EMBO/sd-character-level-ner huggingface dataset:
(D-F) Recruitment of Stx6-positive vesicles to rBCVs in BMMs treated with non-targeting siRNAs (siNT), siRNAs against Arf6 (siArf6) (D), Rab8a (siRab8a) (E) or Rab6a/a' (siRab6a/a') (F) and infected for 24 h with either wild type (2308), ΔbspF, or complemented ∆bspF (ΔbspF::bspF) bacteria. Data are means ± SD of n=3 independent experiments, in which 200 BCVs were analyzed per experiment. Asterisks indicate statistically significant differences (P<0.05, one-way ANOVA followed by Dunnett's multiple comparisons test) between test and control conditions; ns, not significant.
A Electron micrographs of METTL3-knockdown SMMC-7721 cells under hypoxia for 48 h.
(A) MCF10A-eGFP-LC3 cells were left untreated (Control) or treated with 5 μM rapamycin (Rapa), 500 ng/ml TRAIL or 10 ng/ml TNF for 24 h. When indicated, 10 mM 3‐MA or 5 μg/ml TRAIL‐R2 antagonist antibody was added 1 h before the drugs. Representative confocal images (20 μm scale bars) and the percentages of cells with LC3 translocation are shown.
Peak amplitudes of Ca2+ release in cells of the indicated genotypes in response to GPN (F). All values represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
Whole-mount immunofluorescence of E18 mesenteries fixed immediately after dissection (left panel) or after 24 h of ex vivo culture (right panel). Note loss of patterning of PROX1high valve LECs and downregulation of FOXP2 expression in flow-abrogated vessels after ex vivo culture.
(A-J) Isotope-labeled carbon tracing experiment showing glucose and lactate metabolism in HBVPs. HBVPs were treated with isotope-labeled nutrients (­­CON: control, [13C6]-glu : 5mM [13C6]-glucose, [13C3]-Lac : 2mM [13C3]-Lactate, [13C3]-Lac-20 : 20mM [13C3]-Lactate in glucose free media) for 12hr and analyzed by a Q-exactive MS spectrometry. Barplots show relative fraction of unlabeled (M0) and labeled forms (M1~6) in various metabolites including A. Glucose, B. Lactate, C. Citrate, D. Aconitate, E. α-ketoglutarate (αKG), F. Succinate, G. Malate, H. Aspartate, I. Alanine, J. Glutamate. (n=3 from independent experiments.)
(G) H&E, SOFG and Immunofluorescence analyses of the spine specimen of PGIS model at 30 Weeks compare to baseline. GP: Growth plate. n=5 per group.
F Real-time PCR analysis of Ido1 and Tgfb1 transcripts in pDCs transfected with p110α-, β-, δ-specific, or negative control (nc) siRNA and stimulated for 18 h with TGF-β, normalized to the expression of Gapdh and presented relative to results in unstimulated cells (dotted line, 1-fold).
(C) Figures show the presence of differentially expressed genes within the analyzed single cells. Black color indicates cells with RPKM values above 40 for Pax3, 300 for Stmn2, 200 for Slc1a3 and 100 for Mbp
(F) Intestinal permeability was assessed by measuring FITC-dextran (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.
c-fos and c-fostg mRNA expression levels in H2-c-fosLTR/Egfrwt OS cells treated for 24h with Erlotinib (10µM) or DMSO as control (n=4 independent cell lines)
(E) Immunostaining assay of NKX2-1 (red) in control and SOX1KO cells on day 25 of ventral neural differentiation. Scale bar, 100 μm.
C. Schematic of disease-associated mutations in POT1. CTCL - cutaneous T cell lymphoma, CMM - cutaneous malignant melanoma, CLL - chronic lymphatic leukemia, CP - Coats plus syndrome.
Liver sections from control, BDL, and BDL/R-III-treated mice were stained with Sirius red. Scale bar, 200 μm..
Urea production from each group was determined by a commercially available urea assay kit.
Schematic representation of the fluxes for three scenarios: (i) no ATP-release and Pi-production (left, black dots in A-C), (ii) moderate ATP-release, Adenosine (A) and Pi-production (middle, grey triangles in A-C), and (iii) high ATP-release, A and Pi-production (right, white squares in A-C). If there is no ATP-release (left), there is a constant flux of Pi from the fungus via the apoplast to the plant and a constant flux of sugars in the inverse direction. The energy for these fluxes is provided by the phosphate gradient between fungus and plant and the sugar gradient between plant and fungus. At a moderate ATP-release and Pi-production rate (middle, value 1 on the x-axis, grey triangles in A-C), there is no Pi-flux from the fungus to the apoplast anymore. The unchanged uptake of sugars is now energized by the proton pump of the fungus. In this condition, the plant retrieves the cleaved Pi originating from the ATP-release via the H/P cotransporter, a transport which is energized by both, the sugar gradient and the proton pump. At a high ATP-release and Pi-production rate (right, value 2 on the x-axis, white squares in A-C), there is a larger Pi-uptake by the plant and a Pi-uptake by the fungus. Both processes are energized by larger activities of the proton pumps.
Cells from E5.5 epiblast were separated into 8 groups (I-VIII) basing on the average expression of epithelial, mesenchymal, and glycolysis markers (H). The average expression of three groups of markers were summarized in (J).
(C) Parkin-mediated ubiquitination limits BAK activation. HeLa+HA-Parkin cells were treated with antimycin A and oligomycin (AO) for 2 h prior to induction of apoptosis with 1 µM of each of the BH3 mimetics ABT-737 and S63485 (BH3 mim) for 1 h. Intracellular flow cytometry was performed using the conformation-specific anti-BAK antibody G317-2. Representative histograms are shown and the fold increase in mean fluorescence intensity (MFI) is plotted from three independent experiments with error bars showing SD. Data are normalised to untreated control.
Protein expression and mRNA levels of p53+/+ and p53-/- HepG2 cells treated with control siRNA or three separated sets of SREBP2 siRNAs for 72 hours as indicated.
(G-I) qRT-PCR measurement of transcripts of Ifnb1 (G), Il6 (H) and Il1b (I) in mouse colon 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<0.0001; ns, not significant.
B The partial sequences of the F9 gene from a healthy subject (left), the patient (middle) and a carrier (right).
HEK293 cells transfected with Flag-DDX5 were lysed and immunoprecipitated with anti-Flag antibodies. The bound proteins were along with WCE from untransfected (-) and Flag-DDX5 (+) transfected cells were Western blotted with anti-FLAG, anti-methylarginine antibodies (MeR).
fluorescence microscopy results (B) showing the translation activities of the Cnot6l 3"-UTR (WT and CPE mutated) in GV- (maintained by 2 μM milrinone) or MII- (released from milrinone) arrested oocytes. GFP signal indicated translational activation of Cnot6l 3"-UTR. An in vitro transcribed and polyadenylated mCherry mRNA was co-microinjected as a positive control. Scale b
D) Paclitaxel-only treated HFs showed a significant (adjusted p value = 0.0001 [****]) increase in the number of pH3+ ORS cells following drug washout. Palbociclib treatment alone had no significant effect on the number of pH3+ ORS cells. There was a trending, yet non-significant, increase in the number of pH3+ ORS cells in HFs dual treated with palbociclib plus paclitaxel. Ordinary one-way ANOVA with multiple comparisons performed using N of 9-10 HFs from 3 patients. Values plotted represent the mean total number of cells counted per HF analysed. Error bars are standard error
(b) Mean plots show the changes of TE subfamily expression in each cell cluster upon the Emx1-Cre/Trim28-KO. A differential expression analysis performed with DESeq2 (described in material and methods) showed upregulated TEs in cell types in which Trim28 was deleted (excitatory neurons, astrocytes, oligodendrocytes and oligodendrocyte precursors), (indicated with red dots: p-adj < 0.01, log2FC > 3). The specific upregulated elements and their fold changes are listed in bar graphs under each mean plot. In cell types in which Trim28 was not deleted, TE expression remained unaffected (inhibitory neurons and microglia).
Kaplan-Meyer survival analysis of control, Tgif1KO, KC and KTC mice. A regular mosaic two-colors line was used to discriminate between control and Tgif1KO mice.
A. Illustration of the promoters of HSP70.3, HSP70.4 and HSP90.1. Relevant regulatory motifs and promoter regions that were assessed in ChIP experiments (C) or in vitro DNA-binding studies are shown with purple and grey lines, respectively.
Figure 6 - Immediate late genes (ILGs) translate signal duration into response amplitude. A: Upper panel: pERK2 log2 fold changes upon different input scenarios (sustained: 4OHT; two-hour pulse: 4OHT+U0126). Lower panel: Response amplitude across temporal clusters and signal durations. Bold lines show median cluster amplitude at each time point.
A: GO analysis of biological processes among Group IV target genes, showing enrichment of networks in the endothelial-hematopoietic transition.
E. Growing and differentiated podocytes were treated with SA (300 µM, 30 min) and stained for TRAPPC2 or Sec24C and eIF3. Scale bar, 10 µm. The graphs show quantification of TRAPPC2 and Sec24C (mean intensity) in SGs. Mean ± s.e.m. of three independents experiments. ****p<0.0001, Student's unpaired two-tailed t-test.
Representative 5hmC profiles during AA+2i conversion of WT and Kdm3b-KO pre-iPSC with POU5F1 binding in pre-iPSCs and mESCs. Loci were assigned to the nearest gene.
(B) Fed rat liver lysosomes were incubated with 1 mM CaCl2 (+Ca2+) in an isotonic buffer in the absence or presence of a cocktail of protease inhibitors (PI). Samples were subjected to Triton X‐114 extraction, sucrose density gradients centrifugation and LAMP‐2A immunoblot.
C Caspase activity in HCT116 cells either transfected with control (Ctrl), ATF4- or CHOP-targeting siRNAs and treated as indicated (NEN (N) 1.2 µM, Domperidone (D) 30 µM). Data information: Data are presented as mean (SD) and were analyzed by two-way ANOVA with Tukey post-hoc test (C (N=3), E (N=4), F (N=4).
(G) H&E or (H) MyHC staining was performed on TA or Dp muscles from Ctrl or YY1dKO mice. Quantifications of the numbers of MyHC+ fibers per area of TA or Dp muscles are shown on the right (n=3 mice, each). Scale bar = 100 µm.
Representative images of mCherry-Atg8a (red) (G) in Drosophila larval fat body in which dMitf or dMitf-2KQ (K445Q/K450Q) was overexpressed. Drosophila (cg-GAL4/+) was used as the control and DAPI staining (blue) was used to indicate the cell nucleus (Scale bars, 10 µm).
Representative Western blots generated using extracts from HN31 cells stably expressing the MCOLN1 shRNA. Samples treated with exogenous cholesterol for 3 hours are indicated at the bottom. Primary antibodies used are indicated on the right.
E. Parasites EK-GFP or its S37A mutant were synchronized and parasites were allowed to mature to schizonts/segmentors. The graph shows average number of merozoites per schizont from three biological replicates. Each replicate represents an average of merozoites from 30-40 schizonts. (mean± SEM, n=3; biological replicates, *p<0.05, t-test).
(C) Human Ewing Sarcoma histology samples were analyzed by immuno-histochemistry using PAR antibody. Scale bar represents 100 mm.
(D) From the seven tumors arising from BRAFi-resistant cells, the common genes (enriched) have been extracted. Ninety-seven genes including SMAD3, BIRC3 and SLC9A5 are detected in all these 7 tumors.
D) Viable progeny counts of wild-type and noNSUN strains at 20°C and 25°C (D). Automatic counting was done using a Matlab script which processed plate images in real-time. Data information: In (D), data are presented as mean ± SEM, unpaired two-tailed Student's t-test.
(E) SMAD3 and SLC9A5 gain-of-function increases invasion capability of melanoma cells. Invasion assays for engineered cells lines (melanoma spheroids): CTR; 501Mel 2+, SMAD3; 501Mel 2+cells overexpressing SMAD3. Two other cell lines overexpressing SLC9A5 or BIRC3 have been tested. Explanation for ratio calculation is detailed in Fig. EV3A. Results obtained from two biologically independent experiments. (n=5, 4, 6 and 3 spheroids, respectively).
E. Western blot analysis for CCNA, CCNB and Actin (loading control) expression in lysates from MDA-MB-231 cells treated or not with 1 µM Cer.
(E) Graphic summary of EUC1 genetic interactions as tested in (A-D) and Appendix Fig. S10. Arrows indicate negative genetic interactions upon cold (blue), heat (red) or DMSO stress (black), dashed grey arrows indicate epistatic relationships.
(E) Incubation scheme: GUVs (14 nmol lipid) containing preassembled t-SNAREs (14 pmol Syx1/SNAP-25) were mixed on ice with the indicated Munc18-1 constructs (90 pmol) and subsequently SUVs (2.5 nmol lipid) containing Synaptotagmin1 (3 pmol) and Synaptobrevin/VAMP2 (8 pmol) were added. The fusion reaction was started by warming up the liposomes to 37 °C. Calcium (100 µM final concentration) was added after 2 minutes.
Three-week-old WT C57BL/6 mice were infected with 1E6 PFU of WT-ONNV at the metatarsal region of the footpad. (A) Viremia progression in ONNV-infected mice were monitored over 2 weeks (n=5). Viremia is detected with ONNV nsP1 probe via qRT-PCR.
(A) Model of Q cell position and migration direction in C. elegans L1 Larvae. Green arrow indicates that Q cells migrate along the AP body axis, whereas the dotted red arrows indicate that Q cells are potent to move towards the DV direction.
C Hh reporter activity assay in wild type and Grk2-/- 3T3 cells transfected with the equivalent wild type and mutant kinase domain forms of mouse Grk2, Grk2K220R, Grk2K220M and Grk2D335N after 24h Shh-N and SAG treatment. Data represent the mean and ± SD (n=3). Unpaired Students t-test was used for analysis. ****P<0.0001; **P<0.01; *P<0.05; and n.s. (not significant).
(L-M) GlyS gene expression, monitored using a MiMIC transposon insertion (MI01490), showed expression in the larval muscle (L) but not the fat body (M) (green, GFP; blue, DAPI).
Genome browser tracks showing open chromatin (DNase-Seq or ATAC-Seq) and ChIP-Seq in Th0, Th1 and Th17 cells at the Il17a locus (Carr et al., 2017, Ciofani et al., 2012, Vahedi et al., 2012). The grey box indicates a DHS which binds JUND.
B) Quantification of the percentage of activated microglia and infiltrated monocyte present in Sfrp1-/- and controls brains 3 days after infusion of saline or LPS (n=5 animals per genotype and condition). Error bars represent Standard Error. Statistical significance: **P<0.01 by two-way ANOVA followed by Bonferroni's multiple comparisons test.
(A) Respiratory chain enzyme activities of control (blue), COX1∆ (red) and COX2∆ (green) cybrids. Enzyme activities were measured in three experimental replicates. Data are expressed as the percentages of control cells, and indicated as means ± SD. Mann-Whitney U test was applied for statistical analyses. Variations between controls and mutants: α, p<0.05; γ, p<0.001. Specific variations between COX1∆ and COX2∆ mutants: ∗p<0.05.
E, F As in (A), except that DNA damage is induced using UV‐C irradiation (E) or 16 h hydroxyurea treatment (F). Similar results were obtained in at two separate experiments.
Rmi1, a component of the Sgs1-Top3-Rmi1 (STR) complex, is hyper-phosphorylated on S/T-Q motifs in rad9Δ cells.
GFP-trap-based co-immunoprecipitation (CoIP) assay demonstrating a complex formed by PABP, Paip1, and SUD. GFP: green fluorescent protein.
Indicated cells were exposed, or not, to adipocyte EV from primary adipocytes from lean mice fed a normal diet (ND) or obese mice fed a high fat diet (HFD) for 24h. Then, cells were fixed, stained with BODIPY and counterstained with DAPI. Left panel, confocal microscopy observation. Right panel, quantification of BODIPY staining area per cell (n=5 for SKMEL28 and n=6 for 1205Lu).
A Schematic diagram of NKG2D-ligands combination and dissociation model. NKG2D binds and dissociates with multiple ligands at different initial on-rates (kon-initial) and off-rates (koff). Ubiquitous mechanical forces in vivo regulate the disassociation of NKG2D and ligands.
(C) Western blot analyses of RNF5 and SCAP in shCtrl and shRNF5 PKM2 KO MDA-MB-231 cells.
B, D. CCL2 effects on MCH neurons of MCH-CFP knock-in mice recorded in current-clamp mode. Representative trace of the effects of CCL2 on MCH neurons (B). The CCR2 antagonist INCB3344 prevents the small hyperpolarization of MCH neurons elicited by CCL2.
K Capillary-like structures in HUVECs treated with the tumor-conditioned medium (TCM) from control HCCs and METTL3-knockdown HCCs cultured under hypoxic conditions for 48 h. Quantification of the number of tubes with image J in K-1. Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.
E Protein levels of LC3 I/II in METTL3-knockdown & FOXO3-overexpression SMMC-7721 cells under hypoxia for 48 h.
b, c, Punctate GFP-LC3 fluorescence in WT MEFs but not in Atg5-/- MEFs. b, Representative photographs. c, Graphical presentation of the percentages of WT MEFs and Atg5-/- MEFs with punctate GFP-LC3 fluorescence.
A) DnaK binding to cellulose-bound peptide array. Sequences of the aggregating cores are indicated in the top of the panel, the GKs flanking them in each instance are indicated above the blots.
IFN-γ release of NK cells stimulated by indicated MICA mutants at a concentration of 11nM (D) and 22nM (E). Data information: bars in (E), and data point in (F) represent mean values. Error bars represent mean ± SEM for biological triplicate experiments. **P < 0.01, ***P < 0.001, **** P <0.0001 (two-tailed unpaired t-test).
JurkatTat cells were treated with 7 µM of each compound, 50 nM PMA or left untreated (No drug control) for 24 h. B Cell surface CD69 expression was measured by flow cytometry. Data information: For statistical analysis, mean and SE for the results are determined from three biological replicates (n=3). Statistical significance, as determined by ratio paired t test is indicated: ***, P= 0.0008; ns, no significant difference.
Immunoblot analysis of lysates prepared from SAMHD1+/+ or -/- THP-1 cells treated for 24 h with ara-C and HU, as indicated. Representative of 3 independent experiments.
(B) Basal SMAD3-signature in six melanoma cell lines (S for sensitive to BRAFi and R for Resistant).
Formation of LC3 puncta in HeLa cells overexpressing GFP-GCN5 with or without Baf treatment
C Pearson's coefficient of IDO1 colocalization with EEA1 in P1.HTR cells transfected and treated as in (B), with each point representing colocalization within an image stack. Data represent mean ± SD (n > 20 cells from two independent experiments).
(F) qRT-PCR analyses of SREBPs downstream genes in Ctrl and HA-RNF5 OE MCF7 cells (n=3). Data information: Data are displayed as means ± SD. Statistical significance was assessed using two-tailed Student's t-test, ∗p < 0.05, ∗∗p < 0.01 and ∗∗∗p < 0.001.
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 control HER-2 CAR-T cells or those in which PTPN2 had been deleted by CRISPR RNP. Mice were injected with IL-2 (50,000 IU/day) on days 0-4 post adoptive CAR-T cell transfer and tumour growth monitored.
(i) Detrended Venus::HES5 fluorescent intensity timeseries (after z-scoring) corresponding to examples in (h); red arrows indicate in-phase peaks.
(H) The frequency of CX3CR1+ macrophages among CD45+CD11b+ population (n = 8). Data information: Data were representative and were the median ± interquartile range from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.
(c) Schematic indicating the correspondence between Venus::HES5 spatial oscillator represented as detrended level and phase angle characteristics; the spatial oscillator traverses repeated cycles including start (HES5 low-orange arrowhead), middle (HES5-teal arrowhead) and end (HES5 low-red arrowhead) which in phase space corresponds to phase angles 0, π and 2π respectively.
a, Macrophages were stimulated with LPS (100 ng ml-1) for the indicated time period. The number of endogenous LC3 dots within each cell was counted. The results shown are mean + s.d. (n > 100).
Enzymatic activity of ASS1 was examined by di-phosphate release from the argininosuccinate synthesis reaction. whole cell extracts prepared from SW-1116 cells expressing LOC113230, shLOC113230, or vector were subjected for in vitro ASS1 enzymatic assays, and purified enzymatic dead mutant ASS1 K165Q and ASS1 K176Q proteins were used as controls.
(I) Twenty most significantly DE genes comparing blue vs red cells ranked by FDR.
Quantitative data showing changes in the volume of spheroids derived from ME180 cells growing in a 3D hanging-drop culture system in the absence or presence of AREG (20 ng/ml, 8 days). Each bar represents mean ± SEM (n = 5). Bars with different letters are significantly different from each other (P = 0.0030).
A Primary mousecardiomyocytes were treated with H2O2 (1 mM) for 3 hours and cardiomyocyteviability was determined by flow cytometry. Representative results of flow cytometry analysis.
(E) IFNγ-primed WT, Irgm2-/-, Casp1-/-Casp11-/- and Irgm2-/-Casp1-/-Casp11-/- BMMs were treated with LPS (5 µg/ml) for 4 hours and subsequently stained with anti-ASC antibody and Hoechst stain (DNA/nuclei). Representative images are shown with white arrows pointing at ASC specks. Number of ASC specks per nuclei was quantified. Scale bars: 20 µm.
(e) NIH 3T3 cells stably expressing EGFP-Parkin were incubated in the absence or presence of CCCP (30 μM) for 4 h, after which whole-cell homogenates as well as cytosolic, ER and mitochondrial fractions were prepared and subjected to immunoblot analysis. Scale bar (a-d), 10 μm.
Mice were treated as described in Fig 1A. Fungal ITS2 rDNA gene sequence was performed in each group. Fungal-taxon-based analysis at the phylum level in feces of mice. Color from blue to red indicates enrichment of fungus.
Comparison of the SiE5′NT structural homology model (green) with the crystal structure of human E5′NT (PDB id 4H2I, red) with 32% sequence identity. C. Comparison of the SiE5′NT structural homology model (green) with the crystal structure of Thermus thermophiles 5′NT (2Z1A, blue) with 36% sequence identity. *: position of the loop involved in dimerization of human E5′NT.
Protein expression of ALDH1A1 and ALDH1A2 during the culture activation of HSCs. Cell lysates were prepared from HSCs at 3 days after plating (HSCs-d3) and from HSCs after passage 1 (P1), 2 (P2), and 3 (P3), and analyzed by Western blotting.
A. Schema of the experimental paradigm used for drug administration. Mice were injected daily with THC (5 mg/kg) or vehicle (Veh) during adolescence, from PND 30 to 45. SB258585 (SB, 2.5 mg/kg) or rapamycin (Rapa, 1.5 mg/kg) were administered concomitantly with THC or vehicle. Electrophysiological recordings were performed from PND 60.
(B) Cumulative distribution of 3'-UTR lengths of down- and up-regulated genes in either compartment. Two-sample Kolmogorov-Smirnov test; ns > 0.05, *p-value < 0.05.
MIAPaCa-2, Suit-2, Capan-2 and Panc-1 cells were transfected with empty vector (EV), wild-type (TGIF1) or phosphorylation mimic mutant (TGIF1.2TD) of TGIF1. Cells were selected with neomycin for 2-3 weeks, and counted using an automatic cell counter (D) (n=6).
I Immunoassay of IRF3, SP1 and Tubulin in the nuclear and cytoplasmic fractions of the HEK293T cells overexpressed with indicated constructs for 24 hours and stimulated with VSV for 6 hours. Tubulin and SP1 served as cytoplasmic and nucleic protein loading control respectively. Data information: * Data are representative of two or three independent biological replicates