EMBO/sd-character-level-ner huggingface dataset:
Figure 5(A) Western blot for RNA Pol II among proteins pulled down with anti-DDX5 (up) and for DDX5 among proteins pulled down with an anti-Pol II antibody (down). (B) Global increase in RNA Pol II signals after silencing of DDX5 (lv-shD) in HGC-27 cells. Average RNA Pol II ChIP-seq signal at all RNA Pol II peak regions. Upper subpanel: negative control, Lv-NC; lower subpanel: silencing of DDX5, lv-shD. (C) Reads per million mapped reads (RPM) of RNA Pol II ChIP-seq signals of genes in human genome. (D) KEGG Pathway analyses of over-lapped Differential expressed genes (DEGs) in both lncPSCA-overexpression cells and the DDX5-konckdown cells identified multiple pathways involved in cancer biology, with the P53 and MAPK signaling pathways as two of the most markedly changed pathways. (E) RNA Pol II ChIPseq and RNAseq signals of PMAIP1, CDKN1A, SESN2 and SESN3 in HGC-27 cells. Red bars represent the RNA Pol II ChIPseq signal. Orange or blue bars represent the RNAseq signals of HGC-27 cells overexpressing lncPSCA (lncP) or with silenced DDX5 (shD), respectively. (F) Validation of candidate downstream genes of the lncPSCA-DDX5 axis identified through the integrated analyses. qRT-PCR was performed for PMAIP1, CDKN1A and SESN2 genes upon overexpression of lncPSCA (lncP), silencing of DDX5 (shD) or lncPSCA konckout. Error bars indicate the SEM. Data show one representative example of three biological replicates. (G) ChIP-qPCR assays was performed for PMAIP1, CDKN1A and SESN2 genes and demonstrated that significantly decreased RNA Poll II enrichment around TSS of PMAIP1, CDKN1A and SESN2 in various stable lncPSCA konckout GC cell lines. Left subpanel: RNA Pol II ChIP-qPCR fragments a, b and c on PMAIP1, CDKN1A and SESN2 genes; middle and right subpanels: RNA Pol II ChIP-qPCR results of PMAIP1, CDKN1A and SESN2 genes in MGC80-3 (middle) and HGC-27 cells (right). Data show one representative example of three biological replicates. (H) Correlations between lncPSCA levels and the mRNA levels of the P53 signaling PMAIP1, CDKN1A and SESN2 genes in gastric cancer tissues Discovery cohort (n = 96) and Validation cohort (n = 30). RNA levels were determined by qRT-PCR relative to GAPDH. The r values and P values are from Pearson's correlation analysis.
Figure 3A. Averaged ΔCm traces induced by 200-ms depolarization in the presence and absence of dynasore. Endocytic inhibition by dynasore (Dyna) was estimated by comparison of Cm traces recorded during 1-3 min (KD) and 5-10 min (KD + Dyna and Ctrl + Dyna) after whole-cell dialysis. B, C. Endo-5s and Cm jumps recorded as in (A). D. Averaged ΔCm traces induced by 200-ms depolarization in the presence and absence of dynole-34-2TM (Dynole). Cm traces and endocytic rate were measured as in (A) except that 10 μM dynole-34-2TM with 0.1% DMSO was dialyzed into patched cells. E, F. Endo-5s and Cm jumps as in (D). G, H. Averaged ∆Cm traces and Endo-5s recorded from KD neurons under control conditions (0.1 % DMSO). I. KCl-evoked FM 1-43 uptake in DRG neurons after 10-min pre-incubation with 0.1% DMSO (control) or with 100 μM dynasore.
Figure 3(A) Analysis of DNA content by flow cytometry of G1 phase synchronized wild type, rad52∆, rad51∆, mus81∆ and pol32∆ cells and further released into S phase. Cells were synchronized in G1 with α -factor, treated with DMSO or 100 µM CPT, let in G1 for 1 h, and released into S phase. Three biological replicates have been performed. (B) (C) Analysis of DNA content by flow cytometry of G1 phase synchronized wild type, rad3-102, rad3-102 rad51∆, rad3-102 mus81 and rad3-102 mus81-dd cells and further released into S phase. Cells were synchronized in G1 with α-factor, untreated or irradiated with 20 J/m2 UV-C, let in G1 for 2h, and released into S phase. Three biological replicates have been performed.
Figure 1Phenotypes of 4-d-old Col, two cbf1 mutants (cbf1-1 and cbf1-2) and two CBF1-OE lines (CBF1-myc and CBF1-flag) grown at 22°C in darkness (D) or continuous W, R, FR, and B light. Scale bar = 1 mm.   Hypocotyl lengths of Col, two cbf1 mutants and two CBF1-OE lines grown at 22°C in D or continuous W, R, FR, and B light. Error bars represent SD from 20 seedlings. *P < 0.05, **P < 0.01 and ***P < 0.001 (two-tailed t-test) for the indicated genotype compared with Col. NS, not significant.
Poliovirus entry, translation, and RNA replication are unaffected by treatment with inhibitors of vesicle acidification.Figure 5(A) H1-HeLa cells were infected with PV at an MOI of 50 pfu/cell. Cells were pulsed at the indicated h.p.i with 35S-labeled methionine for 1 h then lysed. Lysates were run on SDS-PAGE. Expected viral proteins are labeled according to recognized banding patterns. (B) Triplicate plates of H1-Hela cells were infected with PV at an MOI of 0.1 pfu/cell, virus RNA and host GAPDH RNA were measured by qRT-PCR. Virus RNA levels were normalized to GAPDH levels using the delta-Ct method. NH4Cl treatment was as described in Figure 4, and Guanidine HCl (2 mM) was added to the media at the time of infection. The data shown are pooled from three replicate experiments, and the titer of cell-associated virus collected at 6h.p.i. from each replicate was determined by plaque assay. (C) Triplicate plates of 293T cells were treated with 20 mM 3-MA for 2 hours prior to infection, and kept under treatment throughout infection. PV infections were done at an MOI of 0.1 pfu/cell. RNA levels and virus titers were analyzed as in (B). ** p<0.01, *** p<0.0001.
Figure 2A, overview of the NodLabel procedure, using a viSNE layout of CyTOF single-cell events. Left side, point color indicates channel values for four example channels. Right side, traditional hierarchical gating was used on a subset of samples to identify 8 major immune compartments, which was then used to train a logistic regression classifier (Nod) that applied labels for canonical leukocyte phenotypes to all samples (NodLabel). B, heatmap of log10 scaled PBMC community frequencies for all samples (n = 42 patients × 2 timepoints = 84 samples). Clinical variables are depicted for all samples across the top of the heatmap; convalescent post-symptom onset anti-CHIKV antibody titer and viral titer (which was measured during the acute phase) are both in units of log10 dilutions. Hierarchical clustering (using complete linkage) was applied to both samples (X axis) and communities (Y axis). Four major clusters of communities and two major clusters of samples (largely separating acute and convalescent samples) are highlighted. C, fold changes in log10 frequencies for PBMC communities between acute and convalescent phase samples, filtered to a significance threshold of FDR < 0.05 (moderated paired t-test, mixed effects model). Error bars represent the 95% confidence interval. The acute phase frequency for each community is depicted with the purple heatmap. *, FDR-adjusted P (FDR P) < 0.05; **, FDR P < 0.01, ***, FDR P < 0.001.
Fig.Figure 3Total lipid levels in WT, pldα6 and COM without and with 10 μM GA3. Leaf samples (15 seedling each) from 4-leaf stage rice (Dongjin background) were collected and lipids were extracted and profiled using ESI-tandem mass spectrometry. Values are means ± SD (n = 3 biological replicates)). MGDG, monogalactosyldiacylglycerol; DGDG, digalactosyldiacylglycerol; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PS, phosphatidylserine; PA, phosphatidic acid. Phospholipid species in WT, pldα6 and COM. Leaf samples (15 seedling each) from 4-leaf stage rice (Dongjin background) were collected and the different phospholipid species including carbon number and double bond number were determined. Values are means ± SD (n = 3 biological replicates). GA3 was dissolved in ethanol and seedlings treated with the same ethanol concentration were used as control.
Figure 7Schematic representation of the MeCP2 protein, with the methyl binding domain (MBD) highlighted in red and the transcriptional repression domain (TRD) in blue. Patients' mutations investigated in this study are indicated. Representative immunostaining of primary cilia and MeCP2 in cultured human fibroblasts from healthy controls (CTRL, n=3) and RTT patients. Fibroblasts were starved for 24 h and then stained for acetylated α-tubulin (green), MeCP2 (red) and DAPI (blue). Scale bar 50 µm. Histograms indicate (mean ± S.E.) the percentage of MeCP2 positive cells Histograms indicate (mean ± S.E.) the percentage of ciliated cells in control and RTT fibroblasts The effect of tubacin (TUB) treatment (250 nM, 24 h) on primary cilium length of controls (CTRL) and RTT fibroblasts is reported. The graph indicates the mean ± S.E of the cilium length analyzed in untreated (n=130 CTRL; n=73 705delG; n=57 Q244X; n=68 R255X) and treated cells (n=25 CTRL; n=26 705delG; n=26 Q244X; n=49 R255X) (***p<0.001 vs untreated CTRL, §p<0.05 vs corresponding mutated untreated fibroblasts by two-way ANOVA, followed by Bonferroni post hoc test). Statistical analysis reported a significant treatment effect (F (1,429) = 26.56; p<0.0001) and a significant genotype (F(3,429) = 42.85; p<0.001).
Figure 2 (A) An experimental tracing model of CD45+ leukocytes in "KikGR" mice using a photoconvertion system. Colour conversion from KikGR green to KikGR red occurred in liver cells upon violet light irradiation. In the tumour-bearing- or tumour-conditioned media (TCM)-stimulated- KikGR mice, and the cells later moved into the lungs. The KikGR red cells, obtained from TCM-stimulated- liver and lungs, were isolated by a cell sorter and CD45 microbeads, and these purified cells were used for microarray screening  (B) KikGR red cells were detected in the TCM-stimulated- liver and lungs after liver exposure to violet light (arrow). Images taken from animals with no light exposure were also shown (scale bar, 100 μm)  (C) Flow cytometric quantifications of photoconverted HepELs in TCM (3 times)-stimulated KikGR mouseliver and lungs. Cells were isolated 72 h after photoconversion. Ratio was calculated as the number of photoconverted cells (KikGR redin comparison with the number of liver or lung cells pre-sorted with CD45-beads. Shown are averages (N = 5) with SEM and Welch"s t-test  (D) Surface marker analyses of photoconverted KikGR cells. Vertical axes represent ratio of each marker+ cell/photoconverted KikGR cell. Shown are averages (conCM, control: N = 4, TCM: N = 9) with SEM and Welch"s t-test  (E) Representative immunostaining images of FX expression in NK1.1+, CD11c+, B220+ and CD4+ cells in tumour-bearing lungs (scale bar, 10 μm)
Figure 2(A) The ROD-A and ROD-B protomers are related by 2-fold symmetry and interact through two main regions positioned between residues 485-690 and 1790-2125. (B) A particular prominent interaction of ROD-A and ROD-B consists in the insertion of the 655-680 loop of one protomer into a cradle formed by the bending C-terminal region of the second protomer. (C) Zwilch interacts very prominently with only one of the two ROD protomers, sandwiched between the N-terminal β-propeller and residue 850. A few interactions also link Zwilch to the C-terminal region of the second protomer. (D) A rotated view shows that ZW10 forms a highly bent, U-shaped complex with a relatively small inter-protomer interface. (E) The 2-fold axis of the complex (shown in Figure 1B) crosses the interface between ZW10-A and ZW10-B. (F) Molecular details of the interface between ZW10-A and ZW10-B with side chains of residues involved.
Figure 2(A - G) Changes in plasma level of key metabolites compared to time baseline (solid line) based on untargeted metabolomics measurement in metabolic cofactor supplementation study. The upper and lower box limits represent the 25% quantiles. The upper and lower error bars correspond to 75% quantiles. * Denotes significance (one-way ANOVA; FDR <0 .05). (H) Spearman correlation (visualized by Circlize) between plasma levels of supplemented metabolic cofactors and key metabolites associated with high liver fat and insulin resistance. * Denotes significance ( FDR <0 .05).
Figure 6(A) Images of a cortical slice before (t = 0) and after (t = 15.6 s) pressure ejection of a high KCl pulse that elicits a CSD (top panels), showing that the propagating CSD is associated with a change in light transmittance. Scale bar: 500 µm. The traces below show representative changes in intrinsic optical signal (IOS) relative to background measured in a WT and a KI cortical slice during CSD propagation at increasing times and distances from the KCl puff, as indicated in color code in the right image on the top. The velocity of CSD propagation, obtained from the rate of horizontal spread of the change in IOS, in these two representative WT and KI slices is 3.11 and 4.14 mm/min, respectively.(B) Stimulation threshold for CSD induction (CSD threshold) and rate of CSD propagation (CSD velocity) in WT (n = 24; N=3) and KI (n = 27; N=8) cortical slices from P22-23 mice. CSD threshold is expressed as duration of the first KCl pulse eliciting a CSD. CSD threshold is 28% lower (Mann Whitney U test, P < 0.0001) and CSD velocity 21% higher (unpaired t-test: P< 0.0001) in KI compared to WT mice.
a, Apg7 and Apg3 are necessary for attachment of Apg8 to PE.figf4a, Apg7 and Apg3 are necessary for attachment of Apg8 to PE. Δapg cell lysates were subjected to SDS-PAGE containing 6 M urea, and immunoblotted with anti-Apg8 antibody. b, Autophagic activity in apg3 mutants. Wild-type, Δapg3 and apg3C243A cells were grown in rich medium (open bar) and subjected to nitrogen starvation for 4 h (filled bar). The autophagic activity of each cell was assessed by measuring the alkaline phosphatase activity. The apg3C243A mutant showed defective autophagy.
Re-localization of the RNA decapping machinery upon PNRC1 expression A.Figure 4A. Confocal microscopy images of RFP or RFP-PNRC1-expressing cells stained for DCP1α, DDX6 and LSM1. RFP-PNRC1-transfected cells are indicated with arrowheads. Scale bar: 10µm. B. Quantification of cells classified according to the P-body localization of the three stained proteins. The average ± SD of 3 independent experiments is reported. C. Nucleolar fractionation performed on LacZ or PNRC1-expressing HeLa cells. Total lysates, cytoplasmic (Cyto), nucleoplasmic (Nucl) and nucleolar (No) fractions were collected. UBF1, RNA PolII and MEK2 were used as markers for the nucleolar, non-nucleolar and cytoplasmic fractions, respectively. The electrophoretic mobility of proteins in the nucleoplasmic lanes is slightly diminished due to nuclear lysis buffer composition. D. Densitometric quantification of DCP1α nucleolar pool obtained from the western blot shown in panel (C) and normalized upon the amount of nucleolar UBF1 and the levels of DCP1α in the input fraction. E. Confocal microscopy images of HeLa cells silenced for the endogenous DCP1α and expressing a shRNA-resistant GFP-DCP1α in combination with RFP or RFP-PNRC1 transgenes (green: GFP, red: RFP, blue: DAPI, scale bar: 5µm).
a) H4 cells expressing mCherry–GFP–LC3 were treated overnight with the indicated compounds, fixed, stained with Hoechst 33342 and imaged by automated acquisition.figf3(a) H4 cells expressing mCherry-GFP-LC3 were treated overnight with the indicated compounds, fixed, stained with Hoechst 33342 and imaged by automated acquisition. Representative images of an overlay of GFP (green), mCherry (red) and Hoechst (blue) are shown with a scale bar equivalent to 10 μm. Bars represent the mean GFP- and mCherry-positive LC3 puncta per cell and data points represent values from 18 imaged fields in two wells from one experiment. b) HeLa cells expressing GFP-Parkin were treated with PIK-III for 12 h followed by the addition of CCCP for 12 h, fixed, stained for endogenous Tom20 and imaged. Representative images of an overlay of Tom20 (red) and Hoechst (blue) are shown with a scale bar equivalent to 50 μm. Bars represent the mean cellular Tom20 staining intensity per cell and data points represent values from four wells from one experiment. (c) H4 cells expressing GFP-p62 were treated overnight with the indicated compounds, fixed, stained with Hoechst 33342 and imaged. Representative images of an overlay of GFP (green) and Hoechst (blue) are shown with a scale bar equivalent to 10 μm. Bars represent the mean GFP-positive puncta area per cell and data points represent values from 18 imaged fields in 2 wells from one experiment. (d) Steady-state levels of autophagy markers visualized by western blotting in H4 GFP-p62 cells treated overnight with 0.5 μM AZD8055 or 5 μM PIK-III. (e) Steady-state levels of p62, LC3 and GAPDH visualized by western blotting in PSN-1 cells treated for 48 h with the indicated doses of PIK-III. (f) Steady-state levels of p62, LC3 and GAPDH visualized by western blotting in Panc10.05 cells treated for 48 h with the indicated doses of PIK-III. (g) RKO cells expressing inducible HA-ATG4B-C74A were treated with doxycycline (DOX induction) for five days and then incubated in DOX-free medium for 24 h (DOX washout). Bafilomycin A1 was added with or without PIK-III at the beginning of the washout period (lanes 5 and 6). Steady-state levels of ATG4B, LC3 and GAPDH were visualized by western blotting. Uncropped images of blots are shown in Supplementary Fig. 7.
Apoptosis inhibition cannot restore hematopoiesis in the absence of CHK1.Figure 7Representative dot-plots and quantification of E13.5 fetal liver LSKhi/LSKlow cell phenotypes observed in embryos of the indicated genotypes. N=21 for Chk1fl/+, N=5 for Chk1fl/- Vav-Cre, N=16 for Chk1fl/+ Vav-BCL2, N=5 for Chk1fl/- Vav-Cre Vav-BCL2, N=2 for p53-/- Chk1fl/+ and N=4 for p53-/- Chk1fl/- Vav-Cre. Flow cytometry-based analysis of LSK cells stained with antibodies specific for CD34 and Flt3, to discriminate LT- and ST-HSC from MPP within the LSK subset in fetal livers of embryos of the indicated genotypes. Left: N=25 for Chk1fl/+, N=7 for Chk1fl/+ Vav-Cre and N=7 for Chk1fl/- Vav-Cre. Right: N=16 for Chk1fl/+ Vav-BCL2, N=6 for Chk1fl/+ Vav-Cre Vav-BCL2 and N=5 for Chk1fl/- Vav-Cre Vav-BCL2. Analysis of the colony formation potential of E14.5 total fetal liver cells of the indicated genotypes in methylcellulose. N=3 for controls (pooled; 1 Chk1fl/+, 2 Chk1fl/+ Vav-Cre), N=3 for Chk1fl/- Vav-Cre and N=3 for Chk1fl/- Vav-Cre Vav-BCL2. Western blot analysis of fetal liver cells of the indicated genotypes (each lane represents an embryo) at E14.5 using the indicated antibodies.
Binding of caldendrin and calmodulin to a 49 amino-acid fragment of the myosin Va protein including the first IQ motif is mutually exclusive.Figure 2A Schematic of caldendrin and calmodulin competition assay. A construct containing the GFP-tagged caldendrin binding peptide (aa 742 - 791) of myoVa (GFP-myoVa IQ1) was purified via GFP-trap beads from HEK293T cell lysate enriched with bacterially produced calmodulin (CaM). The CaM-associated construct (Input) was then incubated with lysate from HEK293T cells expressing either cald-tagRFP or tagRFP only. B Western blot analysis of competition co-immunoprecipitation experiment in HEK293T cells. In the presence of Ca2+, caldendrin binds strongly to the IQ1 fragment (upper arrow), while tagRFP by itself does not bind (lower arrow). Detection using a calmodulin antibody indicated that Ca2+-dependent binding of caldendrin reduced the amount of CaM bound to the IQ1 motif relative to the control (tagRFP only). MW = molecular weight marker. C Quantification of the normalized relative intensity of cald-tagRFP (left) and CaM bands (right) in western blot analysis of three independent experiments as shown in B. Shown is mean ± SEM. Upper: Ca2+ greatly increases cald-tagRFP binding to GFP-myoVa-IQ1. Lower: When Ca2+ is available, the simultaneous presence of cald-tagRFP leads to a reduced binding of CaM compared to the control (tagRFP). D D CD spectroscopy reveals distinct secondary structure elements of the myoVa IQ1-containing peptide in water and ammonium acetate solution. Far-UV CD spectra of the myosin peptide acquired either in ultrapure water (black) or in ammonium acetate buffer (red; 0.5nm step size, 3sec/point, 25μs sample period, 3 repeats each, T = 20.0 ± 0.3 °C). E Pie chart indicating structure elements of the myoVa IQ1-containing peptide in ammonium acetate solution calculated from spectra shown in (D). F Native MS analysis of ion saturation for CaM. Ca2+ carried along from purification is detected on CaM in native MS. Without further supplementation with ions, intact CaM shows primarily its high affinity calcium binding sites occupied (left), while in the same analysis myoVa peptide selectively and preferentially binds only to the fully Ca2+-saturated CaM species (right). Additional unassigned peaks represent unspecific adducts of Na+ and Mg2+ ions. G Native MS analysis of ion saturation for caldendrin. Supplemented by an excess of 200 µM Ca2+ and 100 µM Mg2+, caldendrin displays myoVa peptide binding to both fully Ca2+-saturated and 2 Ca2+-bound species (right), which are also both detectable for the intact caldendrin protein in the same analysis (left). H No ternary complex is observed when CaM and caldendrin are mixed together with excess myoVa peptide in native MS. The individual proteins bind individually to myoVa peptide indicating competition for the same or closely located epitope. Fraction of caldendrin degrades into a 28kDa fragment, which has lost it affinity towards myoVa peptide almost completely.
Figure 9Once internalized in donor cells (A) recombinant humanα-synucleinfibrils are mainly targeted to lysosomalvesicles (and found to a lesser extend in early and recycling endosomes). Lysosomalvesicles containing α-synucleinfibrils transfer from donor to (B) acceptor cells inside TNTs. Once in the acceptor cells, α-synucleinfibrils induce the formation of de novo α-synucleinaggregates (seeding). We propose that (A) α-synucleinfibrils accumulated inside lysosomes would impair their function leading to cellular stress (e.g., oxidative stress). In turn this would induce TNTs formation allowing spread to (B) healthy cells in order to lower the burden of α-synucleinfibrils inside lysosomes. α-synucleinfibrils would then escape lysosomes possibly by inducing LMP. Once free in the cytoplasm they would recruit soluble α-synuclein and induce de novo formation of α-synucleinaggregates. As a consequence α-synucleinfibrils would propagate from stressed to unstressed cells through TNTs contributing to the intercellular spreading of the pathology. Because endogenous α-synuclein when aggregated is targeted to lysosomesin vivo, we propose a similar mechanism occurring for endogenously formed aggregates (C).
Figure 5(A) Mean plasma concentration vs time profiles after single dose. (B) Mean plasma concentration profiles for 91 days of dosing and post-dose concentrations up to day 121. (C) Time vs CSF concentration profiles after single dose of CNP520 (Mean ± SEM, n = 6-8). (D) Dose-CSF concentration profiles after 3 months of dosing (Mean ± SEM, n = 22-24).
Figure 3Induction of chr XV loss in three independent diploid co/co clones containing a conditionally stable chr XV centromere (left panel), suppresses choline auxotrophy. After culture on solid YPGal, cell patches were replica-plated on SD-plates with or without choline, uracil and 5-FOA, as indicated (right panel), and incubated at 30 oC for 4 d. Growth of ten-fold serial diluted engineered co S(2n-1) and evolved co S#3 and S#4 on C+/- I+/- SD at 30 oC for 4 d. Choline supplementation induces endoduplication of chr XV in aneuploid cho2opi3 suppressors. Growth phenotype on SD C- and C+ (4 d at 30 oC) and absolute copy number of chr I, IV, VI, IX and XV as determined by qPCR and FACS after culturing co S#4 in SD C+ for the number of days indicated with daily passage to fresh medium at OD600 0.05. Representative data are shown with chromosome copy number presented as mean value from 2 assays using primers complementary to non-coding regions on the left and right arm of each chr, respectively, with the individual values indicated. Serial dilutions of the strains indicated were spotted on SD C+/- I+/- and incubated at 30 oC for 4 d.