EMBO/sd-character-level-ner huggingface dataset:
(b) Detection of NSP2-rich condensates formed in RV-infected cells using DNA-PAINT approach. Transient binding and dissociation of a Cy3B-dye labelled ssDNA probe P1* (complementary to ssDNA P1) generates blinking at the target sites (ON/OFF) used for stochastic super-resolution imaging.
Representative confocal images of CAD cells cultured in control conditions or treated with 0.2% DMSO, 200 µM H2O2, 200 ng/mL Wnt7a, 10 μM KN-93, 200 ng/mL Wnt7a plus 10 μM KN-93, 1 μM TAT or 200 ng/mL Wnt7a plus 1 μM TAT for 4 h. Cells were fixed and stained with WGA (green) and DAPI (blue). Percentage of TNT-connected CAD cells with each of the indicated treatments.
(c) Relative enrichment of H3K4me3 at APX2 and HSP18.2 in control non-primed (NP), SA187-colonized non-primed plants (NP+187), 37°C-primed (P) and 37°C-primed SA187-colonized plants (P+187) at 24 and 72 h after priming as determined by chromatin immunoprecipitation-qPCR for the indicated regions of APX2 and HSP18.2 (Fig 3F). Data information: For H3K4me3 enrichment analysis, amplification values were normalized to input and H3 and region 1 of non-primed (NP) plants. All treatments are compared with direct 44°C HS treatment for statistical significance. All plots represent the means of 3 biological replicates. Error bars indicate SE. Asterisks indicate a statistical difference based on the Student's t-test *P ≤ 0.05; **P ≤ 0.01; **P ≤ 0.001 for differences between NP in comparison to NP+187, P and P+187 treatments.
B Electron microscopy images showing typical sizes of WT and Aldh5a1−/− mice liver mitochondria. Bar, 0.5 μm.
D. Immunoprecipitation and western blotting were performed in OSCs upon RNAi treatment (kd). Even without the association of Yb, Armi, SoYb, and Vret associated. Yb and Armi remained bound to each other upon SoYb or Vret depletion. The level of SoYb (input) decreased upon Vret depletion. Likewise, the level of Vret (input) decreased upon SoYb depletion.
Measurement of dependency and flexibility of the OCR to either of Gln, FA, Glc; the assay was carried out according to the MitoFuel protocol (see Material and Methods); the superimposed bars (whose sum corresponds to the capacity) are means ± SEM of n=3 independent biological replicates (3 technical replicates each);
D, E, Time course analysis of the accumulation of NoVΔB2 RNA1 determined by RT-qPCR (D) and 21-to 23-nt vsiRNAs determined by deep sequencing (E, two independent sets) from BALB/c suckling mice infected with NoVΔB2. Mice, n=3, in each independent analysis. Data are shown as mean±SD. Normalization was done by β-actin mRNA levels for NoVΔB2 RNA1 (D) or by mature miRNAs for vsiRNAs (E). Accumulation levels of NoVΔB2 RNA1 or vsiRNAs at 3 dpi are set as 100%, respectively.
The drawing at left schematizes the svb locus, with position of the E3N enhancer. Close-up shows E3N sequence that correspond to binding sites for Pnt (red) and TCF (green). Right subpanels are pictures of posterior midguts showing expression of wild-type E3N-lacZ (E3Nwt), or E3N-Pnt-mt, and E3N-TCF-mt, as seen from X-Gal staining (cyan blue).
(j) FKBP15 was depleted in HeLa cells as in e. A representative blot from three independent experiments in triplicate is shown. Error bars indicate s.e.m.
(c) Quantitative PCR analysis of cytosolic mtDNA in LPS-primed BMDMs incubated for 1 h with rotenone (5 μM) or vehicle (DMSO) before ATP stimulation.
(D) HeLa-GFP-Parkin cells transfected with siMTPAP were incubated with 1 µM valinomycin for the indicated times. Western blotting was performed using the indicated antibodies. Data are representative of three independent experiments
D-E, cell viability of (D) Du145TXR or (E) MCF-7ADR treated with indicated agents for 72 hours. One-way ANOVA was used to analyze statistical differences. Mean with ± SD. Data information: Results are representative of three independent experiments.
Effect of endocytosis inhibition on TrkB-FL downregulation. The infarcted area of the ipsilateral hemisphere (I) was compared to the corresponding region of the contralateral area (C). Results from representative mice injected with dynasore or vehicle are shown. Different exposures are presented to facilitate visualization of dynasore effects on TrkB-FL and f32. Quantitation of TrkB-FL and TrkB-T1 in the infarcted area. Normalized protein levels are expressed relative to those of the corresponding contralateral region.
A. BMDM cells were infected with VSV (MOI, 0.1) or HSV (MOI, 5) for the indicated times. Cell lysates were analyzed by immunoblotting with the indicated antibodies.
(J) IF for Ccny (a), Ccnyl1 (b) and LRP6 (c) (low-density lipoprotein receptor-related protein 6) phosphorylated at T1479 (pLRP6) in the neocortex of E13.5 control embryos. White arrowheads in (a,b) indicate apical membrane / cortex, shown at higher magnification in the insets. High levels of LRP6 phosphorylation are detected in mitotic APs (c, white arrowheads). Scale bar 50 μm. (K) IF for Ccny(a), Ccnyl1(b) and pLRP6(c), each together with IF for Tbr2, in the neocortex of E12.5 control embryos. White arrowheads in the insets of (a, b) depict Ccny/l1 puncta in Tbr2+ BPs. High levels of LRP6 phosphorylation are detected in mitotic BPs (c, inset, white arrowhead). DNA staining for mitotic pLRP6+ BP shown in bottom right inset (c, green arrowhead). Scale bar 20 μm.
(a) Dot- or ring-shaped GFP-LC3 (LC3 dot) signals in S2 cells expressing both PGRP-LE and GFP-LC3 under the control of an actin promoter (PGRP-LE GFP-LC3) or GFP-LC3 alone (GFP-LC3) after infection with wild-type or Δhly L. monocytogenes or after 1.5 h of incubation with 5 μM rapamycin (rap). -, no infection.
p62immunohistochemistry (IHC) staining in humanbrain tissue.G-I Hematoxylin and eosin (H&amp;amp;E) staining (G) and p62immunohistochemistry analysis (H, I) of a CCM surgical sample (case n° 6 in Appendix Table S1) containing normal vessels in the peri-lesional area, which served as an internal control. Notice marked p62-positive staining in endothelial cells lining a CCM lesion (H, arrows) and p62-negative staining in endothelial cells lining a normal peri-lesional vessel (I, arrows). Scale bars: (G) 300 μm; (H, I) 100 μm. Background staining in brainparenchyma surrounding CCM lesions may be attributed to either cell debris or p62 immunoreactivity in neuronal cells and glial cells.
(B) Immunoprecipitation analysis of HEK293T cells expressing Flag-MAVS and HA-RNF34 together with Myc-Ub (K6, K11, K27, K29, K33, K48, or K63 only) as indicated. Anti-Flag immunoprecipitates were analyzed using immunoblotting with an anti-Myc or anti-Flag antibody. Levels of the transfected proteins were analyzed using immunoblotting with an anti-HA, anti-Myc or anti-Flag antibody. Cell-based studies were performed independently at least three times with comparable results.
Effect of cl-HK2pep on human B-CLL cells freshly isolated from patients. cell death, measured by cytofluorimetric analysis of Annexin V-FITC and 7-AAD staining Cells are treated with 5 µM cl-HK2pep; PD150606 (50 μM) is pre-incubated for 1 h. Experiments are carried out on samples from at least 10 patients and on CD19+, primary B lymphocytes from 5 healthy controls.
E. Representative images of two hybrid assays testing the interaction between the full-length Sir3 and full-length Sae2 proteins in WT cells expressing or not high levels of Sir4 (oeSir4 and WT respectively).
C. TUNEL staining revealed a significantly higher number of apoptotic cells in tunicamycin-treated Nox4 KO mice. n=4/group.
(A-C) HeLa cells transfected with control, VAMP3 siRNA for 4 days were transfected during the last 20 hr with ATG9L1-pEGFP and labeled with anti-EEA1 (for early endosomes) or anti-RAB11 (for recycling endosomes). The histogram in (C) shows the quantification of the colocalization of mATG9 in EEA1 or RAB11 (Manders' coefficient). Error bars, SEM. ∗∗∗p < 0.001.
Area changes of hCOs of different groups at different time points. The area of single hCO from all different batches were analyzed. Each plot represented one hCOs (Day 5, n=12; day 11, n=12; day 14, n=44; day 24, n=26; day 30, n=46; day 40, n=98; day 50, n=63; day 60, n=24 for each group from 4 independent experiments).
C, Quantification of the mini-nesprin-2G accumulation of cells migrating through narrow constrictions. Note that the mutant construct does not accumulate at the front of the nucleus. Error bars correspond to the standard deviation. Mini-nesprin-2G: n=10 cells over 4 biological replicates; Mutant: n=11 cells over 4 biological replicates. A Wilcoxon signed-rank test is used to compare matched samples, stars(*P< 0.05, **P < 0.01) denote comparisons to the measurement at the side, and pounds (#P < 0.05, ##P < 0.01) denote a comparison to the "before" time point.
(E) Electropherograms of sequenced RT-PCR amplicons generated using splenic RNA of a Braf+/floxAVKA (left) and a Braf +/AVKA;Cre mouse (right). RT-PCR amplicons were generated using the primers E14fwd and E16revNEW. Note the double peaks at the first position corresponding to the threonine/serine and alanine codons (indicated by red arrows).
c, In-gel fluorescence assay showing myristoylated ARF1 T31N mutant (a GDP-locked mutant) or ARF1 Q71L (a GTP-locked mutant) after in cells co-expressing IpaJ or catalytic mutants as indicated. Equal loading of ARF1 (middle panel) and IpaJ (lower panel) was determined by western blot analysis.
(B, C) The severity of the rosacea-like phenotypes was evaluated with the redness area (B) and score (C) (n = 5 for each group). **P <0.01, comparison between Tsc2+/- (LL37) and Tsc2+/+ (LL37) group. ##P <0.01, comparison between Tsc2+/+ (LL37) and Tsc2+/+ (Control).
A-C. Analysis of TCR nanoclustering by EM in OT-II WT and CCR5-/- naïve cells (A; n = 6 cells/genotype; WT: 3427, CCR5-/-: 3528 particles), and IL-2- (B; WT, n = 8 cells, 15419 particles; CCR5-/-, n = 6 cells, 5410 particles) or IL-15-expanded lymphoblasts (C; WT, n = 8 cells, 27518 particles; CCR5-/-, n = 7 cells, 22696 particles). A representative small field image at the top of each panel shows gold particle distribution in the cell surface replicas of anti-CD3ε-labeled cells; at bottom, quantification (mean ± SEM) of gold particles in clusters of indicated size in WT (gray bars) and CCR5-/- cells (red). Insets show the distribution of clusters of one, two, three, four, or more than four particles, and statistical analysis.
(A) Flow cytometry quantification of BV-2 Siglec-F expression levels. Cells were cotreated with 0-10 ng/mL IFNγ and 0-10 μM tofacitinib. Values are geometric mean fluorescence intensities (gMFI). Bars indicate mean ± 95% CI; n = 2-4 replicates; *: p < 5e-2, **: p < 1e-2, ***: p < 1e-3, ****: p < 1e-4; ns: not significant, using unpaired Student's t-test, two-sided. Dotted line indicates mean of untreated group.
(E) Epifluorescence and phase contrast microscopy of living tul1∆ and tul1∆ sec13-4 mutants expressing GFP-Orm2 (green) and dsRed-HDEL (red) incubated at 26°C or shifted for 90 minutes to the non-permissive temperature (37°C). Data information: Scale bars 5µm.
The Venn diagram shows the degree of overlap between genes up-regulated by CoCl2 treatment and those down-regulated in the ADAR1-depletion and CoCl2 -treated cells.
(H) CellTiterGLO®-based assay measuring cellular ATP levels of the CX-5461-resistant (CX) and CX-5461-everolimus combination therapy-resistant (CMB) cells treated with metformin as indicated for 48 hours.
(E) Overexpression of DSCR1 reduced the luciferase activity, while removing all methylation sites in the miR-124 promoter increases it. Values are shown as mean ± SEM, and tested for statistical significance by one-way ANOVA followed by Bonferroni post hoc test. N = 3 for each condition, *P< 0.05.
(D) Modest perturbation of scFD20 for RBD-ACE2 interaction. A sensor with RBD immobilized was soaked in 200 nM of scFD20 before being further soaked in scFD20-containing buffer with (red) or without (blue) 25 nM of ACE2 for BLI signal recording. As a control, the ACE2-RBD interaction was monitored in the absence of scFD20 (black).
(d,e) Growth of BSF (d) and PCF (e) trypanosomes in the absence (black lines, −Tet) or presence (red lines, +Tet) of 1 μg ml−1 tetracycline for the indicated number of days. Values are mean±s.d. (n=3).
High-performance liquid chromatography-electrochemical detection quantitation of (a) striatal DA and its metabolites (b) dihydroxyphenylacetic acid (DOPAC) (c) Homovanillic acid (HVA) and (d) 3MT levels at three different time points (1, 2 and 12-month-old) in Pgam5 WT or KO mice.
A Quantification of the band intensities following streptavidin-based pulldown assays using the in vitro-translated biotinylated CbpCT4 and FLAG-tagged autophagy-related proteins shown in Fig EV2A.
D, E GST-pulldown assays using GST-CbpFR6 derivatives and lysates from 293T cells expressing GFP-Atg14 CCD or GFP. The bound proteins were analyzed by immunoblotting using an anti-GFP antibody. Each GST-CbpFR6 derivative-bound bead was confirmed by Coomassie brilliant blue (CBB) staining.
G Immunoblotting of phosphorylated PKC (p-PKC), ERK, phosphorylated ERK (p-ERK) and β-actin (control) (left) with relative quantification (right). Data are expressed as mean ± SEM from three independent experiments. *P = 0.0119, **P = 0.0034 (Student's t-test).
(C) The graph shows the mean ± s.e.m. of the percentage of nuclear TFEB translocation in Ezrin-inhibited cells and subjected to the silencing of PPP3CB. At least 3 independent experiments were performed. Mann and Whitney test (siPPP3CB vs siCTRL) *p ≤ 0.05.
(k) Real-time PCR analysis of LAMP2A mRNA in naive and memory CD4+ T cells obtained from young human donors (26 ± 2 years of age; n = 3) or old human donors (72 ± 6 years of age; n = 6) and activated for 24 h as in a; results were calculated by the change-in-cycle-threshold method (2−ΔCt) relative to those of the gene encoding β-actin. *P = 0.047 and **P = 0.0033 (Mann-Whitney).
(d) Nuclear P-ERK/LC3-II colocalization in serum-fed cells. IF showing P-ERK (green)/LC3 (red) colocalization in 2 h serum-fed NIH/3T3 cells. Native images (top)/images with colocalization in white pixels (bottom) are shown. Scale bar, 5 μm.
(C) Track length of single mCherry-positive clones derived from U2OS (EGFP/STGC-mCherry/LTGC-5034) cells after Cas9/sgRNA-1731 or Cas9n/sgRNA-1731 cleavage was analyzed by sequencing PCR products from genomic DNA at repair junctions. The numbers of the total events analyzed after Cas9 and Cas9n cleavage are shown on the top with the numbers of events using BIR-EJ indicated in brackets. Group means are shown. Error bars represent ± SD. Dashed lines (2.2 kb and 1.1 kb) indicate the upper and lower limits of track length that can be scored by this reporter.
(b-c) Notch1+ progenitors are able to generate Lgr5+ stem cells and contribute to epithelial renewal in homeostasis; however, do not contribute to regeneration after colitis (N=4 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars=50μm. Data are represented as mean ± SD analyzed using two-way ANOVA with Sidak's multiple comparisons test. ****P≤0.0001.
(C) Heatmaps showing Log2 FC (relative to the DMSO/Control condition) for 5 ERS UP and LIVER-ID genes issued from RT-qPCR analyses of MPH pre-treated with 500nM JQ1 (left) or 0.01µM MZ1 (right) followed by addition of 1µM thapsigargin (ERS) for 4h (3 to 6 independent experiments). Two-way ANOVA with Bonferroni's post-hoc test was used to assess statistical significance.
quantification of capillaries per myocyte (N). (N=5 to 7 mice/group, scale bar: 50µm). **P<0.01. One-way ANOVA with Sidak´s multiple comparisons test.
Scheme of the experiment verifying if the HO-1+/+ niche is able to reverse phenotype of HO-1-/- LT-HSCs.
(A) Immunoblot analysis of fibronectin, pSmad2/3, total Smad2/3, and GAPDH (loading control) in cell lysates from MCF10A-pIND20-HPN cells without hepsin overexpression. The graph depicts quantification of pSmad2/3 normalized to total Smad2/3 levels, compared to siCtrl (N = 3 biological repeats). (B) Immunoblot analysis of cell lysates (pSmad2/3, total Smad2/3 and vinculin as loading control) and concentrated cell culture supernatant (anti-V5 for TGFβ) from MCF10A-pIND20-HPN pL6-TGFβ1-V5 cells without hepsin overexpression. Ponceau staining is shown as a loading control for the western blot with concentrated culture supernatant. The graph depicts quantification of pSmad2/3 normalized to total Smad2/3 levels, compared to siCtrl (N = 3 biological repeats).
(B) Cells were pulse-labelled with [35S]methionine and chased on non-radioactive starvation medium. Aliquots were taken at the indicated times and acid-soluble small peptides generated by proteolysis were determined.
(A) Effect of Tet2 and Tet3 single deficiency on osteoclastogenesis. TRAP-stained cells (left panel) and the number of TRAP-positive cells with more than three nuclei (right). Scale bar, 100 μm. (n = 6 (control and Tet2Rank-/-) and n = 3 (Tet3aRank-/-) biological replicates
F. GSEA of gene markers of clusters 2 and 3 (lost upon Ssrp1 KO, blue) versus clusters 8 and 9 (emerged upon Ssrp1 KO, red).
(A qRT-PCR for the expression level of TFAM in ten HCC cell lines, one normal liver cell line (LO2) and two non-tumor liver tissues. (n = 3 independent experiments). Data information: Graphs show mean ± s.e.m., two-tailed unpaired t-test. **P < 0.01.
Immunoblot analysis of p62, actin, LC3 I/II in KO+KRIT1 and KRIT1-KO cells. Where indicated, cells were treated with 100 nM Torin1 for 4 h or 500 nM rapamycin for 4 h. The results are representative of three independent experiments.
(D) Cell proliferation rates of PC3-B2 cells with CTH knockdown. Cell proliferation assay was performed by MTS reagent. Data information: Data shown represent the means ± SD (n=3 biological replicates). Student's t-test was used for the statistical analysis (*P<0.05; **P<0.01; ***P<0.001).
A, B Temporal expression of Snail genes in the intestinal tract in (A) embryonic E12.5 to E18.5 and (B) postnatal P0 to P20 measured by qRT-PCR. Shown are means ± SD.
(B) CH12F3-2A cells were transfected with siRNAs along with empty vectors or vectors expressing various zinc finger mutants of Phf5a (Phf5aR-MF). Twenty-four hours after transfection, the cells were stimulated by CIT for another 24 h, and then examined for CSR. The efficiency of IgA switching was calculated relative to the value obtained for siControl and empty vector-transfected cells. The data are compiled from three independent experiments. The values are presented as mean ± sd (n=3). Statistical significance was performed in reference to siControl by two-tailed unpaired Student's t-test ( *** p ≤0.001). See Supplementary Fig.S8 for a representative data set.
(h) Photographs showing heart sections after SA-β-gal staining; original magnification, × 200; scale bar, 40 μm. SA-β-gal-positive cells were quantified (n=4 per group). Five images per mouse were taken on brightfield and DAPI staining was used to count the total cell number per section.
The 171-amino acid sequence of vBcl-2 is indicated at the top with the α-helical structures numbered according to previous publication [25]. Colored boxes denote the BH 1-4 domains in vBcl-2. "+" : positive interaction, "−" : no interaction. L: linker region; TM: transmembrane domain; Triple arrows denote the alanine substitutions at Ser85-Gly86-Arg87 within the BH1 domain of vBcl-2.
E Major satellite RNA with respective piRNA target sequences. piR major-a and b target the sense strand of major satellite transcripts at their cleavage sites. The MIWI slicer activity results in 125- and 119-nt cleavage products.
(E) EphB4 depletion in B16F10 cells; immunoprecipitation/immunoblotting; control: no infection; pLKO: infection with control lentivirus; shEphB4: infection with silencing lentivirus.
Cac and its accessory subunits are present on the lysosomes. Under normal conditions of activity requiring basal levels of autophagy, Cac allows for calcium efflux from endo/lysosomes to provide for SNARE-mediated fusion of autophagic vacuoles to lysosomes and subsequently efficient degradation of unwanted cellular material and to maintain neuronal homeostasis. In the absence of Cac, there is a block in the autophagic flux and lysosomal fusion, leading to an accumulation of fusion-primed autophagic vacuoles. This subsequently results in an accumulation of improperly formed proteins or damaged organelles, such as mitochondria in the neurons, and causes neurodegeneration.
B Coomassie brilliant blue staining and MS analysis of Hwa-associated proteins after immunoprecipitation (Flag pull-down). Right (outlined text), thirteen matched peptide sequences that correspond to ZNRF3. Hwa-MF, Myc-Flag-tagged Hwa.
b) Overexpression of α-synucleinA53T mutant upregulates LC3-II level and Thr 145-phosphorylated EndoB1 in cultured neurons. Lower panel shows quantified data as means ± s.e.m.; n=3.
B. MEF WT cells were transfected with plasmids as indicated for 24 hr and treated with either DMSO or TH for 4 hr followed by analysis of the protein levels of p-eIF2α, total eIF2α, CHOP, and Endouc-Flag. GAPDH served as an internal control. Protein levels relative to each internal control were presented at each lane. The results obtained from the two trials are shown on the left and right.
E. Quantified relative changes in Nmd4-TAP average levels in light and monosome/polysome fractions in upf1∆ and upf2∆ strains (100% correspond to levels in the wild type strain). Indicated p-values correspond to the Welch t-test, single-sided comparison of 4 replicate experiments (individual values are indicated as dots). Error bars correspond to SD
Human bronchial epithelial BEAS-2B cells were infected with the influenza A/Scotland/20/74 (H3N2) virus (IAV) at MOI=1 for 4 h, and subsequently treated or not with 4 mg/mL of succinate (Suc) for 20 h. (e) Human bronchial epithelial BEAS-2B cells were infected with a A/Scotland/20/74 (H3N2) virus (IAV) carrying a wild-type NP (NP WT) or with the corresponding mutated virus bearing a NP with a K87R substitution (NP K87R). Cells were infected by either virus at MOI=1 for 4 h, then washed and treated or not with 4 mg/mL of succinate for 20 h. Localization of NP proteins was analyzed by confocal immunofluorescence microscopy. Scale bar: 10 µM. Pictures are representative of three independent experiments. (f) Relative nuclear intensity of NP was determined by using the Intensity Ratio Nuclei Cytoplasm Tool. Data information: Data are represented as the mean ± SEM of 3 biological replicates without 2 technical replicates each. at least 10 (f) random images were analysed per treatment with a minimum of 5 cells per field. Statistical analysis was performed using the Mann-Whitney test (*P < 0.05).
MISTRG mice were reconstituted or not at birth with human CD34+ cord blood HSPC, and intravenously injected with 1x106 primary DLBCL cells at six weeks of age. The lymphoma burden at the study endpoint was quantified in the bone marrow of reconstituted and un-reconstituted animals by flow cytometric staining for the indicated surface markers.
(A) Inhibitory pairs showing the inhibitory mRNA codons (red) and the optimal codons (green). Schematic representation of the in vitro elongation reactions performed using the reconstituted yeast translation system. Pelleted 80S initiation complexes (3 nM) are incubated with aminoacyl-tRNAs (15 to 25 nM), elongation factors (1 µM), GTP, and ATP. Reactions are quenched with KOH and the products resolved by electrophoretic TLCs.
A. Pure tone audiogram recorded from one of the probands, showing severe to profound bilateral asymmetric hearing loss.
(D) Cumulative population doublings of KP and KPΔNF1 cells cultured with 2.0 or 0.5 mM glutamine (n = 4 biological replicates).
B. Sensitivity of MCF7 and MCF7aTT cells to heat shock at 45 oC as determined by trypan blue staining. The graph shows means +/- SD, n = 3. Numbers indicate p values.
J) Plaque assays were performed with RH+GRA15WT, RH+GRA15TRAF2mut or RH+GRA15TRAF2/6mut (n=3).