EMBO/SourceData huggingface dataset:
Figure legend: "C. Left panel, in vivo FLIM-FRET measurements in interphase BJH2B-2FPs control ESCs (top) and BJH2B-2FPs Mki67-/- ESCs (clone #1). Mean FRET efficiency is displayed using a continuous pseudo-colour scale from 0 to 25%. Scale bars, 10 µm. Right panel, box-and-Whisker plots represent the FRET efficiency (%) in WT ESCs (n = 77 cells) and Mki67-/- ESCs clones clone #1 (n = 86 cells), #2 (n = 95 cells) and #3 (n = 110 cells). The thick line represents median, the boxes correspond to the FRET % values from the 25-75th percentiles of the median, and the whiskers cover the 10-90 percentiles value range. ****, p &lt; 0.0001, Mann-Whitney test."
NCBI gene IDs:
"H2B: 
Mki67: 4288"
Figure legend: "B. Left panels, nucleosome-rich foci segmentation in naive ESCs and EpiLCs using the FRENETIC tool. Nuclei are outlined with yellow dashed lines. Scale bars, 10µm. Right panel, Box-and-Whisker plots of the mean number of foci per nucleus in naive BJH2B-2FPs ESCs (n = 150 cells) and in primed EpiLCs (n = 137 cells). The thick line represents median, the boxes correspond to the number of foci from the 25-75th percentiles of the median"
NCBI gene IDs:
"H2B: "
Figure legend: "Strep-Tactin pull down  of GIDAnt (strep-tagged at Gid8 C-terminus) probing binding  of Gid1057-292 and Gid4117-362 to the complex visualized with Coomassie-stained SDS-PAGE. The experiment was performed with WT and C-terminal deletion (∆C) of the substrate receptors (∆289-292 (FEIA) and ∆359-362 (FEFA) for Gid10 and Gid4, respectively) and WT and mutant (mut, Gid5W606A/Y613A/Q649A) GIDAnt."
NCBI gene IDs:
"Gid5: 854795"
Figure legend: "Lysates from wildtype and ∆Gid2 yeast  strains expressing endogenously tagged 3xFLAG-Gid10 that were grown at 42°C for one hour, and then returned to 30°C for the indicated timepoints  were run on an SDS-PAGE gel and immunoblotted  with αFLAG and αPGK."
NCBI gene IDs:
"Gid2: 851842"
Figure legend: "Lysates from wildtype, Gid5W606A,Y613A,Q649A, and Gid10∆C strains expressing endogenously tagged 3xFLAG-Gid10 that were grown at 42°C for one hour, and then returned to 30°C for the indicated timepoints  were run on an SDS-PAGE gel and immunoblotted  with αFLAG and αPGK."
NCBI gene IDs:
"Gid10: 852957
Gid5: 854795"
Figure legend: "Lysates from wildtype, ∆Gid4, and Gid4∆C strains expressing endogenously tagged 3xFLAG-Gid10 that were grown at 42°C for one hour, and then returned to 30°C for the indicated timepoints  were run on an  SDS-PAGE gel and immunoblotted  with αFLAG  and αPGK."
NCBI gene IDs:
"Gid4: 852402"
Figure legend: "Wildtype and  Gid10 overexpressing yeast  strains expressing  endogenously tagged Gid4 were grown for 19 hours in YPE, and transitioned to YPD  for the indicated timepoints. Lysates were run on an SDS-PAGE gel and immunoblotted  with αFLAG  and αPGK. Points represent mean, error bars represent standard deviation (n&gt;3 biological replicates)."
NCBI gene IDs:
"Gid10: 852957"
Figure legend: "A. RT-PCR analysis of the expression of β-actin, Trpv1, Trpv2, Trpv3 and Trpv4 using mouse differentiated brown adipocytes after 29 (upper) and 35 (lower) thermal cycles with (RT (+)) and without (RT (-)) reverse transcription (RT). Control (Ct.) lanes indicate the results with each plasmid DNA as a template."
NCBI gene IDs:
"β-actin: 11461
Trpv1: 193034
Trpv2: 22368
Trpv3: 246788
Trpv4: 63873"
Figure legend: "B. Results of real-time RT-PCR analysis of Trpv1, Trpv2, Trpv3 and Trpv4 expression using mouse differentiated brown adipocytes. Expression levels of mRNA were normalized to that of the ribosomal protein gene (36B4), a housekeeping gene un-affected by adipogenesis. Data are presented as mean ± SEM, n = 6."
NCBI gene IDs:
"36B4: 
Trpv1: 193034
Trpv2: 22368
Trpv3: 246788
Trpv4: 63873"
Figure legend: "C. Results of real-time PCR analysis of Trpv1, Trpv2, Trpv3 and Trpv4 expression using mouse interscapular brown adipose tissue (iBAT). mRNA expression levels were normalized to that of 36B4. Data are presented as mean ± SEM, n = 5."
NCBI gene IDs:
"36B4: 
Trpv1: 193034
Trpv2: 22368
Trpv3: 246788
Trpv4: 63873"
Figure legend: "D. Western blot results of TRPV2 and tubulin from WT and TRPV2KO brown adipocytes. Upper bands in the TRPV2 blots likely indicate glycosylated forms."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "E. Averaged traces of [Ca2+]i changes in response to 500 µmol/L 2APB in differentiated brown adipocytes from WT (black) and TRPV2KO (red) mice. One µmol/L NE was used to confirm differentiation. Five µmol/L ionomycin was used to confirm cell viability. Ratio values correspond to the real [Ca2+]i of differentiated mousebrown adipocytes. Data are presented as mean ± SEM, n = 149 of WT cells, and n = 112 of TRPV2KO brown adipocytes; ** P &lt; 0.01. Unpaired Student's t-test."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "A. Results of real-time RT-PCR analysis of Trpv1, Trpv2, Trpv3 and Trpv4 expression in mouse pre-adipocytes and differentiated brown adipocytes. Expression levels of mRNA were normalized to those of 36B4. Data are presented as mean ± SEM, n = 6. * P &lt; 0.05 vs. pre-adipocytes. Unpaired Student's t-test."
NCBI gene IDs:
"36B4: 
Trpv1: 193034
Trpv2: 22368
Trpv3: 246788
Trpv4: 63873"
Figure legend: "C and D. Comparison of the numbers of 6 day-differentiated mouse brown adipocytes (C) and triglyceride levels (D) in the cells from WT and TRPV2KO mice with different differentiation media. 1/10 suppl. indicates differentiation medium ten-time-diluted with DMEM. Mean ± SEM, n = 8, ** P &lt; 0.01 vs. control group, ##P &lt; 0.01 vs. WT group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "A. Basal mRNA expression of Ucp1, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (Pgc1α), peroxisome proliferator-activated receptorγ(Pparγ) and β3-adrenergic receptor 3 (Adrb3) in the differentiated brown adipocytes from WT and TRPV2KO mice. Data are presented as mean ± SEM, n = 5; ** P &lt; 0.01 vs. WT. Unpaired Student's t-test."
NCBI gene IDs:
"Adrb3: 11556
Pparγ: 19016
Pgc1α: 19017
TRPV2: 22368
Ucp1: 22227"
Figure legend: "B and C. Changes in Ucp1 (B) and Pgc1α(C) mRNA expression in the differentiated brown adipocytes from WT and TRPV2KO mice with and without 10 µmol/L isoproterenol (ISO) for 4 h. Data are presented as mean ± SEM, n = 5; ** P &lt; 0.01 vs. DMSO group; # P &lt; 0.05; ## P &lt; 0.01 vs. WT group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"Pgc1α: 19017
TRPV2: 22368
Ucp1: 22227"
Figure legend: "D and E. Changes in Ucp1 mRNA expression (D) and non-esterified fatty acid (NEFA) release (E) in the differentiated brown adipocytes from WT and TRPV2KO mice with or without 10 µmol/L forskolin for 4 h. Data are presented as mean ± SEM, n = 6; * P &lt; 0.05; ** P &lt; 0.01 vs. DMSO group; ## P &lt; 0.01 vs. WT group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"TRPV2: 22368
Ucp1: 22227"
Figure legend: "F and G. Changes in Ucp1 mRNA (F) and Pgc1α mRNA (G) in the differentiated brown adipocytes treated with 10 µmol/L ISO alone or 10 µmol/L ISO plus 10 µmol/L BAPTA-AM for 4 h. Data are presented as mean ± SEM, n = 6; * P &lt; 0.05; ** P &lt; 0.01 vs. DMSO group; ## P &lt; 0.01 vs. ISO group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"Pgc1α: 19017
Ucp1: 22227"
Figure legend: "B and C. Changes in food intake (B) and water intake (C) from 3-weeks to 8-weeks of ages between WT and TRPV2KO mice (n = 6)."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "D. Weights of tissues related to energy metabolism normalized to their body weights in WT and TRPV2KO mice (n = 15)."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "E. The expression levels of mRNA related to energy metabolism in iBAT from WT and TRPV2KO mice. mRNA expression levels of Ucp1, Pgc1a, Ppary, Adrb3, cytochrome c oxidase subunit 4 isoform 1 (Cox4i1), PR domain containing 16 (Prdm16), Ucp2, lipoprotein lipase (Lpl) and cluster of differentiation 36 (Cd36) were examined and normalized to the levels of 36B4. Data are presented as mean ± SEM, n = 15; * P &lt; 0.05 vs. WT group; ** P &lt; 0.01 vs. WT group. Unpaired Student's t-test."
NCBI gene IDs:
"36B4: 
Adrb3: 11556
Cd36: 12491
Cox4i1: 12857
Lpl: 16956
Ppary: 19016
Pgc1a: 10891
Prdm16: 70673
TRPV2: 22368
Ucp1: 22227
Ucp2: 22228"
Figure legend: "A. Representative morphological results of iBAT by hematoxylin and eosin staining from 8-week WT and TRPV2KO mice. Scale bars indicate 100 μm.B. Comparison of lipid droplet size histograms from 8-week-old WT (black) and TRPV2KO (red) iBAT with hematoxylin and eosin staining. Mean values are 9.5 ± 0.2 µm in 8-week-old WT adipocytes, and 14.7 ± 0.2 µm in 8-week-old TRPV2KO adipocytes (P &lt; 0.01). 1000 to 1400 droplets were counted. Data are presented as mean ± SEM, n = 4.C. Comparison of adipocyte size histograms from 8-week-old WT (black) and TRPV2KO (red) iBAT with hematoxylin and eosin staining. 800 to 1000 cells were counted. Data are presented as mean ± SEM, n = 4.D. Mean diameters of adipocytes in 8-week-old WT mice (black) and TRPV2KO mice (red). Mean values are 15.8 ± 0.4 µm in 8-week-old WT adipocytes, and 19.8 ± 0.3 µm in 8-week-old TRPV2KO adipocytes. Data are presented as mean ± SEM, n = 4; * P &lt; 0.05 vs. WT group. Unpaired Student's t-test."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "A, B, C and D. Changes in mRNA expression of Ucp1 (A), Pgc1α (B), Pparγ (C) and Trpv2 (D) in iBAT of WT and TRPV2KO mice before (25oC), after 1 day and 3 days cold (4oC) exposure. Mean ± SEM, n = 5 - 8; * P &lt; 0.05; ** P &lt; 0.01 vs. 25oC group; # P &lt; 0.05 vs. WT group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"Pparγ: 19016
Pgc1α: 19017
Trpv2: 22368
TRPV2: 22368
Ucp1: 22227"
Figure legend: "E and F. Western blot results of UCP1 protein in iBAT from WT and TRPV2KO mice before (25oC) and after 3 days cold (4oC) exposure (E). Comparison of UCP1 protein levels before and after cold exposure in iBAT from WT and TRPV2KO mice (F). Mean ± SEM, n = 6; * P &lt; 0.05 vs. 25oC group; # P &lt; 0.05 vs. WT group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "G and H. Averages of core body temperatures (G) and activities (H) of WT and TRPV2KO mice with or without cold (4oC) exposure. Data are presented as mean ± SEM, n = 5; * P &lt; 0.05 vs. WT group. Unpaired Student's t-test."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "A, B and C. Changes in mRNA expression of Ucp1 (A), Pgc1α (B) and Pparγ(C) from WT and TRPV2KO iBAT 4 h after intraperitoneal administration (i.p., arrows) of saline or a selective β3-adrenergic receptor agonist, BRL37344 (600 µg/kg body weight). Mean ± SEM, n = 5 - 7; * P &lt; 0.05 vs. saline group; # P &lt; 0.01 vs. WT BRL37344 administration group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction."
NCBI gene IDs:
"Pparγ: 19016
Pgc1α: 19017
TRPV2: 22368
Ucp1: 22227"
Figure legend: "D and E. Average traces of changes in iBAT temperature (D) or rectal body temperature (E) from WT and TRPV2KO mice after BRL37344 (600 µg/kg body weight) administration (i.p., arrows). Mean ± SEM, n = 5. * P &lt; 0.05 vs. WT group. Unpaired Student's t-test."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "F and G. iBAT NE turnover rates (F) and rate constants k (G) in WT and TRPV2KO mice upon cold exposure (4oC) for 4 h. Data are presented as mean ± SEM, n = 8."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "A. Body weight changes between WT and TRPV2KO mice treated with high fat diet (HFD) for continuous 8 weeks from 13-week-old."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "B and C. Blood glucose level (B) and plasma insulin level (C) of WT and TRPV2KO mice after 8-week HFD treatment."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "D. Weights of tissues related to energy metabolism in WT and TRPV2KO mice after 8-week HFD treatment."
NCBI gene IDs:
"TRPV2: 22368"
Figure legend: "E. mRNA expression of Ucp1 and Pgc1α in iBAT from WT and TRPV2KO mice after 8-week HFD treatment. All data are presented as mean ± SEM, WT mice (n = 6), TRPV2KO mice (n = 8); * P &lt; 0.05; ** P &lt; 0.01 vs. WT group. Unpaired Student's t-test."
NCBI gene IDs:
"Pgc1α: 19017
TRPV2: 22368
Ucp1: 22227"
Figure legend: "(a) Western blot analysis showing the replacement of endogenous Beclin 1 with Beclin 1-EGFP in Becn1-/-;Becn1-EGFP/+ mice, as detected by an anti-Beclin 1 antibody."
NCBI gene IDs:
"Beclin 1: 56208
Becn1: 56208"
Figure legend: "(b) Coomassie-stained SDS-PAGE showing the Beclin 1-interacting proteins immuno-isolated from brain and liver of the 'rescued' mice (lanes 2 and 4) and of control Becn1+/- littermates (lanes 1 and 3), using an anti-GFP antibody. Proteins in the gel bands were extracted and identified by mass spectrometry as Vps15/p150 (band 1), Vps34/class III PI(3)K (band 3), UVRAG (band 4), Beclin 1-EGFP (band 5), Atg14L (band 6, asterisk, gi|27369860) and Rubicon (band 2, asterisk, gi|45708948). UVRAG levels varied with different affinity-purification conditions, suggesting an unstable association of UVRAG with the complex."
NCBI gene IDs:
"Beclin 1: 56208
Becn1: 56208"
Figure legend: "(d) Western blot analysis of Atg14L, Rubicon, Vps34 and Beclin 1 in gel filtration fractions from wild-type mouse liver extract showed co-elution of these proteins in fractions 38-45. Atg14L was also eluted in later fractions 51-56. The fractions for the peak elution of thyroglobulin (670K) and γ-globulin (158K) are indicated by arrows. Control siRNA-transfected NIH 3T3 cell lysate was loaded as a positive control (labelled as 1) for the migration position of the Atg14L protein on SDS-PAGE; Atg14L siRNA-transfected NIH 3T3 cell lysate was loaded as a negative control (labelled as 2)."
NCBI gene IDs:
"Atg14L: 100504663"
Figure legend: "(a) Beclin 1 or Atg14L siRNA reduced Atg14L levels and increased p62/SQSTM1 and LC3 II levels under normal and nutrient-starvation conditions in NIH 3T3 cells."
NCBI gene IDs:
"Atg14L: 100504663
Beclin 1: 56208"
Figure legend: "(b) Compared with control siRNA, Atg14L siRNA decreased long-lived protein degradation in NIH 3T3 cells under normal (*P = 0.007) and starvation (*P = 5 × 10−6) conditions (one-tailed Student's t-test with equal variances, n = 4). This difference was diminished when the starved cells were treated with 3-methyladenine (3MA, 10 mM), a PI(3)K inhibitor."
NCBI gene IDs:
"Atg14L: 100504663"
Figure legend: "(c) Vps34 kinase assay. HEK 293T cells were co-transfected with Myc-Vps34-Vps15 and Flag-Atg14L or Flag vector, either in the absence or in the presence of Beclin 1-EGFP. Myc-Vps34-Vps15 was immunoprecipitated by anti-Myc antibody for the in vitro kinase assay. The resulting radioactive PI(3)P was separated by thin-layer chromatography (TLC), quantified and normalized against the amount of immunoprecipitated Myc-tagged Vps34 as measured by western blot (upper panel). The quantified results (lower panel) show that overexpressing Atg14L significantly upregulated Vps34 kinase activity by 2.5-fold, but only when Beclin 1 was also overexpressed (*P = 0.04, one-tailed Student's t-test with unequal variances, n = 5)."
NCBI gene IDs:
"Atg14L: 22863
Beclin 1: 8678
Vps34: 5289
Vps15: 30849"
Figure legend: "(e) Electron microscopy images show large structures (asterisks) that are often enwrapped with double membranes in the HEK 293T cells co-transfected with Atg14L-EGFP and Beclin 1-AsRed: concentric membrane 'rings' (panel 1); two large structures (3-5 μm in diameter, panel 2) containing material with high electron density (inset, enwrapping double membranes); numerous autophagosomes (arrows, panel 3) in the cytoplasm; immuno-electron microscopy image of a Atg14L-Beclin 1 structure (labelled with anti-GFP antibody and developed by DAB, panel 4) enwrapped with concentric membrane 'rings'. M, mitochondria; N, nucleus. Scale bar, 500 nm."
NCBI gene IDs:
"Atg14L: 22863
Beclin 1: 8678"
Figure legend: "(b) Overexpression of Rubicon resulted in increased levels of p62 under both normal and nutrient-starved conditions in HEK 293 cells either stably expressing (upper rows) or transiently transfected with (lower rows) Rubicon-EGFP. The control cells were either stably expressing or transiently transfected with the EGFP-N3 vector."
NCBI gene IDs:
"N3: 
Rubicon: 9711"
Figure legend: "(c) Vps34 kinase activity. HEK 293T cells were co-transfected with Myc-Vps34-Vps15 and Flag-Rubicon or Flag vector, either in the absence or in the presence of Beclin 1-EGFP. Myc-Vps34-Vps15 was immunoprecipitated by an anti-Myc antibody and used for the in vitro kinase assay. The resulting radioactive PI(3)P was separated by TLC, quantified and normalized against the amount of immunoprecipitated Myc-tagged Vps34, as measured by western blotting (upper panel). The quantified results (lower panel) show that overexpressing Rubicon significantly downregulated the Vps34 kinase activity to 0.58-fold, but only without Beclin 1 overexpression (*P = 0.04, one-tailed Student's t-test with unequal variances, n = 4)."
NCBI gene IDs:
"Beclin 1: 8678
Rubicon: 9711
Vps34: 5289
Vps15: 30849"
Figure legend: "(d) Effect of overexpressing Flag-Rubicon on autophagosome acidification, as monitored by mCherry-GFP-LC3 fluorescence. HeLa cells were transiently co-transfected with mCherry-GFP-LC3 and Flag-Rubicon (or control Flag vector). Cells co-expressing mCherry-GFP-LC3 and control Flag vector contained many red-only puncta along with yellow (indicating the presence of both red and green) puncta, suggesting the presence of both autolysosomes and nascent autophagosomes (upper panel). In contrast, cells co-expressing mCherry-GFP-LC3 and Flag-Rubicon contained primarily yellow or white puncta, suggesting the presence of only nascent autophagosomes (lower panel, white arrows). Notably, some cells, which were co-transfected with mCherry-GFP-LC3 and Flag-Rubicon but expressed high levels of mCherry-GFP-LC3 and undetectable levels of FLAG-Rubicon, contained many red-only puncta (lower panel, yellow arrows). (e) Quantification of the results in d show that overexpressing Flag-Rubicon markedly reduced the percentage of red-only puncta (mCherry-LC3) from 39% in the control Flag vector-transfected cells to 2% in the Flag-Rubicon-transfected cells (*P = 2 × 10−26, one-tailed Student's t-test with unequal variances, n = 30), indicating that overexpression of Rubicon blocks autophagosome acidification or maturation. See Supplementary Information, Fig. S6 for full scans of blots in a-c."
NCBI gene IDs:
"Rubicon: 9711
LC3: 440738///81631///84557"
Figure legend: "(a) Colocalization of Rubicon-EGFP-associated structures with the late endosome/lysosome marker Lamp1 (arrows) in HeLa cells transfected with Rubicon-EGFP. Note that some of the Rubicon-EGFP-associated structures show a 'ring' shape (yellow arrows). Scale bar, 10 μm."
NCBI gene IDs:
"Rubicon: 9711"
Figure legend: "(b) Partial colocalization of Rubicon-EGFP-associated structures with the MVB marker LBPA (arrows) in HeLa cells transfected with Rubicon-EGFP. Scale bar, 10 μm."
NCBI gene IDs:
"Rubicon: 9711"
Figure legend: "(c) Representative ultrastructural images show aberrant expansion of late endosomal/lysosomal structures in HEK 293T cells overexpressing Rubicon-EGFP. These abnormal organelles are large in size, with high (orange arrows) or low (black arrows) electron density. Some enclose small vesicles (purple arrows) and some resemble the MVB (blue arrows). Scale bars, 500 nm."
NCBI gene IDs:
"Rubicon: 9711"
Figure legend: "(d) Representative ultrastructural images show late endosome/lysosome-like structures that are labelled with anti-GFP gold particles (panels 3, 4) in HEK 293T cells transiently transfected with Rubicon-EGFP. These structures are enwrapped by double membranes (panel 4 inset) and co-labelled by anti-GFP (developed by DAB) and anti-Lamp1 (gold enhanced) (panels 5-7) antibodies. Note that mitochondria are mostly negative for Rubicon-EGFP (panel 4). The negative controls are without antibody (panels 1-2). M, mitochondria. Scale bars, 200 nm."
NCBI gene IDs:
"Rubicon: 9711"
Figure legend: "(c) Subcellular localization of transiently transfected Rubicon-EGFP, RubiconΔRUN-EGFP, RubiconΔC-EGFP or RubiconΔRUNΔC-EGFP in HeLa cells. In contrast to punctate Rubicon-EGFP and RubiconΔRUN-EGFP, RubiconΔC-EGFP and RubiconΔRUNΔC-EGFP were dispersed in the cytoplasm. ΔRUN, RUN domain deletion; ΔC, cysteine-rich domain deletion. Scale bars, 10 μm."
NCBI gene IDs:
"Rubicon: 9711"
Figure legend: "(d, e) Absence of full-length Beclin 1 (d) or Beclin 1-CE mutant (e) (red) on the Rubicon-EGFP-positive structures (green) in HEK 293 cells stably expressing Rubicon-EGFP. These cells were transiently transfected with either Beclin 1-AsRed (d) or Flag-Beclin 1-CE (e; that is, the Flag-tagged Beclin 1 mutant containing both CCD and ECD, which mediate the Beclin 1-Rubicon interaction as shown in Supplementary Information, Fig. S3h). Scale bars, 10 μm."
NCBI gene IDs:
"Beclin 1: 8678"
Figure legend: "(f) The formation of the Rubicon-EGFP-positive structures was not affected by siRNA knockdown of Beclin 1 in HEK 293 cells stably expressing Rubicon-EGFP."
NCBI gene IDs:
"Beclin 1: 8678
Rubicon: 9711"
Figure legend: "mtON-expressing animals in a complex I mutant background (gas-1) were scored for locomotion speed in the presence of food by counting body bends per minute. mtON activation rescued the decreased locomotion of the gas-1 mutant background, one-way ANOVA with Tukey's post hoc test, -ATR, +light vs. +ATR, +light *p = 0.0145, +ATR, +light vs. wildtype (WT) *p = 0.0008 (-ATR, -light vs +ATR, +light p = 0.0272, +ATR, -light vs. +ATR, +light p = 0.0332, all conditions vs WT, p &lt; 0.001, n = 30, 30,30,41,41 animals each bar from left to right). Data show mean ± standard deviation."
NCBI gene IDs:
"gas-1: 181646"
Figure legend: "Locomotion was assessed by counting body bends per minute. Wild type animals were compared to aak-2(ok524) mutant animals. 2-sample, 2-tailed unpaired t-test *p &lt; 0.0001, wild type n = 35, aak-2 n = 39 animals across at least 3 days. Data show mean ± standard deviation."
NCBI gene IDs:
"aak-2: 181727"
Figure legend: "(C) Immunocytochemistry showing post-synaptic marker PSD-95 (red), pre-synaptic marker Synapsin-I (green), dendritic marker Map2 (blue) and co-localization of PSD-95 and Synapsin-I from dissociated Nedd4-2 WT or Nedd4-2 cKO hippocampal neurons at DIV 16. Representative secondary dendrites (left) and quantification of colocalized synaptic puncta number and area (right) (n = 36 for Nedd4-2 WT and Nedd4-2 cKO neurons) are shown. Scale bar: 5 µm."
NCBI gene IDs:
"Nedd4-2: 83814"
Figure legend: "(F) A train of high frequency stimulation (HFS; 100 Hz for 1s) induced early-phase LTP (E-LTP) at Schaffer collateral synapses in Nedd4-2 WT (n = 7 slices from 6 mice) and Nedd4-2 cKO (n = 6 slices from 5 mice) mice. Representative fEPSP traces were recorded before and 60 min after LTP induction (Scale bars: 0.5 mV, 5 ms). Summary bar graphs showing the fEPSP slopes measured 50-60 min after a HFS at Schaffer collateral synapses was on the right. (G) Late-phase LTP (L-LTP) induced by four trains of HFS in Nedd4-2 WT slices (n = 7 slices from 7 mice) and Nedd4-2 cKO slices (n = 9 slices from 8 mice). Representative fEPSP traces were recorded before and 180 min after LTP induction (Scale bars: 0.5 mV, 5 ms). Summary bar graphs showing the fEPSP slopes measured 160-180 min after L-LTP induction at Schaffer collateral synapses was on the right. "
NCBI gene IDs:
"Nedd4-2: 83814"
Figure legend: "(B) Barnes maze test from Nedd4-2 WT (n = 8) or Nedd4-2 cKO (n = 8) mice (6-8 weeks old). Schematic representation of Barnes maze (top left). Mice were trained for 4 days with three training trials on each day to locate the escape box (black circle). Learning curve during 4 training days was shown by the escape latency and the number of errors before escaping (top right). Schematic representation of Barnes maze on probe trials (bottom left). Quadrant occupancy on probe trial at day5 and at day12 (bottom right) were assessed by the time spent in the target area (green quadrant)."
NCBI gene IDs:
"Nedd4-2: 83814"