EMBO/sd-character-level-ner huggingface dataset:
Figure 4(A, B) Co-immunoprecipitation of ectopically expressed Myc-CDC20 with ectopically expressed Flag-p65 in HEK293T cells. (C Co-immunoprecipitation of ectopically expressed Myc-CDC20 with endogenous p65 and ectopically expressed Flag-p65 with endogenous CDC20 in HEK293T cells. D) Co-immunoprecipitation of ectopically expressed Myc-CDC20 with endogenous p65 and ectopically expressed Flag-p65 with endogenous CDC20 in HEK293T cells. (E, F) Co-immunoprecipitation of endogenous CDC20 with endogenous p65 in HEK293T cells. (G) Co-immunoprecipitation of purified GST-CDC20 protein with endogenous p65 in HEK293T cells and the construct of GST-CDC20. Whole cell lysates (WCL) were subjected to perform GST pull-down analyses with purified GST-CDC20 and GST as a negative control. (H) Co-immunoprecipitation of purified GST-p65 protein with endogenous CDC20 in HEK293T cells and the construct of GST-p65. Whole cell lysates (WCL) were subjected to perform GST pull-down analyses with purified GST-p65 and GST as a negative control.
Figure 4Diagrams of the reporter assay vectors DRGFP and EJ5GFP for measuring HDR and Distal-EJ, respectively. Detection of the Xist foci by RNA-FISH, with or without dox addition for 96 h (N >200 each). A representative image with percentage of Xist-positive cells is shown [magenta: Xist, cyan: DAPI.]. Detection of the number of X-linked Atrx gene foci by DNA-FISH, with or without dox addition for 96 h (N >100 each), performed as described in Figure 1C. Estimated repair events. The flow cytometry plots are shown in Figure EV4. The percentage of GFP-positive cells in TX-DRGFP#11 and TX-EJ5GFP#23 was normalized to the transfection efficiency detected by the VENUS expression vector. Dox (-) was set to 1 and the ratio of relative GFP-positive cells is shown (n=3).
Figure 3A In vitro kinase assays were performed as outlined in Materials and Methods with purified recombinant EDC3 (0.2μg) and Pim1 (0.2μg). Samples were analyzed by Western blotting with the indicated Abs. B In vitro kinase assay with EDC3 (0.2μg) and AKT (0.1μg). Samples were analyzed by Western blotting with the indicated Abs. C PC3-LN4 cells containing a doxycycline (DOX) inducible Tripz-Pim1 vector were treated with 50 or 100 ng/ml DOX for 48 h and subsequently incubated with DMSO or PIMi (PIM447, 3 µM) for 24 h. Western blots were probed with the indicated Abs. D PC3-LN4 cells was treated with PIMi (PIM447) at increasing doses (0, 3, 5, and 10μM) for 24 h. Extracts were subjected to Western blotting with the indicated Abs. Relative values of phospho-signals were indicated below p-EDC3 blot by quantification of intensity for p-EDC3 S161 levels using ImageJ (NIH). p-EDC3 S161 levels were normalized to levels of total EDC3 within the respective samples and compared to the p-EDC3 S161 levels in the untreated samples. E PC3-LN4 was treated with PIMi (PIM447, 3μM), AKTi (GSK690693, 5μM), or the combination for 24 h. Extracts were subjected to Western blotting with the indicated Abs. F PC3-LN4 CRISPR-Ctr and Pim1 KO cells were treated with PIMi (PIM447, 3μM), AKTi (GSK690693, 5μM), or the combination for 24 h. Extracts were subjected to Western blotting with the indicated Abs.
Figure 3(A) Localization of GFP-Pgc1 in are1Δ are2Δ lro1Δ dga1Δ cells in presence (no LDs) or absence of DOA10 (no LDs doa10Δ). The ER was visualized by expression of Sec63-Cherry. Scale bar: 5 µm. (B) GFP-Pgc1 was expressed under the ADH1 promoter; LD formation was stimulated by galactose-induced expression of DGA1 in are1Δare2Δlro1Δ. Fluorescence microscopy was used to follow GFP-Pgc1 localization over time. LDs were visualized upon staining with the neutral lipid dye MDH. Scale bar: 5 µm. (C) Photo-conversion of tdEOS-Pgc1 expressed under the ADH1 promoter; LD formation was stimulated by galactose-induced expression of DGA1 in are1Δare2Δlro1Δdoa10Δ cells. The red square marks the photo-converted region. The time (in minutes) after photoconversion is indicated. Arrowheads point LDs containing photoconverted tdEOS-Pgc1. Scale bar 5µm. (D) FRAP experiment of GFP-Pgc1 in wt and doa10Δcells. Representative examples are shown. The bleached areas are marked by red squares and include a LD adjacent to ER. The time (in seconds) after photobleaching is indicated. Each graph shows average fluorescence intensities for 10 cells normalized to pre-bleached plotted over time. Error bars indicate standard deviation.
Cell adhesion is regulated by DHHC5/Golga7b.Figure 710x brightfield images of A431 cells treated with non-targeting siRNA at time 0 (left) and after 48 hours (right) of 5 ng/ml EGF treatment. 10x brightfield images of A431 cells treated with DHHC5 siRNA at time 0 (left) and after 48 hours (right) of 5ng/ml EGF treatment. Quantification of cell scattering of A431 cells, showing a significant increase in cell scatter after 48 hours of DHHC5 knockdown and therefore a decrease in cell adhesion was observed. 10x brightfield images of A431 cells treated with non-targeting siRNA at time 0 (left) and after 48 hours (right) of 5ng/ml EGF treatment. 10x brightfield images of A431 cells treated with Golga7b siRNA at time 0 (left) and after 48 hours (right) of 5ng/ml EGF treatment. Quantification of cell scattering of A431 cells, showing a significant increase in cell scatter after 48 hours of Golga7b knockdown and therefore a decrease in cell adhesion, was observed. Plot showing the resistance of A431 cells from a trans-epithelial electrical resistance assay treated with either DHHC5 siRNA, Golga7b siRNA or non-targeting siRNA. A significant reduction in TEER demonstrates a decrease in cell adhesion after both DHHC5 and Golga7b depletion.
Cdk5-mediated Thr 145 phosphorylation of EndoB1 is required for induced autophagy and cell death in neurons.figf8Cdk5-mediated Thr 145 phosphorylation of EndoB1 is required for induced autophagy and cell death in neurons. Starvation, treatment with MPTP/MPP+ and overexpression of the α-synucleinA53T mutant increase the level of EndoB1 Thr 145 phosphorylation by Cdk5/p35 in neurons. Phosphorylation of EndoB1 promotes its dimerization and recruitment of the UVRAG/Beclin 1 complex to induce autophagy.
Figure 2A CFU-MK assays with CD34+ cells expressing AS-RBM15. MK colonies staining for acetylcholinesterase activity were counted (right). P value was calculated using Student's t test (n=3, mean ± SD). B The number of CD41+CD42+ mature MK cells was determined by FACS analysis. CD34+ cells expressing sh-AS-RBM15 were grown in pro-MK medium containing thrombopoietin and stem cell factor (TPO/SCF) for five days (n=4, mean ± SD). C Schematic diagram of AS-RBM15 truncations, FL (full-length), ∆5 (nt463-2611), ∆3 (nt1-471), and Exon1 (nt1-175). Exon 2 (blue) contains repeat element (SINE/Alu). D FACS analysis of CD34+ cells grown in pro-MK medium and expressing AS-RBM15 full length or Δ5 or Δ3. The CD41+CD42+ cell percentages were analyzed using one way ANOVA, ** P<0.01, (n=4, mean ± SD). E The percentage of CD41+CD42+ cells in CD34+ cells expressing AS-RBM15 Exon 1 were determined by FACS analysis after these cells were grown in pro-MK medium for five days. P value was calculated by t test, p<0.01, (n=3, mean ± SD).
Figure 3A Example of the mapping results. Wild allele frequency in progeny of a cross of the gab1-1 temperature sensitive allele to the YJM975 strain (y-axis) along the yeast genome (x-axis) at the permissive 26°C (blue) and restrictive 34°C (TS allele loss-of-function, cyan). The allele frequency change between the two temperatures is used in mapping. Labels: selected loci in the cross. Blue regions: called suppressor loci. B B Suppressors are plentiful. The average number of suppressor loci per cross (y-axis) at a given allele frequency change cut-off (x-axis) with either the wild allele beneficial (blue) or the reference allele beneficial (yellow). Vertical line at an allele frequency change of 0.2: the cut-off used for calling suppressor loci. C Suppressors are reproducible across TS alleles. Allele frequency change of suppressor loci in crosses using different TS alleles of the same gene (x- and y-axis) crossed with the same wild strain. Colours: gene and wild strain combinations. D D Suppressors are reproducible across wild strains. Allele frequency change of suppressor loci at 34°C in crosses using the same TS allele and a different wild strain (x- and y-axis). Colours: TS alleles.
Figure 3A Schematic illustration of domain structure of Arabidopsis PAP8 fused to GFP. cTP, chloroplast transit peptide; NLS, nuclear localization signal. B Transiently expressed PAP8FL-GFP (full-length coding sequence of PAP8 fused to GFP) in onion epidermal cells displays a dual localization in the nucleus (white arrowhead) and in plastids (yellow arrowheads). C Immuno-blots for the detection of PAP8 in total protein extracts (Col-0 Tot) the nuclear fraction (N) and the plastidic fractions (EP, etioplast; CP, chloroplast) of etiolated (Dark) or photomorphogenic (Light) Arabidopsis seedlings by immuno-Western blotting using a PAP8 antiserum (PAP8). As control, a mixture of antisera raised against Histone 3 (H3) and the large subunit of ribulose 1, 5-bisphosphate carboxylase/oxygenase (RbcL) was used to evaluate reciprocal contaminations. The lanes are extracted from the same blots provided in the Source Data file. D-G Co-expression analysis of PAP8FL-GFP (D) with PAP8ΔcTP-RFP (E) in onion epidermal cells; (F) green and red channels merged; yellow arrowheads show plastids; white arrowheads show nuclei as observed with DIC, differential interference contrast in (G); FL, PAP8 full length ORF; ΔcTP, deletion of the cTP; scale bars equal 20 µm. H Confocal imaging on Arabidopsis cotyledons expressing PAP8ΔcTP-GFP, details of a few palisade cells (see Fig. S7B for a view in a cross section between the two cotyledons); magenta, auto-fluorescence of the chloroplast; the white arrowhead shows a nucleus; scale bar equals 5 µm. I,J Confocal imaging on Arabidopsis cotyledons stably expressing pP8::PAP8ΔNLS-GFP; ΔNLS, deletion of the NLS (I) during skotomorphogenesis and (J) after 24h light; Yellow arrowheads show the GFP signal; the picture is a merge of different channels: GFP in green, Pchl,: protochlorophyllide, or Chl: chlorophyll in magenta marked with arrowheads, and propidium iodide, showing the waxy cuticle in red, the empty space correspond to the layer of highly vacuolated epidermal cells.
Analysis of molecular dynamics simulations of SecYEG in the lipid bilayer.Figure 4A-F (A, D): Average all-atom atomic fluctuations (RMSF; root mean square fluctuations) for SecY (A) and SecE (D). The mean RMSFs are projected onto the 3D structures of SecY/SecE and colored according to the color scales starting from blue (low mobility) to red (highly mobile). (B, E): Overlay of the SecY (B) or SecE (E) representative structure (red) onto the corresponding starting structure (dark cyan). Parts that show a pronounced structural change are explicitly shown as cartoon representation, and the movements are highlighted by arrows. (C, F): Visualization of displacements along the 1st (golden arrows) PC computed for the joint, five 1 µs long MD simulations for SecY (C) and SecE (F). The amplitudes of the motions were scaled, and a cutoff for small displacements was applied for best graphical representation. Distribution of lipids during MD simulations. Grids represent the 3D density of phosphatidylcholine (PC; blue) and phosphatidylglycerol (PG; red) groups from the lipid bilayer. The densities were normalized to the number of considered conformations, which are identical in both cases.
Figure 4 Figure 4. Basins of attraction predicted from systematic perturbations of patterns with shallow attachment gradients. A. Relative distribution of the final patterns (indicated on the right) observed after sampling all alignment angles of the MinD attachment template from 0 to 90 degrees. The MinD recruitment rate was set to a constant value kdD = 0.1. The data shows the increase in the incidence of multistability as the cell size is increased beyond minimal values for cell length and cell width. B. Fractions of the final patterns in cells of 9- and 10-µm length after sampling all alignment angles of the MinD attachment template from 0 to 90 degrees. The data shows that increasing the MinD recruitment rate facilitates multistability.
Figure.Figure 2ChIP-seq peaks identified for Mta1 and Mta2 (left), Mta1 and Mta3 (middle) or Mta2 and Mta3 (right) are plotted by enrichment for each protein. Peaks called for both proteins are indicated in the overlap. Overlap of peaks identified by ChIP-seq for each MTA protein in wild type ES cells. Total peak numbers are indicated below each protein name. Each ChIP-seq dataset was made from biological triplicates.   Comparison of Mta1 and Mta2 peaks with Chd4 peaks, as in Panel (B).   ChIP-seq enrichment for indicated proteins or histone modifications is plotted across different subsets of Mta-bound sites. Mta1/2/3 refers to peaks identified in all three ChIP-seq datasets, whereas "Mta1 Only", "Mta2 Only" or "Mta3 Only" refer to peaks only called for that protein. Average enrichment of density plots are plotted for different subsets of Mta ChIP-seq peaks.
Figure 1HeLa and cyclin F Knock-Out (CCNF K/O) cells were treated with Kinase ChemoGenomic Set (KSGS) in 384 well format. After 72 Hours (h) viability was measured using rezasurin. Flowchart representation (left). Robust Z-score difference is plotted for data acquired at 1 μM concentration (right). Cell survival measured using rezasurin and compared to controls treated with DMSO (expressed as relative proliferation %). Cells were treated with the indicated inhibitors at 0.1 and 1 μM concentration. Cell survival measured using rezasurin and compared to controls (0) treated with DMSO (expressed as relative proliferation %). Cells were treated with UCN-01 at the indicated concentrations. Differences in viability of HeLa and CCNF K/O cells after treatment with specific Chk1i (LY2603618) at the indicated concentrations plotted on a log10 scale to measure differences in IC50. Number of cells was measured in HeLa and CCNF K/O cells left untreated or treated with Chk1i (LY2603618) for 24h, 48h, or 72h as indicated. (n.s. = non-significant). Cell viability measurements using Propidium Iodide staining for HeLa and CCNF K/O cells after treatment with Chk1i (LY2603618). U-2-OS cells were seeded and transfected with non-targeting siRNA siNC (Negative Control) or siCyc F. 24 hours after transfection, cells were treated with UCN-01, or Chk1i (LY2603618) at indicated concentrations for 3 days before viability was measured. Cell viability measurements using Propidium Iodide staining in U-2-OS cells transfected with non-targeting siNC and siCyc F and treated with Chk1i (LY2603618) as indicated.
Variety of actins selected for this study and analysis strategies.Figure 1A Simplified phylogenetic tree showing mainly the Dikarya subkingdom and including the external branches Homo sapiens (Hs) and Arabidopsis thaliana (At). The Id. column indicates amino acid sequences percentage identities, ranging from 100% (green) to 84% (magenta) identity for eukaryotic actins to S. cerevisiae's actin, and 60-62% (black) for archaeal actins. Squares outlines are solid or dotted for sequences deriving from existing species or ancestral reconstruction, respectively. The "coded by" column indicates which coding sequences were originally used to code genes of interest. Nucleotide sequence identities are ranging from 100% (blue) to 76% (orange) compared to S. cerevisiae's actin coding sequence. B Amino acid sequence of Saccharomyces cerevisiae actin. Arrows denote all the positions that are mutated in at least one of the actin variants tested in this study. C Schematic representation of S. cerevisiae actin 3D structure (1YAG (Vorobiev et al, 2003)), showing that mutations cover all regions of the protein. Dots indicate where mutations are located, using a different color code for all actins studied here. D Schematic showing the mutagenesis strategies applied in this study, enabling to question respectively the importance of actin's intron, the nucleotide sequence, the amino acid sequence, and the effect of expressing copolymers. Green color indicates whether modifications are brought in the coding sequence (leading to expression of wild-type Act1 protein (pink) or in the amino acid sequence (leading to expression of an Act1* actin ortholog).
Figure 1(A-B) Coronal brain section, bregma: - 2.88 from The Mouse Brain Atlas shows the site of injection in the CA1 cell body layer of the right hippocampus (A). 8 h post-injection, majority of the injected Fib-Tau-1N3R-ATTO550 (red) is taken up by the corpus callosum of the injected side (B). Images are shown at low (left, 10X) and high (right, 63X) magnification. Data information: Scale bar, 100µm in the left panel in (B), 10µm everywhere else. Representative images of the distribution of Fib-Tau (red) 8 h and 24 h after injection. Dendrites are immunolabeled using MAP2 antibody (green). 8 h after injection, both diffused and clustered distribution of exogenous Fib-Tau is observed in stratum oriens and CA1 cell body region No exogenous Fib-Tau is detected in the adjoining cortex, stratum radiatum and entrorhinal cortex 24 h after injection, clustered distribution is primarily restricted to the pyramidal (CA) cell body layer (D). Uptake of Fib-Tau is seen in some cells in both stratum oriens and pyramidal cell body layer (D). Paired-t-test performed between '8/24h-right' and '8/24h-left'; Unpaired t-test performed between '8h-left' and '24h-left' columns (n is number of animals: 6 for 8h and 5 for 24h); ***p<0.001, **p<0.01, *p<0.05, ns= not significant. Note: The images presented in panels C and D were independently acquired images under non-identical exposure setting at low magnification for display purpose Data information: Scale bar, 10µm Representative images of the distribution of Fib-Tau (red) 8 h and 24 h after injection. Dendrites are immunolabeled using MAP2 antibody (green). 8 h after injection, both diffused and clustered distribution of exogenous Fib-Tau is observed in stratum oriens The number of Fib-Tau clusters per µm2 within stratum oriens decreases between 8 h and 24 h post-injection (G). A similar decrease in the total fluorescence (clusters + diffused) is observed indicating the diffusion and/or clearance of exogenous Fib-Tau (H). Paired-t-test performed between '8/24h-right' and '8/24h-left'; Unpaired t-test performed between '8h-left' and '24h-left' columns (n is number of animals: 6 for 8h and 5 for 24h); ***p<0.001, **p<0.01, *p<0.05, ns= not significant. Panels (E and F) are shown for same exposure and are used for quantification. Data information: Scale bar 10µm
mediated cell death mechanism is independent of inflammatory responses (A, B) Production of cytokines TNF-α, IL-1, IL-6, CXCL15 (A), or chemokines Ccl5, Cxcl10, Icam1 (B) in the A20-/-Socs6+/+, A20+/+Socs6+/+, A20-/-Socs6-/- and A20+/+Socs6-/- BMDMs after Mtb stimulation.Figure 8(A, B) Production of cytokines TNF-α, IL-1, IL-6, CXCL15 (A), or chemokines Ccl5, Cxcl10, Icam1 (B) in the A20-/-Socs6+/+, A20+/+Socs6+/+, A20-/-Socs6-/- and A20+/+Socs6-/- BMDMs after Mtb stimulation. Data are shown as the mean ± s.e.m. of n = 3 biological replicates. (C-E) Cell death mechanisms (C), cell viabilities (D), or Mtb growth rates (E) of A20-/-Socs6+/+, A20+/+Socs6+/+, A20-/-Socs6-/- and A20+/+Socs6-/- BMDMs stimulated with Mtb. Z-VAD treatment concentration was 20 μM and the treatment time was 24 hours. Data are shown as the mean ± s.e.m. of n = 3 biological replicates. (F) Schematic representation of miR-342 regulated anti-Mtb immunity.
Figure 5A. Significantly altered metabolites (FDR<0.2; P<0.05, n=5/group) in presymptomatic (P150) heart tissue of GRAC (red) and GROX (green) mice Bar graph represent mean±S Statistics for graph one-way ANOVA followed by Tukey"s B. Significantly altered metabolites (FDR<0.2; P<0.05, n=5/group) in liver tissue of GRAC (red) and GROX (green) mice Bar graph represent mean±S Statistics for graph one-way ANOVA followed by Tukey"s C-F. Concentrations of the TCA cycle intermediates (C) fumarate and (D) malate, (E) adenylate energy charge and (F) NADH/NAD+ ratio (n=5/group) Bar graph represent mean±S Statistics for graph one-way ANOVA followed by Tukey"s (G) Proline concentratio in heart tissue at P200 (# below detection limit Bar graph represent mean±S mRNA expression of proline synthesis-related genes (n=6/group)) (H) Aldh18a1 and (I) Pycr1 at P150 box plots of mRNA expressions represent quartiles, minimum, and maximum value (relative fold change "FC&qu Statistics for graph one-way ANOVA followed by Tukey"s
Figure 5NK cell-mediated killing of RELA ArCK cells was compared to clones harboring an empty vector. ArCK RELA knock out cells were generated and the NK cell-mediated cytotoxicity was measured as described in the method section. Dot plot of individual data points and mean were presented. n=2 biological replicates; ArCK-c1 vs ArCK RELA-c1, p= 0.70, n.s.; KS test. The effect of inactivating RELB on NK cell-mediated cytotoxicity in ArCK cells. The same experimental methods were used as described in (A). n=3 biological replicates; ArCK-c1 vs ArCK RELB-c1, p= 0.47, n.s.; KS test. Measurement of RelA protein levels in RELA KO single cell clones generated in RPE1-hTERT cells. Measurement of RelB protein levels in RELB KO single cell clones generated in RPE1-hTERT cells. The effect of inactivating both RELA and RELB on NK cell-mediated cytotoxicity in ArCK cells. n=2 biological replicates; ArCK-c1 vs ArCK RELA RELB- c1, p= 0.0014; KS test. Measurement of RelA and RelB protein levels in RELA RELB double KO single cell clones generated in RPE1-hTERT cells. ArCK or euploid proliferating control cells were treated with either DMSO or the NF-κB inhibitor BMS-345541 (5 μM) for 48 hours before assessing NK cell-mediated cytotoxicity. The drug was washed out during the NK cell co-culture assay. n=3 biological replicates; mean± SEM. ArCK vs ArCK NF-κB inhibitor, p< 0.0001; KS test. (H, I) The effect of inactivating both RELA and RELB on NK cell-mediated cytotoxicity in 7-day doxorubicin (H) and nutlin3-treated (I) cells. n2 biological replicates; Doxo-c1 vs. Doxo RELA RELB-c1, p = 0.02. Nutlin-c1 vs. Nutlin RELA RELB-c1, p = 0.44, n.s.; KS test.
Figure 6(A) Representative Western blot analysis of protein extracts of late pupae heads (85-95h) from control, Ythdf#0/ Ythdf#0 and Fmr1∆50/Fmr1∆50 flies. The membranes were probed with anti-Profilin or anti-Actin antibodies. (B) Quantification of Profilin protein levels (mean ± SD) obtained from three independent protein-extraction and Western blot analysis as in (A). Quantification was performed using Fiji. p<0.005 = **; p<0.05 = *, measured with unpaired t-test. (C) Quantification of chic mRNA levels (mean ± SD) obtained from six independent RNA extractions from control, Ythdf#0/Ythdf#0 and Fmr1∆50 late pupae heads, via real-time PCR analysis. Statistical analysis using unpaired t-test show no significant difference between the samples. (D) Immunofluorescence analysis of adult chic/+ and chic/+; Ythdf#0/Ythdf#0 using anti-FasII antibody. Scale bar: 50 μm. Pink dashed lines highlight the normal and fused β-lobes. (E) Quantification of the penetrance of β-lobe fusion phenotype for the indicated genotypes. Bars are labelled with the number of replicates.