EMBO/SourceData huggingface dataset:
Figure legend: "J, K Untreated and MARS/MARS2 knockdown NE4C cells were treated with Hcy (20 μM) or HTL (10 μM), and superoxide (K) levels (n=4) in cells were detected 6 h after the start of the respective treatment and quantified relative to untreated NE4C cells. Error bars indicate SEM. Data were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"MARS: 216443
MARS2: 212679"
Figure legend: "D Upon switching N-Hcy substrate lysine (K) sites to nonmodifiable tryptophan (W), the N-Hcy unmodifiable mutants displayed lower specific activity than the wide-type (WT) SOD. SOD1 (WT, K23W, K122W, K128W, and 3KW) and SOD2 (WT, K44W, K51W, K98W, K106W, K178W, and 5KW) were expressed in HEK293T cells. The catalytic activity of affinity-purified SOD proteins was determined and normalized to protein levels. Wild-type SOD1 and SOD2 activities were set at 100% (n=4). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"SOD1: 6647
SOD2: 6648"
Figure legend: "E, F Hcy and HTL treatment in NE4C cells increased N-homocysteinylation of SODs and decreased their activities. Flag-tagged SOD1 and SOD2 were each ectopically expressed in NE4C cells. The cells were transferred to serum-free DMEM with or without 20 μM Hcy (E) or 10 μM HTL (F) 6 h before harvesting. After affinity purification, the specific activities of SOD1 and SOD2 were determined and normalized to SOD1 and SOD2 activity in untreated cells. Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
SOD1: 6647
SOD2: 6648"
Figure legend: "G N-Hcy SOD levels were down-regulated in MARS/MARS2 knockdown cells. Flag-tagged SOD1 and SOD2 were each over-expressed in untreated and MARS/MARS2 knockdown NE4C cells. After affinity purification, the N-Hcy levels and relative specific activities of purified SOD1 and SOD2 were determined and quantified relative to the NE4C cells (n=4). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
MARS: 216443
MARS2: 212679
SOD1: 6647
SOD2: 6648"
Figure legend: "D Levels of β-catenin in untreated and MARS knockdown NE4C cells were detected (n=3) with the presence or absence of 20 μM Hcy in the culture media. Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"MARS: 216443"
Figure legend: "NE4C cells were co-transfected with NRX-Flag and DVL1-Myc plasmids and treated with different concentrations of Hcy (E) The relative amount of DVL1 that coimmunoprecipitated (co-IPed) with NRX-Flag was determined (n=3). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
Myc: 
DVL1: 13542
NRX: 18230"
Figure legend: "NE4C cells were co-transfected with NRX-Flag and DVL1-Myc plasmids and treated with different concentrations of HTL (F). The relative amount of DVL1 that coimmunoprecipitated (co-IPed) with NRX-Flag was determined (n=3). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
Myc: 
DVL1: 13542
NRX: 18230"
Figure legend: "G NRX-Flag and DVL1-Myc were co-transfected in untreated or MARS knockdown NE4C cells. The relative DVL1 levels that co-IPed with NRX-Flag were determined and quantified (n=3) for treated and control cells cultured with or without 20 μM Hcy. Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
Myc: 
DVL1: 13542
MARS: 216443
NRX: 18230"
Figure legend: "Flag-tagged SOD1 and SOD2 were co-over-expressed in NE4C cells cultured in DMEM and supplemented with Hcy or HTL. (H) The levels of β-catenin in cells with and without SOD1/2 expression were determined (n=3). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons."
NCBI gene IDs:
"Flag: 
SOD1: 
SOD2: "
Figure legend: "Flag-tagged SOD1 and SOD2 were co-over-expressed in NE4C cells cultured in DMEM and supplemented with HTL. (I) Relative levels of DVL1 that co-IPed with NRX-Flag were quantified in SOD-expressing and control cells cultured with or without 10 μM HTL (n=3). Data are presented as the mean ± SEM and were compared using an unpaired Student's t test. nsnot significant, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. One-way ANOVA with Dunnett's correction was used for multiple comparisons. "
NCBI gene IDs:
"Flag: 
SOD1: 6647
SOD2: 6648
SOD: 6648///6647"
Figure legend: "(A-B) Primary cilia are enriched at branch points and the greater curvature of the aorta of wild type mice, schematized in (A) and quantified in (B). The color in (A) indicates which side of the aorta is quantified in (B). Numbers indicate the region of the aorta (A) whose proportion of ciliated cells is quantified in (B). Error bars are +/- 1 S.E.M and n=7 mice. (C) Aortic endothelial cilia are ablated in Tek-Cre Ift88C/- mice. Endothelial cells and cilia are labeled by staining for Pecam1 and Arl13b, respectively. Scale bars are 10μm."
NCBI gene IDs:
"Cre: 
Ift88: 21821
Tek: 21687"
Figure legend: "(B) Loss of EC cilia by Tek-Cre increases atherosclerosis in the aortas of Apoe-/- mice on a high-fat high-cholesterol diet as visualized by Oil Red O (ORO) staining (left panels) whereas loss of cilia genes in blood by Mx1-Cre has no effect (right panels).(C) Cropped views of the boxed areas in (B) showing increased atherosclerosis in mice with Tek-Cre but not Mx1-Cre mediated loss of Ift88 in the aortic arch.(D-G) Scatter plots of the percent ORO-positive area of the thoracic aorta in (D-E) Tek-Cre and (F-G) Mx1-Cre mice, separated by (D, F) females and (E, G) males. Tek-Cre Apoe-/- Ift88C/- mice had a 58.9% (p=0.0135, Student's 2-tailed t-test, n=13 control and n=10 mutant mice) and 67% (p=0.0106, Student's 2-tailed t-test, n=17 control and n=14 mutant) increase in ORO-positive area versus control littermates in females and males, respectively. Mx1-Cre Apoe-/- Ift88C/- mice had no significant difference in ORO-positive area in females (p=0.6643, Student's 2-tailed t-test, n=7 control and mutant mice) or males (p=0.9381, Student's 2-tailed t-test, n=9 control and n=7 mutant mice). Black bars represent the mean and error bars are +/- 1 S.E.M. Aortas depicted in (B-C) are red in the scatter plots."
NCBI gene IDs:
"Cre: 
Apoe: 11816
Ift88: 21821
Mx1: 17857
Tek: 21687"
Figure legend: "(A) Transcripts for the inflammatory cytokines Il1b, Il6, Tnf1 and Tgfb1, the adhesion molecules Vcam1 and Sele, the lymphocyte marker Nos2 and macrophage marker Cd68, and the NFκB responsive genes Tnfaip3 and Hmox1 were upregulated in aortas from Apoe-/- mice lacking EC cilia by RT-qPCR, while transcripts of the Hh target genes Gli1, Ptc1, and Ptc2 were not. Error bars are +1 S.E.M. n=8 control and n=10 mutant mice of mixed sex. P-values calculated by Student's 2-tailed t-test."
NCBI gene IDs:
"Apoe: 11816
Cd68: 12514
Gli1: 14632
Hmox1: 15368
Il1b: 16176
Il6: 16193
Nos2: 18126
Ptc1: 19206
Ptc2: 19207
Sele: 20339
Tgfb1: 21803
Tnf1: 21926
Tnfaip3: 21929
Vcam1: 22329"
Figure legend: "Immunoblot  analysis of phosphorylated ERK1/2 (P-ERK1/2), phosphorylated p38  (P-P38), phosphorylated JNK1/2 (P-JNK1/2), phosphorylated p65  subunit of NF-κB (P-P65), total P65, MEKK2, TRAF2, TRAF3, TRAF6, NEDD4L, and actin  in HeLa  cells transfected with Nedd4l siRNA (siNedd4l) or control RNA (siNC) (A) , treated with  IL-17 for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. Densitometry  of MEKK2  was relative to actin. All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 23327"
Figure legend: "Immunoblot  analysis of phosphorylated ERK1/2 (P-ERK1/2), phosphorylated p38  (P-P38), phosphorylated JNK1/2 (P-JNK1/2), phosphorylated p65  subunit of NF-κB (P-P65), total P65, MEKK2, TRAF2, TRAF3, TRAF6, NEDD4L, and actin  in Nedd4l+/+ and Nedd4l-/- MEFs  , treated with  IL-17 for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated proteins relative to that of total proteins, respectively. Densitometry  of MEKK2 was relative to actin. All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "Immunoblot  analysis of phosphorylated p38  (P-P38), phosphorylated p65  subunit of NF-κB (P-P65), total P65, MEKK2, NEDD4L, and actin  in Nedd4l+/+ and Nedd4l-/- primary  lung epithelial cells (C), or Nedd4l+/+ and Nedd4l+/- astrocytes (D) , treated with   IL-17  for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. Densitometry  of MEKK2  was relative to actin. All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "(E) Immunoblot  analysis of phosphorylated p65  subunit of NF-κB (P-P65), total P65, phosphorylated p38  (P-P38), total P38, MEKK2, NEDD4L, and actin  in HeLa  cells transfected with Myc-tagged NEDD4L，Myc- tagged NEDD4L-CA(C942A), or Myc- tagged Null plasmids, treated with   IL-17  for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. Densitometry  of MEKK2  was relative to actin. All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Myc: 
NEDD4L: 83814"
Figure legend: "(F)Immunoblot  analysis of MEKK2, TRAF2, TRAF6, NEDD4L, and actin  in Nedd4l+/+, Nedd4l+/-, and Nedd4l-/- MEFs. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. Densitometry  of MEKK2  was relative to actin. All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "(G)Immunoblot  analysis of MEKK2  in lysates of Nedd4l+/+ and Nedd4l-/- MEFs  treated with CHX  (50 μg/ ml) for indicated time. (H)The intensity values were measured by Image J software to calculate half-life of MEKK  protein ( n = 3 biological replicates). Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. Densitometry  of MEKK2  was relative to actin. All experiments were performed three times, and representative data are shown. Significant differences were tested using a two-tailed Student's t-test. *P&lt;0.05, **P&lt;0.01. NS, no significance."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "(C)Immunoblot  of HA-tagged MEKK2 co-immunoprecipitated with anti-Myc  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing HA-tagged MEKK2  and Myc-tagged wild-type NEDD4L  or mutant NEDD4L  with C2 (∆C2), WW (∆WW) or HECT (∆HECT) domain deleted. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"HA: 
Myc: 
MEKK2: 10746
NEDD4L: 83814"
Figure legend: "(D)Immunoblot  analysis of MEKK2  and NEDD4L  in Nedd4l+/+, and Neddl4- /- treated with DMSO, 20μM MG-132, or 0.2 μM bafilomycin A1 (Baf A1) for 6 h. Densitometry  of MEKK2  was relative to actin. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 83814
Neddl4: 83814"
Figure legend: "(F)Immunoblot  analysis of K48-, K63-linked, and total ubiquitination  of MEKK2  following precipitation of MEKK2  with MEKK2-specific antibody from lysates of Nedd4l+/+ and Nedd4l-/- MEFs  treated with  MG-132. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "(G)Immunoblot  analysis of total ubiquitination  of Flag-tagged MEKK2 following precipitation of MEKK2  with Flag-tagged specific antibody from lysates of HEK293T  cells co-transfected with plasmids expressing Flag-tagged MEKK2  and Myc-tagged wild-type NEDD4L  or mutant NEDD4L  with C2 (∆C2), WW (∆WW) or HECT (∆HECT) domain deleted. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Flag: 
Myc: 
MEKK2: 10746
NEDD4L: 83814"
Figure legend: "(H)Immunoblot  analysis of total ubiquitination  of Flag-tagged MEKK2  following immunoprecipitating MEKK2  with anti-Flag  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing Flag-tagged MEKK2, Myc-tagged NEDD4L, and HA-tagged wild-type or K6O, K11O, K27O, K29O, K33O, K48O, K63O mutant Ub. (I)Immunoblot  analysis of total ubiquitination  of Flag-tagged MEKK2  following immunoprecipitating MEKK2  with anti-Flag  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing Flag-tagged MEKK2, Myc-tagged NEDD4L, and HA-tagged wild-type or K6R, K11R, K27R, K29R, K33R, K48R, K63R mutant Ub. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
MEKK2: 10746
NEDD4L: 83814
Ub: 7311///6233///7316///7314"
Figure legend: "(J)Immunoblot  analysis of total ubiquitination  of Flag-tagged MEKK2  following immunoprecipitating MEKK2  with anti-Flag  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing Flag-tagged MEKK2, increased dosage of Myc-tagged NEDD4L, and HA-tagged wild-type, K27O, or K63O mutant Ub. Data information: All experiments were performed three times, and representative data are shown."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
MEKK2: 10746
NEDD4L: 83814
Ub: 7311///6233///7316///7314"
Figure legend: "(A, Immunoblot  analysis of phosphorylated p38  (p-p38), phosphorylated NF-κB p65  (P-P65), MEKK2  and actin  in HeLa  cells (A) transfected with Mekk2  siRNA (siMekk2) or control RNA (siNC) and stimulated with IL-17 (HeLa  cells 50 ng/ml, for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Mekk2: 10746"
Figure legend: "B) Immunoblot  analysis of phosphorylated p38  (p-p38), phosphorylated NF-κB p65  (P-P65), MEKK2  and actin  in MEFs (B) transfected with Mekk2  siRNA (siMekk2) or control RNA (siNC) and stimulated with  IL-17 MEFs  100ng/ml) for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Mekk2: 26405"
Figure legend: "(C,  Realtime PCR analysis of  Il-6, Cxcl2, and Ccl20  mRNA expression in HeLa  cells (C) transfected with siRNA (siMekk2) or control RNA (siNC) and stimulated with   IL-17 (HeLa  cells 50 ng/ml, for indicated time  (n = 3 technical replicates). Data information: Data are shown as the mean ± s.e.m. of technical replicates. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Ccl20: 6364
Cxcl2: 2920
Il-6: 3569
Mekk2: 10746"
Figure legend: "D)  Realtime PCR analysis of  Il-6, Cxcl2, and Ccl20  mRNA expression in MEFs (D) transfected with siRNA (siMekk2) or control RNA (siNC) and stimulated with IL-17 MEFs  100ng/ml) for indicated time  (n = 3 technical replicates). Data information: Data are shown as the mean ± s.e.m. of technical replicates. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Ccl20: 20297
Cxcl2: 20310
Il-6: 16193
Mekk2: 26405"
Figure legend: "(E) Immunoblot  analysis of phosphorylated p38, phosphorylated NF-κB p65  (P-P65), NEDD4L, MEKK2  and actin  in HeLa  cells transfected with control RNA (siNC), Nedd4l  siRNA (siNedd4l), Mekk2  siRNA(siMekk2) or Nedd4l  siRNA plus Mekk2  siRNA (siNedd4l+ siMekk2), and stimulated with   IL-17(50 ng/ml) for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Mekk2: 10746
Nedd4l: 23327"
Figure legend: "(F) Immunoblot  analysis of phosphorylated p38, phosphorylated NF-κB p65  (p-p65), NEDD4L, MEKK2  and actin  in Nedd4l+/+ and Nedd4l-/-MEFs  transfected with Mekk2  siRNA (siMekk2) or control RNA (siNc), and stimulated with   IL-17 (100 ng/ml) for indicated time. Data information: Numbers between two blots  indicate densitometry  of phosphorylated  proteins relative to that of total proteins, respectively. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Mekk2: 26405
Nedd4l: 83814"
Figure legend: "(G, Realtime PCR  analysis of  Il-6, Cxcl2, and Ccl20  mRNA expression in HeLa  cells (G) treated as described in (E) (n = 3 technical replicates). Data information: Data are shown as the mean ± s.e.m. of technical replicates. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Ccl20: 6364
Cxcl2: 2920
Il-6: 3569"
Figure legend: "H) Realtime PCR analysis of  Il-6, Cxcl2, and Ccl20  mRNA expression in MEFs (H) treated as described in (F) (n = 3 technical replicates). Data information: Data are shown as the mean ± s.e.m. of technical replicates. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Ccl20: 20297
Cxcl2: 20310
Il-6: 16193"
Figure legend: "(B) Realtime PCR  analysis of Il-6, Cxcl2, and Ccl20  mRNA expression in HeLa  cells transfected with HA-tagged MEKK2  S520A or control vector, and stimulated with IL-17 (50 ng/ml) for indicated time  (n = 3 technical replicates). Data information: Data are shown as the mean ± s.e.m. of technical replicates. All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"HA: 
Ccl20: 6364
Cxcl2: 2920
Il-6: 3569
MEKK2: 10746"
Figure legend: "(E)Immunoblot  analysis of Ser520 phosphorylation of MEKK2 immunoprecipitated  from HeLa  cells transfected with Tak1-specific (siTak1) or control RNA (siNC), and then stimulated with  IL-17 (50 ng/ml) for indicated time. Data information: All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Tak1: 7182"
Figure legend: "(F)Immunoblot  analysis of Myc-tagged NEDD4L co-immunoprecipitated with anti-HA  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing Myc-tagged NEDD4L and HA-tagged wild-type MEKK2 or mutant MEKK2  (S520A). Data information: All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"HA: 
Myc: 
MEKK2: 10746
NEDD4L: 83814"
Figure legend: "(G)Immunoblot  analysis of total ubiquitination  of HA-tagged MEKK2  and HA-tagged MEKK2(S520A) following precipitation of MEKK2  with anti-HA  antibody from lysates of HEK293T  cells co-transfected with plasmids expressing HA-tagged MEKK2  or HA-tagged MEKK2(S520A) together with Myc-tagged NEDD4L  and Flag-tagged Ub. Data information: All experiments were performed two times, and representative data are shown."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
MEKK2: 10746
NEDD4L: 83814
Ub: 7311///6233///7316///7314"
Figure legend: "A and B) Confocal microscopy images showing mitochondrial fragmentation in HBV- and HBx-expressing cells, respectively. Huh7 cells were transiently transfected with HBV (A) or the HBx-flag construct (B). At 2 days post-transfection, cells prestained with MitoTracker (Mito, white) were immunostained with anti-HBsAg (A, green) and anti-flag (B, green) antibodies, respectively. In the zoomed images, typical tubular mitochondria in untransfected cells and fragmented mitochondria in transfected cells are shown."
NCBI gene IDs:
"HBx: 944566"
Figure legend: "(D-F) Confocal immunofluorescence showing mitochondrial translocation of Drp1 in HBV- and HBx-expressing cells, respectively. Huh7 cells transfected with HBV (D and E) or HBx-flag construct (F) were immunostained with antibodies specific to TOM20 (red), Drp1 (D, green), and phospho-Drp1 (Ser616) (E and F, green), respectively. HBV and HBx gene expression (white) was verified using anti-HBsAg (D and E) and anti-flag (F) antibodies, respectively. In the zoomed images, the yellow color indicates the merge of Drp1 or phospho-Drp1 (Ser616) with mitochondria. (A, B, D, E, and F) Transfected (+) and untransfected (−) cells are marked. Nuclei were stained with DAPI (blue)."
NCBI gene IDs:
"HBx: 944566"
Figure legend: "(D) Mfn2 protein in whole cell lysates extracted from HepAD38 cells transfected with non-targeting (NT) and Parkin (P) siRNA, respectively, for 48 h was immunoprecipitated by anti-Mfn2 antibody, followed by immunoblotting (IB) with anti-ubiquitin (Ub) antibody. Normal mouse IgG was used as a control for immunoprecipitation (IP). The protein expression was analyzed by Western blotting with antibodies specific to Mfn2, Parkin, and β-actin proteins. ("
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(E) Intracellular mRNA levels of Parkin, PINK1, and LC3B were analyzed by real-time qRT-PCR. GAPDH was used to normalize changes in Parkin, PINK1, and LC3B gene expression."
NCBI gene IDs:
"GAPDH: 2597
LC3B: 81631
Parkin: 5071
PINK1: 65018"
Figure legend: "(B) Huh7 cells transiently expressing Mito-mRFP-EGFP were transfected with HBV, HBx-flag, and HBV-ΔX constructs, respectively, for 48 h. Cells were immunostained with antibodies specific to HBsAg and flag (white), respectively. Nuclei were stained with DAPI (blue). Transfected (+) and untransfected (−) cells are marked. In the zoomed images, fluorescence signals indicate the expression of Mito-mRFP-EGFP targeting mitochondria: yellow color, no mitophagy; red color, mitophagy."
NCBI gene IDs:
"HBx: 944566"
Figure legend: "(A-C) Parkin silencing accelerates HBV-induced mitochondrial apoptotic signaling. HepG2 and HepAD38 cells grown in the absence or presence of tetracycline were transfected with non-targeting (NT) and Parkin siRNA, respectively, for 72 h. Cells were used for Western blot analysis using antibodies specific to the indicated proteins (A), caspase-3/7 activity assay (B), and TUNEL assay (C)"
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(B) The DDL transcripts and growth phenotype of ddl-6 and ddl-7. DDL transcripts were detected in fully expanded leaves of four-week-old plants by qRT-PCR (left panel). The expression of DDL in WT Col-0 was set as 1. Plants grown under 12-hr light/12-hr dark condition for 4 weeks are shown (right panel). Bar=1cm."
NCBI gene IDs:
"DDL: 821601
ddl: 821601"
Figure legend: "(C) ddl-6 and ddl-7 are more susceptible to Pst DC3000 infections. Leaves of four-week-old plants were inoculated with Pst DC3000 at OD600=5x10-4. Bacterial numbers were counted at 0 and 3 dpi. Leaf pictures were taken at 3 dpi."
NCBI gene IDs:
"ddl: 821601"
Figure legend: "(D) The ddl-1 mutant in the Ws background is more susceptible to Pst DC3000 infection."
NCBI gene IDs:
"ddl: 821601"