EMBO/sd-character-level-ner huggingface dataset:
hTauAT causes elevation of Ca++ levels in CA3 hippocampal neurons at resting state and after membrane depolarization through extrasynaptic NMDA receptors.Figure 4A. Slices (DIV15) from control mice were loaded with the Ca++ sensitive dye Fura-2AM. Ratiometric images are presented at baseline and after application of high potassium. Note the increase in intracellular Ca++ ([Ca++]i) after KCl application.B. Slices (DIV15) from hTauAT mice were loaded with the Ca++ sensitive dye Fura-2AM. Ratiometric images at baseline and after application of high potassium in area CA3 are depicted. Note the increase in [Ca++]i (false color legend) under both conditions in hTauAT slices compared to controls. C. Electrophysiological example traces (control = black; hTauAT = red) of excitatory postsynaptic field potentials (fEPSP) depicts examples of depolarizations that are induced by a single high potassium chloride application in stratum pyramidale (s.p.) of area CA3 in slices in which calcium imaging experiments were conducted. The example depolarization evokes averaged calcium influxes into neurons depicted in the calcium imaging graph. The graph shows the mean of [Ca++]i changes in response to high KCl in stratum radiatum and stratum pyramidale of area CA3 in Fura2-AM loaded hippocampal slices. After depolarization [Ca++]i rises up to ~600 nM in hTauAT slices (red trace, n=6 slices, prepared from at least three animals), compared to ~300 nM in control slices (black trace, n=6 slices; prepared from at least three animals). Note that even under resting conditions [Ca++]i is elevated to ~120nM due to hTauAT expression. D. Quantification of the maximum [Ca++]i from ratiometric images as depicted in (A) and (B) after background subtraction and selection of regions of interest (10 circles of fixed diameter) in stratum radiatum border to stratum pyramidale of area CA3. Under resting conditions [Ca++]i was elevated in transgenic slice cultures (~120 nM, n=11) compared to controls (~80 nM, n=8). Slices were incubated with one of the following channel blockers: Nifedipine (NIF, VGCC; Ctrl n=8; A152T: n=7), APV (NMDAR; Ctrl n=7; A152T n=8), ifenprodil (IFEN, NMDAR; Ctrl n=8; A152T n=7), memantine (MEM, NMDAR; Ctrl/A152T n=6), 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX; AMPAR; Ctrl n=8; A152T n=7)), tetrodotoxin (TTX, VGNaC; Ctrl n=4; A152T n=5), tetanus neurotoxin (TeNT, neurotransmitter release; A152T n=6) or in Ca++ free buffer (Ctrl n=10; A152T n=7). For each experiment slice preparations from at least three different mice were used. One-way ANOVA followed by Tukey's post-hoc test; Ctrl: F(7/51) .3,533; p=0.0036; A152T: F(8/55)=5,230; p<0.0001.For an overview of drug concentrations see EV Table 1.E. Quantification of the maximum peak increase in intracellular calcium in the same slices than in (D) after high KCl stimulation. One way ANOVA followed by Tukey's post-hoc test Ctrl: F(7/45)=4,080; p=0.0015; A152T: F(8/53)=7,580; p<0.0001).Error bars represent SEM; One-Way ANOVA *p<0.05; **p<0.01 and ***p<0.001.
Figure 1(A) Overlay of 15N-1H HSQC spectra of 15N-labeled Ca2+/CaM by itself (red peaks) and after addition of saturating, unlabeled PSD-95 (1-21) (blue peaks) or saturating, unlabeled PSD-95_pT19 (green peaks). All NMR experiments were recorded at 600 MHz 1H frequency. (B) Chemical shift perturbation of CaM amide resonances in the absence vs. presence of PSD-95_pT19. Chemical shift difference (CSD) plotted on the vertical axis was defined as CSD = {(HNA - HNB)2 + (15NA - 15NB)2}1/2 , where "A" and "B" designate free and bound states of CaM. HN and 15N represent amide 1H and 15N chemical shifts, respectively. Perturbations greater than the average were used as active ambiguous restraints in the Haddock docking calculation (see Methods). (C) Representative data from IPAP [15N-1H]-HSQC spectra of 15N-labeled Ca2+/CaM bound to PSD-95_pT19 in the absence (blue) and presence of 17 mg/ml filamentous bacteriophage Pf1 (red). Residual dipolar couplings (RDCs) for backbone HN resonances are calculated (in Hertz) as the difference in splitting for the 15N-{1H} doublet components (red peaks) relative to the isotropic 1JNH coupling (blue peaks). RDC values are calculated to be +40, +30, +20, +20, and -20 Hz for I100, I27, N137, D64, and I130, respectively. (D) Correlation between observed RDCs (panel C) versus RDCs calculated from the final NMR derived structure of Ca2+/CaM bound to PSD-95_pT19. The correlation coefficient (R) equals 0.99 and Q is 0.11.
Figure 9In our MT-flux model, interpolar MTs are slid apart by the collaborative activity of the MT-crosslinking motors EG5 and KIF15, supported by sequential contribution of CENP-E at KTs in prometaphase and KIF4A on chromosome arms in metaphase. CENP-E at laterally attached KTs during early mitosis interacts with antiparallel MTs and slides them apart. During chromosome alignment to the metaphase plate, when CENP-E is partially stripped away from the KTs, KIF4A gradually takes over, promoting MTs to flux towards the poles.
Figure 2A. RNA-seq was performed on WT, mutant, and null p53 low passage cell lines. Principle component analysis (PCA) highlights distinct genetic profiles based on p53 status. B. Relative fold change in expression level of endocytic recycling genes in invasive vs. non-invasive cells, and in mutant vs. WT p53 cells based on microarray and RNA-seq analysis, respectively. C. qPCR analysis of recycling-related gene expression in mutant p53 relative to WT p53 cells (red and black bars, respectively). Graphs represent mean ± SEM (n=3 biological replicates for Rab11-FIP1, Rab25, Myo5b and Clic3; n=2 biological replicates for Rab5). Rab11-FIP1 *p=0.0109, Rab25 **p=0.0021, Myo5b ***p=0.0001, Clic3 **p=0.0051, Rab5 no significant differences (n.s.). (Unpaired t-test).
Divergent genes are under relaxed selective constraints.Figure 6APA divergent genes have higher dN/dS ratios compared to conserved genes in each tissue (Mann-Whitney U tests, **P < 0.01; ***P < 0.001). The boxplot shows the Q1 to Q3 quartile values (the box limits), the median (the horizontal green line) and values within the 1.5 * IQR (the whiskers). Divergent genes have higher APA variability between replicates compared to conserved genes in each tissue (Mann-Whitney U tests, ***P < 0.001). The boxplot shows the Q1 to Q3 quartile values (the box limits), the median (the horizontal green line) and values within the 1.5 * IQR (the whiskers). Spearman correlation between allelic difference in dominant PAS usage and total gene expression level (shown for liver as an example). Frequency of sequence variants in major PAS flanking region (-200 nt, 100 nt) for all-divergent genes, some divergent genes and conserved genes. The numbers of genes in each group are indicated in the legend. Scaling law, major PASs with moderate usage have larger allelic PAS usage difference (Mann-Whitney U tests, *P < 0.05; ***P < 0.001). The boxplot shows the Q1 to Q3 quartile values (the box limits), the median (the horizontal green line) and values within the 1.5 * IQR (the whiskers). Similar SNV densities in PAS flanking regions (- 200 nt, 100 nt) of major PASs between genes with different major PAS usage (Mann-Whitney U test, **P < 0.01). The violin plot shows the median (the white dots), Q1 to Q3 quartile values (the thick black lines), 1.5 x IQR (the thin black lines) and kernel density distribution with the range of the observed data.
Retinoic acid induces COUP-TFI and COUP-TFII during atrial differentiation.Figure 4A, B Line plot illustrating relative mRNA levels of (A) COUP-TFI and (B) COUP-TFII in VM and AM differentiations from day 5 through day 9 (left) and in GFP+CMs at day 31 (right); n = 3.Data information: Data are presented as mean ± SEM. In (A, B), *P < 0.05, **P < 0.01, ***P < 0.001 by unpaired t-test. In (A), left panel, P = 0.03, 0.02, 0.03, 0.005 and 0.0004 for comparison of COUP-TFI expression between AM and VM at days 5, 6, 7, 8 and 9 of differentiation. In (A), right panel, P = 0.0002 for comparison of COUP-TFI expression at day 31 between AM and VM. In (B), left panel, P = 0.02, 0.03, 0.006, 0.004 and 0.003 for comparison of COUP-TFII expression between AM and VM at days 5, 6, 7, 8 and 9 of differentiation. In (B), right panel, P = 0.0001 for comparison of COUP-TFII expression at day 31 between AM and VM. CT = control differentiation; hESC-atrial (AM); hESC-ventricular (VM). C, D COUP-TFI (C) and COUP-TFII (D) immunofluorescence at day 31 in AM (top) and VM (bottom). Scale bars: 40 μm.
Figure 3(A) ROS burst in WT and rgi5x after elicitation with 100 nM flg22. Shown is the kinetic of ROS production over 40 min -/+ SE, n=8 biological replicates. RLU = Relative light units. Similar results were obtained in 3 independent experiments. (B) Ethylene production was measured in the indicated genotypes 3.5 h after elicitation with mock or 500 nM flg22. Ethylene accumulation was normalized to the average of WT responses to flg22 set as 1. Shown is the mean of n=18 biological replicates from 3 pooled experiments -/+ SD (one-way ANOVA, Tukey post-hoc test, a-b p<0.001; a-c, p<0.001; b-c, p<0.001). (C) 5-day-old seedlings of WT and rgi5x were treated with 100 nM flg22 for 7 days before measuring fresh weight. Shown is the mean of relative fresh weight compared to the MS medium control -/+ SD, n=16 biological replicates (Students T-test, ***p<0.001). Similar results were obtained in 3 independent experiments. (D) Mean colony-forming units (cfu) of Pto DC3000 COR- 3 days after spray infection of the indicated genotypes; n=7-8 biological replicates from 2 pooled experiments -/+ SD (one-way ANOVA, Tukey post-hoc test, a-b p<0.001; a-c p<0.001, b-c p<0.05). (E) Ethylene production was measured in WT and rgi5x and rgi5x pRGI3::RGI3 #2 and #3 3.5 h after elicitation with 500 nM flg22. Ethylene production was normalized to the average of WT responses to flg22 set as 1. Shown is the mean of n=8 biological replicates from 2 pooled experiments -/+ SD (one-way ANOVA, Dunnett post-hoc test, a-b p<0.05). (F) 5-day-old seedlings of the indicated genotypes were treated with 100 nM elf18 for 7 days before measuring fresh weight. Shown is the mean of relative fresh weight compared to the MS medium control -/+ SD, n=36 biological replicates from 3 pooled experiments (Students T-test, ***p<0.001).
Figure 5(A) Genomic distribution of ING5 determined by ChIP-seq analysis. ChIP was performed in HepG2 cells with antibodies against ING5 followed by deep sequencing. The raw data were analyzed by MACS with the cutoff of p value < 1e-5 and FDR < 0.001. (B) Binding density of ING5 across its specific binding sites visualized by deepTools. The heatmap shows the normalized ChIP-seq tag counts ordered by signal strength. (C) Venn diagram from cross analysis of down-regulated genes obtained from RNA-seq analysis in JFK-overexpressing and ING5-depleted HepG2 cells with genes targeted by ING5 from ChIP-seq. GO enrichment analysis of 140 potential target genes using DAVID is shown. (D) ChIP-seq track at the representative promoter of target genes. The red rectangles indicate the peak regions/binding sites of ING5 on the target genes promoter.
Figure 2(A) Expression of chemokine receptors was assessed by microarray analysis of different CD4+ T cell populations. Statistical analysis revealed a strong upregulation of most of the chemokine receptors covered in the array for Th17iv/Tnaive (column2), Th17eae/Tnaive (column 3) and MOG35-55 induced EAE recovered CD4eae/Tnaive. (B) Microarray signal intensities of strongest regulated genes from (A) are shown in detailed statistical analysis for the different T cell subgroups. Values are depicted as signal intensity mean ± SEM from three independent experiments. Statistical significance was determined using one-way ANOVA with post-hoc Tukey Test for multiple comparisons. P-values < 0.05 were regarded as statistically significant. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.
within the C-terminal transactivation domain(A) Doxycycline (Dox) induction of EBNA2 in DG75Dox HA-EBNA2 cells treated for 24 hours.Figure 3(A) Doxycycline (Dox) induction of EBNA2 in DG75Dox HA-EBNA2 cells treated for 24 hours. Co-immunoprecipitates of HA-EBNA2 and endogenous PLK1 are visualized by Western blotting. (B) EBNA2/PLK1 co-precipitates were submitted to kinase reactions using [γ-32P] ATP in the absence (control) or presence of 50 ng recombinant active PLK1. (C) EBNA2 co-precipitates were submitted to kinase reactions in the absence (control) or the presence of the PLK1 inhibitor Volasertib (40 nM). (D) EBNA2 candidate phosphorylation mutants were expressed in DG75 B cells and tested for PLK1 binding by co-immunoprecipitations followed by Western blotting. (E) Immunoprecipitates were submitted to kinase reactions but samples were treated with Volasertib (40 nM) (+) or treated with solvent only (-). (F) GST EBNA2 fragment 246-487 wt and mutant S457A/T465V were treated with recombinant active PLK1 (+) in the presence of [γ-32P] ATP in vitro or left untreated (-). CRS, an artificial PLK1 test substrate was used as a positive control. (G) Schematic presentation of EBNA2 phosphorylation sites by CDK1 and PLK1. (H) HA-tagged EBNA2 candidate phosphorylation mutants were expressed in DG75 B cells and tested for activation of an EBNA2/CBF1 responsive promoter reporter luciferase plasmid. Activation of the reporter gene is shown as relative response ratio normalized to Renilla luciferase activity and shown relative to wt activity. (I) GST-pull down assay using GST-EBNA2 446-474 as a bait to purify cellular proteins from DG75 cells followed by Western blotting and quantification of signals obtained by GST and p300 specific antibodies. Relative binding affinities (rel. p300 bindg.) are normalized to the wt signal. Since 3 lanes of the original blot were excised a broken line marks the borders between two parts in the figure.
Figure 1(A) NSCLC expressing single site mutants of EGFR, PC9 (3X106) or H3255 (8X106), were seeded in 10-cm dishes. On the next day, complete media were replaced with media containing serum (1%) and the cells were treated for 24 hours with different EGFR-specific TKIs (erlotinib, 50 nM; osimertinib, 50 nM, or afatinib, 10 nM), either alone or in combination with 2XmAbs (cetuximab and trastuzumab, 5 μg/ml each). Thereafter, cells were washed with cold saline and extracted. Proteins were separated using gel electrophoresis and transferred onto nitrocellulose membranes. After blocking, membranes were incubated overnight with the indicated primary antibodies, followed by incubation with horseradish peroxidase-conjugated secondary antibodies (60 minutes), and treatment with Clarity™ Western ECL Blotting Substrates (Bio-Rad). ECL signals were detected using the ChemiDoc™ Imaging System (Bio-Rad) and images were acquired using the ImageLab software. Signals (relative to Control) were quantified and normalized to the signals of GAPDH (numbers shown below each lane). for 24 hours with different EGFR-specific TKIs (erlotinib, 50 nM; osimertinib, 50 nM, or afatinib, 10 nM), either alone or in combination with 2XmAbs (cetuximab and trastuzumab, 5 μg/ml each). (B) PC9 cells (1X106) were seeded in 6-well plates and treated After washing with acidic buffer (glycine 100 mM, pH 3.0), cells were incubated with fluorescently-labelled antibodies against EGFR, HER2 and HER3, and surface expression levels of each receptor were analyzed using flow cytometry. The normalized fluorescence intensity is shown as averages + SEM of four experiments. with different EGFR-specific TKIs (erlotinib, 50 nM; osimertinib, 50 nM, or afatinib, 10 nM), either alone or in combination with 2XmAbs (cetuximab and trastuzumab, 5 μg/ml each). (C) PC9 cells were seeded on coverslips and treated for 24 hours Cells were washed in acidic buffer, fixed in paraformaldehyde (4%) and incubated with specific primary antibodies, followed by an Alexa Fluor 555-conjugated secondary antibody (pseudo colored in green). DAPI (blue) was used to stain nuclei. Images were captured using a confocal microscope (40X magnification).
Evolutionary dynamics of MXEs in mammalian evolution.Figure 5  Figure 5 -Evolutionary dynamics of MXEs in mammalian evolution. Clusters of validated MXE were sorted by chromosome and chromosomal position. The names of the corresponding genes and the cluster-IDs are given in the outermost circle and the presence of the respective MXEs (MXE clusters) in other annotations and mammals is indicated by coloured bars. Because the generation of the set of MXE candidates was based on the GenBank annotation, we analysed the presence of the validated MXEs in complementary annotations. Thus, the outer circles show whether the validated MXEs are also annotated as MXEs in Ensembl and Aceview, and whether the validated MXEs are present at all as exons in the Ensembl annotation as indicated by the legend. The lengths of the bars denote the percentage of matching exons for each cluster. For comparison, we show the annotation as MXE in two different Ensembl versions highlighting the dynamics of exon annotations over time. The comparison of the GenBank with the latest Ensembl annotation (v. 37.75) showed considerably less exons annotated as MXEs (58) in Ensembl although these include six of the 'novel exons' (Appendix Fig. S1). The presence of the respective validated MXEs in each of the analysed 18 mammals is shown by coloured bars. The 18 mammals, their phylogenetic relation and the total numbers of MXEs shared with human are presented at the bottom. The innermost circle represents the number of exons within each cluster of MXEs.
Figure 4Scatter plots representing the association of CSF PGRN with different cognitive tests. Only the subjects of the Alzheimer's continuum group (n = 474) were included. In all tests studied, higher levels of CSF PGRN were associated with worse cognitive performance (namely, lower scores in ADNI-Mem, ADNI-EF and MMSE and higher scores in ADAS-Cog11, ADAS-Cog13 and CDR-SB). The analysis and the graphs are excluding PGRN outliers; including them rendered similar results (Appendix Table S6). Abbreviations: ADAS-Cog, Alzheimer's disease Assessment Scale - cognitive subscale; ADNI-Mem: ADNI memory composite score; ADNI-EF: ADNI executive function composite score; CDR-SB: clinical dementia rating Sum of Boxes; MMSE, Mini-Mental State Examination.
Figure 6(A) Domain organization of TAX1BP1 (NP_006015.4) and derived variants. Coiled-coil regions were defined by PCOILS using a 28 amino acid window and cutoff of 0.5. SKICH, SKIP carboxyl homology domain; CC, coiled-coil; Z1 and Z2, ubiquitin-binding zinc finger (UBZ) domains; N, NBR-interacting domain. (B) A summary of TAX1BP1 variants' activity in complementation and flux analyses. For complementation analysis, ATG7KO/TAX1BP1KO K562 cells expressing tf-NBR1 were electroporated with BFP-TAX1BP1 constructs and BFP-positive cells were analyzed for red:green ratio (for underlying data, see Appendix Figure S2A and B). For flux analysis, tf-TAX1BP1 variants were transfected into TAX1BP1KO K562 cells and assessed for red:green ratio by flow cytometry (for underlying data, see Appendix Figure S2C and D). In all experiments, median red:green ratios were used to compare populations. (C) HEK293T cells were transfected with either myc-TAX1BP1WT or myc-NBR1WT and indicated TagBFP-V5-TAX1BP1 variants. Extracts derived from transfected cells were immunoprecipitated (IP) with anti-TagBFP magnetic beads. Input and eluates were resolved by SDS-PAGE followed by immunoblotting (IB) with indicated antibodies. (D) HEK293T cells were transfected with myc-NBR1WT and indicated TagBFP-V5-TAX1BP1 variants. Extracts derived from transfected cells were immunoprecipitated (IP) with anti-TagBFP magnetic beads. Input and eluates were resolved by SDS-PAGE followed by immunoblotting (IB) with indicated antibodies.
Figure 4Representative Southern blots showing DSB repair products of indicated mutants in regular mating type switching (H-1400 assay). Viability of indicated mutants are shown. (mean ± SD; n = 3). Data information: Welch's unpaired t-test was used to determine the p-value Percentage of BIR product among all repair products by 6 hr are shown. (mean ± SD; n = 3). Data information: Welch's unpaired t-test was used to determine the p-value Graphs show analysis of repair efficiency compared to uncut parental band (left) (mean ± SD; n = 3) and repair efficiency compared to WT (right) at 6 hrs after DSB induction (right). Data information: Welch's unpaired t-test was used to determine the p-value Data information: χ2 test is used to determine the p-value
| Characterization of the inferred factor associated to the differentiation state of the cell of origin.Figure 3(a) Beeswarm plot with Factor 1 values for each sample with colors corresponding to three clusters found by 3-means clustering with low factor values (LZ), intermediate factor values (IZ) and high factor values (HZ) (b) Absolute loadings for the genes with the largest absolute weights in the mRNA data. Plus or minus symbols on the right indicate the sign of the loading. Genes highlighted in orange were previously described as prognostic markers in CLL and associated with IGHV status (Maloum et al, 2009; Morabito et al, 2015; Plesingerova et al, 2017; Trojani et al, 2012; Vasconcelos et al, 2005) (c) Heatmap of gene expression values for genes with the largest weights as in b (d) Absolute loadings of the drugs with the largest weights, annotated by target category (e) Drug response curves for two of the drugs, stratified by the clusters as in a
Stress inversely correlates with correction of GAA activity by rhGAA.Figure 3A, B, C. Correlations between the levels of single stress indicators and correction of GAA activity by rhGAA in 6 different PD fibroblasts. ROS production and lipid peroxidation inversely correlate with the GAA levels attained in cells after incubation with rhGAA for 4 hours. The analysis of correlation was calculated, and the coefficient of Pearson is indicated. D D, E. Spider web charts show the trend of the four variables in each of the 6 PD cell lines analyzed after 4 (D) and 24 hours (E) of incubation with rhGAA and support the inverse relationships between the stress levels and correction of GAA activity. Multiple correlation coefficient was calculated; the increase in oxidized glutathione (GSSG level), that is complementary to the reduction of reduced glutathione (GSH), is indicated. Data information: the scales used in D and E have been adjusted to the GAA activity at different time points.
FBXO2 targets GAS and is involved in xenophagy.Figure 3A, B Co-localization of GFP-FBXO2 and mCherry-LC3 in GAS-infected cells. HeLa cells transfected with the indicated EmGFP-FBXO (green) and mCherry-LC3 (magenta) were infected with WT GAS for 2 h; scale bar, 10 μm. Representative confocal images (A) and (B) percentages of FBXO-positive cells. C Enlarged image of GAS-associated FBXO2 Graphs show the signal intensities of EmGFP-FBXO2 and mCherry-LC3 measured along the arrows in the merged image. Green and red arrows indicate the signal peaks observed in EmGFP-FBXO2 and mCherry-LC3, respectively. White arrow indicates bacteria that are targeted by FBXO2 but not by LC3. D Time course of FBXO2 and LC3 recruitment during GAS infection. E, F Localization of EmGFP-FBXO2 in GAS-infected cells. HeLa cells transfected with GFP-FBXO2 (green) were infected with the indicated GAS strains for 2 or 4 h at an MOI of 100; scale bar, 10 μm. Representative confocal images at 4 h of WT GAS, ΔgacI, and ΔgacI::gacI (E) and (F) percentages of FBXO2‐positive cells.