Journal: PLoS ONE

Article Title: Time resolved 3D live-cell imaging on implants

doi: 10.1371/journal.pone.0205411

Figure Lengend Snippet: CYTO-ID Red labeled human gingival fibroblasts were treated with or without chlorhexidine. CYTO-ID Red labeled gingival fibroblasts, fixed with 4% w/v PFA in PBS and subsequently stained with DRAQ7 served as a positive control for the LIVE/DEAD staining: (A) CYTO-ID Red, (B) DRAQ7, and (C) their overlay. Labeled gingival fibroblasts without addition of chlorhexidine served as a negative control after DRAQ7 staining: (D) CYTO-ID Red, (E) DRAQ7, and (F) their overlay. CYTO-ID Red labeled gingival fibroblasts were treated with 132 mM chlorhexidine for 2 hours prior DRAQ7 staining: (G) CYTO-ID Red, (H) DRAQ7, and (I) their overlay. Arrows show live cells without DRAQ7 nucleus staining. The samples were examined under the CLSM (Leica TCS SP2). Scale bars: 100 μm.

Article Snippet: The non-toxic DRAQ7 DNA dye was able to pass cell membrane of compromised cells, since they were fixed with 4% w/v PFA in PBS (335.2, Carl Roth GmbH, Germany) to generate a positive control of cell damage Consequently, the fibroblasts had damaged cell membranes and emitted both dyes, the CYTO-ID Red was located at the cell membranes and the DRAQ7 at the nuclei ( ).

Techniques: Labeling, Staining, Positive Control, Negative Control

Journal: PLoS ONE

Article Title: Time resolved 3D live-cell imaging on implants

doi: 10.1371/journal.pone.0205411

Figure Lengend Snippet: CYTO-ID Red labeled human gingival fibroblasts were treated with different concentrations of chlorhexidine for 8 hours prior DRAQ7 staining. LIVE/DEAD stained gingival fibroblasts after treatment with 18 μM chlorhexidine: (A) CYTO-ID Red, (B) DRAQ7, and (C) their overlay. LIVE/DEAD stained gingival fibroblasts after treatment with 36 μM chlorhexidine: (D) CYTO-ID Red, (E) DRAQ7, and (F) their overlay. LIVE/DEAD stained gingival fibroblasts after treatment with 72 μM chlorhexidine: (G) CYTO-ID Red, (H) DRAQ7, and (I) their overlay. LIVE/DEAD stained gingival fibroblasts after treatment with 181 μM chlorhexidine: (J) CYTO-ID Red, (K) DRAQ7, and (L) their overlay. The samples were examined under the CLSM (Leica TCS SP2). Scale bars: 200 μm.

Article Snippet: The non-toxic DRAQ7 DNA dye was able to pass cell membrane of compromised cells, since they were fixed with 4% w/v PFA in PBS (335.2, Carl Roth GmbH, Germany) to generate a positive control of cell damage Consequently, the fibroblasts had damaged cell membranes and emitted both dyes, the CYTO-ID Red was located at the cell membranes and the DRAQ7 at the nuclei ( ).

Techniques: Labeling, Staining

Journal: PLoS ONE

Article Title: Time resolved 3D live-cell imaging on implants

doi: 10.1371/journal.pone.0205411

Figure Lengend Snippet: (A) MIP of the live cell stain with CYTO-ID Red (green) and dead cell stain with DRAQ7 (red) at the different time points. Rectangles indicate area of zoomed in versions of each MIP. (B) Fluorescence intensity profile of the MIPs (see corresponding image above in A). The profile was measured top-down and averaged for the full width of the titanium implant. (C) The difference spectrum for consecutive profiles in B.

Article Snippet: The non-toxic DRAQ7 DNA dye was able to pass cell membrane of compromised cells, since they were fixed with 4% w/v PFA in PBS (335.2, Carl Roth GmbH, Germany) to generate a positive control of cell damage Consequently, the fibroblasts had damaged cell membranes and emitted both dyes, the CYTO-ID Red was located at the cell membranes and the DRAQ7 at the nuclei ( ).

Techniques: Staining, Fluorescence

Journal: bioRxiv

Article Title: Paired CRISPR screens identify mitochondrial metabolism and UBE2H as aneuploid-specific dependencies in human cancer cell lines

doi: 10.64898/2026.04.26.720636

Figure Lengend Snippet: Validation and mechanistic analysis of UBE2H A-D) Competition assay results showing fold dropout of sgRNAs targeting negative controls (ROSA26, AAVS1), positive controls (CDK9, CDC7), and UBE2H in A) SNU1 near-tetraploid control cells, B) SNU1 aneuploid subclone 114 (trisomy 9, 19), C) SNU1 aneuploid subclone 12 (trisomy 5, 10,17; pentasomy 2), D) SNU1 aneuploid subclone 24 (trisomy 1,8,10,14; DiY; pentasomy 5). Percent dropout is normalized relative to positive and negative controls. E) Colony formation following AZ3146 treatment (250 nM) relative to ethanol vehicle control in HCT116 wild-type cells, three UBE2H knockout clones, and UBE2H cDNA rescue clones. P-values from two-sided t-test relative to wild-type are shown. One sided t-test for overexpression clones rescue relative to knockout. F) Change in percentage of Annexin V and/or DRAQ7-positive cells following 96 h treatment with AZ3146 (1 µM), relative to ethanol-treated controls in HCT116 wild-type and UBE2H-KO clones. Two-sided t-tests. G) Diagram of sample preparation for Mass Spectrometry analysis. H-J) g:Profiler gene group enrichment analysis of mass spectrometry data. Protein abundance downregulated in HCT116 in H) AZ3146 treated versus wild-type, I) UBE2H-KO versus wild-type and J) AZ3146 treated UBE2H-KO versus AZ3146 treated wild-type cells. K) UBE2H RNA expression correlated to aneuploidy score in TCGA human tumor data. Pearson correlation and corresponding p-value. L) UBE2H RNA expression stratified by chromosome arm 7q copy number status; with 7q arm loss (-1), neutral (0) and gain (1) in TCGA data. Two-sided t-test p-values are shown. M) UBE2H RNA expression correlated to aneuploidy score for samples with a neutral copy of chromosome arm 7q in TCGA data. N) UBE2H RNA expression and aneuploidy score Pearson correlation coefficient and -log₂(p-value) per tumor types (TCGA). All significant correlations labeled with tumor abbreviation.

Article Snippet: Cells and media were harvested, resuspended in 100 μl annexin buffer and stained with AnnexinV FITC conjugate (Fisher Scientific, A13199) and then with 1 μl of DRAQ7 dead cell dye (Fisher Scientific, D15106).

Techniques: Biomarker Discovery, Competitive Binding Assay, Control, Knock-Out, Clone Assay, Over Expression, Sample Prep, Mass Spectrometry, Quantitative Proteomics, RNA Expression, Labeling