EMBO/sd-character-level-ner huggingface dataset:
Blastocyst (E4.5) and diapause embryos stained for Ronin, Sox2 and Sox17. Egg cylinder stage (E5.5) embryo stained for Ronin and Sox17. Nuclei are counterstained with DAPI.
Immunoprecipitation using FLAG antibody in lysates from HEK 293T cells transfected with plasmids expressing HOXA4 truncation mutants and TEAD1.
A. Purified trophozoite-stage iRBCs and matched uRBCs were labeled with one of ten 13C-substrates (listed in purple). All mass-to-charge (m/z) features identified by LC-MS were extracted and isotopologues grouped. 13C-labelled and 12C-labelled isotopologue groups were compared to identify m/z features in each cell type and that were differentially labelled between iRBC and uRBC. Putative metabolite identities were then confirmed with authentic standards, MS/MS spectral matching, 13C-labelling profile, and exact mass. The observed metabolic network of each cell type was then constructed using the draft metabolome and 13C-labelling information and compared to the predicted P. falciparum metabolome reported by Huthmacher et al. (2010).
(A) Immunofluorescence images of quadriceps muscle using p62 and Lamp1 or -2 antibodies. Quadriceps section from a 9-mo-oldVCP-WT mouse, age-matched VCP-RH transgenic, 12-mo-oldVCP-RH transgenic, and IBMPFD patientmuscle biopsy are shown. Open arrows highlight p62 and Lamp1/2 colocalization, and closed arrows show regions of only p62immunofluorescence. Single myofibers containing RVs are outlined in the merge panels.
A Phylogenic tree showing the relationship of the various vertebrate Grk genes and the Drosophila gprk genes
Western Blot analysis of starved p53f/f Rb1f/f Osx-Cre OS cells, pre-treated with DMSO (1:1000) or Afatinib (5µM) for 30 minutes and stimulated with EGF (50ng/ml) as indicated
F-H. Analysis of GSDMDNterm oligomers bound to lipid membranes of E. coli extract polar lipids. F. GSDMDNterm oligomers assembled into arcs, slits and rings leading to transmembrane (TM) pores or not transmembrane aggregate (n = 218). G. Height of GSDMDNterm oligomers protruding from the lipid membrane. Bars represent mean and error bars represent s.e.m. (n = 218). H. Distribution of the diameters of rings formed by GSDMDNterm oligomers. The average distribution was 21.2 ± 5.6 nm (n = 164; average ± s.d.) and the bin size was 3 nm.
HER-2-E0771 mammary tumour cells (2x105) were injected into the fourth inguinal mammary fat pads of female HER-2 TG mice. Six days after tumour injection HER-2 TG mice received total body irradiation (4 Gy) followed by the adoptive transfer of 10x106 HER-2 CAR-T cells generated from C57BL/6 splenocytes transfected with GFP versus Ptpn2 siSTABLE™ FITC-conjugated siRNAs two days before adoptive CAR-T cell transfer. Mice were injected with IL-2 (50,000 IU/day) on days 0-4 after adoptive CAR-T cell transfer and tumour growth was monitored. CD45+CD3+CD8+ mCherry+ CAR-T cells numbers were determined in HER-2-E0771 positive tumours and spleens by flow cytometry 21 days post adoptive transfer.
C, D. Western blot of ZFP207 and OCT4 of mouse ESCs during (C) RA-induced and (D) EB-mediated differentiation.
D. Quantification of the number of esg-GFP+ cells, Dl+ cells, pH3+ cells in experiments (A-C). n is indicated. The numbers of quantified guts from left to right are: 15, 18, 17, 15, 18, 17, 15, 18, and 17. Data information: Error bars represent SDs. p-values for lifespan curves (N) were calculated by the log-rank test. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
A Clonogenic survival assays were carried out in wild‐type (WT), USP45 knockout (KO) or USP45 KO cells re‐expressing wild‐type USP45 (RESWT) or catalytically inactive USP45 [Cys199Ala] (RESCA). The cells were treated with the indicated doses of mitomycin C (MMC) 16 h. Medium was changed and number of colonies quantified after 10 days. Each data point is the average of 3 experiments undertaken with 6 replicates ± SD.
(b) MEFs stably expressing EGFP-FKBP38(N402K), mCherry-FKBP38 and FLAG-Parkin were incubated in the absence or presence of CCCP (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to FLAG (M2). The fluorescence of EGFP-FKBP38(N402K) and mCherry-FKBP38 was also monitored directly.
(H) Incubation scheme: GUVs (14 nmol lipid) containing Syx1 (14 pmol) were preincubated with the indicated Munc18-1 constructs (90 pmol) at room temperature for 30 min. Subsequently, samples were incubated with soluble SNAP-25 (128 pmol) and SUVs (2.5 nmol lipid) containing Synaptotagmin1 (3 pmol) and VAMP8 (8 pmol) for 5 min on ice. Lipid mixing was started by increasing the temperature to 37 oC.
F) There is no significant difference in number of spots in HRPA-1HsLCWTmScarlet lines with or without Fyn, although there seems to be a trend of reduced spots in HRPA-1HsLCD290VmScarlet lines in animals also expressing Fyn*; this difference is not statistically significant (ANOVA). N = 12 animals per genotype. G) After exposure to 22 hours paraquat induced oxidative stress there is no significant difference between HRPA-1HsLCWTmScarlet lines with or without Fyn, although there seems to be a trend of reduced spots in HRPA-1HsLCD290VmScarlet lines in animals also expressing Fyn*; this difference is not statistically significant (ANOVA). N = 12 animals per genotype.
e, LPS-induced production of IL-1b from macrophages with the indicated phenotype.
Evolution of Cα-Cα distances of the two pairs of residues GluN1-N492/GluN2B-S188 and GluN1-K495/GluN2B-N192 during the fitting
Potassium currents recorded from mature Clrn2clarinet/+ (A, P15) and Clrn2clarinet/clarinet (B, P16) apical-coil OHCs. Currents were elicited by depolarizing voltage steps (10 mV nominal increments) from -144 mV to more depolarized values from the holding potential of -84 mV. Note that the current characteristic of mature OHCs, The size of IK,n, measured in isolation as the deactivating tail currents (difference between instantaneous and steady-state inward currents) for voltage steps from the holding potential to −124 mV, was 545 ± 115 pA, (n=5) in Clrn2clarinet/+ and 595 ± 67 pA, (n=7) in Clrn2clarinet/clarinet OHCs.
A. HEK293 cells were co-transfected with CDKL5NLS (wild type "WT" or kinase-dead "KD" K42R mutant) and either FLAG-EP400 (left), FLAG-ELOA (middle) or FLAG-TTDN1 (right). 24 h later cells were incubated with H2O2 (500 µM) for 15 min before being harvested and lysed. Protein extracts were subjected to immunoprecipitation with anti-FLAG-agarose beads. Precipitates were subjected to SDS-PAGE and blotting with antibodies shown (bottom panels) or staining with Coomassie Brilliant Blue (top panels). The bands corresponding to the FLAG-tagged proteins were excised from the gels in A. and processed for mass spectrometric detection of relevant phospho-peptides. Three independent co-transfection experiments were done for every condition.
(E) ChIP-qPCR analysis of the ATF4 promoter and 2000bp upstream of the region of interest (ATF4-Control) from MEF cells that were untreated (control), starved for 2 h, or treated with Tunicamycin (0.1 µg/ml) for 16 h. Amplification regions are indicated by arrows. Chromatin DNA was immunoprecipitated with antibodies for anti-TFE3. Bar graphs show the amount of immunoprecipitated DNA detected by the real-time PCR assay. Values were normalized to the input and plotted as relative enrichment compared to untreated conditions (means ± SD of three independent experiments, students t-test, *p < 0.05, **p < 0.01).
D In situ hybridisation for transcripts of ptch2, olig2 and nkx2.2 in 24hpf smohi1640 mutant embryos injected with mRNA encoding mSmo and mSmoSA (n=6 for each sample). Scale bars, are 100μm (lateral view), 50μm (sections).
D. HeLa cells transfected with HA-hnRNPK were left untreated (Steady state) or treated with SA (300µM, 30 min) or SA+Dinaciclib (10 µM, 150 min) and then immunostained with anti-HA and anti-G3BP antibodies. Data information Scale bars, 10 µm.
(K) De novo motif prediction by DREME revealed the enrichment of canonical YY1 motifs in the above binding regions.
Mice were transplanted with B-cell depleted human PBMC and then received CD8-LVCD19CAR (filled circle) or PBS (open circle). As control, CD8-LVCD19CAR or PBS were injected into mice transplanted with non-depleted PBMC. Data represent mean ± SD for all groups (CD8-LVCD19CAR: n=6 in D, n=4 in G; CD8-LVRFP: n=4; PBS: n=4 in G, all others n=3).
(G-I) qRT-PCR measurement of transcripts of Ifnb1(G), Cxcl10 (H) and Il6 (I) in mouse stomach tissues harvested from mice of indicated groups. The data shown are mean ± SEM of n=5 mice from 1 of 3 biological replicates with similar results. Each symbol indicates the value of 1 mouse from n = 5 mice per group. Statistical significance was determined by one-way ANOVA test followed by Tukey's multiple comparisons post-hoc test between all groups. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001; ns, not significant.
B. M-CSF induced mouse bone marrow derived macrophages (BMMs) were stimulated with 20 ng/mL mouse recombinant IL-4 (B) in the absence or presence of PGE2 ± varying concentrations of TP-16 for 12 hr. The mRNA levels of selected M2 markers (Arg-1 and Ym-1) were measured by q-PCR. Data are normalized to β-actin expression levels (n=3).
A Chromatin immunoprecipitation assays were performed using JurkatTat LTR-DsRed, clone 11. The cells were treated for 24 h with PH02 and/ or PEP005, and ChIP was performed using antibodies against histone H3K9-me3 (left panel) and histone H3K9-ac (right panel). The results are presented relative to ChIP with anti-histone H3 antibodies.
(D) Schematic presentation of multiple inflammatory cytokines from inflammatory cell up-regulate hyperstimulation of CaSR through NF-κB/p65 and JAK/Stat3 pathways. Hyperstimulation of CaSR induce osteogenic differentiation through PLCγ signalling pathway in osteogenic precursor cell to promote pathological new bone formation in AS.
(E) Neurons were treated with 3 nM decylTPP and MitoQ10 for 48 hr and stained with TMRM and fluorescence intensity analyzed via confocal microscopy (n = 3, >16 cells/experiment).
(d) Functional classification of the Sα region binding proteins identified by iChIP.
(C) The relative difference in TMRE FI between non‐fusing mitochondria and fusing mitochondria, calibrated against the whole‐cell average.
Recycling yield and maintenance rate per cell volume. (C) Recycling yields and (D) maintenance rate measured as described in Fig. 2 are normalized per cell volume and plotted versus the previous growth rate of the cultures they refer to (see color legend at the top and Table EV3). The normalized yield is constant within the uncertainty. Maintenance rate increases significantly with a slope of (0.99±0.55) h, matching the increase of the death rate, (1.1±0.4) h, shown in Fig 2B. Solid black lines show linear fits on log transformed data, using weighted least square fits.
H) FACS-assisted quantification of CellROX-DeepRed fluorescence intensity in ES and 2-cell-like cells. Measurements were obtained from 2 independent biological replicates. *** P < 0.005; Mann-Whitney U test.
(a-c) Heart-to-body-weight ratios (a), cardiomyocyte diameters (b) and cardiac fibrosis (c) in Sham-operated mice and mice treated with intravenous injection of either scrambled control (Scr) or miR-132 inhibitors (Ant-132) after TAC. These mice were analysed 3 weeks after TAC (n=4-11). PSR, picrosirius red staining.
E. Representative stitched image showing mTFP (green), Venus (yellow), DAPI (blue) and ERG1/2/3 (purple) fluorescence from BMECs and laconic-infected HBVPs on a 2 well chamber.
L. Immunofluorescence analysis of SSEA1 in shScr, sh1 and sh2 ESCs. DAPI was used as the nuclear marker. Scale bars, 20 μm.
NEDD8 affinity resin shows enrichment of endogenous neddylated proteins in WT and NEDP1 KO cells. Recombinant HALO-NEDP1 C163A (CA) conjugated to HALO-Link beads was used as an affinity resin to enrich for neddylated proteins in lysates from HEK 293 WT and NEDP1 KO cells. Enriched proteins were resolved by SDS-PAGE and processed for Western blot analysis with NEDD8 or Ubiquitin antibodies. HALO-NEDP1 CA specifically enriches for NEDD8-reactive proteins in both WT and NEDP1 KO cells, but does not enrich for Ubiquitin-modified proteins in either cell line.
D Quality of SDD model fitting to tFT-Bcd ratio for different Bcd diffusion coefficients and lifetimes. For each pair of these parameters, the fluorescence correction ε is left as a free parameter for fitting. The colormap is the log of the fitting function (Methods). The white lines correspond to parameter combinations that produce a gradient with a length constant λ=75μm (solid) and λ=95μm (dashed).
(B) 3rd instar larval fat bodies were stained by BODIPY (green) for lipid droplets and DAPI (blue) for nuclei. Overexpressing wild-type or site-mutated RDH/CG2064 increases the lipid droplet size in larvae with DGAT1 overexpression (ppl>DGAT1). Scale bar represents 25 µm.
J. Analysis of cell death after overnight recovery of HeLa cells treated or untreated with CDKi (SNS-032; Flavopiridol or Dinaciclib, 1 µM, 150 min) and then treated or not with SA (500 µM, 3 h). Images were acquired automatically by OPERETTA microscope. Values indicate the percentage of the total number of nuclei (stained with DAPI) positive for BoBo-3 staining. Mean ± s.d. of one representative experiment out of three independent replicates. ns: not significant, ****p<0.0001, One-way ANOVA with Dunnett's multiple comparison test.
E) Skin organoids derived from WT or Pvt1 inducible KO cells were grafted to nude mice. The regenerated skin was analyzed by H/E staining.
C) Quantification of the total fluorescence from phagocytized pHrodo-labelled E. coli bioparticles and percentage of phagocyting cells in the CD11b+;GFP+ microglial population (n=3-5 animals per genotype and condition). Error bars represent Standard Error. Statistical significance: **P<0.01, ***P<0.001 by two-way ANOVA followed by Bonferroni' s multiple comparisons test.
Figure 5. TGFβ signaling activity in smooth muscle cells in human left main coronary arteries with various degrees of atherosclerosis.(A&amp;amp;C&amp;amp;E) Representative images of immunofluorescence staining for TGF (red), p-Smad2 (red), or p-Smad3 (red) from patients with No/mild, moderate, or severe disease. Nuclei were counter-stained with DAPI (blue). Scale bar: 16 m.(B&amp;amp;D&amp;amp;F) Medial TGF area and percentage of medial p-Smad2, and p-Smad3 positive SMCs (***p<0.001 compared to No/mild disease; one-way ANOVA with Newman-Keuls post hoc test for multiple comparison correction).A full table of p-values for this figure is shown in Appendix Table S1.
The OHC stereocilia measurements at both P8 and P16 (C) show a significant difference in height of Clrn2+/+ stereocilia compared to Clrn2clarinet/clarinet in: e.g. for the shortest row at P8: Clrn2+/+: 0.6188 ± 0.0944 p.µm (n=27); Clrn2clarinet/clarinet: 0.2948 ± 0.1029 p.µm (n=27) (p<0.0001, Mann-Whitney ranks comparison), and at P16: Clrn2+/+: 0.579 ± 0.06179 p.µm (n=27); Clrn2clarinet/clarinet: 0.07282 ± 0.1626 p.µm (n=27) (p<0.0001, Mann-Whitney ranks comparison). Note the amount of value points equal to zero at P16. (D) Conversely, IHC stereocilia measurements at P8 and P16 did not show a difference between Clrn2+t/+ and Clrn2clarinet/clarinet in: for the shortest row at P8: Clrn2+/+: 0.8808 ± 0.1753 p.µm (n=27); Clrn2clarinet/clarinet: 0.9313 ± 0.1217 p.µm (n=27) (p=0.2244, unpaired t-test); and at P16: Clrn2+/+: 0.6784 ± 0.1171 p.µm (n=23); Clrn2clarinet/clarinet: 0.6063 ± 0.1855 p.µm (n=26) (p=0.2436, Mann-Whitney ranks comparison).
Protein expression of STRA6 during the culture activation of HSCs. Cell lysates were prepared from HSCs at 3 days after plating (HSCs-3d), and from HSCs after passage 1 (P1), 2 (P2), and 3 (P3), and analyzed by Western blotting. Lysates from NIH3T3 cells were used as a negative control. The separating lines demarcate bands that come from non-consecutive lanes of the same gel.
D458 cell lines were treated with PBS (vehicle, black) or with ActivinB (green). Immunoblot of phosphorylated Smad2 (P-Smad2), total Smad2 and β-actin in response to ActivinB stimulation for 24 hours. Quantification of P-Smad2 (P-S2) to β-actin are shown on right panels. Bars represent the mean ± SD. Number of replicates is n≥3.
Pom1 amplitude increases with Tea4 concentration at the pole. Linear regression (black line) in the log-log scale shows a slope smaller than one indicative of a sub-linear relationship between Pom1 and Tea4 at the pole (see also Fig. 2B) and thus buffering of Tea4 fluctuations. Each dot corresponds to one average Tea4 and corresponding Pom1 profiles as in (C-D). The trans-phosphorylation model predicts the slope to be 2/3 (red line), close to the observed 0.63 (black line) and within the two SE confidence interval (shaded area). Each data point is weighted by its inverse variance of the mean in the linear regression.
(C) Quantification of Arf6 activity (GTP-Arf6) in HeLa cells transfected to produce either mCherry and Arf6-HA or mCherry-BspF and Arf6-HA by G-LISA. Data are means ± SD of n=3 independent experiments, normalized to mCherry-producing controls. The asterisk indicates a statistically significant difference (P = 0.0026, unpaired Student's t test) between BspF-producing and control conditions.
I Luciferase reporter assay with indicated response element constructs in human HEK293T cells co-transfected with or without p53 expression vector.
D. Quantification of three categories of midguts treated with the pH indicator Bromophenol Blue in Drosophila carrying esgts-GAL4-driven UAS-lacZ (control), Las RNAi, or Las RNAi with ALA administration. The numbers of quantified guts from left to right are 90, 90, and 90. Error bars show SD of three independent experiments. Data information: The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
Immunoblotting of the streptavidin precipitates of the mixture of biotin (100 μM) or biotin-Palbociclib (100 μM) and the lysates of HEK293T cells transfected with Flag-STING (C) The data shown are representative of n=3 biological replicates.
ChIP analysis of c-Jun binding to sequences in SPP1 or TNC promoters. (E) Diagrams of SPP1 and TNC promoters showing positions of primer pairs, flanking c-Jun/AP-1 consensus sites, that were used for qPCR following ChIP with an antibody against c-Jun.
J, Functional analysis of GABAergic signalling shows increased responsiveness to GABA antagonist PTZ in both onset and overall locomotor activity (n=24; ****p<0.0001; one way ANOVA).
D, TolB undergoes both rotation and translation when transitioning from the full (red) to the partial translocon (orange). The C-terminal β-propeller domain of TolB, which binds the ColE9 TBE, moves toward OmpF in the OM by ~8 Å along the rotation axis.
Pearson correlation of transcripts per million (TPM) of WT and Kdm3b-KO pre-iPSC upon DMSO or AA+2i treatment for 2 or 10 days and mESC, reprogramming populations from Chronis et. al (2017), (labelled as CC).
Immmunohistochemistry of fetal organoids for C Ass1 D Sis and E Arg2. Quantification of 3 slides per staining, 7 to 10 organoids / spheroids per slide. Scale bars: 50µm.
E) Representative western blot of the solubility analysis of GK variants upon overexpression in E. coli K12. Bands show Soluble (Sol) and Pellet fractions after centrifugation at 17,100 g for 15 mins. "-DnaK" indicates expression in E. coli K12 DnaK knockout line, "+ Dnak" indicates co-expression of pKJE7, encoding DnaK, DnaJ and GrpE.
C. Expression of BR-regulated genes in bes1-DxhsfA1qM, as compared to its parents and respective wild-types analyzed by qPCRs. Data show the mean ±SD. n=3 biological repeats, each measured in 3 technical replicates, normalized to UBC. Statistically significant difference at P≤0.05 of results is indicated with different letters and was determined by Student's t-test.
H: Dot plots corresponding to measurements at 15 min of spreading: Each dot represents one cell. Horizontal bars represent the mean ± SEM. Mann-Whitney test. Data are representative of three experiments.
(e) Phase synchronisation measure (see Materials and Methods) of the detrended Venus::HES5 spatial oscillator measured over time in E10.5 Venus::HES5 spinal cord periodic slices treated in DMSO vs DBZ conditions up to 10h; dots indicate DMSO (21 kymographs, n=3 experiments) and DBZ (19 kymographs, n=4 experiments); bars indicate mean and SD; 2 tailed Mann-Whitney test with significance ****p<0.0001.
A) Experimental design. ESC cultures were supplemented with increasing concentrations (see Table EV1) of 20 distinct metabolites for 48 hours. The abundance of the Zscan4+ and 2-cell-like cells was quantified by FACS according to the reporters
C Verification of the binding specificity of NKG2D with different ligands. Data information: Every dot represents the adhesion frequency of one cell-bead pair and the experimental data came from at least two to three repeated trials. Horizontal lines represent mean values. Error bars represent mean ± SEM.
C. Genome-wide scatter plot of IP and input normalized (norm.) RNA read counts per gene for the mean of the triplicates; n=21,754; r, Pearson's correlation coefficient between IP and input.
(D) HeLa cells were transfected with 10 nM control (n=84) or Nup50 siRNA (n=171), 20 nM control (n=101) or Nup50 siRNA (n=157) and 40 nM control (n=86) or Nup50 siRNA (n=204). 72 h post transfection, cells were fixed with 4% PFA and stained with antibodies against Nup50 and mAB414, chromatin was labeled with DAPI. Scale bars: 50 µm. Quantitation of the mAB414 rim intensity at three different Nup50 RNAi and control oligo concentrations. The means are indicated as diamonds, error bars show the standard deviations. P-values have been calculated from a student t-test comparing the mean between the experimental conditions.
R-loop unwinding assay in presence of increasing DDX5. The top panel shows a typical image obtained after the assay. The bar graph (bottom) shows the quantification. The average is expressed as percentage unwinding, and standard error of the mean (S.E.M.), n=4.
Percentage of non-classical monocytes in each sample group were calculated (B). each dot represents an individual. Brown-Forsythe and Welch ANOVA test was used and data were shown as means±SD. *, P<0.05; **, P<0.01; NS, non-significant. Data information: Brown-Forsythe and Welch ANOVA test was used and data were shown as means±SD.
(c,d) Frozen sections of indicated livers were subjected to LC3/LAMP1 immunostaining and DAPI counterstaining (c). Co-localization between LC3 and LAMP1 was quantified (d). Boxed areas in fluorescence images are magnified in right-most panels (c). Scale bar, 5 μm (c). All data are shown as mean±s.e.m. ***P0.001 (Student's t-test). Molecular weight markers are indicated in kDa.
D. Table showing the type of movement found for wild-type, mutant 2, mutant 5, and mutant 13 in a modified single-molecule assay with and without ATP. Classification of type of movement is based on two repetitions of different dynein preparations.
A) Apical Myo-II localization as marked by Sqh-GFP is disrupted in round (stage 2/3) and elongated (stage 6) egg chambers. Red arrows point to the seperation of Myo-II at cell junctions, indicating that actomyosin is no longer correctly linked to adherens junctions. Live confocal imaging. Scale bars = 5 μm.