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receptors  (New England Biolabs)


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    Structured Review

    New England Biolabs receptors
    Receptors, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 78 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/surface+surface+colocalization/SNAP-Surface+649/pmc05347553-233-5-11
    Average 95 stars, based on 78 article reviews
    receptors - by Bioz Stars, 2026-11
    95/100 stars

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    Related Articles

    Purification:

    Article Title: A mechanism of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence
    Article Snippet: .. Purified Gal4-SNAP-VP16 was labeled with SNAP-Surface-649 (New England Biolabs) as in ref. 51 . ..

    Labeling:

    Article Title: A mechanism of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence
    Article Snippet: .. Purified Gal4-SNAP-VP16 was labeled with SNAP-Surface-649 (New England Biolabs) as in ref. 51 . ..

    other:

    Article Title: Membrane lipid composition and endocytosis modulate Wingless release from secreting cells
    Article Snippet: SNAP labelling reagents used: SNAP-surface488 (NEB, S9124S), SNAPCell-TMR-Star (NEB, S9105S) and SNAP-surface649 (NEB, S9159S).


    Article Title: Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins.
    Article Snippet: Lysates were incubated with Strep-tactin 4Flow high capacity resin (Cat# 2- 12500-010, IBA Lifesciences, Göttingen, Germany) at 4 °C for at least 30 min. After washing five times with the same buffer, proteins were eluted with 2.5 mM desthiobiotin (Cat# D1411-500MG, Sigma-Aldrich, St. Louis, MO, USA).

    Article Title: Class A and B GPCRs trigger rapid Gα s translocation to late and slow recycling endosomes
    Article Snippet: SNAP-Surface 649 (#S9159S) was purchased from NEB (Ipswich, Massachusetts, USA).

    Incubation:

    Article Title: Wnt-dependent Frizzled clustering is required for Dishevelled phosphorylation but insufficient for β-catenin stabilization.
    Article Snippet: Wnt–βcatenin signaling begins when Wnt ligands engage the receptors Frizzled (Fzd) and LRP5 or LRP6 (LRP5/6), leading to the recruitment and phosphorylation of the intracellular protein Dishevelled (Dvl), which is necessary for stabilization of the transcriptional coactivator βcatenin.. Understanding the mechanisms by which ligand binding to Fzd activates Wnt–βcatenin signaling is crucial for rational ligand design to selectively modulate Wnt responses in the context of diseases and tissue regeneration.. Here, we determined that ligandinduced Fzd clustering was the initiating event for the recruitment and phosphorylation of the downstream signaling mediator Dvl.

    Article Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.
    Article Snippet: .. In brief, HEK293T cells were plated in 6-well plates at a density of 6 × 105 cells per well and cultured at 37 °C with 5% CO2 for 24 h. The cells were then transfected with the plasmids encoding SNAP- AR TI CL E IN P RE SS tagged wild-type mGlu7 or mutants and EAAT1 at a ratio of 9:1 with a final concentration of 1 μg ml–1, and cultured for 48 h. Next, the cells were labelled with 100 nM SNAP-Surface 649 (New England Biolab) in culture medium at 37 °C for 1 h. Then, crosslinking buffer containing 1.5 mM dichloro (1,10-phenanthroline) copper (CuP, Sigma), 16.7 mM Tris, pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 1 mM CaCl2 or a blank control buffer (crosslinking buffer without CuP) was added to the cells and incubated at room temperature for 20 min. .. The reaction was stopped by incubating with 10 mM N-ethylmaleimide at 4 °C for 15 min, then the cells were lysed with 30 μl CellLytic M (Sigma) at 4 °C for 1 h. The cell lysate was centrifugated at 12,000g, 4 °C for 30 min and the supernatant was mixed with SDS loading buffer at room temperature for 10 min.

    Cell Culture:

    Article Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.
    Article Snippet: .. In brief, HEK293T cells were plated in 6-well plates at a density of 6 × 105 cells per well and cultured at 37 °C with 5% CO2 for 24 h. The cells were then transfected with the plasmids encoding SNAP- AR TI CL E IN P RE SS tagged wild-type mGlu7 or mutants and EAAT1 at a ratio of 9:1 with a final concentration of 1 μg ml–1, and cultured for 48 h. Next, the cells were labelled with 100 nM SNAP-Surface 649 (New England Biolab) in culture medium at 37 °C for 1 h. Then, crosslinking buffer containing 1.5 mM dichloro (1,10-phenanthroline) copper (CuP, Sigma), 16.7 mM Tris, pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 1 mM CaCl2 or a blank control buffer (crosslinking buffer without CuP) was added to the cells and incubated at room temperature for 20 min. .. The reaction was stopped by incubating with 10 mM N-ethylmaleimide at 4 °C for 15 min, then the cells were lysed with 30 μl CellLytic M (Sigma) at 4 °C for 1 h. The cell lysate was centrifugated at 12,000g, 4 °C for 30 min and the supernatant was mixed with SDS loading buffer at room temperature for 10 min.

    Transfection:

    Article Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.
    Article Snippet: .. In brief, HEK293T cells were plated in 6-well plates at a density of 6 × 105 cells per well and cultured at 37 °C with 5% CO2 for 24 h. The cells were then transfected with the plasmids encoding SNAP- AR TI CL E IN P RE SS tagged wild-type mGlu7 or mutants and EAAT1 at a ratio of 9:1 with a final concentration of 1 μg ml–1, and cultured for 48 h. Next, the cells were labelled with 100 nM SNAP-Surface 649 (New England Biolab) in culture medium at 37 °C for 1 h. Then, crosslinking buffer containing 1.5 mM dichloro (1,10-phenanthroline) copper (CuP, Sigma), 16.7 mM Tris, pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 1 mM CaCl2 or a blank control buffer (crosslinking buffer without CuP) was added to the cells and incubated at room temperature for 20 min. .. The reaction was stopped by incubating with 10 mM N-ethylmaleimide at 4 °C for 15 min, then the cells were lysed with 30 μl CellLytic M (Sigma) at 4 °C for 1 h. The cell lysate was centrifugated at 12,000g, 4 °C for 30 min and the supernatant was mixed with SDS loading buffer at room temperature for 10 min.

    Concentration Assay:

    Article Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.
    Article Snippet: .. In brief, HEK293T cells were plated in 6-well plates at a density of 6 × 105 cells per well and cultured at 37 °C with 5% CO2 for 24 h. The cells were then transfected with the plasmids encoding SNAP- AR TI CL E IN P RE SS tagged wild-type mGlu7 or mutants and EAAT1 at a ratio of 9:1 with a final concentration of 1 μg ml–1, and cultured for 48 h. Next, the cells were labelled with 100 nM SNAP-Surface 649 (New England Biolab) in culture medium at 37 °C for 1 h. Then, crosslinking buffer containing 1.5 mM dichloro (1,10-phenanthroline) copper (CuP, Sigma), 16.7 mM Tris, pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 1 mM CaCl2 or a blank control buffer (crosslinking buffer without CuP) was added to the cells and incubated at room temperature for 20 min. .. The reaction was stopped by incubating with 10 mM N-ethylmaleimide at 4 °C for 15 min, then the cells were lysed with 30 μl CellLytic M (Sigma) at 4 °C for 1 h. The cell lysate was centrifugated at 12,000g, 4 °C for 30 min and the supernatant was mixed with SDS loading buffer at room temperature for 10 min.

    Control:

    Article Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.
    Article Snippet: .. In brief, HEK293T cells were plated in 6-well plates at a density of 6 × 105 cells per well and cultured at 37 °C with 5% CO2 for 24 h. The cells were then transfected with the plasmids encoding SNAP- AR TI CL E IN P RE SS tagged wild-type mGlu7 or mutants and EAAT1 at a ratio of 9:1 with a final concentration of 1 μg ml–1, and cultured for 48 h. Next, the cells were labelled with 100 nM SNAP-Surface 649 (New England Biolab) in culture medium at 37 °C for 1 h. Then, crosslinking buffer containing 1.5 mM dichloro (1,10-phenanthroline) copper (CuP, Sigma), 16.7 mM Tris, pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 1 mM CaCl2 or a blank control buffer (crosslinking buffer without CuP) was added to the cells and incubated at room temperature for 20 min. .. The reaction was stopped by incubating with 10 mM N-ethylmaleimide at 4 °C for 15 min, then the cells were lysed with 30 μl CellLytic M (Sigma) at 4 °C for 1 h. The cell lysate was centrifugated at 12,000g, 4 °C for 30 min and the supernatant was mixed with SDS loading buffer at room temperature for 10 min.



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    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 <t>colocalization.</t> 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.
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    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 <t>colocalization.</t> 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.
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    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 <t>colocalization.</t> 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.
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    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 <t>colocalization.</t> 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.
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    µGUIDEs as engineered signaling centers to locally stimulate kidney organoid vascularization. a,b), <t>Colocalization</t> of EC networks and emerging epithelial structures in human iPSC‐based kidney organoid cultures. a), Day 7 immunofluorescence staining showing PAX2+ RVs and CD31+ ECs. Scale bars: 1 mm (left) and 500 µm (right). b), Day 17 Immunofluorescence staining highlighting WT1+ glomeruli, LTL+ proximal tubule cells, and CD31+ ECs. Scale bars: 1 mm (left), 500 µm (right). c), Schematic representation of the µGUIDE deposition within kidney organoids. d), 3D simulation of the kidney organoid transwell culture depicting the VEGF gradient formation from starPEG‐sGAG µGUIDEs using a reaction‐diffusion model. The simulations show the concentration profiles of freely diffusing VEGF (normalized by initial µGUIDE loading) between two adjacent µGUIDEs, 100 µm above the organoid base (dashed line in the schematic on the top left). The µGUIDE integral charge density (P1) is concluded to determine the duration of the VEGF gradient, from short‐term (hours) to long‐term (days). e), Phase contrast images of kidney organoids with P1 5 P2 3.6 µGUIDEs at day 0 (left; scale bar: 1 mm) and day 7 (right; scale bar: 200 µm). The arrowhead in the right image indicates a µGUIDE. f), Day 7 confocal images of kidney organoids cultured with VEGF‐loaded µGUIDEs (w/ VEGF), unloaded µGUIDEs (w/o VEGF) and no µGUIDEs (w/o µGUIDE). Scale bars, 1 mm. g), Quantitative analysis of the EC response (CD31 coverage area) to VEGF gradients around and between µGUIDEs at day 7. Control regions of interest (ROIs) of identical size were positioned in organoids without µGUIDEs. h,i), Analysis of the interactions between RVs and ECs. h), Confocal images of day 7 organoids stained for PAX2+ RVs and CD31+ ECs, with magenta indicating the contact area. Scale bar, 500 µm. i), Quantitative analysis of the RV‐EC contact. For all experiments, µGUIDEs with a diameter of ≈ 182 µm were used. Data are shown as mean ± s.d. ( n = 4).
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    Image Search Results


    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.

    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

    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.

    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

    µGUIDEs as engineered signaling centers to locally stimulate kidney organoid vascularization. a,b), Colocalization of EC networks and emerging epithelial structures in human iPSC‐based kidney organoid cultures. a), Day 7 immunofluorescence staining showing PAX2+ RVs and CD31+ ECs. Scale bars: 1 mm (left) and 500 µm (right). b), Day 17 Immunofluorescence staining highlighting WT1+ glomeruli, LTL+ proximal tubule cells, and CD31+ ECs. Scale bars: 1 mm (left), 500 µm (right). c), Schematic representation of the µGUIDE deposition within kidney organoids. d), 3D simulation of the kidney organoid transwell culture depicting the VEGF gradient formation from starPEG‐sGAG µGUIDEs using a reaction‐diffusion model. The simulations show the concentration profiles of freely diffusing VEGF (normalized by initial µGUIDE loading) between two adjacent µGUIDEs, 100 µm above the organoid base (dashed line in the schematic on the top left). The µGUIDE integral charge density (P1) is concluded to determine the duration of the VEGF gradient, from short‐term (hours) to long‐term (days). e), Phase contrast images of kidney organoids with P1 5 P2 3.6 µGUIDEs at day 0 (left; scale bar: 1 mm) and day 7 (right; scale bar: 200 µm). The arrowhead in the right image indicates a µGUIDE. f), Day 7 confocal images of kidney organoids cultured with VEGF‐loaded µGUIDEs (w/ VEGF), unloaded µGUIDEs (w/o VEGF) and no µGUIDEs (w/o µGUIDE). Scale bars, 1 mm. g), Quantitative analysis of the EC response (CD31 coverage area) to VEGF gradients around and between µGUIDEs at day 7. Control regions of interest (ROIs) of identical size were positioned in organoids without µGUIDEs. h,i), Analysis of the interactions between RVs and ECs. h), Confocal images of day 7 organoids stained for PAX2+ RVs and CD31+ ECs, with magenta indicating the contact area. Scale bar, 500 µm. i), Quantitative analysis of the RV‐EC contact. For all experiments, µGUIDEs with a diameter of ≈ 182 µm were used. Data are shown as mean ± s.d. ( n = 4).

    Journal: Advanced Materials (Deerfield Beach, Fla.)

    Article Title: Microgels With Electrostatically Controlled Molecular Affinity to Direct Morphogenesis

    doi: 10.1002/adma.202409731

    Figure Lengend Snippet: µGUIDEs as engineered signaling centers to locally stimulate kidney organoid vascularization. a,b), Colocalization of EC networks and emerging epithelial structures in human iPSC‐based kidney organoid cultures. a), Day 7 immunofluorescence staining showing PAX2+ RVs and CD31+ ECs. Scale bars: 1 mm (left) and 500 µm (right). b), Day 17 Immunofluorescence staining highlighting WT1+ glomeruli, LTL+ proximal tubule cells, and CD31+ ECs. Scale bars: 1 mm (left), 500 µm (right). c), Schematic representation of the µGUIDE deposition within kidney organoids. d), 3D simulation of the kidney organoid transwell culture depicting the VEGF gradient formation from starPEG‐sGAG µGUIDEs using a reaction‐diffusion model. The simulations show the concentration profiles of freely diffusing VEGF (normalized by initial µGUIDE loading) between two adjacent µGUIDEs, 100 µm above the organoid base (dashed line in the schematic on the top left). The µGUIDE integral charge density (P1) is concluded to determine the duration of the VEGF gradient, from short‐term (hours) to long‐term (days). e), Phase contrast images of kidney organoids with P1 5 P2 3.6 µGUIDEs at day 0 (left; scale bar: 1 mm) and day 7 (right; scale bar: 200 µm). The arrowhead in the right image indicates a µGUIDE. f), Day 7 confocal images of kidney organoids cultured with VEGF‐loaded µGUIDEs (w/ VEGF), unloaded µGUIDEs (w/o VEGF) and no µGUIDEs (w/o µGUIDE). Scale bars, 1 mm. g), Quantitative analysis of the EC response (CD31 coverage area) to VEGF gradients around and between µGUIDEs at day 7. Control regions of interest (ROIs) of identical size were positioned in organoids without µGUIDEs. h,i), Analysis of the interactions between RVs and ECs. h), Confocal images of day 7 organoids stained for PAX2+ RVs and CD31+ ECs, with magenta indicating the contact area. Scale bar, 500 µm. i), Quantitative analysis of the RV‐EC contact. For all experiments, µGUIDEs with a diameter of ≈ 182 µm were used. Data are shown as mean ± s.d. ( n = 4).

    Article Snippet: Here, two surfaces were created for the respective source channels, and the surface‐surface colocalization Imaris XTension was applied.

    Techniques: Immunofluorescence, Staining, Diffusion-based Assay, Concentration Assay, Cell Culture, Control