custom-made knime analysis pipeline (termed ‘track-based colocalization analysis (with recursive track pairing and particle number correction)  (KNIME GmbH)

Journal: bioRxiv

Article Title: Loss of Parkin Disrupts Nuclear and Mitochondrial Programs Required for Muscle Regeneration

doi: 10.64898/2026.03.20.712989

Figure Lengend Snippet: A-B ) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in in situ fixed, freshly sorted quiescent and 4h in vitro activated MuSCs ( n =48-55 cells from 3 mice in each group and experimental condition). C) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. D) Colocalization of PARKIN to TOM20-labeled mitochondria expressed in absolute volume of PARKIN + structures overlapping with mitochondria per cell ( n =25-36 cells from 3 mice in each group and experimental condition). E) Proportion of TOM20-labeled mitochondria labeled with PARKIN, computed using data presented in panel D and total mitochondrial content (Fig. S1A). F) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and PARKIN-labeled structures (red) in each of the experimental conditions examined. The volume of PARKIN overlapping with mitochondria is shown in yellow in the right-end panels, where mitochondria and PARKIN + surfaces have been removed to highlight changes in colocalization. G) Total cellular PARKIN content in the indicated experimental conditions. H) Parkin transcript levels in MuSCs purified from muscles that were fixed in situ in healthy uninjured conditions or at 15, 30, 60, 90 and 120 min after CTX injury. Data is taken from (GSE163856 ). All data are presented as mean ± SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs. I) Changes in the transcript levels of ubiquitin- and receptor-dependent mitophagy in three transcriptomics datasets (GSE70736, GSE55490, GSE47177 , , ) that compared quiescent and in vivo activated MuSCs 36-72h following muscle injury with CTX or BaCl 2 . Each dot represents data from an individual dataset and a specific timepoints. Genes shown where differentially expressed in all datasets with a q value of less than 0.05. Level of statistical significance shown is based on the average q value.

Article Snippet: Volume reconstruction and surface/surface colocalization analysis was performed in Imaris using fixed settings.

Techniques: In Situ, In Vitro, Labeling, Purification, Muscles, Two Tailed Test, Ubiquitin Proteomics, Transcriptomics, In Vivo

Journal: bioRxiv

Article Title: Loss of Parkin Disrupts Nuclear and Mitochondrial Programs Required for Muscle Regeneration

doi: 10.64898/2026.03.20.712989

Figure Lengend Snippet: A-C) Parkin transcript and protein levels in FACS-purified MuSCs from MuSC Park2 +/+ and MuSC Park2 -/- mice 1 week after the last tamoxifen treatment ( n =4 mice per group). Protein abundance was quantified as the total volume of PARKIN + structures (B) in cells labeled with antibodies against PARKIN and TOM20 ( n =11-70 cells from 2-4 mice per group,) (C). D-E) transcript abundance expressed in Transcript Per Million (TPM) for genes involved in Parkin- and Receptor-mediated mitophagy ( n =3 mice per group). F-G) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in freshly sorted quiescent and 4h in vitro activated MuSCs ( n =41-52 cells from 3 mice in each group). H) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. All data are presented as mean ±SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs.

Article Snippet: Volume reconstruction and surface/surface colocalization analysis was performed in Imaris using fixed settings.

Techniques: Purification, Quantitative Proteomics, Labeling, In Vitro, Two Tailed Test