EMBO/sd-character-level-ner huggingface dataset:
Non-apical divisions occur in the posterior epiblast before and at the onset of gastrulation.Figure 5(a) 3D reconstruction from wholemount lightsheet imaging of an E5.75 Hex-GFP (green, anterior marker) embryo, stained for nuclei (DAPI, grey) on the left, mitosis (Phh3, magenta) and F-actin (Phalloidin, grey) on the right. (b) Z-slice (left) and 3D reconstruction (right) from wholemount lightsheet imaging of an E6.25 embryo stained for a posterior marker (Eomesodermin, cyan), mitosis (Phh3, magenta) and F-actin (Phalloidin, grey). (a', b') Mitotic Index (Phh3/DAPI) in percentage at the anterior and posterior regions of E5.75 (a') and (b') E6.25 embryos. Posterior region includes the PS region, as it could not be precisely discriminated. (a", b") Ratio of non-apical mitosis (non-apical Phh3 over total Phh3, normalized by number of nuclei) in percentage in the anterior and posterior region of E5.75 (a") and E6.25 (b") embryos.
Figure 2A Kaplan-Meier overall survival curves of mice transplanted with GB2 cells (Left panel), GB13 cells (Middle panel) or GB16 cells (Right panel) infected with the indicated lentivirus (1 × 104 cells, 7 mice per group). The y-axis indicates the percent survival. B Mice were transplanted with the indicated number of GB2 cells infected with a control (Empty) or shSIRT2-expressing (shS2 #1) lentivirus. Six weeks after transplantation, mice (3 or 4 animals, see number of dots) were sacrificed and the expression levels of human β-actin mRNA were quantified by qRT-PCR. C H&E staining of tumors that were developed in mice implanted with GB16 cells that had been infected with a control (Empty) or shSIRT2-expressing (shS2#1) lentivirus. Scale bar, 1 mm. An image with higher magnification is shown on the right (scale bar, 50 μm). D The effect of AK7 on the deacetylation of acetyl-tubulin (Left panel) and the proliferation of GB2 cells (Right panel). (Left panel) Immunoblotting analysis of the effect of AK7 (20 μM) on deacetylation of acetyl-tubulin/tubulin were performed on day 3 in Right panel. Bars indicate mean ± s.d. (n = 3). E Ten days after intracranial transplantation of GB2 cells (1.0 × 104 cells), AK7 was intraperitoneally administrated for 4 weeks (15mg/kg, twice/week). After eight weeks, mice (4 or 5 animals, see number of dots) were sacrificed and the expression levels of human β-actin mRNA was quantified by qRT-PCR.
Figure 3A. Yeast two-hybrid analysis of IDAP1 and IDAP2 interactions. Yeast cells expressing the indicated proteins from the pGAD-T7 (AD) and pGBK-T7 (BD) vectors were plated onto medium lacking Leu and Trp (SD-LT) (left) or medium lacking Leu, Trp, Ade and His (SD-LTHA) (right). B. Pull-down assays showing that IDAP1 and IDAP2 interact with each other. MBP-IDAP1 and GST or GST-IDAP2 were co-expressed in E. coli BL21 (DE3). GST or GST-IDAP2 was purified with GST affinity beads. The eluted proteins and total proteins with or without IPTG treatment were separated by SDS-PAGE and stained with Coomassie brilliant blue. A, GST+MBP-IDAP1; B, GST-IDAP2+MBP-IDAP1. C. Split luciferase complementation assays showing that IDAP1 interacts with IDAP2 in N. benthamianaleaves. 1, IDAP1-nLUC+cLUC; 2, IDAP1-nLUC+IDAP2-cLUC; 3, nLUC+IDAP2-cLUC; 4, nLUC+cLUC; 5, IDAP2-nLUC+cLUC; 6, IDAP2-nLUC+IDAP1-cLUC; 7, nLUC+IDAP1-cLUC. Three biological replicates were performed, and similar results were obtained. D. BiFC analysis of the interaction between IDAP1 and IDAP2 in Agrobacterium-infiltrated N. benthamianaleaves. YFP signals (green) and the overlay of the YFP signals and the DAPInuclear stain (blue) are shown. YFPC, C-terminal region of YFP; YFPN, N-terminal region of YFP. Three biological replicates were performed, and similar results were obtained. Scale bar: 50 μm. E. Co-localization of IDAP1 and IDAP2 in the nucleus. The nuclear distribution of IDAP1 and IDAP2 was analyzed by immunostaining using anti-Myc (green) and anti-Flag (red) in wild-type plants or the F1 heterozygous plants expressing Myc-tagged IDAP1 and Flag-tagged IDAP2 under their native promoters. DNA was stained with DAPI (blue). The frequency of nuclei displaying each interphase pattern is shown on the right. Upper panel: WT; Lower panel: F1 offspring of a cross between the IDAP1-3 Myc and IDAP2-3 Flag transgenic plants.
Figure 6 [a] Representative image of DIV15 dissociated cultured neurons used. Scale bar: 100 µm.  [b] (top) Cartoon schematic illustrates SyGCaMP6f targeting and action. (bottom) Image shows typical punctate SyGCaMP6f expression at DIV15. Scale bar, 20 µm.  [c] Representative images of fluorescence responses in synaptic terminals expressing SyGCaMP6f to a train of 10 stimuli at 10 Hz in dissociated hippocampal neurons derived from wild type and mutant mice. Scale bar: 5 µm.  [d,e] Mean SyGCaMP6f responses to three rounds of 10 APs stimulation from mice of the following genotypes; WT (n = 1946 synapses, 9 coverslips, 3 animals), Xrcc1Nes-Cre (n = 3313, 12, 4), Parp1+/- /Xrcc1Nes-Cre (n = 2272, 9, 3), and Parp1-/- /Xrcc1Nes-Cre (n = 2122, 11, 3). Data are from three or more independent experiments per genotype/treatment type, combined into one experimental data set and plotted on three separate graphs for clarity. Dashed lines in panels e and f are the WT and/or Xrcc1Nes-Cre curves transposed from panel d for comparative purposes.  [f] Response to chronic treatment with the PARP inhibitor, KU 0058948 Hydrochloride (1 µM) for 9-11 days prior to imaging for Xrcc1+/+ (n = 1264 synapses, 8 coverslips, 3 animals) and Xrcc1Nes-Cre (n = 2231, 10, 4) mice. Data are from three or more independent experiments per genotype/treatment type, combined into one experimental data set and plotted on three separate graphs for clarity. Dashed lines in panels e and f are the WT and/or Xrcc1Nes-Cre curves transposed from panel d for comparative purposes. Summary histogram of the mean (± SEM) of the integrated fluorescence responses for all individual synapses for each condition. Synapse number is the same as in (D-F). Responses are significantly higher in Xrcc1Nes-Cre synapses versus both WT and Parp1-/-/Xrcc1Nes-Cre (one-way ANOVA, *p < 0.0033, and pairwise student's t-tests).
Figure 5(a) 264 common genes were identified down-regulated by both deficiency for YAP/TAZ and deficiency for ATF4, among which were known ATF4 targets, such as SLC7A11 and CHAC1. HLE cells were transfected with siCtrl, siYAP/TAZ or siATF4 and cultured with 6μM Sorafenib for 18 hours and RNA was subjected to next generation RNA sequencing. Venn diagram analysis was conducted using VENNY 2.1.0. (b) Quantitative RT-PCR analysis verified that depletion of YAP/TAZ or ATF4 declined the expression levels of SLC7A11 and CHAC1. HLE cells were transfected with siCtrl, siY/T or siATF4 and cultured with 6μM Sorafenib for 18 hours. Quantitative RT-PCR was conducted to determine SLC7A11 and CHAC1 mRNA levels. Data are shown as mean ± standard deviation (SD).Statistical significance was calculated using Two-way ANOVA. Results represent 3 independent experiments. (c) Binding of ATF4 to DNA fragments containing the AARE binding motif in the promoters of SLC7A11 and ATF3. ChIP was performed on HLE cell lysate with antibodies against ATF4 and rabbit IgG as control. DNA fragments were amplified using the primers specific for AARE binding motif in the SLC7A11 promoter region. The non-coding region NC10 served as negative control. Data are shown as mean ± standard deviation (SD). Statistical significance was calculated using one-way ANOVA. Results represent 3 independent experiments. (d) Schematic representation of the ATF4 binding motif AARE located at - 95bp of the SLC7A11 promoter region. YAP/TAZ were predicted to interact with ATF4 binding to the AARE binding motif in the promoter of SLC7A11. (e) Binding of YAP and TAZ to DNA fragments containing the AARE binding motif in the SLC7A11 promoter. ChIP was performed on HLE cell lysate with antibodies against YAP and TAZ and rabbit IgG as control. DNA fragments were amplified using the primers specific for AARE binding motif in the SLC7A11 promoter region. The non-coding region NC10 served as negative control, and the bona fide TEAD target genes CYR61 and ANKRD1 served as positive controls. Data are shown as mean ± standard deviation (SD). Statistical significance was calculated using one-way ANOVA. Results represent three independent experiments. (f) Schematic representation of the ChIP-ReChIP strategy to test whether YAP/TAZ bind to the AARE binding motif within the SLC7A11 promoter via binding to ATF4. (g) YAP/TAZ bind to DNA fragments containing the AARE binding motif within the SLC7A11 promoter via ATF4. HLE cells were cultured with 6μM Sorafenib for 18 hours before harvest. In a 1st round ChIP ATF4 was immunoprecipitated with antibody against ATF4, rabbit IgG was used as control. DNA-protein immunocomplexes were eluted and in a 2nd round ChIP antibody against YAP/TAZ was used to precipitate DNA fragments which were then amplified and analyzed by quantitative PCR for the AARE motif in the SLC7A11 promoter. NC10 served as negative PCR control. Data are shown as mean ± standard deviation (SD). Statistical significance was calculated using one-way ANOVA. Results represent three independent experiments.
Type I IFN signaling is retained in dormant PCa cells in bone metastases (A) PKH26 (PE)-labelled RM1 (V500/eCFP) cells were injected intracardiac (IC) into C57BL/6 mice and FACS-isolated from bones with evident tumor burden (8 individual mice across 5 independent experiments) from day 16 onward and individual dormant and proliferating cells were isolated for scRNA-seq.Figure 1(A) PKH26 (PE)-labelled RM1 (V500/eCFP) cells were injected intracardiac (IC) into C57BL/6 mice and FACS-isolated from bones with evident tumor burden (8 individual mice across 5 independent experiments) from day 16 onward and individual dormant and proliferating cells were isolated for scRNA-seq. Representative tumor burden at the whole mouse level and in bone shown by bioluminescence with representative FACS plots of PKH+ (PE/V500) and PKH- (V500) RM1 cells and bone marrow cells (grey). (B) goana gene ontology (GO) analysis (limma) of all DE genes enriched in proliferating (PKH-; n = 32) cells compared to dormant cells (PKH+; n = 28). Gene sets appear in order of significance (p value) with color representing fold enrichment and bar width indicating the number of genes in each process. (C) goana GO analysis (limma) of all DE genes uniquely enriched in PKH+ compared to PKH- cells. Gene sets appear in order of significance (p value) with color representing fold enrichment and bar width indicating the number of genes in each process. (D) INTERFEROME database classification of differentially expressed (DE) genes retained in dormant cells into predicted type I and/or II IFN regulated genes (IRGs). (E) Heatmap of relative BASiCS-derived log2(denoised counts + 1) of type I IRGs (upregulated > 2-fold in the INTERFEROME in at least one dataset) that are differentially expressed between all dormant and active cells with no residual over-dispersion. Mice IDs for each sample are indicated, along with type I IRGs that are identified as such in at least 30 INTERFEROME datasets. Genes are displayed if detected in at least 10 samples per population. Samples with zero counts for individual genes are represented in white. (F) Dot plot of BASiCS-derived log2(denoised counts + 1) of key DE IRGs expressed in > 5 dormant cells associated with immune-activatory processes (among one of the most enriched types of biological pathway determined by GO analyses) present for all single cells ranked by ExpLogFC (Fig. 1c). Open circles are zero counts. Bars indicate mean expression.
Figure 3(A) Numbers of quantified O-glycopeptides identified with ETD fragmentation with either dimethyl labeling or TMT labeling approach in COSMC KO or WT background, respectively. (B) Numbers of differentially glycosylated peptides in the two approaches, using select filters on quantification values. (C) Numbers of unambiguous unique differential O-glycosites identified with the two different approaches. The stacked bar graph differentiates between glycosites identified on peptides with single and multiple HexNAc/HexHexNAc modifications. (D) The Venn diagram represents overlap between differential single HexNAc/HexHexNAc glycosites in the three differential datasets (pooled targets from both approaches). (E) Analysis of differential glycosites identified with the TMT labeling approach using the Qluqore Omics Explorer software. The heatmap represents O-glycosites most significantly contributing to sample variation, using ANOVA with a q value cutoff of 0.1, where each compared sample consists of three individual KO clones. Each horizontal line depicts the median quantification of glycopeptides contributing to the same glycosite. Alternative differentially glycosylated site positions are separated by semicolons on sites derived from glycopeptides with multiple HexNAc/HexHexNAc modifications. (F, G) GO term analysis of differentially glycosylated protein identifications from both approaches (DAVID, q ≤ 0.05, Benjamini adjusted). (F) GO terms found in all differential datasets associated with subcellular location and common glycoprotein properties. (G) Differential GO terms, found in only one of the three differential datasets. p value (Benjamini multiple comparison adjusted) of 0.05 is marked with a dashed line. (H) Top downregulated unambiguous single HexNAc/HexHexNAc targets found in all three clones of individual GALNT KO (not changed in other isoforms) with the TMT labeling approach.
Figure 7Smc5/6 complex first uses its ATPase activity to associate with DNA. After loading onto DNA, binding of the positively charged patch (DNA sensor) in the Smc5 ARM domain further activates the Nse2 SUMO ligase. Nse1, Nse3, Nse5 and Nse6 subunits of the Smc5/6 complex are not shown in the figure
Figure 1The schematic of human CAMP transgenic mouse strain. LL-37(4 kD) detection by Western blotting. Prior to loading, samples were centrifuged through 10 kD ultrafiltration membranes and the equal amount of ultrafiltrate (19μg/lane) subject to immunoblotting. High-molecular-weight proteins (GAPDH) were not detected in ultrafiltrate. The CFU of PAO1 was measured by culturing in ultrafiltrate (upper panel) or retentate (lower panel) of mouse BALF samples from indicated mice. Initial additions of PAO1 were 1 × 103 CFU. Coculture duration, 6h. n=3. The bacterial CFU (per gram) in lungs of indicated mice with and without PAO1 infection (5 × 106 CFU) for 6, 24 and 48 hours. n=3. Error bars, S.E.M. Representative histological sections of indicated lungs with PAO1 infection (5 × 106 CFU) for 6 hours. H&E staining. Scale bar, 1000 μm (upper panel) and 50 μm (lower panel). Histopathological injury score of indicated mouse lungs with PAO1 infection (5 × 106 CFU) for 6 h and 24 h based on blinded expert judgement. n=3. Error bars, S.E.M. Gene expression level of IL-1β and IL-6 of indicated mouse lung with PAO1 infection (5 × 106 CFU) for 6 h and 24 h. n≥3. Error bars, S.E.M. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001.
Bax forms ring-like structures on fragmented mitochondria during apoptosis.Figure 1A Left: Overlay image of a confocal recording of an apoptotic U2OS cell surrounded by non-apoptotic cells labeled with Bax (green) and Tom22 (red). Bax translocates to the mitochondria in apoptotic cells. Right: Individual display of the two color channels as shown in the overlay image. The asterisk denotes the apoptotic cell. Scale bars: 10 µm. B, C Dual color image of an apoptotic U2OS cell decorated with antibodies against Bax (green) and Tom20 (red). The Bax signal was recorded in the STED mode and the Tom20 signal in the diffraction-limited confocal mode. (B) and (C) display the same data set. The small images are magnifications of the areas indicated by the rectangles. In (B) the color table was adjusted to the brightest Bax signal in the image resulting in a clear display of the clusters. In (C) the color table was adjusted such that the dimmer Bax-rings are visible and the clusters are saturated. The arrows point to Bax-rings. Scale bars: 1 µm. D Optical sections of an apoptotic mitochondrion labelled for Bax (green) and Tom22 (red). Shown are three optical sections and a maximum intensity projection of the entire image stack. Scale bar: 0.5µm. E Bax-rings on apoptotic mitochondria of various mammalian cell types. Shown are apoptotic mitochondria labelled for Bax (green) and Tom22 (red) in HT1080, SH-SY5Y, HeLa and CV-1 cells, as indicated. Scale bars: 0.5 µm. F Quantification of the diameter of Bax-rings in apoptotic U2OS cells. Only the long ring-axis was measured. Bax-rings smaller than 200 nm exist, but were not considered.
Lethal response of different genotypes to increasing doses of TNF and generation of consomic mice.Figure 1Mice were injected with three different doses of TNF and mortality was observed for 96 h. Ratios of deaths/total are displayed. Statistical significance of the differences in survival was calculated relative to the B group or the B.S.chr6 BB group. Student's t-test using unpaired comparisons and two-tailed analysis. ***P < 0.001 and ****P < 0.0001. Breeding scheme for the generation of B.S.chr6 consomic mice for the distal part of chr6. After N10 generations of backcrossing, an intercross was performed resulting in progenies carrying at least 40-cM-sized haplotypes of B homozygosity (black), BS heterozygosity (green) or S homozygosity (grey). The location of the Tnfrsf1a gene is indicated.
Figure 1A. Western blot detection of PEX13, ATG7, SMURF1, and FANCC in HeLa/GFP-LC3cells transfected with the indicated siRNA. Asterisk denotes non-specific band. B. Representative images of GFP-LC3 colocalization with mCherry-capsid at 10 h after Sindbis virus (strain AO30) infection of HeLa/GFP-LC3 cells treated with the indicated siRNA. siPEX13 oligo #2 is shown; similar results were observed with three other siPEX13oligos. Arrowheads denote representative colocalized GFP-LC3/mCherry-capsid puncta. Scale bars, 10 μm. C. Quantification of colocalized GFP-LC3 and mCherry-capsid puncta normalized to the number of mCherry-capsid puncta per cell (% colocalization) in the experiment shown in (B). Bars are mean ± SEM of triplicate samples (~100 cells analyzed per sample). Similar results were observed in more than three independent experiments. ***p<0.001; one-way ANOVA with adjustment for multiple comparisons. See Fig EV1A and B for quantification of mCherry-capsid puncta per cell and GFP-LC3 puncta per cell from the same experiment. D. Western blot detection of Pex13 in MEFs of indicated genotype. Asterisks denote non-specific bands. E. Quantification of colocalized GFP-LC3 and mCherry-capsid puncta normalized to the number of mCherry-capsid puncta per cell (% colocalization) at 8 h after Sindbis virus (AO28 strain) infection in MEFs of the indicated genotype. Bars are mean ± SEM of triplicate samples (~100 cells analyzed per sample). Similar results were observed in more than three independent experiments. *p<0.05; two-tailed unpaired t-test. See Fig EV1G and H for quantification of mCherry-capsid puncta per cell and GFP-LC3 puncta per cell from the same experiment. F. Western blot detection of p62 and LC3 in MEFs of indicated genotype treated with 100 nM Baf A1 or DMSO vehicle and cultured in normal medium (starvation "-") or EBSS (starvation "+") for 3 h. Similar results were observed in three independent experiments. G. Quantification of GFP-LC3 puncta in MEFs of indicated genotype treated with 10 nM Baf A1 or DMSO vehicle and cultured in normal medium or HBSS (starvation "+") for 3 h. Bars are mean ± SEM of triplicate samples (~100 cells analyzed per sample). *p<0.05; two-tailed unpaired t-test. NC, nonsilencing control.
Teicoplanin and dalbavancin but not vancomycin repress the entry of 2019-nCoV into different cell types.Figure 3.types.A, HEK293T cells were infected with HIV-luc/2019-nCoV pseudoviruses and then incubated with teicoplanin at various concentrations. The intracellular luciferase activity was measured at 48 h post-infection. The IC50 was calculated using GraphPad Prism software.B software.B, Huh7 cells were infected with HIV-luc/2019-nCoV pseudoviruses and then incubated with teicoplanin at various concentrations. The intracellular luciferase activity was measured at 48 h post-infection. The IC50 was calculated using GraphPad Prism software.C A549 cells were incubated with dalbavancin (D) at various concentrations and infected with HIV-luc/2019-nCoV pseudoviruses. The intracellular luciferase activity was measured at 48 h post-infection. Ordinary one-way ANOVA test was used for this analysis. dalbavancin D, A549 cells were incubated with vancomycin at various concentrations and infected with HIV-luc/2019-nCoV pseudoviruses. The intracellular luciferase activity was measured at 48 h post-infection. Ordinary one-way ANOVA test was used for this analysis. Left: Chemical structure of vancomycin
/6 complexes determined by cross-linking mass-spectrometry (XL-MS) and cryo-electron microscopy (cryo-EM).Figure 1A. Reconstitution of Smc5/6 and Nse5/6 complexes. Left panel, schematic depiction of the composition and organization of the yeast Smc5/6 'core' hexamer and the Nse5/6 dimer. Middle panel, elution profiles for analytical gel filtration (Superose 6 Increase 3.2/300) of the Smc5/6 core hexamer, the Nse5/6 dimer and a holo-complex obtained by mixing of dimer and hexamer. Measured by absorption at 280 nm. Right panel, peak fractions were analysed by SDS-Page and Coomassie Brilliant Blue staining. B. Circular representation of lysine-lysine inter-subunit cross-links identified by mass spectrometry (XL-MS) in buffer containing 250 mM NaCl. For simplicity, cross-links between proteins (or domains) are grouped, and the thickness of the lines indicate the total number of crosslinks of this particular type. Smc5 and Smc6 proteins are divided into N- and C-terminal head domains (HD) and coiled-coil arms (CC) as well as the central hinge domain. For a full representation of individual inter-subunit as well as intra-subunit cross-links C. Cross-links obtained within and between Smc5 and Smc6 subunits of the Smc5/6 octamer. A cross-link that did not match to the elongated rod-shaped particle is displayed by a dashed line in red colours. The cartoon on the right shows the dimer of folded Smc5 and Smc6 proteins, with examples of intra- and interlinks within the coiled-coil arms indicated with yellow and red lines, respectively. D. Selected 2D class averages obtained by cryo-electron microscopy of the yeast Smc5/6 hexamer. Representative classes with dimers of Smc5/6 hexamers are displayed (left images). Emerging details are indicated schematically (right panel).
Pex10, Pex11, and Pmp47 do not colocalize with Pex14.Figure 3.(A) FM images of pex3 atg1 cells grown for 16 h on MM-M/G. Cells produced Pex14-mCherry and C-terminal mGFP fusions of the indicated proteins. (B) WB analysis of WT (1) and pex3 atg1 cells (2), grown for 6 or 16 h on MM-M/G. (C) FM images showing mGFP-fluorescence in pex3 atg1 cells producing Pex14-mCherry (control) or Pex14-mCherry together with the indicated mGFP fusion protein. Cells were grown for 6 h on MM-M/G. (D and E) iEM of pex3 atg1 cells using α-Pex5 (D) or α-alcohol oxidase antibodies (E). (F) Cell fractionation of the two indicated strains (seperated by the horizontal broken line). Postnuclear supernatants (PNS) were subjected to differential centrifugation resulting in a 30,000 g organelle pellet (P) and supernatant fraction (S). (G) Flotation analysis of the organelle pellet showing the distribution of the indicated proteins in the top (1) to bottom (10) fractions. (H) Colocalization of Pex8-GFP and Pex14-mCherry in pex10 cells.