EMBO/sd-character-level-ner huggingface dataset:
Figure 4A. Immunoblot analysis (IB) of histone modifications in stably transfected HT1080 cell lines expressing EGFP, FUS‑DDIT3‑EGFP or EWSR1‑FLI1‑EGFP. Antibodies against H3K27Ac, H3K27me3, H3K4me3 and histone loading control H4 for detection of histone modifications and antibodies against EZH2 and loading control GAPDH to evaluate catalytic PRC2 amount. Immunoblot analysis with GFP antibody is shown to verify expression of FET fusion oncoproteins and EGFP. One representative immunoblot is shown. Graphs showing amount of protein (H3K27me3, H3K4me3, ratio H3K27me3/H3K4me3, H3K27Ac, and EZH2) quantified from immunoblots relative each corresponding loading control H4 or GAPDH, normalized to parental HT1080. Mean ± SEM is shown with individual replicates indicated by circles from two experiments with stable transfection and by squares from two experiments with transient transfection (24h and 48h , n=4. Student's t-test, ns= not significant, *p<0.05, **p<0.01, ***p<0.001. Original data for all quantifications, including p-values, are shown as source data. C. SWI/SNF opposes the Polycomb complex PRC2. The catalytic subunit of PRC2, EZH2, catalyzes the trimethylation of Lys27 on histone H3 (H3K27me3), a chromatin modification associated with closed chromatin, leading to downregulation of polycomb-regulated genes. FET-fusion binding to SWI/SNF might compromise the function of SWI/SNF, including polycomb opposition. In particular, genes downregulated when FUS-DDIT3 is overexpressed in HT1080 cells (RNA-seq data, n=3, compared to control, n=4) overlap with upregulated gene-sets after EZH2 knockdown, NIPP1 knockdown and HDAC knockdown, and BAF57 (SMARCE1) reconstitution in a SMARCE1 null cell line. RNA-seq data of HT1080 wt (n=4), HT1080 EGFP (n=4), HT1080 FUS-DDIT3-EGFP (n=3) and HT1080 EWSR1-FLI1-EGFP (n=4) were generated and genes > two-fold regulated were analyzed using the molecular signature database (MSigDB). Gene lists were compared to the gene-set collection "chemical and genetic perturbations" and top 20 gene sets for each comparison are shown in the source data. q‑values (FDR-adjusted p‑values) are indicated in parentheses. D. Schematic presentation of FET family of fusion oncoproteins, targeted DNA sequences and associated tumors. Left: FET N-terminal fusion partners and binding to SWI/SNF. Center: C-terminal transcription factor fusion partners and their DNA target sequences (JASPAR database). Right: Tumor types caused by respective fusion oncogene. Note tumor type specificity for each fusion oncoprotein and that the FET NTDs replace each other as fusion partners in some entities. Only a selection of the FET family fusion-oncoproteins and tumors is shown as more members are continuously discovered.
Effects of MAB treatment on the immune response of DMD patients.Figure 6Panel A: viral and donor specific T-cell responses were measured by IFN-γELISpot at different time points: before the beginning of treatment (PRE), prior to each infusion and 2 months after the fourth infusion. Infusions are indicated by arrows. Patient's peripheral blood mononuclear cells (PBMC) were challenged with irradiated autologous lymphoblastoid cell lines (EBV line host), with cytomegalovirus glycin extract (CMV antigen)(Gehrz et al, 1987) and with the following irradiated cells harvested from the donor: untreated mesoangioblasts (MABdonor), MAB activated by 48 hour-exposure to 500 IU/mL IFN-γ (γMABdonor), myotubes differentiated from MAB (myotubesdonor) and PBMC (PBMCdonor). Polyclonal stimulation (phytohemagglutinin, PHA) was used as positive control. Donor PBMC were challenged with autologous targets as negative controls. Results are expressed as number of specific cells/105PBMC and calculated according to the following formula: number of spots produced by patient's PBMC - number of spots produced by donor's PBMC. Results for patientsPt 01, Pt 02, Pt 03, Pt 05 and Pt 06 are shown. Panel B: dystrophin specific T-cell responses were measured by IFN-γ ELISpot at two time points: before the beginning of treatment (PRE, white bar) and 2 months after the fourth infusion (black bar). PBMC were challenged with a library of 15-mer overlapping peptides covering the protein sequence (pool 1-8). Polyclonal stimulation (phytohemagglutinin, PHA) was used as positive control. The grey area represents the threshold calculated on a cohort of healthy donors. Results for Pt 01, Pt 02, Pt 03, Pt 05 and Pt 06 are shown.
Figure 2Three types of GSC (GBM4, GBM6, and GBM8) were transfected with miR-10bASO, and gene expression was analyzed 24 hours later by the Affymetrix microarrays. The heatmaps colors intensity demonstrate altered expression of the genes (up- or down-regulated relative to the mock treated samples) with the fold change > 1.2 and p < 0.05 in at least two out of the three GSC cultures.A. The genes associated with "cell cycle" bioterm have been selected using Ingenuity Pathway Analysis. The treatment with the miR-10b inhibitor is indicated as "miR-10b-i". B. The genes associated with "RNA splicing" bioterm have been selected using Gene Ontology (GO). The treatment with the miR-10b inhibitor is indicated as "miR-10b-i". Arrows depict the genes selected as candidate direct targets for further study. C. miR-10b binding motifs are enriched in 5'UTRs of the genes up-regulated by miR-10b ASO. The graph shows the probability that enrichment of the miR-10b motifs in mRNAs up-regulated vs. unchanged (p<0.05) by anti-miR-10b does not occur by chance. D. The miR-10b octamer motifs' composition of the 5'UTRs was compared between transcripts up- and down-regulated on the microarrays. The relative frequencies of various miR-10b binding motifs are shown, indicating that mostly miR-10b 3'-end binding motifs are enriched in the up-regulated mRNAs.
– Tau protein mediates the proneurogenic effects of environmental enrichment.Figure 6A Representative images of control housing (CH) and environmental enrichment (EE) cages.B Schematic diagram of the experimental design. C-D Representative images of DCX+ cells in the DG of CH and EE animals (C), and quantification of the number of DCX+ cells of WT and Tau-/- animals in CH or EE conditions (D). E Representative images of 8-week-old newborn granule neurons labeled with IdU (red) belonging to WT CH, WT EE, Tau-/- CH and Tau-/- EE mice.F-G Quantification of the number of 8-week-old IdU+ cells (F) and apoptotic fractin+ cells (G).
enzymes that contribute to CMG-MCM-7 ubiquitylation during DNA replication termination in C.Figure 1Model for the priming and elongation of ubiquitin chains on substrates of cullin ubiquitin ligases in metazoa. See text for details. Family tree for the E2 ubiquitin conjugating enzymes encoded by the C. elegans genome. For each of the indicated groups, a single plasmid was generated to express RNAi to the component genes (see Materials and Methods). Summary of RNAi screen to detect synthetic lethality, upon combining ubxn-3 RNAi with a plasmid expressing RNAi to lrr-1 or to one of the groups of E2 enzymes indicated in (B). Summary of synthetic lethality data for the screen described in (C). Worms were fed on the indicated proportions of bacteria expressing RNAi to ubxn-3, lrr-1, E2 enzyme groups G1-G6, or else containing empty vector as indicated. The data represent the means and standard deviations from three biological replicates. Synthetic lethality resulting from the combination of RNAi to E2 group 5 and RNAi to ubxn-3 was deconvolved in similar experiments to those in (D), using plasmids expressing RNAi to individual E2 enzymes as indicated. Synthetic lethality resulting from the combination of RNAi to E2 group 5 and RNAi to ubxn-3 was deconvolved in similar experiments to those in (D), using plasmids expressing RNAi to pairs of E2 enzymes, as indicated. GFP-psf-1 worms were fed on bacteria containing a single plasmid expressing the indicated RNAi treatments, before preparation of embryonic cell extracts and isolation of GFP-PSF-1 by immunoprecipitation. The indicated factors were monitored by immunoblotting. The presence of GFP-PSF-1 on mitotic chromatin (indicated by white arrows) was monitored by spinning disk confocal microscopy (see Materials and Methods), in GFP-psf-1 mCherry-Histone H2B worms that were fed on bacteria containing a single plasmid expressing the indicated RNAi treatments ('Control' = empty vector). NEB = nuclear envelope breakdown. The scalebars correspond to 5 µm. Analogous experiments to those in (D, E) to deconvolve the synthetic lethality induced by RNAi to ubxn-3 in combination with E2 group 6.
Figure 5A Mouse pups born following spermatocyte injection (left) and the birth rates following embryo transfer (right). The numbers in the graph indicate: (number of pups born)/(number of embryos transferred). B Histology of the testis of a Stx2repro34 mouse. Arrowheads indicate multinucleated cells containing spermatocyte-like nuclei. There are no spermatids or spermatozoa. Bar = 50 μm. C An MII oocyte injected with a putative spermatocyte nucleus from a multinucleated cell in a Stx2repro34 mouse testis, showing the typical paired meiotic chromosomes. Bar = 20 μm. D A multinucleated cell isolated from a Stx2repro34 mouse testis, showing four nuclei. Differential interference contrast (left) and Hoechst-stained (right) images. Bar = 10 μm. E Left: mouse pups born following microinjection with putative primary spermatocyte nuclei isolated from multinucleated cells; Right: birth rate of pups following Stx2repro34 spermatocyte microinjection. F Genomic sequencing confirming the origin of pups from Stx2repro34 spermatocytes. Arrows indicate the expected point mutation of Stx2repro34. Y indicates a hybrid status with T and C bases.
Blebbing of chromatin from nucleus to cytoplasm in senescent cells is associated with loss of nuclear envelope integrity.Figure 3.Blebbing of chromatin from nucleus to cytoplasm in senescent cells is associated with loss of nuclear envelope integrity. (A) Herniation of H3K27me3-positive chromatin into the cytoplasm of OIS cells. Yellow boxed area is magnified in bottom panels. Bars: (top panels) 10 µm; (bottom panels) 5 µm. (B) Quantitation of lamin B1 gaps or herniations in OIS. Mean ± SEM, n = 2; P < 0.01. (C) Isolated nuclei of senescent cells are permeable to both 70- and 500-kD dextrans, indicating impairment of the barrier function of nuclear envelope. Dark nuclei exclude fluorescent dextran. Bars, 10 µm. (D) Quantitation of results from C. Mean ± SD, n = 4; P < 0.000001 for both 70- and 500-kD dextrans. (E) Representative OIS SAHF+ nucleus showing dextran permeability. Bars, 10 µm. (F) Quantitation of dextran 70 uptake in SAHF+ and SAHF− OIS cells. P < 1.9 × 10−5. (G) In individual nuclei, chromatin extrusion and dextran intrusion occurred in close physical proximity. Right-hand panels are expanded from yellow boxed areas on the left. Bars: (left) 10 µm; (right) 2 µm.
Effects of cancer-derived EVs on AA consumption by fibroblasts.Figure 3A,B. Decreases of leucine, arginine, and lysine (A) as well as production of ammonium (B) in the conditioned medium (CM) of NIH3T3 cells at 30 min after the LRK mixture was added to starved cells that were pretreated with EVs or PBS (n=3 biological replicates for each group). C. Intracellular levels of leucine, arginine, and lysine in NIH3T3 cells collected 30 min after the LRK mixture was added to starved cells (n=3 biological replicates for each group).
a) RagAQ66L and RagCS75N activate TORC1 in the absence of amino acids.figf3(a) RagAQ66L and RagCS75N activate TORC1 in the absence of amino acids. Each Rag construct (200 ng) indicated was co-transfected with HA-S6K (20 ng) into HEK293 cells. Cells were starved of amino acids for 1 h before collection. Phosphorylation and protein levels were determined by immunoblotting with the appropriate antibodies, as indicated. (b) RagAT21N and RagCQ120L block S6K phosphorylation in response to amino acid (AA) stimulation. pcDNA3 (200 ng, lanes 1 and 2) or each indicated Rag construct was co-transfected with HA-S6K into HEK293 cells. Cells were starved of amino acids for 1 h (-AA) and either remained in the starvation medium or were stimulated with amino-acid-containing-medium (+AA) for 30 min before collection. Phosphorylation and protein levels were determined by immunoblotting with the appropriate antibodies, as indicated. (c) RagAT21N and RagCQ120L suppress insulin-induced stimulation of S6K phosphorylation. pcDNA3 (200 ng, lanes 1 and 2) or each indicated Rag construct was co-transfected with HA-S6K (20 ng) or GST-Akt (100 ng) into HeLa cells. Cells were serum-starved overnight and stimulated with insulin (400 nM) for 30 min. Phosphorylation and protein levels were determined by immunoblotting with the appropriate antibodies, as indicated. Full scans of blots are provided in Supplementary Information, Fig. S6.
Figure 5A. Remazol brilliant blue assay. The absorbance of supernatants from the reaction containing purified and RBB-labelled E. coli peptidoglycan and the indicated protein (50 µg) were measured at =595 nm after incubation for 0.5 or 4 hours at 37°C. The results shown are the average and standard deviation from triplicate reactions (n=3). Asterisks indicate significant differences compared to the buffer (NS, non significant; **, p < 0.01; ***, p < 0.001). The supernatant of the reaction after 4 hours of incubation is shown on bottom. B. Peptidoglycan hydrolysis. The decrease of the absorbance of the M. luteus peptidoglycan suspension in presence of the indicated protein (50 µg) was measured at =600 nm at 37°C over time. The experiment was performed in triplicate and a representative result is shown.
Figure 5 Figure 5. Definition of MGC specific genes and increased phagocytosis but reduced killing in MGC A Volcano plot of microarray data of BMMΦ stimulated with LP for 6 days, as log2 fold-change to unstimulated. Black dots indicate <2 fold differentially expressed genes with significantly upregulated genes in red and downregulated genes in blue. Piecharts show the MGC specific set of genes defined by significantly differential expression in LP and nutlin3a (10µM) stimulated BMMΦ compared to LP stimulation alone.  B Heatmap of gene expression pattern in BMMΦ after 6 days of stimulation with LP or LP and nutlin3a (n3a) (10µM). Depicted are standardized log2 differences (subtract mean divided by standard deviation) of all significantly upregulated genes in MGC in comparison to untreated and n3a-treated MΦ. Gene array was performed with 2 independent biological replicates per group. C Representative images of BMMΦ and LP stimulation derived MGC of day 6 with internalized 1µm and 10µm beads and staining for immunofluorescence by phalloidin (turquoise) and quantification of bead uptake after 24 hours by FACS. Depicted are 3 independent experiments with mean; scale bar, 20 µm. D Representative image of 11day old BMMΦ infected with BCG-RFP (MOI15) for 48 hours and addition of dead-cell marker DAPI (blue), indicating apoptotic cells; scale bar, 20 µm. E Representative image of 11day old BMMΦ infected with undefined-RFP (MOI15) for 7 days, fixed and stained with phalloidin (green) and DAPI (blue) for immunofluorescence; scale bar, 50µm. F BMMΦ were infected with MGC-RFP for 6 days (yellow dashed-line) and applied on MGC from BMMΦ stimulation with LP for 6 days (white dashed-line) for live-cell imaging of 24 hours; scale bar, 20µm. G BMMΦ and MGC from BMMΦ stimulation with LP for 6 days were quantified for uptake of apoptotic BMMΦ at indicated times after addition, by FACS. Depicted are mean ± SEM of 3 independent experiments.  H BMMΦ and MGC, from BMMΦ stimulation with LP for 6 days, were infected with BCG of indicated MOI. Cells were lysed after 72 hours and plated on 7H11 agar for CFU quantification after 3 weeks. *p < 0.05, **p < 0.01, ****p < 0.0001 (two-tailed unpaired t-test).
Figure 8(A) Activity of mAb 2A10 on sporozoite speed and displacement: Data are displayed in box and whisker plots with whiskers displaying the 10 to 90 percentiles and values below and above the whiskers shown individually. Horizontal lines show the median. For the displacement data, percentage values indicate the fraction of tracks displacing over 75 microns. Statistical analysis: Mann-Whitney, p=0.0001 (speed data) and p=0.0098 (displacement data). Data shown originates from the analysis of 5 videos obtained at 5 separate imaging sessions, which generated a total number of 217 (naïve) and 136 (2A10) sporozoite tracks. (B) Activity of mAb 2A10 on the proportion of motile sporozoites (left panel) and blood vessel entry (right panel). Four-minute videos of mice inoculated with mAb 2A10 and naïve controls were manually counted at 10 min post P. falciparum sporozoite inoculation. 5 videos for each condition, from 5 independent imaging sessions were scored for motility. 4 videos per condition from 4 independent imaging sessions were analyzed for blood vessel entry. Statistical analysis: Percent motile, Mann-Whitney, p=0.0317; Blood vessel entry, Fisher's exact test, p=0.0163   (C) Activity of human mAbs 10 and CIS43, specific for P. falciparum CSP, and VRC01, an isotype control human mAb specific for HIV-1, on the proportion of motile sporozoites (left panel) and blood vessel entry (right panel). Four-minute videos of mice inoculated with the indicated mAbs were taken 10 min after sporozoite inoculation and manually counted. Data are pooled from 7 biological replicates, naïve and VRC01 (n=2), naïve and mAb 10 (n=2), VRC01 and CIS43 (n=3). No comparisons were statistically significant (Mann-Whitney for percent motile and Fisher's exact test for blood vessel entry).
single cell analysis of published liver cell atlas.Figure 1.liver cell atlas visualized by tSNE, colored by cluster number. Cluster number information is provided by the authors. liver cell atlas visualized by tSNE, colored by major cell type compartments. Clusters were collapsed into major cell types based on their canonical markers. The dotplot showing cell type marker expression of all cell types. The violin plot of ACE2 gene expression of all major cell types.
Figure 4(A) A model of the regulation of physiological cell death in EC-committed EBs based on our epistatic analysis and previous known gene interactions. (B and B') Number of ECs over time (left), number of EBs over time (middle), and probabilities of EB loss through apoptosis (right graph). The simulation starts with 1000 EC cells in all figures In (B) a challenge at day 1 imposes a loss of 500 EC cells (black dashed vertical line). In (B') two successive challenges are imposed: one at day 1, reducing by half the number of ECs (as in B), and a second one at day 3, causing a loss of 200 cells. (C) All EBs show Diap1-GFP expression but at varying levels, consistent with EB death fate being tuned by apoptotic input counteracting survival signals. Data information: (n= 17, 13, 12, 10, 21, 24). P values were calculated using one-way ANOVA Bonferroni corrected (****, P < 0,0001). (D) Quantification of the number of Diap1-GFP+. Note that in p35-expressing midguts reared in 'Low', GFP levels are not increased, consistent with the p35 protein suppressing apoptosis downstream of Diap1. Data information (n= 17, 13, 12, 10, 21, 24). P values were calculated using one-way ANOVA Bonferroni corrected (****, P < 0,0001). (E) Quantification of the number of newly renewed ECs in the indicated genotypes after 7 days Increase in EB numbers and EC turnover in the EGFRact midgut reflects both suppression of EB deaths and the non-autonomous stimulation of ISC in this background. Data information: (n= 17, 13, 12, 10, 21, 24). P values were calculated using one-way ANOVA Bonferroni corrected (****, P < 0,0001). (F) Representative images acquired using the same laser intensity are shown for Diap1-GFP in the indicated illustrative examples. Scale bar, 100µm.
β-Coronavirus lineage B entry with human ACE2 is clade-specifica, β-Coronaviruses, including SARS-CoV, interact with the host cell receptor via the Receptor Binding Domain (RBD) in spike (PDB: 5X5B, 2AJF) .Figure 1:β-Coronavirus , including SARS-CoV, interact with the host cell receptor via the Receptor Binding Domain (RBD) in spike (PDB: 5X5B, 2AJF) . SARS-CoV spike was engineered with silent mutations to facilitate cloning novel RBD sequences in place of the SARS spike RBD. SARS spike amino acid numbers are indicated for silent cloning sites and the RBD in grey and orange, respectively. outline of experimental workflow. Westernblot of producer cell lysates and concentrated reporter particles. BHK cells were transfected with either human ACE2 or empty vector, subsequently infected with VSV-reporter particles pseudotyped with chimeric spikes, luciferase was measured and normalized to no pseudotype as a readout for cell entry. Shown are the data for 3 replicates.
TBK1 deficient in the autophagy adaptor binding domain does not reduce HTTex1 72Q eGFP S13A/S16A aggregates: (A) Western blot of soluble HTT (ab-MAB5492), HTT pS13 (ab-CHDI-90001039-1) and HTT aggregates (ab-MAB5492), upon coexpression of the HTTex1 72Q eGFP or HTTex1 72Q eGFP S13A/S16A variant with TBK1 KD, TBK1 or TBK1 Δ690-713 for 48 hour in HEK293 cells.Figure 7(A) Western blot of soluble HTT (ab-MAB5492), HTT pS13 (ab-CHDI-90001039-1) and HTT aggregates (ab-MAB5492), upon coexpression of the HTTex1 72Q eGFP or HTTex1 72Q eGFP S13A/S16A variant with TBK1 KD, TBK1 or TBK1 Δ690-713 for 48 hour in HEK293 cells. (B) The graph indicates the calculated fold changes in HTT, HTT pS13 ratio to total HTT and HTT aggregates all compared to the levels in TBK1 KD from the experiments like in A (bottom panel normalized to Tubulin, n=3). (C) Representative immunofluorescence images of eGFP HTTex1 72Q or its phosphorylation-deficient variant S13A/S16A upon coexpression with TBK1 KD or TBK1 or TBK1 Δ690-713 (ab-anti-Myc) with for 48 hour in HEK293 cells (scale bar 20μm). (D) The graph indicates the percentage of co-transfected cells presenting aggregates upon expression of the indicated kinase, from the experiments like in C (n=3).
Fig.Figure 5Abrogation-of-restriction assay in FRhK4 cells expressing restrictive rhesus TRIM5. FRhK4 cells were co-transduced with a fixed dose of HIV-1 GFP (5×107 genomes/ml) and increasing doses of HIV-LUC ΔCA-SP1 mutants Rescue of GFP infectivity was assessed by flow cytometry. Data are singlet % GFP values and two repeats of the experiment are shown. See also Appendix figure S3. Statistical analyses were performed using 2-way ANOVA with multiple comparisons. * P<0.05, ** P<0.01, *** P<0.001. Abrogation-of-restriction assay in FRhK4 cells expressing restrictive rhesus TRIM5. FRhK4 cells were co-transduced with LPV-treated HIV-LUC viruses Rescue of GFP infectivity was assessed by flow cytometry. Data are singlet % GFP values and two repeats of the experiment are shown. See also Appendix figure S3. Statistical analyses were performed using 2-way ANOVA with multiple comparisons. * P<0.05, ** P<0.01, *** P<0.001.