Journal: Journal of Cellular and Molecular Medicine

Article Title: CXCL16 and oxLDL are induced in the onset of diabetic nephropathy

doi: 10.1111/j.1582-4934.2009.00761.x

Figure Lengend Snippet: Involvement of CXCL16 and CD36 in the uptake of oxLDL. (A) DiI-oxLDL uptake was analysed after the pre-treatment of podocytes with an IgG control antibody (control), a CXCL16 blocking antibody (+C16 Ab), a CD36 blocking antibody (+CD36 Ab), or both antibodies (+C16 Ab + CD36 Ab). After pre-incubation of human podocytes with the blocking antibodies, cells were incubated for 4 hrs with 100 μg/ml DiI-oxLDL (red) and subsequently washed with PBS and fixed in methanol/0.02% EDTA. In addition, cells were stained with DAPI to visualize the nuclei (blue). (B) Semi-quantitative analysis of the fluorescence intensity of DiI-oxLDL in cells pre-treated with a control IgG antibody (control), a CXCL16 antibody (C16 Ab), a CD36 antibody (CD36Ab) or with a combination of both antibodies (C16AB+CD36Ab). Mean fluorescence of DiI-oxLDL was measured with an image software from Keyence. (C) DiI-oxLDL uptake was analysed after pre-incubation of the primary tubular cell line HRCEpiC with an IgG control antibody (control), a CXCL16 blocking antibody (+C16Ab), a CD36 blocking antibody (+CD36Ab) or the combination of both blocking antibodies (+C16Ab+CD36Ab) and visualized by immunofluorescence microscopy. After pre-incubation of HRCEpiC with the different blocking antibodies, cells were incubated for 4 hrs with 100 μg/ml DiI-oxLDL (red) and subsequently washed with PBS and fixed in methanol/0.02% EDTA. The cells were stained with DAPI to visualize the nuclei (blue). (D) Fluorescence intensity of DiI-oxLDL in HRCEpiC pre-treated with an IgG control antibody (control), a CXCL16 antibody (C16 Ab), a CD36 antibody (CD36Ab) or the combination of both antibodies (C16Ab+CD36Ab) was determined with the BZ-Analyzer software (Keyence). Data represent mean ± S.D. *** P < 0.001; ** P < 0.01 considered statistically significant compared to the control. (E) Podocytes were fixed with 4% paraformaldehyde and CD36 expression was investigated using monoclonal CD36 and Cy3 coupled secondary antibodies (red). The cells were stained with DAPI to detect the nuclei (blue) of the cells. Fluorescence analyses were performed with a LSM 510 Meta confocal laser-scanning microscope (Carl Zeiss, Jena, Germany). (F) Podocytes were fixed with methanol and incubated with CXCL16 antibodies followed by Alexa 488 coupled secondary antibodies (green). Cells were than incubated with DAPI to visualize nuclei (blue). Fluorescence analyses were performed with a LSM 510 Meta confocal laser-scanning microscope (Carl Zeiss).

Article Snippet: Primary human renal cortical epithelial cells (HRCEpiC) were supplied from Provitro (Berlin, Germany) and cultured according to the manufacturer’s instructions.

Techniques: Control, Blocking Assay, Incubation, Staining, Fluorescence, Software, Immunofluorescence, Microscopy, Expressing, Laser-Scanning Microscopy

Journal: Computers in biology and medicine

Article Title: GILEA: In silico phenome profiling and editing using GAN Inversion.

doi: 10.1016/j.compbiomed.2024.108825

Figure Lengend Snippet: Fig. 2. Reconstruction visualization of GILEA and quantitative comparison of drug responses between the baseline [7] and 𝑑𝖫𝖤𝖠(Proposed). a (VERO) and f (HRCE): The reconstructed samples obtained by GILEA. b (VERO) and g (HRCE): The quantitative comparison between the hit score [7] and 𝑑𝖫𝖤𝖠with the latent representations of all concentrations. c (VERO) and h (HRCE): The violin plot of overall comparison between the hit score [7] and 𝑑𝖫𝖤𝖠. d (VERO) and i (HRCE): The quantitative comparison between the hit score [7] and 𝑑𝖫𝖤𝖠with the latent representations of optimal drug concentration. e (VERO) and j (HRCE): The hierarchical clustering of top 50 drug compounds (if exist) w.r.t. the 5 largest eigenvalues of the latent representations of optimal drug concentration.

Article Snippet: For VERO and HRCE cell-lines, Remdesivir and GS-441524 are consistently identified as effective compounds w.r.t. individual fluorescent channels as well as all channels, which supports the clinical utility of Remdesivir approved by U.S. Food and Drug Administration (FDA).2 Meanwhile, the heterogeneous effects of Chloroquine and Hydroxychloroquine are also revealed in our refined analysis.

Techniques: Comparison, Concentration Assay

Journal: Computers in biology and medicine

Article Title: GILEA: In silico phenome profiling and editing using GAN Inversion.

doi: 10.1016/j.compbiomed.2024.108825

Figure Lengend Snippet: Fig. 4. Identification of drug-concentration dependent effects and visual interpretation for key drugs of interest in the HRCE cell-line. a, The proposed 𝑑𝖫𝖤𝖠of different drug concentrations for individual and all fluorescent channels. Here, we report the mean 𝑑𝖫𝖤𝖠(with standard deviation) averaged on 4 randomly sampled cell collections. b, The PCA plots and phenotypic transitions driven by manipulating the largest (top) and 5 largest (bottom) principal component(s). The bounding box indicates the reconstructed image.

Article Snippet: For VERO and HRCE cell-lines, Remdesivir and GS-441524 are consistently identified as effective compounds w.r.t. individual fluorescent channels as well as all channels, which supports the clinical utility of Remdesivir approved by U.S. Food and Drug Administration (FDA).2 Meanwhile, the heterogeneous effects of Chloroquine and Hydroxychloroquine are also revealed in our refined analysis.

Techniques: Concentration Assay, Standard Deviation