EMBO/sd-character-level-ner huggingface dataset:
An siHif1α was used to evaluate its involvement in the glycolytic phenotype of Pink1 KO cells.f3(a) RT-qPCR analysis of Hif1α mRNA abundance in MEF transfected with siHif1α, or siControl (100 nM), after 72 h. (b) siHif1α effectively knockdowns expressed Hif1α cDNA WT, but not a Hif1α cDNA silent mutant form refractory to siHif1α (Hif1α cDNA REFR.) in mice MEF. (c) RT-qPCR analysis of the relative mRNA abundances of Glut1, Glut3, Hk2 and Gapdh in WT and Pink1 KO mice MEF transfected with siControl or siHif1α. ß-Actin mRNA was used for normalization, and all data are expressed as the change relative to WT-siControl. (d) Western blot against HIF1α in WT and in Pink1 KO mice MEF transfected with siHif1α or siControl shows the efficacy of the siHif1α at knocking down endogenous HIF1α; ß-actin was used as loading control. As shown, siHif1α partially prevented the increase in GLUT1, HK2 and GAPDH protein abundances. The increased rate of lactate released after 4 h of incubation (e) and glycolytic flux (f) observed in the Pink1 KO MEF was prevented by siHif1α. siHif1α was also effective at preventing the endogenous increased HIF1α protein (g), as well as the increased glycolytic flux (h) observed in Pink1 KO primary neurons. Only representative western blots are shown; the replicates and the semi-quantitative estimation of the band intensities are shown in the Supplementary Information.
Figure 1(A) Schematic of microfluidic chip. (B) Schematic of working principle for cell screening based on stiffness differences. (C) The screening efficiency of four different types of chip was detected in 4T1 cells. n =100. Data information: Kruskal-Wallis test (C) The data represent mean ± SD of three independent experiments. (D) The stiffness of cells screened from the outlet or backflow inlet was measured by AFM. n = 100. Data information: Mann-Whitney test (D) The data represent mean ± SD of three independent experiments. (E) The number of soft 4T1 or MCF-7 cells from the outlet was calculated after treatment with or without Cyto (5 μM) or Jas (50 nM) for 4 hr or 12 hr, respectively. Data information: one-way ANOVA (E). The data represent mean ± SD of three independent experiments.
Distributions of the OFS and the IFS lifetime pairs for individual molecules.Figure 5(A, B) 2D-histograms of lifetime pairs obtained for trajectories exhibiting single exponential behavior. N is the number of traces used. Scale bar shows relative density normalized by the number of molecules. Above and to the right of each panel are stacked histograms of, respectively, the OFS and the IFS lifetimes of the analyzed molecules (open bars) and the photobleaching time of molecules showing no transitions (black bars). Data from three independent measurements were combined for presentation. (C) The mean lifetimes of the molecules falling within 30 % of the most populated bins of the 2D-histograms (yellow to red). The open blue bar represents the calculated mean OFS lifetime for WT GltPh Shown are means and standard errors of the mean of at least three independent measurements.
Figure 2A, B, Joint analysis of nonCM scRNA-seq data from uninjured hearts and hearts at 2, 7, and 14 dpi with LIGER. A, All nonCM visualized on tSNE. B, top, NonCM from each time point visualized on the tSNE embedding in (A). Data was down-sampled to the same cell number at each time point. B, bottom, Pie charts showing contribution of different cell types at each time point. C-F, Zoom-in analysis of macrophages identified in (A). C, tSNE plot colored by MC subpopulations. D, Expression levels of representative markers of each MC subpopulation color-coded and mapped to tSNE embeddings in (C) (top), and corresponding representative GO terms for each subpopulation (bottom). E, Dynamics of MC subpopulations during heart regeneration as shown by the proportion of each subpopulation in total nonCM or total MC. F. Expression of tnfa and csf3b in MC at each time point. G, Fluorescent in situ hybridization for cd74a, tnfa, and ctsc at 7 dpi, respectively. mpeg1 was used to label all MC cells. The blue boxed region is highlighted in the zoom-in image to the right. Scale bar = 50 μm. A stands for arium, V stand for ventricle and OFT stands for outflow tract. White dashed lines outline the heart and the yellow dashed lines indicate approximate resection plane.
Figure 2 [A] Plants grown with 0.05 MS and GMVs (G 0.05) showed hyper-induction of IPS1 and PS2 gene expression in both shoots and roots, compared to plants grown with 0.05 MS alone (C 0.05). Values are means ± SE of three biological replicates.  [B] Root acid phosphatase activity as detected by the blue color from the 5-bromo-4-chloro-3-indolyl phosphate p-toluidine salt (BCIP) treatment. Image contrast enhanced for improved visualization of the blue color in roots Supplementation of Pi to the nutrient-deficient plants (0.05 + Pi) significantly reduced hyper-accumulation of anthocyanin (C) triggered by GMVs. Data information: The boxplots show representative data from three independent experiments (n=12). Whiskers represent the min to max data range, the median is represented by the central horizontal line. The upper and lower limits of the box outline represent the first and third quartile. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test within each group of the same DAT. Supplementation of Pi to the nutrient-deficient plants (0.05 + Pi) significantly reduced hyper-induction of IPS1 gene expression (D) triggered by GMVs. Data information: The boxplots show representative data from three independent experiments (n=12). Whiskers represent the min to max data range, the median is represented by the central horizontal line. The upper and lower limits of the box outline represent the first and third quartile. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test within each group of the same DAT.  [E] Pi supplementation to the 0.05 MS medium partially restored GMV-induced plant vigor, as indicated by increases in total leaf area per plant. [F] A low Pi level (LP), which was equal to 1/20 of that in the 0.5 MS medium, in plant growth medium blocked GMV-induced plant vigor. Data information: The boxplots show representative data from three independent experiments (n=12). Whiskers represent the min to max data range, the median is represented by the central horizontal line. The upper and lower limits of the box outline represent the first and third quartile. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test within each group of the same DAT.  [G] The Arabidopsis phr1phl1 mutant showed substantially decreased growth-promotion, compared to the wild type plants. Data information: The boxplots show representative data from three independent experiments (n=12). Whiskers represent the min to max data range, the median is represented by the central horizontal line. The upper and lower limits of the box outline represent the first and third quartile. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test within each group of the same DAT.
Figure 3A Meta-analysis of 363 cutaneous melanoma from TCGA (skin cutaneous melanoma, PanCancer Atlas) (http://www.cbioportal.org/) showing the percentage of samples with genetic alterations of DDR1 and DDR2. Cases with missense (green) and truncating (blue) mutations, amplification (red) and mRNA overexpression (pink) are indicated; gray, individual cases. B Immunohistochemical analysis of DDR1 and DDR2 levels on human melanoma tissue microarrays. Representative IHC images and quantification (right bar histograms) of DDR1 and DDR2 expression in normal skin, naevus, primary melanoma (PM) and lymph node melanoma metastases (MM). Scale bar, 100 µm. Histological scoring of the samples was performed in blinded fashion. Samples were scored as low, medium or high for DDR1 or DDR2 expression (naevus, n = 12; PM, n = 30; MM, n = 20). Immunoblotting of equal amounts of protein extracts from melanoma cell lines (C) using antibodies against DDR1, DDR2 or markers of the melanoma cell differentiation AXL, MITF or SOX10. ERK2, loading control. Immunoblotting of equal amounts of protein extracts patient-derived short-term cell cultures (D) using antibodies against DDR1, DDR2 or markers of the melanoma cell differentiation AXL, MITF or SOX10. ERK2, loading control. Immunoblotting of equal amounts of protein extracts isogenic pairs of parental sensitive and BRAFi-resistant cell lines (E) using antibodies against DDR1, DDR2 or markers of the melanoma cell differentiation AXL, MITF or SOX10. ERK2, loading control. F DDR1 and DDR2 levels increase in dedifferentiated melanoma cells. Box and whisker plots show DDR1, DDR2, MITF, AXL and SOX10 expression among four differentiation melanoma cell states (U, Undifferentiated, n=10; NC, Neural crest-like, n=14; T, Transitory, n=12; M, Melanocytic, n=17) (GSE80829). The expression of AXL, MITF and SOX10 is shown as control markers of cell differentiation. n, number of cell lines representative of each cell state. Central bars represent the median and the whiskers the 10th to 90th percentile of the boxplot. Multiple comparisons were performed using ordinary one-way ANOVA.
Fig.Figure 4A. Overview of central cleft shows path of target RNA. Seed, bridge, and supplemental regions indicated. B. Schematic of pairing between miRNAs (loaded into Ago2) and targets used in equilibrium binding experiments. C. Dissociation constants (Kd) of Ago2-miRNA complexes (containing an AU-rich supplementary region) binding to target RNAs with bridging regions of various lengths. D. Dissociation constants (Kd) of Ago2-miRNA complexes (containing an GC-rich supplementary region) binding to target RNAs with bridging regions of various lengths. Data information: All plotted data are the means of at least three independent replicates. Error bars indicate SEM. E. Fold repression of a luciferase reporter (relative to no target site control) plotted versus affinity (1/Kd) values measured for the same sites in vitro. Data information: All plotted data are the means of at least three independent replicates. Error bars indicate SEM.
Levels of TSC1 and MYC correlate in Burkitt's lymphoma.Figure 2Elevated TSC1 and MYC expression in BL (cohort 1). Example of immune staining of TSC1, MYC, the B-cell marker CD20, and DAPI nuclear DNA-staining in germinal centers of control lymph nodes (upper rows) and samples from BL patients (lower rows). Boxplots at the right show quantification of TSC1 or MYC staining from control germinal centers and BL samples (see materials and methods) (the horizontal line shows the median, whiskers show maximum and minimum data points and the box represents the first to the third quartiles, n=56 fields for tumor samples and n=21 fields for control germinal centers; scale bar = 100 μm). Quantification of immunoblot analysis of TSC expression in BL (cohort 2) (n=13) compared to healthy tonsils (n=3) or reactive lymph nodes (n=3) (mean ± st. dev.) shown in Fig EV2B.
Figure 3(A Effect of inhibitors BKA and CATR on ANT1-VDAC1 binding in 293T cells. B) Effect of inhibitors BKA and CATR on ANT1-VDAC1 binding in 293T cells. Data are presented as means ± S.E.M. (paired t-test, n = 3, biological replicates per group, ** p < 0.01). (C The effect of different amounts of EBV-LMP1 on the binding of ANT1-VDAC1 was detected by CO-IP. D) The effect of different amounts of EBV-LMP1 on the binding of ANT1-VDAC1 was detected by CO-IP. Data are presented as means ± S.E.M. (paired t-test, n = 3, biological replicates per group, * p < 0.05, ** p < 0.01). (E) Two tyrosine sites of ANT1, Y195/Y290 (human origin), were selected and mutated into TAG using a genetic codon extension technique to insert difluorotyrosine into their specific sites to construct two mutant prokaryotic expression vectors of ANT1Y195-F2Y/ANT1Y290-F2Y. (F) Schematic flowchart of the incorporation of F2Y into ANT1. (G) 19F-NMR spectra of ANT1-Y195-F2Y and ANT1-Y290-F2Y after titration with different amounts of LMP1. After incubation at room temperature for 30 min, the nuclei were continuously monitored at 500 MZ for 30 min. (H) 19F-NMR spectra of ANT1-Y195-F2Y and ANT1-Y290-F2Y after titration with different amounts of LMP1-ΔT. After incubation at room temperature for 30 min, the nuclei were continuously monitored at 500 MZ for 30 min.
Activation of autophagy in trisomic and tetrasomic cell lines.Figure 5(A) Abundance changes of the sub‐category autophagy (GOBP) in all analyzed cell lines are depicted. CGH and proteome data are shown. (B) Fluorescence intensity of LC3−positive foci in HCT116 and HCT116 5/4. Right panel: quantification of the fluorescence intensity (non−parametric T−test, **P<0.01). (C) Western blot of LC3‐II shows an increase in all analyzed aneuploids. Similarly, levels of p62/SQSTM1 are increased in aneuploids. Note that p62 is coded on chromosome 5, but its levels are increased in all aneuploids. Tun-diploid HCT116 treated with tunicamycin that activates unfolded protein response and hence autophagy. (D) Representative images of cells after transfection with the double‐tagged mRFP‐GFP‐LC3. Yellow foci represent phagosomes (both GFP and mRFP signals visible), red foci represent lysosomes (only mRFP signal is insensitive to the acidic pH in lysosomes). Bar 10 μm. (E) Total number of LC3 foci within a defined area of each cell (2500 voxels). There are significantly more foci in the HCT116 3/3 cell line (non‐parametric T‐test, P<0.01), the levels in HCT116 5/4 are higher, but the difference from HCT116 is not statistically significant. See also Supplementary Figure S5. Source data is available for this figure in the Supplementary Information.
Fig.Figure 3a, RNAseq differentially expressed genes (DEG) analysis in the adult hippocampus of miR379-410 ko and wt mice. Up- (green) and down- (blue) regulated DEG are indicated by average changes in mRNA levels (ko/wt; log2) (n = 3; q-values represent FDR-corrected P-values; q<0.05); 2170/898 genes were significantly up- and downregulated in miR379-410 mice, respectively. b, GO-Term enrichment analysis of DEG reveals several synaptic cellular components (highlighted in grey). Green and blue bars indicate the percentage of significantly up- and downregulated genes associated with specific GO-Terms, respectively. GO-Terms with more than 300 annotated genes are not shown. c, String-Database protein interaction network. The network is built including String-DB parameters Experiments, Databases and Textmining. Clusters associated with synaptic transmission are enlarged (for the complete network see Fig. EV3b). Green and blue borders indicate significantly up- and downregulated genes, respectively. d, Enrichment analysis of cluster miRNA binding motifs (TargetScan v7.1). miRNAs overrepresented in differentially expressed (DE) transcripts are highlighted in green and blue, respectively. Shown is the natural logarithm (ln) of the wt/ko ratio of binding sites in DE transcripts. Bubble sizes correspond to RPM values in the mouse brain.
FXR1 regulates cytoplasmic Nups by dynein-based microtubule-dependent transport.Figure 7A, B HeLa cells stably expressing GFP-Nup133 were treated with the indicated siRNAs, synchronized by double thymidine block, released for 12 hours, treated with nocodazole to induce granule formation and washed-out as indicated and analysed by immunofluorescence microscopy. The percentage of cells with cytoplasmic GFP-Nup133 granules was quantified in (B), 5200 cells were analysed (mean ±SD, **P < 0.01; ***P < 0.001; N = 3). C-E HeLa cells stably expressing GFP-Nup107 were treated with the indicated siRNAs, synchronized by double thymidine block, released for 12 hours, treated with nocodazole to induce granule formation and washed-out as in (A) and analysed by live video spinning disk confocal microscopy. The selected frames of the movies are depicted and time is shown in minutes. The magnified framed regions are depicted in the lower rows. White arrowheads point to individual GFP-Nup107-positive granules. Yellow arrowheads point to the granules undergoing fusion events. The percentage of cells with fusion/fission events of GFP-Nup107 granules was quantified in (D), 815 cells were analysed (mean ±SD, **P < 0.01; N = 3). The number of fusion/fission events per cell was quantified in (E), 815 cells were analysed (mean ±SD; N = 3).
Figure 6T cells were activated using Alexa568-2C11 and ICAM1 reconstituted lipid bilayers for 5 min, fixed, stained with phalloidin and imaged using SIM. In the graph, n= 50 for WT and 61 for WASP-/-, P value, P***<0.0001, obtained using Mann-Whitney two-tailed test. The graphs in (B) show synaptic levels of indicated proteins, normalized to the mean levels of '+WASP' in each case. For the left graph, n= 48, 46, 52, 46 respectively, and p value, P *= 0.03. For the right graph, n= 50 for WT and n= 61 for WASP-/- in 'Actin', 'Foci', as well as 'pCasL' cases. P values P*** <0.0001, obtained using Mann-Whitney two-tailed test. Synapse breaking behavior of T cells on hydrogels of indicated stiffness, covalently conjugated with 2C11 and ICAM1. These experiments were repeated at least thrice with similar results. In the left graph, n for WT= 14, for WASP-/-, n= 19; P**= 0.0015; in the graph on the right, n for WT= 40, n for WASP-/-= 36, P***= 0.0006, as assessed using Mann-Whitney two-tailed test.
Mass spectrometry analysis of Elongator.Figure 2A. Number of peptides detected of each Elongator subunit purified through Elp4-FLAG pulldown from yeast lacking ELP1, ELP2, or ELP3 as a fraction of the number of Elp4 peptides. Individual data points are represented as circles, while the averages are represented as bars. B. Purified Elongator was incubated with the primary amine crosslinker disuccinimidyl suberate (DSS) and analyzed by mass spectrometry. Schematic representation of the major crosslinking connectivity of Elp123 is shown. C. Major crosslinking connectivity of the Elp456 complex. D. Detailed locations of crosslinked residues plotted onto a domain representation of Elongator. Lysines from two residues found crosslinked together are denoted by black lines.
Daw signaling mediates the effects of Btz on NMJ size.Figure 5(A) log2 fold changes in daw, ltl and frac mRNA in btz2/Df(3R) BSC497 larval carcasses compared to btz2/+, measured by RNA-Seq (blue) or qRT-PCR (green). **, q<0.01; *, q<0.05 by unpaired t-test corrected for false discovery rate with the Benjamini-Hochberg procedure (RNA-Seq) or **, p<0.01; *, p<0.05 by unpaired t-test (qRT-PCR). n=3 for each sample. Error bars show mean ± SD. confocal images of the NMJ on larval muscles 6 and 7 in segment A3, stained with anti-HRP (magenta) and anti-P-Mad (green in B, C) or anti-Dlg (green in D-K). (B) btz2/+ control; (C) btz2/Df(3R) BSC497. confocal images of the NMJ on larval muscles 6 and 7 in segment A3, stained with anti-HRP (magenta) and anti-P-Mad Insets show enlargements of the boxed regions stained with anti-P-Mad. Synaptic P-Mad is lost in btz mutants. (D) UAS-daw RNAi/+ control; (E) BG380-GAL4/+; UAS-daw RNAi/+; (F) mhc-GAL4/UAS-daw RNAi; (G) UAS-daw RNAi/+; repo-GAL4/+; confocal images of the NMJ on larval muscles 6 and 7 in segment A3, stained with anti-HRP (magenta) and anti-P-Mad Insets show enlargements of the boxed regions stained with anti-P-Mad. Synaptic P-Mad is lost in btz mutants. /+; (H) UAS-daw/+; btz2/Df(3R) BSC497; (I) tub-GAL4/UAS-daw; btz2/Df(3R) BSC497; (J) tub-GAL4/UAS-btz; btz2/Df(3R) BSC497; (K) tub-GAL4/UAS-daw. (L) quantifications of the number of boutons normalized to muscle surface area (x1000) in the indicated genotypes. ****, p<0.0001; ns, not significant by unpaired t-test or Mann-Whitney test. n=19 (UAS-daw RNAi/+), n=9 (BG380>daw RNAi; btz/Df; tub>daw), n=23 (mhc>daw RNAi), n=10 (repo>daw RNAi; tub>daw), n=12 (btz/Df; UAS-daw), or n=14 (btz/Df; tub>btz). Error bars show mean ± SEM. Knocking down daw in motor neurons, muscles or glia reduces NMJ size. Expressing UAS-daw with tub-GAL4 rescues NMJ size in btz mutants as efficiently as expressing UAS-btz, but has no significant effect on NMJ size in a wild-type background.
Figure 1A, Histogram showing the distribution of mean gene expression levels. The dashed vertical line represents the cut-off chosen to define the set of expressed transcripts. FPKM, Fragments Per Kilobase of transcript per Million mapped reads B, Heatmap showing the expression profiles (ordered by phase) of 482 rhythmic transcripts (JTK-Cycle, p < 0.05, FDR=0.31) C, Phase distribution of circadian transcripts shown in B D, Scatterplot representation of Gene Ontology (GO) analysis of the rhythmic transcripts e, Cell cycle analysis using flow cytometry showing the fraction of cells in G1, S and G2 phases over a time course experiment (n = 3 per time-point, mean ± SEM) F, Example of six transcripts detected as rhythmic under constant conditions at 25°C or 28°C (JTK-Cycle, p < 0.05)
Overexpression of p38α inhibits autophagy and competes with mAtg9 for binding to HA–p38IP.Figure 6(A) HEK293A cells were transfected with RFP-mAtg9 and Flag-p38 (lanes 2 and 7), RFP-mAtg9, Flag-p38 and HA-p38IP (lanes 3 and 8), or RFP-mAtg9 and HA-p38IP (lanes 4 and 9). RFP-mAtg9 was immunoprecipitated with an anti‐mAtg9 antibody, the co‐immunoprecipitated HA-p38IP was detected with an anti‐HA antibody, and co‐immunoprecipitated Flag-p38 was detected with an anti‐Flag antibody. RFP-mAtg9 was detected with an anti‐Atg9 antibody. (B) HEK293A cells were transfected with RFP-Atg9 and HA-p38IP (lanes 1 and 5), Flag-Flag, Flag-p38, and HA-p38IP (lanes 2 and 6), or Flag-p38 and HA-p38IP (lanes 3 and 7). HA-p38IP was immunoprecipitated with an anti‐HA antibody, the co‐immunoprecipitated RFP-Atg9 was detected with an anti‐Atg9 antibody, and co‐immunoprecipitated Flag-p38 was detected with an anti‐p38α antibody. HA-p38IP was detected with an anti‐HA antibody. (C) HEK293A cells were transfected with Flag-p38α for 24 h. Cells were incubated in either full medium, EBSS, or EBSS plus leupeptin for 2 h, lysed, and analysed for endogenous LC3 lipidation using an anti‐LC3 antibody, and immunoblotted with anti‐Flag antibody. LC3 lipidation was quantified as the amount of LC3II/LC3I (data are represented as mean±s.e.m. of triplicates, n=2 experiments, EBSS control versus EBSS with Flag‐p38α, ***P=0.0026).