EMBO/sd-character-level-ner huggingface dataset:
Figure 5Pyridostatin (PDS) was administered intravenously (i.v.; 7.5 mg/kg/day) and NU-7441 was administered intraperitoneally (i.p.; 10 mg/kg/day), over the indicated periods of time. Vertical dashed line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 5 mice. Error bars represent SEM. P values were calculated at day 39 using an unpaired two-tailed t-test, between treated and untreated tumours, or between the NU-7441+PDS combination and each single treatment. **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001. Pyridostatin (PDS) was administered intravenously (i.v.; 7.5 mg/kg/day) over the indicated periods of time, and paclitaxel (PACLI) was administered intravenously (i.v.; 20 mg/kg/day) on indicated single days. Vertical dashed line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 5 mice. Error bars represent SEM. P values were calculated at day 39 using an unpaired two-tailed t-test, between treated and untreated tumours, or between the PDS+PACLI combination and each single treatment. **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001. Pyridostatin (PDS) was administered intravenously (i.v.; 7.5 mg/kg/day), NU-7441 was administered intraperitoneally (i.p.; 10 mg/kg/day), over the indicated periods of time, and paclitaxel (PACLI) was administered intravenously (i.v.; 20 mg/kg/day) on indicated single days. Vertical dashed line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 5 mice. Error bars represent SEM. P values were calculated at day 63 using an unpaired two-tailed t-test between the NU-7441+PDS+PACLI combination and each double treatment. ****, P ≤ 0.0001. Kaplan-Meier survival curve for mice treated as in (C), with each treatment group containing n = 5 mice. Statistical significance was assessed by Log-rank test (****P <0.0001).
NDST3 deacetylates α-tubulin in the cells and in vitro.Figure 5(A) Immunoblotting analysis demonstrated a large accumulation of α-tubulin acetylated at Lys40 (Ac-α-tubulin) in NDST3 KO RPE1 cells, while the total α-tubulin relative to GAPDH remained unchanged (n = 3 independent cultures, ***P = 0.0008). Data information: Error bars represent ± standard deviation. ns means non-significant. (B) Immunoblotting analysis showed decreased levels of Ac-α-tubulin, but unchanged levels of total α-tubulin relative to GAPDH, in RPE1 cells over-expressing Flag-NDST3 compared to those in Flag-EGFP control cells (n = 3 independent cultures, *P = 0.0399). Data information: Error bars represent ± standard deviation. ns means non-significant. (C) In vitro enzymatic assay quantitating the effect of NDST3 on α-tubulin acetylation. Flag-NDST3 was expressed in HEK 293 cells and immunoprecipitated by anti-Flag beads. Flag-EGFP was used as a control. The immunoprecipitated protein was incubated with purified tubulin heterodimers in vitro, with or without 1 mM NAD+, 400 nM TSA, or 5 mM nicotinamide (NAM) for 2 h at room temperature. The reaction products were examined by immunoblotting against Ac-α-tubulin or total α-tubulin (n = 3 independent experiments, *P = 0.0185, **P < 0.01, ****P < 0.0001). (D) The same in vitro enzymatic assay as in (C), except that the purified tubulin was polymerized in the presence of 20 μM Taxol and 1 mM GTP (n = 3 independent experiments, **P < 0.01, ***P = 0.0001). Data information: Error bars represent ± standard deviation. ns means non-significant.
Figure 5 Responsiveness to gemcitabine (GEM), either alone or combined with Nab-paclitaxel (NAB-P), was evaluated in mice bearing orthotopic HuPa8 in the pancreas. Nab-paclitaxel (25mg/kg) and gemcitabine (150mg/kg) were given i.v. on days 1 and 8 of each 21-day cycle (for a total of 8 treatments). A) Levels of TIMP1, MMP7 and TSP2 in plasma of mice bearing orthotopic HuPa8 at 30, 90 and 150 days after tumor transplantation (mean ± SEM; n≥4 for each group). *p<0.05, (Mann-Whitney). The exact n and p-values are indicated in Table S5A   Responsiveness to gemcitabine (GEM), either alone or combined with Nab-paclitaxel (NAB-P), was evaluated in mice bearing orthotopic HuPa8 in the pancreas. Nab-paclitaxel (25mg/kg) and gemcitabine (150mg/kg) were given i.v. on days 1 and 8 of each 21-day cycle (for a total of 8 treatments) B) Magnetic resonance imaging of HuPa8. Representative images are shown, the white dotted lines indicate tumor masses . Responsiveness to gemcitabine (GEM), either alone or combined with Nab-paclitaxel (NAB-P), was evaluated in mice bearing orthotopic HuPa8 in the pancreas. Nab-paclitaxel (25mg/kg) and gemcitabine (150mg/kg) were given i.v. on days 1 and 8 of each 21-day cycle (for a total of 8 treatments) C) Tumor growth over time measured by MRI; each black arrow indicates one treatment (mean ± SEM; n=4 for each group; 2-way ANOVA with Tukey"s multiple comparison test)  Responsiveness to gemcitabine (GEM), either alone or combined with Nab-paclitaxel (NAB-P), was evaluated in mice bearing orthotopic HuPa8 in the pancreas. Nab-paclitaxel (25mg/kg) and gemcitabine (150mg/kg) were given i.v. on days 1 and 8 of each 21-day cycle (for a total of 8 treatments) D) Levels of the 3 selected biomarkers in plasma of HuPa8 bearing mice, prior to (day 80; at randomization), during (day 120) and after (day 165) the treatments (mean ± SEM; n≥4 for each group; 2-way ANOVA with Tukey"s multiple comparison test). The exact n is indicated in Appendix Table S5B
Figure 7A A schematic drawing of the hypothesis that astrocytes perform phagocytosis on behalf of phagocytosis-deficient microglia. B Representative images of microglial distribution in the cerebral cortex of WT and mutant mice at 3 w. Sections were stained with anti-Iba1 or anti-CD11b antibodies (red). Scale bar, 100 µm. C Quantification of microglial number (n = 5 animals per group, one-way ANOVA). Note that Irf8-/- mice were analyzed by CD11b immunostaining, while other strains were analyzed by Iba1 staining. D Representative images of a spontaneous apoptotic cell and surrounding glial cells in the cerebral cortex of WT and Irf8-/- mice at 3 w. Sections were stained with anti-GFAP (green), anti-CD11b (red) and anti-cleaved caspase-3 (blue) antibodies. 3D images (lower row) were reconstructed from confocal images (upper row) using Imaris software. Arrows indicate cleaved caspase-3+ apoptotic cells. Insets are higher magnification images around apoptotic cells. Scale bar, 20 µm and 5 µm (insets).
Proposed model of antithetical NFATc1–Sox2 and p53–miR‐200c network in pancreatic cancer plasticityA proposed model shows an antidromic NFATc1–Sox2 and p53–miR200c transcriptional network controlling EMT and stemness in pancreatic cancer.Figure 8A proposed model shows an antidromic NFATc1-Sox2 and p53-miR200c transcriptional network controlling EMT and stemness in pancreatic cancer.
Figure 1Time course of avoidance of P. aeruginosa lawn by N2, odr-3(n2150) and odr-3(n2046) worms. n ≥ 3 assays. *** P ≤ 0.001, **** P ≤ 0.0001 as determined by two-tailed unpaired t-test. Error bars indicate SEM. Images of P. aeruginosa lawn at different time intervals showing avoidance response of N2 and odr-3(n2150) mutant worms. Scale bar = 5 mm. Kaplan Meier survival curve of N2, odr-3(n2150) and odr-3(n2046) worms on partial lawn of P. aeruginosa at 25°C.   Kaplan Meier survival curve of N2, odr-3(n2150) and odr-3(n2046)   worms on full lawn of P. aeruginosa at 25°C. Time required for 50% of worms to die (TD50) on partial lawn and full lawn of P. aeruginosa. Individual data points indicate replicates with ~100 worms each. **** P ≤ 0.0001, ns (not significant) P > 0.05 as determined by two-tailed unpaired t-test. n ≥ 3 assays. Error bars indicate SEM. Schematic of young (8 h) and old (24 h) lawn choice assay in a tripartite plate and choice index. n ≥ 3 assays. Individual data points indicate replicates with ~40 worms each. * P ≤ 0.05 as determined by two-tailed unpaired t-test. Error bars indicate SEM. Representative image of intestinal lumen width, indicated by arrows, in N2 worm exposed to P. aeruginosa for 12 h. Scale bar = 50 µm. Quantification for the width of intestinal lumen in N2 exposed to E. coli and P. aeruginosa for 12 h. ns (not significant) P > 0.05 as determined by two-tailed unpaired t-test. n = 3. Error bars indicate SEM.
Figure 3A. List of compounds and their targets. Lysates from BT549 transfected with HA-FGFR1c, 2b, or 4 and stimulated for 8 or 40 min. with Enkamin-E, FGF10, or FGF1, respectively, followed by treatment with either DMSO or the FGFR inhibitor PD173074 (B) BT549 transfected with HA-FGFR2b or HA-FGFR2b_Y656F/Y657F and stimulated with FGF10 for 40 min. (C) T47D treated with DMSO, PD173074 or the EGFR inhibitor AG1478 and stimulated or not with either FGF10 or TGFα for 0, 8, and 40 min. (D) were immunoblotted with the indicated antibodies. E. Protein sequences surrounding T693 (based on Uniprot P00533) of members of the ErbB family were aligned using CLUSTAL O (version 1.2.4). The red box indicates that the amino acid T is followed by a conserved proline. Asterisks below the sequences indicate identical amino acid residues; double dots indicate conserved amino acid residues; single dots indicate semi-conserved substitutions. F, G Lysates from T47D or BT20 treated with DMSO, PD173074, AG1478, or the MEK inhibitors U0126 and MEK162 and stimulated or not with either FGF10 or TGFα (F); T47D or BT20 treated with DMSO, or the p38 inhibitor BMS582949 and stimulated or not with either FGF10 or TGFα (G) were immunoblotted with the indicated antibodies.
Migrating concavin(-) sporozoites lose their cellular integrity A.Figure 7A. Percentage of mosquitoes depositing WT or concavin(-) sporozoites in the skin of a mouse during a bite (left) and sporozoites deposited during a mosquito bite (right). P-values are calculated using the Fishers exact test (left) and the Mann Whitney test (right). Bite transmission experiments were repeated over 3 independent mosquito infections for the KO and 2 independent mosquito infections for the WT. For each mosquito infection 2-3 mice were imaged, for a total of 3-5 ears. B. Maximum fluorescence intensity projections encoded by color for time from movies showing migrating sporozoites after mosquito-bite transmission. Graphs and camembert diagrams below show fraction of motile and immotile sporozoites after 10, 20 and 30 minutes of recording, numbers analysed as well as sporozoite speed. Pooled data from 4-5 WT or 5-8 concavin (-) bite sites per time point. Scale bar: 50 µm. P-values are calculated using the Mann Whitney test. C. Motile WT or concavin(-) sporozoites entering blood vessels during the first hour following micro-injection. Number above bars shows numbers of sporozoites observed. Pooled data from four WT or five concavin(-) experiments. P-values are calculated using the Fishers exact test. D, E (D) Deformation and (E) disintegration of concavin(-) sporozoites migrating in the skin. Individual images corresponding to the frames shown on the right are indicated in distinct colours in the maximum projection (left) of 13-min movies. Arrowheads indicate constrictions of the parasites. Graphs below time-lapse show that deformation and disintegration are preceded by a decrease in speed. Color of dots correspond to the time-points displayed in the time-lapse images. Scale bars: 10 µm. F. Percentage of deformation and disintegration events observed in 54 WT and 57 concavin(-) sporozoites that were tracked for at least 10 min. Pooled data from 5 WT or 10 concavin(-) bite sites. G. Consequence of deformation and disintegration from the 22 sporozoites in F include immobilization and parasite death.
Figure 2(A) Local 4-AP treated crushed sciatic nerve (black: vehicle PLGA films; red: (4-AP)-PLGA films) regained partial walking ability as early as 3 days post-injury compared to vehicle treated group. (*: D5, p= 0.0004; D8, p = 0.0012; D11, p =0.003; D14, p=0.0089; n=6; ANOVA, with post-hoc comparisons using two-tailed unpaired t-test). (B) Local 4-AP treated crushed sciatic nerve (black: vehicle PLGA films; red: (4-AP)-PLGA films) showed faster improvement in NCV restoration compared with vehicle-treated mice, beginning at 21 days post-injury.
Figure 1A. The experimental flowchart to isolate trisomic ES cell lines. B. The molecular events during isolation of trisomic ES cell lines. BsdS: sensitive to blasticidin, BsdR: resistant to blasticidin, PuroS: sensitive to puromycin, PuroR: resistant to puromycin. C. Karyograms of trisomic ES cells shows that these cell lines have extra copies of chromosomes 6, 8, 11, or 15. The Ts6 and Ts11 ES cells harbored isochromosomes of the two identical trisomic chromosomes. Ts, trisomy. D. CGH analysis of trisomic ES cell lines. The relative gene copy number is plotted using a log2 scale. E. CGH analysis of the genome stability of trisomic ES cells. F. CGH analysis of the genome integrity of trisomic ES cell subclones.
Figure 3A) Density maps depicting all DNase-Seq peaks in the order of increasing DNase-Seq tag count signal for CD4 TM compared to TN. On the right are the locations of the defined subset of 2882 pDHSs and the log2 TM/TN fold change in expression of the closest gene to the corresponding DHS. B) Density maps for all DNase-Seq and ChIP-Seq peaks shown in order of increasing DNase-Seq tag count signal for CD4 TB compared to TN. The TN H3K27ac track is from published data (Lara-Astiaso et al, 2014). C) Average DHS signal at 2882 pDHSs and 2882 invariant DHSs in CD4 TN, TB and TM. The locations of the 2882 pDHSs are indicated in (A) and (B). D) Pie chart showing the genomic distribution of pDHSs. E) Average H3K4me2, H3K27ac and BRD4 signal at 2882 pDHSs. F) Plot of the log2 fold change in gene expression following 2 hours PMA/I for CD4TM compared to TN. 1895 genes (black) have a log2 fold change of 1 or above in TM but not TN. G) The distance between the TSS of the 1895 TM specific genes and the nearest pDHS.
Interaction of RsaI to icaR mRNA induces biofilm production (A) Secondary structure model of icaR mRNA.Figure 4(A) Secondary structure model of icaR mRNA. The nucleotides in red are involved in the long-range interaction between the 3' and 5'-UTRs or with RsaI. SD and anti-SD are respectively for the Shine and Dalgarno sequence and for the sequence complementary to the SD sequence. (B) Gel retardation assays show the formation of the complex between RsaI and icaR full length, icaR SUBST, icaR-5'UTR, and icaR-3'UTR. The 5' end-labeled of RsaI was incubated with increasing concentrations of the various mRNAs. UTR is for untranslated region, SUBST stands for the substitution of UCCCCUG sequence by AGGGGAC. This mutation, which is located in the 3'UTR of icaR, significantly destabilizes the long-range interaction, and enhances icaR translation. Lane C represents binding between radiolabelled RsaI and full-length icaR mRNA (50 nM). Due to the rather short migration of the gel, the full-length mRNA is still observed in the pocket. (C) In vivo effect of RsaI on PIA-PNAG synthesis in the S. aureus wild-type (WT) 132 strain, the ∆rsaI mutant, and the strain carrying a deletion of icaR 3'UTR (∆3'UTR). This last mutant strain has been transformed with the pES plasmids expressing rsaI or rsaI mut5. The PIA-PNAG exopolysaccharide biosynthesis was quantified using dot-blot assays. Serial dilutions (1/5) of the samples were spotted onto nitrocellulose membranes and PIA-PNAG production was detected with specific anti-PIA-PNAG antibodies. RsaI was detected in the same samples by Northern blot using a probe directed against RsaI. Ethidium bromide staining of rRNA was used as loading controls of the same gel.
Figure 5(A) Schematic representation of the experimental procedure. Catheters pre-colonized with S. aureus were allowed to form biofilms by incubation at 37ºC (for in vitro dispersion assay) or by subcutaneous implantation in mice (for ex vivo dispersion assay) before being treated in vitro with different mycoplasma strains and estimate biofilm dispersion by crystal violet staining. (B) Representative pictures of catheters from the ex vivo dispersion assay with the indicated strains after crystal violet staining are shown. A staining control based on catheters in which no biofilm is formed was also included. (C, D) Plots showing results obtained from the in vitro or ex vivo dispersion assays with the indicated strains and from the staining control. Each circle represents the OD 595 nm values obtained for individual catheters (n≥4), whereas mean ± s.d. is represented with lines inside each group. Results from one-sided ANOVA followed by Fisher's PLSD test are shown for treatments statistically different from those based on strains not secreting dispersin B (i.e., the WT or CV2 strains). *P ≤ 0.05; **P ≤ 0.005; ***P ≤ 0.0005.
Figure 7The impact of administration of scrambled antimiR (S) or an antimiR directed against miR-34a (A34a) on the abundance of type I alveolar epithelial cells (marked by aquaporin 5, Aqp5) and type II alveolar epithelial cells (marked by pro-surfactant protein C, Sftpc) was assessed in 3-µm sections of paraffin‑embedded lung tissue from P5 mice undergoing normal (21% O2) or aberrant (85% O2) lung alveolarization. DAPI, 4′,6-diamidino-2-phenylindole. In the DAPI images, white lines delineate tissue from airspaces, and in the 85% O2 groups demarcate septa. Antibody specificity was validated by rabbit IgG isotype control primary antibodies. The control experiments for the Aqp5 and Sftpc staining runs are illustrated here. Scale bars, 50 µm.
Figure 5A. Workflow of the quantification of soluble proteins by mass spectrometry. B. Q97-GFP was expressed for 4.5 h in wild type and GAL-Mia40 cells in two biological replicates each. Cells were lysed with NP-40 before soluble proteins were quantified. Mitochondrial proteins (mito.) and members of the mitochondrial carrier family (carrier) are visualized in a volcano plot. P-values were derived from a moderated t-test. Mitochondrial (mito.) and carrier proteins are indicated by yellow and red dots, respectively. Rnq1 is indicated in blue. C. Transcript levels for RNQ1 were measured by qPCR in the strains indicated. D. Antibodies against Rnq1 were used in Western blots to specifically detect the protein in whole cell extracts of yeast cells. E, F. Cell extracts of the strains indicated were separated into soluble (S) and aggregated (P) fractions. Rnq1 was detected by Western blotting. Whole cell extracts (total, T) were loaded for control. The wild type and GAL-Mia40(N) strain shown in F were newly generated. G. Drop dilution experiments of the strains indicated on galactose plates; ev, empty vector. H. Growth curves of the indicated strains at 30°C. I. Cells of the newly made strains were grown on galactose for 1 or 7 days, respectively. Cells were lysed before the distribution of Rnq1 in the soluble and pellet fractions was quantified. Shown are mean values and standard deviations of three independent replicates. J. Mia40 overexpression reduces the toxicity of polyQ proteins. In newly made cells, Q97-GFP is still toxic (though less than in wild type) but after several generations, cells escape sensitivity by loss of Rnq1 nucleation seeds.
FGF7 suppresses IFN-induced ISG expression (A-C) Serum-starved HaCaT keratinocytes were treated with FGF7 (10 ng/ml (A, C) or different concentrations as indicated (B)) and/or IFN-α (500-1000 U/ml) for 12-16 h.Figure 3Serum-starved HaCaT keratinocytes were treated with FGF7 (10 ng/ml (A and/or IFN-α (500-1000 U/ml) for 12-16 h. RNA was analyzed by qRT-PCR for ISGs relative to RPLP0 (A Serum-starved HaCaT keratinocytes were treated with FGF7 different concentrations as indicated (B)) and/or IFN-α (500-1000 U/ml) for 12-16 h. RNA was analyzed by qRT-PCR for ISGs relative to RPLP0 Serum-starved HaCaT keratinocytes were treated with FGF7 (10 ng/ml and/or IFN-α (500-1000 U/ml) for 12-16 h. protein samples by Western blot for total and pSTAT1 (Y701 and S727), IRF1, IRF9 and RSAD2 and GAPDH (C). The vertical line in the RSAD2 blot indicates a place where the gel was broken. Densitometric quantification of the different blots (N=3) is shown on the right. (D) Human primary keratinocytes were starved and treated for 12 h with FGF7 (10 ng/ml) and/or IFN-α (1000 U/ml). RNA samples were analyzed by qRT-PCR for ISGs relative to RPLP0.
APOE promotes subretinal MP accumulation in Cx3cr1GFP/GFP mice.Figure 3Immunohistochemistry of APOE (red) and IBA-1 (green) on a section (A, blue Hoechst) and the subretinal side of a retinal flatmount (B and C) from a 12-month-old Cx3cr1GFP/GFP mouse (representative of 3 independent experiments, experiments omitting the primary antibody immunostaining served as negative controls). ONL: outer nuclear layer; RPE: retinal pigment epithelium. Quantitative RT-PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP monocytes cultured for 24 h in contact with POS of an overlaying retinal explant (n = 4/group per experiment; Mann-Whitney U-test, *P = 0.0286, the experiment was repeated twice with similar results).Quantitative RT-PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP FACS-sorted microglial cells, freshly extracted from adult brain (n = 4-5/group; Mann-Whitney U-test, C57BL/6J versus Cx3cr1GFP/GFP *P = 0.0159).Quantitative RT-PCR of ApoEmRNA normalized with S26mRNA of C57BL/6J and Cx3cr1GFP/GFP peritoneal macrophages cultured for 24 h with CX3CL1. (n = 4/group per experiment; Mann-Whitney U-test, *P = 0.0286. The experiment was repeated twice with similar results). APOE Western blot analysis of equivalent amounts of supernatant protein from CX3CL1-exposed C57BL/6J and Cx3cr1GFP/GFP peritoneal macrophages at 24 h. Soluble Mer receptor tyrosine kinase that is released constitutively from cultured macrophages served as a loading control. The experiment was repeated twice with similar results. 12-month-old IBA-1 stained RPE flatmounts of Cx3cr1GFP/GFP (H) and Cx3cr1GFP/GFPApoE−/− (I) mice.Quantification of subretinal IBA-1+ mononuclear phagocytes in 2-month-old (left) and 12-month-old (right) mice of the indicated strains (n = 9-20/group ANOVA/Dunnett test at 12 months: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann-Whitney U-test at 12 months of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001). Quantification of subretinal IBA-1+ mononuclear phagocytes after 4 days of light challenge of 2-month-old mice of the indicated strains (n = 10-25/group ANOVA/Dunnett test: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann-Whitney U-test of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001). IBA-1- (green) and CD102- (red) stained RPE flatmounts 7 days after laser injury of 2-month-old Cx3cr1GFP/GFP (E) and Cx3cr1GFP/GFPApoE−/− (F) mice.Quantification of subretinal IBA-1+mononuclear phagocytes on the RPE counted on the RPE at a distance of 0-500 μm to CD102+CNV 7 days after the laser injury of 2-month-old mice of the indicated strains (n = 8-10 eyes/group ANOVA/Dunnett test: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann-Whitney U-test of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001).