EMBO/sd-character-level-ner huggingface dataset:
Figure 6We selected six resources and five species for additional experiments. Resources are shown in relation to glycolysis and the citric acid cycle. Species are shown with a phylogenic tree with connections in the correct order but not to scale. Monoculture experiments were performed to determine species' growth rates and lag times for each two-resource environment. For each pair of species, coculture competition experiments were performed in each two-resource environment, and qualitative competitive outcomes were determined There were 44 competitions in which both species could be assigned growth rates and lag times Each point represents one competition. Pie charts summarize the competitive outcomes for cases in which the slow-grower was the fast-switcher (above the Δtlag = 0 line) and in which the slow-grower was not the slow-switcher (on and below Δtlag = 0).
DREADD-based activation of MPOA neurons ameliorates social bonding in Shank2-/- mice (A) Shank2+/+ and Shank2-/- mice were bilaterally injected with a Cre-dependent DREADD virus (pAAV-hSyn-DIO-hM3D (Gq)-mCherry) and (pENN.Figure 6(A) Shank2+/+ and Shank2-/- mice were bilaterally injected with a Cre-dependent DREADD virus (pAAV-hSyn-DIO-hM3D (Gq)-mCherry) and (pENN.AAV.hSyn.HI.eGFP-Cre)) into the MPOA region. After four weeks, a pup-exposure assay was performed once a day for five days after intraperitoneal injection of vehicle or 5 mg/kg CNO (30 min before pup exposure). Maternal behavior was analyzed at the final 20 min of pup exposure on day 5 (test day). (B) Confocal images showing the location and expression of the stereotaxically injected viral constructs in the MPOA region. (a) Merge of GFP(CRE) and mCherry (DREAAD) (scale bar: 500 µm) (b-d) Magnified views of the MPOA region (scale bar: 20 µm), (b) GFP & mCherry merge, (c) GFP, (d) mCherry. The dotted lines outline the MPOA and the third ventricle (middle line). AC, anterior commissure and MPOA, medial preoptic area. (C) A significant genotype x treatment interaction was detected for pup retrieval, two-way ANOVA, effect of genotype: P=0.187, effect of treatment: P=0.759, genotype x treatment interaction: *P=0.031. Shank2+/+ vehicle injected n = 6, Shank2-/- vehicle injected n = 6, Shank2+/+ CNO injected n = 6, Shank2-/- CNO injected n = 7. Data information: All data are presented as mean ± SEM, NS: not significant. AC, anterior commissure and MPOA, medial preoptic area. (D-G) DREADD activation by CNO injection selectively rescues major components of social attachment behavior in Shank2-/- mice: (D) grooming, two-way ANOVA, effect of genotype: *P=0.018, effect of treatment: **P=0.002, genotype x treatment interaction: ***P=0.001. (E) Crouching, two-way ANOVA, effect of genotype: P=0.091, effect of treatment: P=0.869, genotype x treatment interaction: P=0.663, (F) nest building, two-way ANOVA, effect of genotype: P=0.415, effect of treatment: P=0.341 genotype x treatment interaction: P=0.093, (G) Maternal interaction, two-way ANOVA, effect of genotype: *P=0.034, effect of treatment: P=0.149, genotype x treatment interaction: *P=0.045. Shank2+/+ vehicle injected n = 6, Shank2-/- vehicle injected n = 6, Shank2+/+ CNO injected n = 6, Shank2-/- CNO injected n = 7. Data information: All data are presented as mean ± SEM, NS: not significant.
Figure 6Combination gene therapy with IFNα, TNFα and IFNγ, expressed from the Tie2 vector platform. CTRL (Tie2.NGFR), 2 independent experiments, n = 9 mice; IFNα, 1 experiment, n = 2 mice; IFNα/IFNγ, 1 experiment, n= 4 mice; IFNα/TNFα, 1 experiment, n = 3 mice; IFNγ/TNFα, 2 independent experiments, n = 19 mice. (A) Vector copy number (VCN) in peripheral blood at eight weeks post-transplantation (mean ± SD). Combination gene therapy with IFNα, TNFα and IFNγ, expressed from the Tie2 vector platform. CTRL (Tie2.NGFR), 2 independent experiments, n = 9 mice; IFNα, 1 experiment, n = 2 mice; IFNα/IFNγ, 1 experiment, n= 4 mice; IFNα/TNFα, 1 experiment, n = 3 mice; IFNγ/TNFα, 2 independent experiments, n = 19 mice. (B) B-ALL progression in peripheral blood measured as absolute number of OFP+ cells (mean ± SD, each dot represents an individual mouse; * p = 0.0308, ***p = 0.0004 ****p ≤ 0.0001, Two-Way ANOVA with Geisser-Greenhouse correction). Combination gene therapy with IFNα, TNFα and IFNγ, expressed from the Tie2 vector platform. CTRL (Tie2.NGFR), 2 independent experiments, n = 9 mice; IFNα, 1 experiment, n = 2 mice; IFNα/IFNγ, 1 experiment, n= 4 mice; IFNα/TNFα, 1 experiment, n = 3 mice; IFNγ/TNFα, 2 independent experiments, n = 19 mice. (C) Percentage of MHC II+ macrophages identified by F4/80 expression in the spleen (mean ± SD, each dot represents an individual mouse; *p = 0.0484, **p = 0.0049, ordinary One-Way ANOVA). (D) Percentage of CD8+ T lymphocytes within CD45 positive and OFP negative splenic cells (mean ± SD, each dot represents an individual mouse; *p = 0.0356, ordinary One-Way ANOVA). ( Combination of IFNγ gene therapy with immuno-oncology drugs. CTRL (Tie2.NGFR) + antibody isotype, n = 6 mice; CTRL + αCTLA4 antibody, n= 5 mice; CTRL + αLAG3 antibody, n = 5 mice; CTRL + 1-Methyltryptophan (1-MT), n = 5 mice; IFNγ (Tie2.IFNγ) + antibody isotype, n = 7 mice; IFNγ + αCTLA4 antibody, n = 7 mice; IFNγ + αLAG3 antibody, n = 7 mice; IFNγ +1-MT, n = 5 mice. (E) B-ALL progression in peripheral blood measured as absolute number of OFP+ cells (mean ± SD, each dot represents an individual mouse; ns = not significant, **p = 0.001 (CTRL isotype vs IFNγ + αCTLA4); **p = 0.0022 (CTRL isotype vs CTRL + αLAG3), ***p ≤ 0.001, ****p ≤ 0.0001; comparisons are against the corresponding isotype, or as indicated by the lines; Two-Way ANOVA). Combination of IFNγ gene therapy with immuno-oncology drugs. CTRL (Tie2.NGFR) + antibody isotype, n = 6 mice; CTRL + αCTLA4 antibody, n= 5 mice; CTRL + αLAG3 antibody, n = 5 mice; CTRL + 1-Methyltryptophan (1-MT), n = 5 mice; IFNγ (Tie2.IFNγ) + antibody isotype, n = 7 mice; IFNγ + αCTLA4 antibody, n = 7 mice; IFNγ + αLAG3 antibody, n = 7 mice; IFNγ +1-MT, n = 5 mice. (F) Percentage of MHC II+ macrophages identified by F4/80 expression in the spleen (mean ± SD, each dot represents an individual mouse; **p ≤ 0.01, ***p ≤ 0.001, **** p ≤ 0.0001 as compared to CTRL isotype, ordinary One-Way ANOVA). (G) Percentage of CD8+ T lymphocytes within OFP negative BM cells (mean ± SD, each dot represents an individual mouse). S
Fig.Figure 2Schematic of the primary postnatal sympathetic neuron-derived model of HSV-1 latency. Reactivation from latency is quantified by Us11-GFP expressing neurons following addition of the PI3K inhibitor LY294002 (20μM) in the presence of WAY-150168, which prevents cell-to-cell spread. The arrow indicates the time of LY294002 treatment at 5 days post-establishment of latency. n=9 biological replicates. Number of Us11-GFP expressing neurons at 3 days post-LY294002-induced reactivation in P6 SCG neuronal cultures infected with HSV-1 in the presence or absence of IFNα (600 IU/ml), then treated with an α-ΙFNAR1 neutralizing antibody. n=9 biological replicates. RT-qPCR for viral mRNA transcripts at 3 days post- LY294002-induced reactivation of SCGs infected with HSV-1 in the presence or absence of IFNα. n=9 biological replicates. RT-qPCR for viral mRNA transcripts at 20 hours post-LY294002-induced reactivation in SCGs infected with HSV-1 in the presence of absence of IFNα. n=9 biological replicates. Relative amount of viral DNA at time of reactivation (8dpi) in SCG neurons infected with HSV-1 in the presence or absence of IFNα (600 IU/ml). n=9 biological replicates. Quantification of vDNA foci detected by click chemistry at time of reactivation (8dpi) in SCG neurons infected with HSV-1 in the presence or absence of IFNα (600 IU/ml). n=60 genomes from 3 biological replicates. LAT mRNA expression at time of reactivation (8dpi) in neurons infected with HSV-1 in the presence or absence of IFNα (600 IU/ml). n=9 biological replicates.
Figure 1Overlap of the mouse RBP database and the RBP repertoire revealed by the mRNA interactome in mouse ES cells. All the 789 RBPs were subsequently analyzed. The differentially expressed RBPs during embryoid body (EB) differentiation, neural differentiation and cardiac differentiation, which are classified as different clusters. The right line plots show the dynamic expression pattern of each cluster, gray lines represent the expression of all genes in individual cluster, while the red line represents the average expression level. The number on the graph indicates the number of RBPs in the cluster. The expression value was firstly z-score scaled before plotting. EBD4: embryoid body at day 4; EBD8: embryoid body at day8; NSC: Neural Stem Cells; NPC: Neural Progenitor Cell; MES: mesodermal cells; CP: Cardiac Precursors; CM: Cardiomyocytes. The protein-protein interaction (PPI) network between differentially expressed RBPs (pink dot) during EB formation and pluripotency-associated genes (PAG) (green dot). The interaction relationships were download from STRING database. Overlap of the 789 RBPs with the published screen data on mouse ES cells exit-from-pluripotency. The overlapped 29 RBPs may function in exit-from-pluripotency. Gene ontology (GO) enrichment of the above 29 RBPs. The node size of enriched GO terms indicates the number of enriched RBPs, RBPs with the same domains (e.g. RPM) are clustered and filled with the same background color. The domain names are labeled around enriched RBPs. Heatmap showing the expression pattern of the 29 RBPs during EB differentiation.
Figure 6A. Two-hybrid interaction between GBD-AC40 (left) or GBD-Sir4 (right) and different GAD-IN5 or GAD-IN1 constructions. Cells were plated in five-fold serial dilutions on DO-Leu-Trp-His plates. No growth or protein expression defects were detected B. Genome-wide occupancy profiles (top) and heatmaps (bottom) of IN5, WT, and indicated mutants, +/- 1kb upstream and downstream of all tDNAs. C. Genome browser visualization of different HA-IN occupancy for chromosome V (chrV:431129..443275). Occupancy of the indicated integrase is represented in each panel. Control, as panel 3D. The region contains tH(GUG) E2, tK(CUU) E2, tV(ACC) E1, tI(AAU) E1, SNR52 and SCR1, all transcribed by Pol III. D. Detection of Ty5, Ty5ΔTD5+bNLS or Ty1 de novo integration events at HMR and HML loci, SCR1 and upstream of all glycine tDNAs, by PCR using a primer in HIS3 and a primer in the locus of interest. Retrotransposition was induced in cells transformed with WT or mutated pGAL1-Ty5his3AI (Ty5 or Ty5ΔTD5+bNLS) and pGAL1-Ty1his3AI (Ty1). Total genomic DNA was extracted from His+ cells obtained from independent cultures. Nucleosome position (green circles) is indicated on the right of the panels (Brogaard et al, 2012).
Figure 6A Representative western blot analysis of pp53 in WT (n=6), DM (n=6) and PINK1-/-DM mice (n=3). GAPDH served as the loading control (DM ; **p=0.006 vs. WT group, PINK1-/-DM; **p=0.004 vs. DM group). B Measurement of p-selectin translocation to the cell membrane by flow cytometry analysis in WT (n=3), DM (n=3) and PINK1 -/- DM (n=3) miceplatelets. Graphs indicate mean fluorescence intensity (MFI) in each group. (*p<0.05 vs. WT or DM). C Quantification of vessel occlusion time after carotid arterial flow measurement (WT and DM; and PINK1 -/- : **p<0.01 vs. WT or DM). D Plot of carotid arterial flow by Doppler flow probe after 2 min FeCl3 injury, indicative of occlusive thrombosis. Flow was plotted as percentage of baseline flow before injury (DM: n=3, PINK1-/- DM; n=3).
HS3ST4, GPC6, and VCAN are effectors of the MDSC dependent oncogenic properties of TRF2 A Schematic representation of the Matrigel plug assay with BJcl2 cells knockdown for TRF2 target genes.Figure 5A Schematic representation of the Matrigel plug assay with BJcl2 cells knockdown for TRF2 target genes. Immune cells infiltration within the Matrigel plugs was determined by FACS. B-E Percentage of CD11bHi GR1Hi MDSCs (B), CD3- NKp46+ NK cells (C), NKp46+ CD107a+ NK cells (D) or CD69+ NK cells (E) Data information: data are presented by Box plots Min to Max showing all points with median corresponding to the percentages of each cell population among CD45+ or NK cells (n = 8 mice per group; *p < 0.05 and ***p < 0.001; Mann-Whitney test). Analysis of STAT3 phosphorylation by MSC2 cells after 18 hours co-culture with BJcl2 overexpressing or compromised for TRF2 and the target genes (F). Histograms of the pSTAT3 mean fluorescence intensity (MFI) of MSC2 cells when TRF2 was overexpressed and the target gene knocked down (G) Data information MFI of n=3 independent experiment is normalized to controls and represented as fold change of MFI (n = 3 independent experiments; *p < 0.05 and **p < 0.01; Student's t-test). Histograms of the pSTAT3 mean fluorescence intensity (MFI) of MSC2 cells when both TRF2 and its target gene were knocked down (H). Data information: MFI of n=3 independent experiment is normalized to controls and represented as fold change of MFI (n = 3 independent experiments; *p < 0.05 and **p < 0.01; Student's t-test). I Histograms of tumor weights on day 19 after implantation of subcutaneous xenografts containing BJcl2 cells overexpressing or knocked down for HS3ST4 or GPC6 Data information: data are represented as mean +/- SEM (n = 8 mice per group; *p < 0.05, and **p < 0.01; Mann-Whitney test).
Figure 7(A-D) DSE duration and amplitude is decreased in CA1 pyramidal neurons upon ERK pathway inhibition by a pre-treatment with PD98059 (PD; 10 µM) compared to 0.1% DMSO (control).(A) Average EPSC amplitude during 25 s baseline recording prior to DSE induction shows no significant differences in EPSC amplitude between the DMSO and PD pretreated groups (DMSO: 196.36 +/- 16.51 pA, n = 10; PD: 196.42 +/- 18.61 pA, n = 11, p = 0.9).(B) DSE in neurons of DMSO pre-treated slices, induced by a 10s depolarization to 0 mV (arrow). Inset: example traces of 2 averaged EPSCs before (black) and after depolarization (grey).(C) DSE in slices pre-treated with PD. Insets: example traces of 2 averaged EPSCs before (red) and after depolarization (grey).(D) Comparison of DSE between control and PD. PD pre-treatment limits amplitude and duration of DSE. ** = p < 0.01; unpaired T-test with Welch's correction. Numbers in bars represent the number of neurons in each group. (E-H) ERK-pathway inhibition by pre-treatment with PD98059 (PD; 10 µM) blocks the effect of WIN55,212-2 (WIN; 2 µM) on the amplitude of EPSCs recorded in CA1 pyramidal neurons.(E) Average EPSC amplitude during 5 min baseline recording prior to DSE induction shows no significant differences in EPSC amplitude between the DMSO and PD pretreated groups (DMSO: 295.69 +/- 28.73 pA, n = 6; PD: 270.86 +/- 32.14 pA, n = 6, p= 0.6).(F) Effect of WIN application (grey bar, 30 min) on EPSC-amplitude in CA1 pyramidal neurons of 0.1% DMSO (control) pre-treated slices. Inset: example traces of averaged EPSCs of baseline (black) and the last 5 min (grey).(G) Effect of WIN application (grey bar, 30 min) on EPSC-amplitude in CA1 pyramidal neurons of PD pre-treated slices. Inset: example traces of averaged EPSCs of baseline (red) and the last 5 minutes (grey).(H) Comparison of the effect size of the last 5 minutes in both groups shows a significant difference. * = p < 0.05; unpaired T-test. Numbers in bars represent number of slices in each group.
Figure 4Representative confocal (grey) and epifluorescence (blue) images of filipin staining in HUVECs in response to 2 h VEGF-B186 stimulation (left panels). Cellular cholesterol content measured by quantification of fluorescent filipin staining. Data presented as mean ± SEM from a representative experiment performed in triplicates. Statistical evaluation using t-test, p-value: * <0.05. Scale bars, 10 µm. Measurement of cholesterol content (B) in HUVECs after VEGF-B186 stimulation for different time-points. Data presented as mean ± SEM from representative experiments performed in triplicates. Statistical evaluation using t-test, p-value: * <0.05, ** <0.01, *** <0.001 (compared to respective control). Measurement of glucose uptake (C) and FA uptake (D) in HUVECs after VEGF-B186 stimulation for different time-points. Data presented as mean ± SEM from representative experiments performed in triplicates. Statistical evaluation using t-test, p-value: * <0.05, ** <0.01, *** <0.001 (compared to respective control). Colorimetric quantification of non-esterified cholesterol extracted from HUVECs stimulated with VEGF-B186 for 20 min. Data are presented as mean ± SEM of three individual experiments. Statistical evaluation using t-test, p-value: * <0.05. Uptake of a fluorescent cholesterol tracer (TopFluor) in HUVECs after VEGF-B186 stimulation for 20 min or 2 h. Data presented as mean ± SEM from a representative experiment performed in triplicates. Statistical evaluation using one-way ANOVA and Dunnett´s multiple comparisons test, p-value: ** <0.01, *** <0.001 (compared to respective untreated control). Quantification of the major cholesteryl ester (CE) species in HUVECs after VEGF-B186 stimulation for 20 min, analyzed by lipid mass spectrometry. Data presented as mean ± StDev of an experiment performed in triplicates.
CRY-less oscillations are temperature compensated and entrained(A) Detrended traces of bioluminescence recordings of WT and CKO fibroblast at different constant temperature conditions within the physiological range (n=4, solid lines: mean, dashed lines: ±SEM).Figure 2(A) Detrended traces of bioluminescence recordings of WT and CKO fibroblast at different constant temperature conditions within the physiological range (n=4, solid lines: mean, dashed lines: ±SEM). Temperature was changed from 37°C to 32°C halfway through the experiment, as depicted by red/blue shading. Arrows represent medium changes. Note the lack of rhythmicity in the first three days in CKO and the appearance of rhythmicity after the first medium change. (B) Quantification of period from recordings presented in (A). Both WT and CKO oscillations are temperature compensated with respective Q10s of 1.05 and 0.95 (n=3, mean ±SEM). P-values were determined by two-tailed t-test. (C) Bioluminescence of WT and CKO PER2::LUC cells during temperature entrainment (12h 32°C (blue) - 12h 37°C (red)) (n=3, solid lines: mean, dashed lines: ±SEM).
Figure 1(A-B) Immunofluorescence (IF) analysis of IκBα in sections from murine small intestine of 2 month-old WT (A) and Lgr5-GFP reporter mice (B). Scale bars, 50μm. IF analysis of P-IκBα in the intestine of 2 month-old WT (C) and quantification of P-IκBα positivity Scale bars in C, 25 μm IF analysis of P-IκBα in the intestine of 2 month-old Lgr5-GFP reporter mice (D), and quantification of P-IκBα positivity inside the Lgr5-GFP population. A minimum of 30 crypts was counted in 3 Lgr5-GFP mice. Scale bars in D, 50 μm. (E) Distribution of P-IκBα positive cells according to their position in the intestinal crypt from 200 crypts counted. (F) Double IF analysis of 2 month-old murine small intestine sections with the indicated antibodies and quantification of P-IκBα positivity inside the EphB2+ population. 70 crypts were counted. Bars represent mean values ± standard error of the mean (s.e.m). Scale bars, 50 μm. (G) Double IF analysis of murine small intestine sections with the indicated antibodies. Scale bars, 50 μm. (H) Western blot analysis of cytoplasmic (CYT) and nuclear (NUC) extracts from isolated intestinal crypt cells. (I) Western blot analysis of crypt nuclear extracts immunoprecipitated with anti-SUMO2/3 antibody. (J) IF analysis of developing intestines from E12.5 to E17.5 with the indicated antibodies. Scale bars, 25 μm. (K) Representation of IκBα distribution in the indicated genomic regions obtained from ChIP-sequencing analysis (n=4).
Figure 2Outline of the purification of HSATIII-derived AAUG fragments for RNA-MS analysis. HSATIII lncRNA is represented by magenta lines and other nSB-localized RNAs, such as U1 snRNA, are represented by gray lines. Lane numbers in B are indicated by red text. Semi-quantitative RT-PCR validation of the purity of HSATIII lncRNAs. Purified RNAs at each step in A were validated by semi-quantitative RT-PCR. ChIRP using control oligonucleotide was performed as negative control (lane 3). U1 snRNA was examined as an nSB-localized non-HSATIII RNA. RT(-) samples (lanes 6-10) were used as negative controls for PCR without reverse transcription. Input: 10%. RNA-MS analysis of HSATIII lncRNAs digested by RNase T1. Base peak chromatogram (BPC, top panel) and extracted chromatograms (XIC, lower panels) for the RNase T1-digested fragments of the isolated HSATIII lncRNAs. XICs detecting for the negatively-charged ions of AAUGp tetramer without modification (second panel), with one methylation (third panel), and two methylations (bottom panel) . The sequence, mass to charge ratio (m/z) and charge state are indicated. NL; normalization level. Collision-induced dissociation spectra of AAUGp, m6AAUGp and m6Am6AUGp. The product ions are assigned as indicated. LC/MS single nucleoside analysis of the purified HSATIII lncRNAs. Proton adduct of m6A nucleoside (m/z 282) is abundantly detected in UV trace at 260nm (upper panel) as well as in extracted mass chromatogram (lower panel). The base ion (m/z 150.077) of m6A nucleoside (m/z 282.119) is produced spontaneously by cleavage of the N-glycoside linkage during electrospray ionization (inserted mass spectrum).
Figure 3Representative blots showing expression of TP53 and RB1 expression in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells in the presence or absence of HPV E6/E7 oncoproteins at the 7th passage. β-Actin was used as a protein loading control. Growth curves of hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells in the presence of HPV E6/E7 oncoproteins at the 9th passage. Each point represents mean ± SEM of four independent samples. Representative images showing SA-β-gal staining in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells in the presence or absence of HPV E6/E7 oncoproteins at the 7th passage. Quantitative data showing the ratio of SA-β-gal positive cells in hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells in the presence or absence of HPV E6/E7 oncoproteins. Representative images showed SA-β-gal staining in cultured primary hOSE cells in the presence or absence of HPV E6/E7 oncoproteins. Cells were collected and stained at the 13th passage. Scale bar: 25 µm. Right graph showing the ratio of SA-β-gal positive cells in P13 hOSE cells transfected with empty vectors (CTRL-P13) or vectors expressing E6/E7 oncoproteins (E6/E7-P13).
Fig.Figure 5Centrioles first form by de novo biogenesis around E3 and gradually mature, acquire appendages (orange spokes) and recruit PCM (pink circle) to provide a basal body template for cilia and act as MTOCs for mitosis around E7, when the mitotic surveillance pathway is established. The expression of 53BP1 and USP28 precedes the establishment of the pathway and continues until at least E9.5. The embryo development timeline was adapted and modified from (Kojima et al, 2014).