EMBO/sd-character-level-ner huggingface dataset:
Figure 2A Deduced protein structure of Drosophila CG9005/Atossa (Atos) and its murine orthologs, mFAM214A-B, highlighting conserved domains. FAM214A-B are 44-45% identical to Atos. B Macrophages (red) near the germband in Stage 11/12 embryos. Atos tagged at C terminus with HA (HA-antibody, green) and expressed under direct control of macrophage specific promoter. Nucleus stained by DAPI (blue). Data information: Scale bars: 5µm C-D Confocal images or (D) quantification of the macrophages in germband in Stage 12 embryos from the control, atosPBG, and atosPBG expressing Atos itself or variants lacking particular domains. Transgene expression directly from macrophage specific promoter (mac-). For control (n=32 embryos) vs atosPBG mutant (n=56) p<0.0001; vs rescue with mac-atos (n=18) p>0.99; vs rescue with mac-atosDUF- (n=17) p=0.0003; vs rescue with mac-atosChrSeg-(n=21) p=0.0003; vs rescue with mac-atosDUF-/ChrSeg-(n=19) p=0,00014; vs rescue with mac-atosTAD1-/ TAD2- (n=25) p=0.0009, atosPBG mutant vs. rescue with mac-atos p=0.0031. Data information: Germband edge: dotted white line. Mac- indicates direct expression from the srpHemo promoter. (C, macrophage nuclei (red), actin by Phalloidin staining (green). (D One-way ANOVA with Tukey. Mean±SEM, ns=p>0.05, **p<0.01, ***p<0.001, ****p<0.0001. Scale bars: 50µm (C E Confocal images of atosPBG rescued by expressing Atossa's murine orthologs, mFAM214A or B (mFAMA-B) in macrophages, F Quantification of macrophages in the germband in Stage 12 embryos from the control, atosPBG, and atosPBG embryos expressing mFAM214A or B specifically in macrophages (mac-). For control (n=24 embryos) vs. atosPBG mutant (n=56) p<0.0001; vs mac-atos rescue (n=18) p=0.7; vs mac-mFAMA rescue (n=22) p=0.6; vs mac-mFAMB rescue (n=25) p=0.086. For atosPBG mutant vs mac-atos rescue p=0.0006; vs mac-mFAMA rescue p=0.0002; vs mac-mFAMB rescue p=0.0043. Data information: Germband edge: dotted white line. Mac- indicates direct expression from the srpHemo promoter. E) macrophage nuclei (red), actin by Phalloidin staining (green). F) One-way ANOVA with Tukey. Mean±SEM, ns=p>0.05, **p<0.01, ***p<0.001, ****p<0.0001. Scale bars: 50µm E).
Btz acts as an EJC component to control the distribution of mitochondria in muscle.Figure 2(A-K) Confocal xz-sections of larval muscle 6 in segment A3 stained with anti-ATP5A to label mitochondria. The dorsal surface (D) is to the right and ventral (V) to the left. (A) white (w)1118 control; (B) btz2/+ heterozygote; (C) btz2/ Df(3R) BSC497; (D) G14-GAL4/UAS-btz; btz2/ Df(3R) BSC497; (E) Btz-WT; btz2/ Df(3R) BSC497; (F) Btz-HD; btz2/ Df(3R) BSC497; (G) C57-GAL4/+ control; (H) C57-GAL4>UAS-btz RNAi; (I) C57-GAL4>UAS-mago RNAi; (J) C57-GAL4>UAS-eIF4AIII RNAi; (K) C57-GAL4>UAS-blw RNAi. In wild type muscles, mitochondria are present at the dorsal surface (red arrow in A) and also distributed between the fibers (yellow arrow in A), while in btz mutant muscles and in muscles expressing btz, mago or eIF4AIII RNAi they are concentrated at the dorsal surface. Expression of UAS-btz in muscle or the presence of the wild type, but not the HD mutant, Btz transgene restores the wild type distribution to btz mutants. The loss of ATP5A staining in muscles in which blw is knocked down confirms that the signal is specific. (L-N) electron micrographs showing cross-sections of larval muscle 6 in segment A3, with the dorsal surface to the right. Scale bars, 10 μm. (L) btz2/+; (M) Df(3R) BSC497/+; (N) btz2/ Df(3R) BSC497. Yellow arrows indicate examples of mitochondria interspersed between muscle fibers, and red arrows indicate mitochondria at the dorsal surface. Scale bars, 2 μm. (O) quantification of the ratio of the dorsal surface peak of ATP5 intensity to the second highest peak for the genotypes indicated. ***, p<0.001; **p<0.01; *p<0.05; ns, not significant by Mann-Whitney test. n=9 (btz/+), n=11 (Df/+, btz/Df), n=6 (btz/Df; G14>btz, C57-GAL4/+), n=4 (btz/Df; Btz-WT, C57>eIF4AIII RNAi), n=5 (btz/Df; Btz-HD), n=10 (C57>btz RNAi), or n=3 (C57>mago RNAi). Error bars show mean ± SEM. (P) Western blot of wild type (Canton S) and btz2/Df(3R) BSC497 larval carcasses with anti-ATP5A and anti-tubulin. Duplicate samples of 15 ng total protein are shown for each genotype. The overall level of ATP5A is not altered in btz mutant muscles.
Figure 4A. DNA-RNA hybrids in IGVL and IGCL in wild type and h3.3. The DRIP signal is normalised to total input and to wild type IgVλ (*** = p<0.001, ns = not significant, unpaired T-test). B. MNase mapping reveals that loss of H3.3 does not affect average Igλ nucleosome positioning. The red bars indicate the qPCR amplicons for the MNase mapping. The qPCR signals are normalised to the first amplicon at the TSS. Error bars represent 1SD of 2 experimental repeats. C. DNA-RNA hybrids in IGVL of wild type clones either without overexpression of RNAseHI (red, clones 1 and 2, each assayed with three qPCR repeats) or with overexpression of RNAseHI (blue, clones 3 and 4, each assayed with three qPCR repeats) (*** = p<0.001, ** = p < 0.01; unpaired T-test). Expression of hAIDup-FLAG and chickenRNAseHI-YFP in these clones is shown in Figure EV6. D. Rate of Ig diversification in wild type cells with and without overexpression of RNAseHI.
IL-1 signalling inhibition in MPSIIIA mice reduces glial activation.Figure 6Representative images of the hippocampus and cortex (layers II-V) from control and treated mice stained with anti-mouse glial fibrillary acidic protein (GFAP; red)/DAPI (nuclear, blue) to identify activated astrocytes, 20x, scale bar: 50μm Representative images of the hippocampus and cortex (layers II-V) from control and treated mice stained with isolectin B4 (ILB4) to identify activated microglia, 20x, scale bar: 50μ The average number of GFAP positive astrocyte cells over three fields of view per mouse of the hippocampus (C) and the cortex (D) were counted (n=4 mice per group, average of 3 fields of view per mouse). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; **P<0.01, ***P<0.001. Symbols above bars are versus WT The average number of ILB4+ positive microglial cells over three fields of view per mouse of the hippocampus (C) and the cortex (D) were counted (n=4 mice per group, average of 3 fields of view per mouse). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; ***P<0.001. Symbols above bars are versus WT
Metabolic network showing metabolome, transcriptome and proteome changes triggered by pyk1 allele replacement.Figure 3Metabolites, transcripts and proteins are coloured by their abundance ratios in A-strain relative to T-strain (see legend top left for details). For clarity, enzymes without protein or transcript changes are not shown (e.g. most upper glycolysis). Two metabolite pairs are indistinguishable by our LC-MS method (marked as '+' and '#)'.
Figure 7A) Density power radial kymograph of a representative time-lapse movie of the nests expansion process after blocking histoblasts proliferation by overexpressing Dacapo. Each horizontal line displays at each time point (left scale) the mean of the power value at every distance (bottom scale) to the nest-LECs border (vertical black line). Each phase is represented in a colored background with three different densities of purple. Power values color scale is on the right. B) Comparison of the means and standard deviations of the density power radial kymographs in phase 3 for Dacapo overexpressing nests (green) and wild type (purple). C) Surface Stress radial kymograph of a representative time-lapse movie Phases are represented in different densities of brown. Stress values color scale is on the right. D) Comparison of the means and standard deviations of the surface stress radial kymographs in phase 3 for Dacapo overexpressing nests (green) and wild type (brown). E) Density power radial kymograph of a representative time-lapse movie after blocking LECs delamination by overexpressing P35. Power values color scale is on the right. F) Comparison of the means and standard deviations of the density power radial kymographs in phase 3 for P35 overexpressing LECs (green) and wild type (purple). G) Surface Stress radial kymograph of a representative time-lapse movie Phases are represented in different densities of brown. Power values color scale is on the right. H) Comparison of the means and standard deviations of the surface stress radial kymograph in phase 3 for P35 overexpressing LECs (green) and wild type (brown).
Figure 4The Venn diagram showing genes with significantly isoform changes. Pink circle represents genes with highly expressed isoform (FPKM > 5) that emerged during EPC generation. Blue circle represents genes exhibiting isoform proportion changes (delta iso > 0.15) after PLB treatment (PLB vs DMSO). Green circle represents genes with differentially expressed isoforms (FC > 10 & FDR < 0.05) after PLB treatment (PLB vs DMSO). The heatmap shows the expression of the overlapped genes ranked by FC when compared between DMSO vs PLB treated cells. The heatmap was scaled with Z-Score using the log2(FPKM) expression of isoforms of indicated genes. n=2 technical replicates The schematic representation (top) indicates the isoform structure of NUMB_L and NUMB_S. The bottom curve reflects the expression of NUMB isoforms in day 2-APLNR+ cells, day 5-DMSO and day 5-PLB (2.5 nM) treated cells. A Sashimi plot to visualize the mapping of RNA-Seq reads at the exon 11-13 loci of NUMB in day 2-APLNR+ cells, day 5-DMSO-treated and day 5-PLB-treated cells. The top panel is one representative RT-PCR electropherogram showing the inclusion/exclusion of NUMB exon 9 in day 2-APLNR+, day 5-DMSO-treated and day 5-PLB treated cells. The expected isoforms are indicated on the right with exon 9 in blue and constant exons in red. At the bottom is a statistical bar graph of normalized PSI obtained from the RT-PCR electropherogram. P-values were calculated by one-way ANOVA followed by Dunnett's test. Western blotting showing NUMB_S overexpression in sorted GFP+ cells on day 5 during differentiation induced by DOX from day 2.5 to 5. GAPDH was used as the loading control. The bar graph presents the quantification of NUMB_S protein expression. The P-value was determined by an unpaired two-tailed Student's t-test. The representative FACS plots show the frequency of CD31+CD34+ EPCs in the GFP+ population at day 5 with 1.25 nM PLB supplementation alone or in combination with NUMB_S ectopic expression from day 2.5. The bar graph denotes the percentage of CD31+CD34+ in GFP+ cells as described in (F). P-values were determined by an unpaired two-tailed Student's t-test.
Fig.Figure 2(a) PPARγ mRNA expression in sperm from control and MSUS mice. Control n = 15, MSUS n = 13, two-tailed Student's t-test, P = 0.029, t = 2.30, df = 26. (b) Schematic of serum treatment of GC-1 cells. On day 1, cells are transfected with PPRE and luciferase normalization plasmids. Serum is mixed in culture medium at 10% concentration and exposed to cells on day 2. Cells are harvested 24h later (Day 3) and luminescence is measured. (c) Relative luciferase luminescence in transfected GC-1 cells exposed to serum from control or MSUS mice. Numbers correspond to serum from individual animals applied to different cell culture wells. Control n = 17, MSUS n = 22, two-tailed Student's t-test, P = 0.042, t = 2.1, df = 37.
Figure 6A. IF staining of hnRNP U, FUBP1, ILF2, and SRSF1 in normal L2C, E4C, and embryos injected with Control-LNA or LincGET-LNA. The results show that hnRNP U, FUBP1, ILF2, and SRSF1 are present in the nuclei of 2- to 4-cell embryos, and the expression of hnRNP U, FUBP1, and ILF2 increased significantly after LincGET depletion. Normal L2C and 4-cell embryos were collected at phCG 48 hours and 54 hours, respectively. Embryos injected with LNA were collected at phCG 48 hours. Scale bar, 50 μm. Three experimental replicates were performed and about 15 embryos were used in each group. B. Quantification of the fluorescence intensity show that the expression of hnRNP U, FUBP1, and ILF2 increased significantly after LincGET depletion. Two tailed student's t-test was used for the statistical analysis. Related to Figure 6A and Appendix Fig S5. n.s., p > 0.05. C. LincGET depletion in embryos had no effect on RNA levels of Hnrnpu, Fubp1, Ilf2, and Srsf1 measured by SG-qPCR. Three experimental replicates were performed and about 50 embryos were used for each time. Two tailed student's t-test was used for the statistical analysis. n.s., p > 0.05. D. LincGET overexpression in mouse ESCs decreases the protein level of hnRNP U, FUBP1, and ILF2 by western blot. Three experimental replicates were performed and about 1 106 cells were used for each time. E. LincGET overexpression in mouse ESCs had no effect on RNA levels of Hnrnpu, Fubp1, Ilf2, and Srsf1 measured by SG-qPCR. Three experimental replicates were performed and about 1 106 cells were used for each time. Two tailed student's t-test was used for the statistical analysis. n.s., p > 0.05.
ATP8A1 activity is essential for fission of TfnR‐positive membrane carriersCOS‐1 cells were treated with ATP8A1 siRNA1 for 72 h and stained for TfnR.Figure 2A COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h and stained for TfnR. Each image represents the maximum intensity z‐projection of four confocal slices. Intensified images are shown in the bottom row. Red dashed lines and arrowheads indicate nuclei and TfnR puncta, respectively. Scale bars, 10 μm. B COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h and stained for the indicated proteins. Scale bars, 10 μm. C COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h. TfnR‐GFP was transfected 48 h after siRNA transfection. Cells were then imaged with an epifluorescent microscope. Selected stills from Supplementary Movie S1 are shown. The asterisks indicate the tips of the tubules of interest. Scale bars, 5 μm. D The effect of increasing levels of 1,2‐dioleoyl‐PS on the ATPase activity of purified ATP8A1 (WT and E191Q)‐CDC50A complex. The Km and Vmax for the WT complex were 59.1 ± 3.5 μM and 38.7 ± 0.8 μmol ATP/min/mg protein, respectively. E COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h. siRNA‐resistant ATP8A1 (WT or E191Q), and myc‐CDC50A were transfected 48 h after siRNA transfection. Cells were then fixed and stained for TfnR. The graph shows percentages of cells showing aberrant TfnR‐positive tubules as mean ± SD of three independent experiments. At least 50 cells were counted per experiment.
In vivo” treatment with ETP-47037 compound blocks the progression of lung carcinoma.Figure 8Schematic representation of the ETP-47037 treatment protocol. Mice with already developed lungcarcinomas were subjected to computerized tomography (CT) measurements before the start of the treatment. ETP-47037 was given at a dose of 75 mg/kg body weight by oral gavage 8 days out of the ten that the experiment lasted as indicated. At the end of the treatment, a CT was performed for quantification of tumor area and mice were sacrificed for further histological and molecular analysis. Control mice were similarly treated with vehicle. Quantification of tumor growth relative to initial tumor size. Representative CT images are shown to the right. The white arrowhead indicates a tumor within a highly inflammatory region. Quantification of TRF1 levels by immunofluorescence in intestine and lung tumors samples of mice treated with vehicle or with ETP-47037 for 10 days. Representative images are shown to the right (n = 4). Number of cells showing γH2AX foci in intestine and lung tumors samples of mice treated with vehicle or with ETP-47037 for 10 days. Representative images are shown to the right (n = 4).
Figure 3(A) HepG2 cells were stably transfected with vector or FLAG-JFK. Cellular extracts were immunopurified with anti-FLAG immunoafﬁnity resin and eluted with FLAG peptides. The eluates were resolved on SDS-PAGE and silver-stained. The proteins bands were retrieved and analyzed by mass spectrometry. (B) Cellular extracts from HepG2 cells were immunoprecipitated with antibodies against ING5 followed by immunoblotting with the antibodies against the indicated proteins. (C) Extracts from liver tissues of wild-type mice were immunoprecipitated with antibodies against Ing5 followed by immunoblotting with the antibodies against the indicated proteins. (D) GST pull-down assays with bacterially expressed GST-ING5 and in vitro transcribed/translated JFK, CUL1, SKP1, or RBX1. (E) Schematic diagrams of wild-type JFK and JFK mutants. Cellular extracts from HepG2 cells co-transfected with Myc-ING5 and FLAG-JFK or JFK mutants were immunoprecipitated with anti-FLAG followed by immunoblotting with anti-Myc. (F) GST pull-down assays with bacterially expressed GST-JFK or JFK mutants and in vitro transcribed/translated ING5.
Phosphofructokinase 1 is inhibited in glycolytic muscle and glucose is rerouted toward glycogen stores.Figure 3Enzymatic activity of phosphofructokinase in whole tibialis anterior muscle cytosolic homogenates is expressed as mean fold change ± SEM from age-matched WT at 65 days of age *P = 0.016 (WT n = 6, SOD1G86Rn = 7) and 105 days of age ***P < 0.0001 (n = 5/genotype), two-way ANOVA followed by Fisher's LSD post hoc test. Data shown are representative of two independent experiments having similar results. Pyruvate was measured in whole tibialis anterior muscle tissue homogenates. The mean fold change ± SEM compared to age-matched WT are represented with *P = 0.019 at 65 days of age (n = 5/genotype) and *P = 0.041 at 105 days of age (n = 4/genotype), two-way ANOVA followed by Fisher's LSD post hoc test. Data shown are representative of two independent experiments having similar results. Left: Representative Western blot showing glycogen synthase and phosphorylated glycogen synthase levels. Right: Quantification represents the mean ratio of optical densities of glycogen synthase/P-glycogen synthase ± SEM. At 65 days of age n = 6/genotype, *P = 0.0162, and at 105 days of age n = 5/genotype, *P = 0.0163, two-way ANOVA followed by Fisher's LSD post hoc test. Left: Representative microphotographs of PAS staining from WT and SOD1G86R tibialis anterior cross-sections at 65 and 105 days of age showing glycogen-negative (light pink) and glycogen-positive (dark pink) fibers. Scale bar: 200 μm. Right: Quantification of glycogen-negative (−) and glycogen-positive (+) fibers at 65 and 105 days of age. For (−) fibers: **P-values versus WT: 0.0026 at 65 days and 0.0074 at 105 days, for (+) fibers: ##P-values versus WT: 0.0025 at 65 days and 0.0073 at 105 days (n = 5/genotype at 65 days and n = 4/genotype at 105 days, two-way ANOVA followed by Fisher's LSD post hoc test).
Figure 6A RUNX1 expression levels in human CD34+ cells grown in pro-MK medium in a time course were measured by real-time PCR (n=4, mean ± SD). B CD34+ cells were grown in pro-MK medium for 5 days and stained with antibodies against CD41 and CD42 for flow cytometry analysis. The CD41+CD42+ cell percentages were analyzed using one way ANOVA, ** P<0.01, (n=4, mean ± SD). C The mRNA expression levels of RUNX1, RBM15, and AS-RBM15 in RUNX1 knockdown MEG-01 cells were measured by real-time PCR (n=4, mean ± SD). D Chromatin immunoprecipitation using anti-RUNX1 antibody. Immunoprecipitated DNA fragments were measured by real-time PCR using HEL cells expressing shRUNX1 and control (n=4, means ± SD). E CD34+ human cord blood cells were transduced with MIG retroviruses co-expressing A/E (AML1-ETO, aka RUNX1-ETO) and GFP. Around 5 days after transduction, the GFP+CD11b- cells were sorted for real-time PCR (n=4). Also see Fig EV6 for RUNX1-ETO binding profile on RBM15 locus.
Figure 3(a) Experimental testing of the predicted SR (DU) rescuers of DNMT1 via drug combination experiments in 18 NSCLC cell lines insensitive to Decitabine. The matrix displays drug interactions between Decitabine, a DNMT1 inhibitor, and inhibitors of its predicted rescuer genes (X-axis) across 18 NSCLC cell lines (Y-axis) that are insensitive to Decitabine. Row labels present rescuer genes and their inhibitors. Colors in the matrix show whether the interactions found are significantly synergistic (red), antagonistic (green) or non-significant (in gray). Values in the matrix show average synergism (<1 synergism and >1 antagonism Thirteen predicted DU-SR rescuers (red lines), two predicted DD SR rescuers (green lines) of DNMT1 and one random control (JAK3i) were tested. (b) Some SR interactions of DNMT1 occur between genes proximally located on the signaling pathway. DU rescuer genes of DNMT1 are colored blue. (c-e): Functional similarities between gene pairs in the DU-SR network. Comparison of functional similarities between interactions in (i) the DU-SR network (ii) Random-pairs( the network is generated by random pairing between protein-coding genes, having a degree distribution similar to that of the DU-SR network) (iii) shuffled-pairs (the network is generated by shuffling pairing of the DU-SR network). Functional similarities of genes in each pair were evaluated in terms of their: (c) GO similarity, (d) distances in human PPI network and (e) distances in the STRING network The distances denote the number of interactions on the shortest path between the paired genes. The histogram of network distances between gene pairs is displayed for the PPI and STRING networks.
Figure 4(A) Nuclear (Nuc.) and cytoplasmic (Cyto.) fractions of U2-OS cells were analyzed at times indicated after IR exposure by SDS-PAGE western blotting. PARP1 and LDHA are fractionation controls and phospho-specific p65 signals are indicated. Representative gels from n = 3 biological replicates are shown. Right panel: quantitation of nuclear p65 and phosphorylated p65 species (n = 3). Fold changes compared to untreated samples (ut) and time points post IR are indicated on Y and X axes, respectively. (B) U2-OS cells treated with dox to deplete endogenous p65, were irradiated (20 Gy) and transfected with plasmids encoding p65, p65-S276A or p65-S468A, as indicated. Nuclear (N) and cytoplasmic (C) lysates were analyzed by SDS-PAGE at day seven post IR. Representative gel from n = 3 biological replicates is shown. PARP1 and αTubulin serve as fractionation and loading controls. (C) ChIP performed with U2-OS cells irradiated (20 Gy) 1.5h or 7 days prior to assay, or left untreated (UT). Normalized relative enrichment of NFKBIA is shown (relative to input and two non-recruiting reference regions). Left panel: p65 antibody. n = 5 biological replicates with 3 technical repeats per biological replicate. Right: Antibody against p65 pSer468. n = 2 biological replicates with three technical repeats per biological replicate. Statistical significance was determined by ANOVA with Tukey multiple comparisons test. SD shown. * = p < 0.05, ** = p < 0.01, *** = p < 0.001 (D) Kinase proteome array was performed with nuclear fractions of U2-OS cells that were either left untreated (UT) or irradiated (20 Gy) at time points indicated prior to harvest. Kinase binding to membrane was quantitated (n = 2) and only significant results (p < 0.05) are shown. Significance was determined by ANOVA with Tukey multiple comparisons test. (E) U2-OS cells left untreated (ut) or irradiated (20 Gy) 7 days before harvesting, as indicated. Two days prior to harvest cells were transfected with siRNA against GSK3β or scrambled control (Scr). Whole cell lysates were analyzed by SDS-PAGE and western blotting. A representative example from n = 3 experiments is shown. (F) U2-OS cells were left untreated or exposed overnight to 10 mM LiCl, with or without prior irradiation, as indicated, and analyzed as in (E). Representative data from n = 3 experiments are shown. (G) RT-qPCR of U2-OS cells irradiated (20 Gy) either 1.5h or 7 days prior to harvest. CHIR denotes treatment with GSK3 inhibitor CHIR-99021 (10nM overnight). DMSO overnight treatment was used as control. Quantitation was performed and statistical significance obtained from n = 3 replicates, using ANOVA with Tukey multiple comparisons test. SD shown. * = p < 0.05, ** = p < 0.01, *** = p < 0.001.