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RStudio coloc.abf function
Coloc.Abf Function, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/colocalization+functionality/coloc+abf+function/pm38924078-64-32-39
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coloc.abf function - by Bioz Stars, 2026-09

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Loss of Usp15 inhibits Mtb replication and increases K63 ubiquitination colocalization. ( A ) Schematic for shRNA screen in the BV2 cell line infected with luminescent Mtb. ( B ) Heat map shows the average of relative luminescence units when normalized to day 0 and then to the nontargeting control (NTC). ( C ) CFU values of WT Erdman Mtb infected into non-targeting control shRNA (NTC) and Usp15 KD shRNA BV2 cells were normalized for each day to the count on day 0. ( D ) CFUs of WT or BV2 usp15 KO cells infected with WT Mtb. ( E ) Images show Mtb (gray or red) and K63 (gray or green) with DAPI (blue) in WT or BV2 usp15 KO cells. Scale bar: 5 μm. ( F ) Quantification of K63 immunofluorescence colocalizing with mCherry Mtb infected WT or BV2 usp15 KO cells at 16 h post-infection. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: Loss of Usp15 inhibits Mtb replication and increases K63 ubiquitination colocalization. ( A ) Schematic for shRNA screen in the BV2 cell line infected with luminescent Mtb. ( B ) Heat map shows the average of relative luminescence units when normalized to day 0 and then to the nontargeting control (NTC). ( C ) CFU values of WT Erdman Mtb infected into non-targeting control shRNA (NTC) and Usp15 KD shRNA BV2 cells were normalized for each day to the count on day 0. ( D ) CFUs of WT or BV2 usp15 KO cells infected with WT Mtb. ( E ) Images show Mtb (gray or red) and K63 (gray or green) with DAPI (blue) in WT or BV2 usp15 KO cells. Scale bar: 5 μm. ( F ) Quantification of K63 immunofluorescence colocalizing with mCherry Mtb infected WT or BV2 usp15 KO cells at 16 h post-infection. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Ubiquitin Proteomics, shRNA, Infection, Control, Immunofluorescence, Comparison

usp15 deletion in BV2 cells increases LC3-II conversion and colocalization of LC3 with Mtb-associated structures. ( A ) Western blot of LC3-I and LC3-II and ACTB in WT and BV2 usp15 KO cells infected with Mtb. ( B ) Quantification of LC3-II normalized to ACTB. ( C ) Representative immunofluorescence images of mCherry Mtb (gray or red), LC3 (gray or green) in WT (upper panel) or BV2 usp15 KO (lower panel) cells. Scale bar: 5 μm. ( D ) Quantification of LC3 colocalization with mCherry Mtb in BV2 cells. ( E ) Schematic of PI3K inhibition of upstream autophagy initiation via the class III phosphatidylinositol 3-kinase (PtdIns3K) complex. ( F ) CFU of WT Mtb in WT or BV2 usp15 KO cells with or without 5 μM of PIK-III normalized for each day to the count on Day 0. For statistical analysis, we used two-way ANOVA and Tukey’s multiple comparison test.* p<0.05, ** p<0.01, *** p<0.001, **** p<0.000.1. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: usp15 deletion in BV2 cells increases LC3-II conversion and colocalization of LC3 with Mtb-associated structures. ( A ) Western blot of LC3-I and LC3-II and ACTB in WT and BV2 usp15 KO cells infected with Mtb. ( B ) Quantification of LC3-II normalized to ACTB. ( C ) Representative immunofluorescence images of mCherry Mtb (gray or red), LC3 (gray or green) in WT (upper panel) or BV2 usp15 KO (lower panel) cells. Scale bar: 5 μm. ( D ) Quantification of LC3 colocalization with mCherry Mtb in BV2 cells. ( E ) Schematic of PI3K inhibition of upstream autophagy initiation via the class III phosphatidylinositol 3-kinase (PtdIns3K) complex. ( F ) CFU of WT Mtb in WT or BV2 usp15 KO cells with or without 5 μM of PIK-III normalized for each day to the count on Day 0. For statistical analysis, we used two-way ANOVA and Tukey’s multiple comparison test.* p<0.05, ** p<0.01, *** p<0.001, **** p<0.000.1. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Western Blot, Infection, Immunofluorescence, Inhibition, Comparison

Loss of Usp15 in BMDM results in reduced CFU and increased colocalization of LC3 with Mtb-associated structures. ( A ) CFU of WT Mtb in WT or usp15 −/− BMDM normalized to the count at Day 0. ( B ) Representative images of mCherry (gray or red) and LC3 immunofluorescence (gray or green) in WT or usp15 −/− BMDM. Scale bar: 5 μm. ( C ) Quantification of LC3 colocalization with mCherry Mtb in BMDM at 16 h post-infection. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: Loss of Usp15 in BMDM results in reduced CFU and increased colocalization of LC3 with Mtb-associated structures. ( A ) CFU of WT Mtb in WT or usp15 −/− BMDM normalized to the count at Day 0. ( B ) Representative images of mCherry (gray or red) and LC3 immunofluorescence (gray or green) in WT or usp15 −/− BMDM. Scale bar: 5 μm. ( C ) Quantification of LC3 colocalization with mCherry Mtb in BMDM at 16 h post-infection. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Immunofluorescence, Infection, Comparison

The catalytic activity of USP15 is necessary for regulating Mtb replication in BV2 cells. ( A ) Schematic of USP15 with the location of the catalytic dead mutation noted in red. Domain abbreviations are as follows: DUSP (domain present in USP) and UBL (ubiquitin-like domain). The catalytic domains (CD) are noted in blue. ( B ) Complementation of BV2 usp15 KO cells with 3XFlag-USP15WT ( usp15 KO::WT) or 3XFlag-Usp15C269A ( usp15 KO::C269A). Western blot demonstrating 3XFlag-USP15 WT or 3XFlag-USP15 C269A in BV2 cell lines. ( C ) CFU of Mtb infection in BV2 WT with empty vector (WT Empty), BV2 usp15 KO with empty vector ( usp15 KO Empty), BV2 usp15 KO complemented with 3XFlag-USP15 WT ( usp15 KO::WT) or BV2 usp15 KO complemented with 3XFlag-USP15 C269A ( usp15 KO:: C269A). CFU values were normalized to Day 0. ( D ) Representative image of mCherry (gray or red) and K63 immunofluorescence (gray or green) with DAPI (blue) in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. Scale bar: 5 μm. ( E ) Quantification of K63 colocalization with mCherry Mtb in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. ( F ) Representative image of mCherry (gray or red) and LC3 immunofluorescence (gray or green) with DAPI (blue) in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. Scale bar: 5 μm. ( G ) Quantification of LC3 colocalization with mCherry Mtb in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used one-way ANOVA and Tukey’s multiple comparison test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: The catalytic activity of USP15 is necessary for regulating Mtb replication in BV2 cells. ( A ) Schematic of USP15 with the location of the catalytic dead mutation noted in red. Domain abbreviations are as follows: DUSP (domain present in USP) and UBL (ubiquitin-like domain). The catalytic domains (CD) are noted in blue. ( B ) Complementation of BV2 usp15 KO cells with 3XFlag-USP15WT ( usp15 KO::WT) or 3XFlag-Usp15C269A ( usp15 KO::C269A). Western blot demonstrating 3XFlag-USP15 WT or 3XFlag-USP15 C269A in BV2 cell lines. ( C ) CFU of Mtb infection in BV2 WT with empty vector (WT Empty), BV2 usp15 KO with empty vector ( usp15 KO Empty), BV2 usp15 KO complemented with 3XFlag-USP15 WT ( usp15 KO::WT) or BV2 usp15 KO complemented with 3XFlag-USP15 C269A ( usp15 KO:: C269A). CFU values were normalized to Day 0. ( D ) Representative image of mCherry (gray or red) and K63 immunofluorescence (gray or green) with DAPI (blue) in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. Scale bar: 5 μm. ( E ) Quantification of K63 colocalization with mCherry Mtb in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. ( F ) Representative image of mCherry (gray or red) and LC3 immunofluorescence (gray or green) with DAPI (blue) in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. Scale bar: 5 μm. ( G ) Quantification of LC3 colocalization with mCherry Mtb in WT Empty, BV2 usp15 KO Empty, BV2 usp15 KO::WT, or BV2 usp15 KO::C269A. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used one-way ANOVA and Tukey’s multiple comparison test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Activity Assay, Mutagenesis, Ubiquitin Proteomics, Western Blot, Infection, Plasmid Preparation, Immunofluorescence, Comparison

USP15 counters the activity of PRKN. ( A ) Schematic of PRKN’s activity in the context of ubiquitination of Mtb. ( B ) Western blot confirms knockdown (KD) of PRKN in WT or Usp15 KO compared to non-targeting controls (NTC). The percentage of KD is shown below each KD. ( C ) CFU of WT Mtb infected in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. CFU values were normalized to the count at Day 0. ( D ) Representative image of mCherry (gray or red) and K63 immunofluorescence (gray or green) with DAPI (blue) in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. Scale bar: 5 μm. ( E ) Quantification of K63 colocalization with mCherry Mtb in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. ( F ) Representative image of mCherry (gray or red) and LC3 immunofluorescence (gray or green) with DAPI (blue) in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. Scale bar: 5 μm. ( G ) Quantification of LC3 colocalization with mCherry Mtb in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used one-way ANOVA and Tukey’s multiple comparison test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: USP15 counters the activity of PRKN. ( A ) Schematic of PRKN’s activity in the context of ubiquitination of Mtb. ( B ) Western blot confirms knockdown (KD) of PRKN in WT or Usp15 KO compared to non-targeting controls (NTC). The percentage of KD is shown below each KD. ( C ) CFU of WT Mtb infected in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. CFU values were normalized to the count at Day 0. ( D ) Representative image of mCherry (gray or red) and K63 immunofluorescence (gray or green) with DAPI (blue) in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. Scale bar: 5 μm. ( E ) Quantification of K63 colocalization with mCherry Mtb in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. ( F ) Representative image of mCherry (gray or red) and LC3 immunofluorescence (gray or green) with DAPI (blue) in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. Scale bar: 5 μm. ( G ) Quantification of LC3 colocalization with mCherry Mtb in WT with NTC, usp15 KO with NTC, WT with Prkn KD, and usp15 KO with Prkn KD. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used one-way ANOVA and Tukey’s multiple comparison test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Activity Assay, Ubiquitin Proteomics, Western Blot, Knockdown, Infection, Immunofluorescence, Comparison

USP15 depletion in HsMDM leads to decreased Mtb burden and increased LC3 colocalization. ( A ) Representative western blot of knockdown of USP15 in human monocyte-derived macrophages (HsMDMs) from Donor 1 and Donor 2. ( B ) Representative time course from day 0 to day 3 of Mtb CFU in HsMDMs from Donor 2. ( C ) Combined normalized CFU to day 0 from day 3 of Donor 1 (D1), Donor 2 (D2), Donor 3 (D3), and Donor 4 (D4). ( D ) Representative image of mCherry Mtb (gray or red) and LC3 immunofluorescence (gray or green) in HsMDMs from Donor 5 (D5) with NTC or USP15 KD. Scale bar: 5 μm. ( E ) Quantification of LC3 colocalization in HsMDMs from Donor 5 with NTC or USP15 KD. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test.* p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: USP15 depletion in HsMDM leads to decreased Mtb burden and increased LC3 colocalization. ( A ) Representative western blot of knockdown of USP15 in human monocyte-derived macrophages (HsMDMs) from Donor 1 and Donor 2. ( B ) Representative time course from day 0 to day 3 of Mtb CFU in HsMDMs from Donor 2. ( C ) Combined normalized CFU to day 0 from day 3 of Donor 1 (D1), Donor 2 (D2), Donor 3 (D3), and Donor 4 (D4). ( D ) Representative image of mCherry Mtb (gray or red) and LC3 immunofluorescence (gray or green) in HsMDMs from Donor 5 (D5) with NTC or USP15 KD. Scale bar: 5 μm. ( E ) Quantification of LC3 colocalization in HsMDMs from Donor 5 with NTC or USP15 KD. For statistical analysis of CFU, we used two-way ANOVA and Tukey’s multiple comparison test. For statistical analysis of colocalization, we used Student’s t-test.* p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Western Blot, Knockdown, Derivative Assay, Immunofluorescence, Comparison

Inhibition of USP15 by USP15-IN-1 leads to decreased Mtb burden in BV2 cells and HsMDM. ( A ) A 4-point dose response of USP15-IN-1 in WT or BV2 usp15 KO cells infected with Mtb-pLux. ( B ) Combined Relative Luminescence Units (RLU) of Day 3 from Donor 6, Donor 7, Donor 8, and Donor 9. ( C-F ) The 4-point dose response of USP15- IN-1 in ( C ) Donor 6, ( D ) Donor 7, ( E ) Donor 8, ( F ) Donor 9. ( G ) Representative immunofluorescence image of mCherry Mtb (gray or red) and LC3 (gray or green) in HsMDMs from Donor 7 with 0 μM (DMSO control) or 60 μM of 15 IN 1 at 18 h post-infection. Scale bar: 5 μm. ( H ) Quantification of LC3 colocalization in HsMDMs from donor 7. For statistical analysis for Mtb-pLux experiments, we used two-way ANOVA and Tukey’s multiple comparison test. For colocalization analysis, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Journal: Autophagy

Article Title: Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis

doi: 10.1080/15548627.2026.2618632

Figure Lengend Snippet: Inhibition of USP15 by USP15-IN-1 leads to decreased Mtb burden in BV2 cells and HsMDM. ( A ) A 4-point dose response of USP15-IN-1 in WT or BV2 usp15 KO cells infected with Mtb-pLux. ( B ) Combined Relative Luminescence Units (RLU) of Day 3 from Donor 6, Donor 7, Donor 8, and Donor 9. ( C-F ) The 4-point dose response of USP15- IN-1 in ( C ) Donor 6, ( D ) Donor 7, ( E ) Donor 8, ( F ) Donor 9. ( G ) Representative immunofluorescence image of mCherry Mtb (gray or red) and LC3 (gray or green) in HsMDMs from Donor 7 with 0 μM (DMSO control) or 60 μM of 15 IN 1 at 18 h post-infection. Scale bar: 5 μm. ( H ) Quantification of LC3 colocalization in HsMDMs from donor 7. For statistical analysis for Mtb-pLux experiments, we used two-way ANOVA and Tukey’s multiple comparison test. For colocalization analysis, we used Student’s t-test. * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001. Data shown are representative of at least 3 independent experimental replicates.

Article Snippet: The Imaris colocalization function was used to quantify LC3, K63, and K48 colocalization with mCherry Mtb.

Techniques: Inhibition, Infection, Immunofluorescence, Control, Comparison

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