) cell ( d - f ). Cell nuclei were stained with DAPI (blue). Scale bars 10 μm (40x objective). In bar charts ( g ), ( h ) and ( j ) the cell-in-cell rates occurring in the respective cell lines on the left were shown for different combinations of senescent, living and heat-treated dead cells as indicated

Article Snippet: Senescent cells were detected by anti-H3K9me3 antibodies and a fast-blue color reaction (Sigma-Aldrich, Deisenhofen, Germany).

Techniques: Staining

Journal: BMC Molecular and Cell Biology

Article Title: Role of tumor cell senescence in non-professional phagocytosis and cell-in-cell structure formation

doi: 10.1186/s12860-020-00326-6

Figure Lengend Snippet: Kaplan Meier plots for overall survival, metastasis free survival and local recurrence-free survival for the cohort of patients ( a ) of which tissue micro arrays from pretherapeutic biopsies and ( b ) of post-RCT tumor resection were available. c Example of a micro array spot of rectal carcinoma tissue with a diameter of 2 mm that was immunohistochemically double stained by nuclear anti-H3K9me3 (blue, senescent) and anti-E-Cadherin (red membranous). Arrows indicating cell-in-cell events. d Individual cell-in-cell events. e Frequency of counted intraepithelial senescent cells/mm 2 of patients in pre-RCT biopsy and post-RCT central tumor, invasive tumor front and normal tissue. f Frequency of counted intraepithelial cell-in-cell phenomena/mm 2 in patients in pre-RCT biopsy and post-RCT central tumor, invasive tumor front and normal tissue area. Differences between groups were analyzed by unpaired Student’s t-test

Article Snippet: Senescent cells were detected by anti-H3K9me3 antibodies and a fast-blue color reaction (Sigma-Aldrich, Deisenhofen, Germany).

Techniques: Microarray, Staining

Journal: BMC Molecular and Cell Biology

Article Title: Role of tumor cell senescence in non-professional phagocytosis and cell-in-cell structure formation

doi: 10.1186/s12860-020-00326-6

Figure Lengend Snippet: a Part of a TMA immunohistochemical double stained for senescence by nuclear anti-H3K9me3 (blue) and membranous anti-E-Cadherin (red) in rectal cancer. Arrows indicating cell-in-cell events. Zoomed images of the tissue micro array, b a cell-in-cell event in which both involved cells are senescent, c a cell-in-cell event in which both involved cells are not senescent, d engulfed cell is senescent (asterisk marks the cell in the tissue micro array) and ( e ) a cell-in-cell event in which only the engulfing cell is senescent. f Distribution of senescence in the engulfing and in the engulfed cell in all observed cell-in-cell events. Differences were analyzed by the Student’s t-test

Article Snippet: Senescent cells were detected by anti-H3K9me3 antibodies and a fast-blue color reaction (Sigma-Aldrich, Deisenhofen, Germany).

Techniques: Immunohistochemical staining, Staining, Microarray

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Discovery of RNA Binding Small Molecules Using Small Molecule Microarrays

doi: 10.1007/978-1-4939-6584-7_11

Figure Lengend Snippet: Overview of SMM strategy to identify RNA-binding small molecules. Small molecule libraries prepared in 384-well plates are utilized to print onto isocyanate-functionalized slides by the microarrayer. Prepared SMMs are next incubated with the labeled RNA of interest and scanned to detect hits

Article Snippet: Printing of Small Molecule Microarrays MicroGrid II Microarrayer (BioRobotics) or equivalent.

Techniques: RNA Binding Assay, Incubation, Labeling