EMBO/sd-character-level-ner huggingface dataset:
Figure 4A. Transmission EM demonstrates the absence of synaptic ribbons in presynaptic terminals of photoreceptorribbon synapses in RBEKO/KOmice, while synaptic ribbons are readily visible in the terminals of RBEWT/WTmice. Asterisks in A2 and A3 denote photoreceptor active zones of RBEKO/KOmice in which the synaptic ribbon is absent. Except for the absence of synaptic ribbons, the ultrastructural appearance of the presynaptic terminals is comparable to that of RBEWT/WTmice. Abbreviations: sr, synaptic ribbon; pre, presynaptic; post, postsynaptic. Scale bars: 500 nm. B. Transmission EM demonstrates absence of synaptic ribbons in presynaptic terminals of bipolar cellribbon synapses in RBEKO/KOmice, while synaptic ribbons are readily visible in the terminals of RBEWT/WTmice. Except for the absence of synaptic ribbons, the ultrastructural appearance of the presynaptic terminals is comparable to RBEWT/WTmice. Abbreviations are the same as in A. Scale bars: 1 µm (B1, B2, B4, B5); 300 nm (B3, B6).
Fig.Figure 6ApoE-/- mice were treated with vehicle (Veh) or the PKM2 inhibitor shikonin (SKN, 1.2 mg/kg), subjected to partial ligation of the left carotid artery (LCA) and given a cholesterol-rich diet. The right, non-ligated artery (RCA) was used as a control. GSH (green) levels in the RCA and LCA 3 days after ligation. CD31 (red) was included to label endothelial cells. n=5 mice per group (2-way ANOVA and Bonferroni). Scale bars: 50 µm. ApoE-/- mice were treated with vehicle (Veh) or the PKM2 inhibitor shikonin (SKN, 1.2 mg/kg), subjected to partial ligation of the left carotid artery (LCA) and given a cholesterol-rich diet. The right, non-ligated artery (RCA) was used as a control. 3-Nitrotyrosine (3NT, green) levels in the RCA and LCA 3 days after ligation. CD31 (red) was included to label endothelial cells. n=5 mice per group (2-way ANOVA and Bonferroni). Scale bars: 50 µm.
Figure 5(A). I. Steady state mRNA levels of NF54 var genes measured by qRT-PCR. The NF54 line was transfected with a luciferase expression vector and selected for ICAM-1-binding. PFD1235w/PF3D7_0425800 is the transcriptionally dominant var gene expressed by this line. Steady state mRNA levels of each individual var gene are presented as relative copy number to the housekeeping gene arginyl-tRNA synthetase (PFL0900c). II. Immunofluorescence image of PFD1235w surface expressed on ICAM-1 selected NF54-luciferase iRBCs. The punctuate PfEMP1 pattern was detected using an anti-PFD1235w antibody. (B). Short-term (6h) neutrophil killing of unselected NF54 and antibody-selected PFD1235w expressing parasite lines. (C). Flow cytometric quantification of neutrophil interaction with MitoTracker (APC+) stained NF54 iRBCs and antibody-selected PFD1235w expressing iRBC. (D). Percent reduction in parasitemia of NF54 and antibody-selected PFD1235w expressing parasites after 5 days of co-culture with neutrophils, compared to unchallenged parasites (E). var gene transcription profiles measured by qRT-PCR of antibody-selected PFD1235w expressing parasite line cultured in the absence (upper panel) or presence (lower panel) of neutrophils. Steady state mRNA levels of each individual var gene was calculated as in A. I.
∆SxIP and Ask12A alleles cause a synthetic growth defect A: Model of regulatory mechanisms of Dam1c oligomerization.Figure 7A: Model of regulatory mechanisms of Dam1c oligomerization. Both binding of Bim1 to Dam1c and Cdk1-dependent phosphorylation of Ask1 promote oligomerization of the complex, while phosphorylation of Dam1 by Ipl1 prevents oligomerization. B: Serial dilution assay of yeast strains with 6xFlag-tagged Duo1WT or Duo1∆SxIP and Ask1WT, Ask12A or Ask12D. Cells were grown at the indicated temperatures and images were taken two days (25 °C, 30 °C and 37 °C) or four days (16 °C) after spotting. C: Mps1 localizes to unattached kinetochores and phosphorylates Dam1c on proximal microtubules (left). By this, Bim1 associates with Dam1c and the complex is enriched at microtubule plus ends which allows formation of end-on attachments (right). Since phosphorylation of Dam1c does not happen on distal microtubules, association with Bim1 and accumulation at plus ends is restricted to microtubules which are close to unattached kinetochores.
Anti-BDCA2 mAb inhibits IFNα production by pDCs and induces internalization of BDCA2 on the surface of pDCs.Figure 1A, B Whole blood or PBMC were treated with increasing concentrations of 24F4A and stimulated with CpG-A for 16 h at 37°C. Anti-BDCA2-mediated IFNα inhibition in whole-blood assays (A). IFNα levels were detected using human IFNα ELISA. Graph depicts average of duplicate wells of one representative donor (n = 10). IC50 of 24F4A-mediated IFNα inhibition (B) in whole blood (circles) (n = 10) and PBMC (n = 18) from healthy human donors (squares) or SLE patients (triangles) (n = 11). Horizontal bar represents the mean IC50 for each sample type. Error bars represent SD of IC50 between donors. C Anti-BDCA2-mediated internalization in whole-blood assays. Whole blood was treated with increasing concentrations of 24F4A for 16 h. Mean fluorescence intensity (MFI) of BDCA2 was determined with a non-cross-blocking anti-BDCA2 mAb (2D6). Shown is a representative plot of 10 experiments conducted. D The IC50 of 24F4A-mediated IFNα inhibition was compared to the EC50 of 24F4A-induced BDCA2 internalization.
Figure 2(A, B) The bur1-ΔC vac17Δ double mutant exhibits a delay in progression through G1 phase of the cell cycle. Yeast were grown in YPD medium and collected in log phase growth. DNA content was measured using propidium iodide (PI) staining and assessed by flow cytometry. p-value determined with a one-way ANOVA and Tukey post hoc test. ** (p-value < 1 x 10-2). Error bars; SD calculated from at least four independent experiments with at least 100 cells counted in each strain/experiment. (C, D) A bur1-267 mutant also exhibits a delay in progression through G1 phase of the cell cycle. DNA content was measured using PI staining and assessed by flow cytometry. p-value determined with a one-way ANOVA and Tukey post hoc test. **** (p-value < 1 x 10-4). Error bars; SD calculated from at least four independent experiments with at least 100 cells counted in each strain/experiment. (E, F) The bur1-ΔC vac17Δ double mutant shows accumulation of Whi5 in the nucleus. WT, vac17Δ, bur1-ΔC, and bur1-ΔC vac17Δ cells, which express Whi5-3xGFP and Nup188-mCherry from endogenous loci, were incubated at 24 ̊C. Cells were scored for the presence of Whi5-3xGFP in within the nucleus (Nup188-mCherry). Error bars; SD calculated from at least four independent experiments with at least 100 cells counted in each strain/experiment. p-value determined with a one-way ANOVA and Tukey post hoc test. ** (p-value < 1 x 10-2). Error bars; SD calculated from at least four independent experiments with at least 100 cells counted in each strain/experiment. Scale bar, 2 μm.
NDP52+ granules in Listeria‐infected cells have characteristics of pre‐autophagosomal structures.Figure 5(A) HeLa cells transfected with GFP‐LC3 and infected with Listeria WT for 4 h were analysed by IF using an antibody against NDP52. (B) Murine embryonic fibroblasts (MEFs) from WT or ATG16L1‐deficient (ATG16L1 KO) mice infected with Listeria WT for 4 h were analysed by IF using an antibody against ubiquitinated proteins (Ubi). (C, D) HeLa cells infected with Listeria WT for 4 h analysed by IF using antibodies against NDP52 and WIPI‐2 (C) or Galectin‐8 (Gal‐8) and calreticulin (D). (E) HeLa cells infected with Listeria WT for 4 h, in the absence or presence of Wortmannin added during the last hour of infection, analysed by IF using antibodies against NDP52 and WIPI‐2. Scale bars: 5 μm for all panels except (D) (1.5 μm).
Figure 7(A) Analysis of the cell growth rate of control and subject fibroblasts, overexpressing or not an EGFP-tagged version of the wild-type SLC25A46. Experiments were done in independent triplicates. Error bars represent mean +/- SEM and p-values were calculated using t-test. (B) Analysis of the cell area in control and subject fibroblasts, overexpressing or not an EGFP-tagged version of the wild-type SLC25A46. 30 cells were measured in each condition and experiments were repeated three times. Error bars represent mean +/- SEM and p-values were calculated using t-test. (C) Analysis of the senescence-associated β-galactosidase (SA-β-gal) activity in control and subject fibroblasts, overexpressing or not an EGFP-tagged version of the wild-type SLC25A46. Hydrolysis of X-gal results in the accumulation of a distinctive blue color in senescent cells. (D) Quantification of the senescence-associated β-galactosidase (SA-β-gal) activity in each of the experimental condition described in (C). In each condition, 200 cells were analysed. Percentage of positive blue cells corresponding to senescent cells was calculated. Experiments were done in independent triplicates. Error bars represent mean +/- SEM and p-values were calculated using a t-test. (E) Immunoblot analysis from the same samples as in (A), for expression of SLC25A46, regulators of the cell cycle and markers of senescence. SDHA was used as a loading control. (F) Analysis of cell migration capacity of control and subject fibroblasts, overexpressing or not an EGFP-tagged version of the wild-type SLC25A46, using a transwell assay as described in Methods. Cells that migrated through the membrane were identified under a microscope using DAPI staining. Scale Bars: 50 µm. (G) Quantification of cell migration capacity in each of the experimental condition described in (F). In each condition, all cells present in a field were counted and 5 random fields were analyzed per condition. Experiments were done in independent triplicates. Errors bars represent mean +/- SD and p-values were calculated using a student t-test. (H) Analysis of the cell growth rate of primary control fibroblasts treated or not with an siRNA against SLC25A46 for 3 and 6 days. Experiments were done in independent triplicates. Error bars represent mean +/- SEM and p-values were calculated using t-test. (I). Immunoblot analysis from the same samples as in (H), for expression of SLC25A46, regulators of the cell cycle and markers of senescence. SDHA was used as a loading control. (J) Analysis of the cell growth rate of MCF7 breast cancer cells treated or not with an siRNA against SLC25A46 for 3 and 6 days. Experiments were done in independent triplicates. Error bars represent mean +/- SEM and p-values were calculated using a t-test. (K) Immunoblot analysis from the same samples as in (J). SDHA was used as a loading control.
Figure 2Scheme for the piggyBac-based vectors to induce the T-V5-GR-2A-H2BmCherry protein in OCT4-YFP ESCs. Bottom: FACS analysis of the induced T fusion protein and the OCT4-YFP protein. Western blot of the indicated proteins in sorted T-induced ESCs (Oct4-GFP ESCs [left] and OCT4-YFP ESCs [right]). GAPDH was used as a loading control. Heatmap derived from mean-centered expression values (log2 scale) of selected key pluripotency genes. See also Fig EV2C, Dataset EV1 for all the clustered DEGs. PCA of global gene expression in the four distinct T-induced cell populations as shown in (A).
Figure 7Inner ring (grey): Classical transcription-translation feedback loop or the central circadian clock, involving the transcription activator CLOCK and BMAL1 and the transcription targets/repressors Period (Per) and Cryptochrome (Cry). Outer ring (green/yellow): Model of rhythmic GE driven via AS-decay. AS regulates the formation of productive stable or unproductive instable isoforms, thereby regulating the abundance of SR protein mRNA and protein. An additional regulatory layer is achieved through temperature-mediated control of SR protein activity (active SR proteins are indicated by an asterisks), resulting in rhythmic GE of SR proteins themselves and output target genes. GE in response to continuous (top) or single (bottom) input signal (indicated by arrows) is shown in the center.
Fluorescence images of (a) pag2 (strain STK2) and (b) pag3 (strain STK3) mutants of P.Figure 9Fluorescence images of (a) pag2 (strain STK2) and (b) pag3 (strain STK3) mutants of P. pastoris after a 3 h shift to glucose. (b) Arrows show deeply invaginated structures of vacuolar membranes surrounding peroxisomes in the pag3 mutant.
Fig.Figure 5In engraftment mode A - both, the clonal composition (all clonal mutations with AF>30%) and the clonal architecture are captured in the corresponding PDX. In mode B - the composition of the major clone including its characteristic SNVs and CNAs and/or the clonal architecture are remodeled in the PDX by clonal selection; grey - core mutations common for both initial diagnosis and relapse, blue - mutations specific to initial diagnosis, red - relapse-specific mutations.
| REST/NRSF target genes were not enriched at E11.Figure 5A. Volcano plot for DEGs in the embryonic brain of YFO and AFO at E11.5 (n=3 in each group). Green lines indicate a twofold change and p=0.01. Orange dots indicate REST/NRSF target genes. Data information: Data are presented in the volcano plot or line chart format. *p<0.05, ** p<0.01, ***p<0.001, determined by volcano or nominal GSEA P-value. NES, normalized enrichment score. B. GO gene sets in AFO up-regulated genes. C. GO gene sets in AFO down-regulated genes. D. Motif gene sets in AFO up-regulated genes. E. GSEA plots of DEGs for REST/NRSF target gene sets. F. GSEA plots of DEGs for early-fetal gene sets. G. GSEA plots of DEGs for late-fetal gene sets. H. GSEA plots of DEGs for DNA hypo-methylation neighboring gene sets. I. GSEA plots of DEGs for DNA hypo-methylation neighboring gene sets with REST/NRSF binding motifs.
Figure 7(A) Schematic depicting the expected visualization of a cross-linked immunoprecipitation by autoradiogram. Bands corresponding to smRNA-RBP interactions (no RNase digestion) or a smear representing mRNA-RBP interactions (low RNase digestion) by autoradiogram were processed for HITS-CLIP. (B) IGV plots from an hnRNPA1 HITS-CLIP (Huelga et al., 2012) reveals interactions with tRFTyrGUA. (C) IGV plots representing SSB interacting with the tRFTyrGUA in samples that were treated with low levels of RNase digestion. SSB bound tRFTyrGUA reads mapped to multiple loci encoding tRNATyrGUA. (D) Similar to the IGV plots shown in (C), but depicting SSB interactions with tRFTyrGUA loci in samples without RNase digestion. (E) A cumulative distribution in control and hnRNPA1 depleted cells of the stability levels for mRNA transcripts with 3' UTR hnRNPA1 CLIP binding (Huelga et al., 2012). Transfection of tRFTyrGUA led to a significant right-shift in the expression levels of 3' UTR bound hnRNPA1 transcripts. Statistical significance was measured using the Kolmogorov-Smirnov test. (F) Cumulative distribution as in (E). Transfection of locked nucleic acid against tRFTyrGUA and treatment with 200µM H2O2 led to a significant left-shift in mRNA stability of 3'UTR bound hnRNPA1 transcripts. Statistical significance was assessed using the Kolmogorov-Smirnov test. (G) Model of tRNATyrGUA-dependent gene regulatory response to oxidative stress.
Figure 2Volcano plots showing the differential expression of the genes after HNRNPC knock-down in the MCF7 (A) and T47D (B) cells. The ISGs with significant differential expression were marked as red dots. The cutoffs (dashed line) were set at the log2 fold-change > 1.5 or < -1.5 and the P-value < 0.001. Enrichment of the GO and KEGG functional annotations in the up-regulated gene sets upon HNRNPC knock-down in MCF7 (C) and T47D (D) cells. The P-values (-log10) of such enrichments were provided on the y-axis. qPCR measurements of the expressions of ISGs upon knock-down of HNRNPC in MCF7 and T47D cells using siRNA qPCR measurements of the expressions of ISGs upon knock-down of HNRNPC in MCF7 and T47D cells using CRISPR-Cas9 11 TFs involved in the interferon response and signaling, which were identified by MARINa as master TFs upon HNRNPC knock-down. In each row, all genes were sorted (from left to right) by their differential expressions in siHNRNPC vs. control cells. The predicted target genes that are positive or negative regulated by the TF are marked as red or blue bars. All the TFs were sorted by the P-values (FDR-corrected) from the MARINa analysis. Ranks of these 11 TFs among all the master TFs identified by MARINa were provided to the right.
Figure 4(A). Surface representations of the complex structures of PTP-MEG2-C515A/D470A/NSF-pY83, PTP1B-C215A/EGFR-pY992 (PDB: 1EEN), LYP-C227S/SKAP-HOM-pY75 (PDB: 3OMH), PTPN18-C229S/HER2-pY1248 (PDB: 4GFU), and PTP-STEP/pY (PDB: 2CJZ). Crystal structures of PTP-MEG1 (PDB: 2I75), SHP1 (PDB: 4HJQ), PTPH1 (PDB: 4QUN) and SHP2 (PDB: 3B7O). The pY+1 sites are highlighted. (B). Summary of the distance between the Cβ atoms of D335 and Q559 (corresponding to PTP-MEG2 number) of the pY+1 pocket in PTP-MEG2 and other classical non-receptor PTPs bearing the same residues at similar positions.
Purinergic Mechanism of Enteric Gliosis in Postoperative Ileus Gut surgical manipulation and trauma cause inflammation and increase ATP release that activates P2X2 receptors on enteric glia and induces a reactive glial phenotype termed 'enteric gliosis'.Figure 6
a) Localization using confocal microscopy of endogenous DICER (monoclonal antibody 13D6) and NDP52 in HeLa cells treated with RAP or control.figf2(a) Localization using confocal microscopy of endogenous DICER (monoclonal antibody 13D6) and NDP52 in HeLa cells treated with RAP or control. The arrows highlight some examples of co-localization. The lower left insets show higher magnifications of the areas outlined in the main panel. Scale bars, 5 μm. (b) Quantification of DICER co-localization with NDP52. Total fluorescence intensity of DICER co-localized with punctae (>0.2 μm3) of NDP52 was quantified with Volocity software in RAP-treated cells/control-treated cells over several Z-stacked microscope fields per experiment (n = 4, error bars s.e.m.). (c) Localization using confocal microscopy of endogenous DICER (monoclonal antibody 13D6) and HcRed-LC3 in HeLa cells treated with BAF or control. The arrows highlight some examples of co-localization. Insets as in a. Scale bar, 5 μm. (d) Quantification of DICER co-localization with HcRed-LC3 was performed as for NDP52 in b. (e) Confocal microscopy analysis of GFP-DCP1A and HcRed-LC3wt in HeLa cells. Scale bar, 10 μm. (f-i) Localization of DICER (monoclonal antibody 13D6) detected with anti-mouse IgG (10 nm gold beads) by electron microscopy in CQ- (20 μM, 12 h) treated HeLa cells. Mito, mitochondria; MVB, multivesicular body. The black arrows highlight all gold beads. (j) Western blot analysis of fractions from a discontinuous gradient of Histodenz (15%, 20%, 24%, 26%) described to enrich autophagosomes (light AV) and autophagolysosomes (heavy AV; ref. ). HEK293T cells were treated with CQ (20 μM, 16 h). Fractions enriched in multivesicular body and lysosomal markers are indicated. Material that was pelleted by centrifugation at 100,000g (100 K pellet) or that remained in solution after the 100,000g spin (soluble) was not added to the gradient. (k) Western blot analysis of UB and p62 in discontinuous Histodenz gradients (as in j) of HEK293T cells treated with control (DMSO) or CQ. Uncropped images of blots are shown in Supplementary Fig. S3.
Figure 6A Bright-field microscope images of indicated groups (left) and a quantitative analysis of total area of droplets (right). n = 3 biological replicates. 10 μM cGAS, 5 μM G3BP1 and 50 μM KCl, 50 μM MgCl2, 50 μM ZnCl2 were used. Data information: Representative images are shown Scale bars, 10 μm. Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. B cGAMP production assays. Recombinant cGAS (10 μM) and indicated ions (100 μM) were incubated with or without dsDNA (100 nM). The production of cGAMP was analyzed by LC-MS/MRM. n = 3 technical replicates. Data information: Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. C Fluorescent images and analysis of DNA-induced cGAS LLPS in the presence of the indicated reagent. n = 3 biological replicates. 10 μM cGAS, 50 μM of each ion and 100 nM dsDNA were used in these assays. Data information: Representative images are shown Scale bars, 10 μm. The Partition coefficient was calculated as the total fluorescence intensity of droplets / bulk fluorescence intensity of background Hoechst (blue), nuclear staining. Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. D Fluorescent images and analysis of DNA-induced LLPS of cGAS in the presence of different amounts of ZnCl2. n = 3 biological replicates. 10 μM cGAS and 100 nM dsDNA were used in the assay. Data information: Representative images are shown Scale bars, 10 μm. The Partition coefficient was calculated as the total fluorescence intensity of droplets / bulk fluorescence intensity of background Hoechst (blue), nuclear staining. Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. E Fluorescent images and analysis of DNA-induced LLPS of cGAS in the presence of G3BP1 (2 μM) and/or ZnCl2 (20 μM) as indicated. n = 3 biological replicates. Data information: Representative images are shown Scale bars, 10 μm. The Partition coefficient was calculated as the total fluorescence intensity of droplets / bulk fluorescence intensity of background Hoechst (blue), nuclear staining. Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. F cGAMP production assays. Recombinant cGAS (10 μM), G3BP1(10 μM) and ZnCl2 (100 μM) were incubated with or without dsDNA (100 nM) as indicated. The produced cGAMP was quantitatively analyzed by LC-MS/MRM. n = 3 technical replicates. Data information: Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test. NS, non-significant. NT, non-treated. G Immunofluorescence staining of cGAS in HeLa cells stimulated with ZnCl2 (100 μM). The images were acquired by ZEISS LSM 880 Confocal Microscopy. Data information: Representative images are shown Scale bars, 10 μm. Hoechst (blue), nuclear staining.
cay1∆ cells accumulate Tf2 LTR retrotransposon transcriptsChromosome maps of differentially expressed genes in cay1∆ cells shown as fold enrichment over wt.Figure 2Chromosome maps of differentially expressed genes in cay1Δ cells shown as fold enrichment over wt. Red dots are overexpressed genes and Tf2 retrotransposons, blue dots are overexpressed LTR sequences. Northern blot analysis of tlh1/2+, Tf2 retrotransposons, and 18S rRNA (loading control) in wt, cay1Δ, and trichostatin A (TSA)‐treated wt cells. Black arrowhead indicates tlh1/2+ mRNA; red arrowhead unprocessed Tf2 transcripts; and blue arrowhead processed Tf2 transcripts. ChIP analysis of Cay1‐Myc binding to the indicated genomic loci. subtel: subtelomeres; Tf2: Tf2 retrotransposon genes; LTR: Tf2 LTR sequences; Tlh: tlh1/2+ genes; cen: centromeres. Immunoprecipitated DNA is normalized to input DNA and expressed as fold increase over untagged strains (unt). ChIP analysis of H3K9ac, H3K9me3, and total H3 at the indicated genomic loci. Immunoprecipitated DNA is normalized to input DNA and expressed as fold increase over wt after subtraction of values obtained for negative control immunoprecipitations performed with beads only.