EMBO/sd-character-level-ner huggingface dataset:
(D-F) HCT 116 cells were left transfected with a GFP-LC3 plasmid, cultured in complete medium for 24 h, and treated with either vehicle (Co), 100-µM resveratrol, or 100-µM spermidine in the presence or absence of the SIRT1 inhibitor EX527 for 4 h. (D) Representative images. (E) Quantitative data. (B and E) Bars depict the percentages of cells showing accumulation of GFP-LC3 in puncta (GFP-LC3vac; means ± SEM; n = 3; *, P < 0.05). (F) Representative immunoblots showing LC3 lipidation in HCT 116 cells treated with 100-µM spermidine in the presence or absence of EX527. GAPDH, glyceraldehyde 3-phosphate dehydrogenase.
A. Host C57Bl/6 mice were injected with CD45.1+ splenocytes, isolated from SWHEL x Cyp1a1Cre R26R eYFP mice together with SRBC-HEL or SBRC-mock. The transferred mice were treated with 3-MC or vehicle. Readout at d7 post-challenge was eYFP expression in transferred CD45.1+ cells.
(D-F) Flag‐ or HA‐tagged proteins were expressed in HeLa cells, captured on Flag‐ or HA‐beads and subjected to immunoblotting as indicated. In all experiments, the inputs represent 2.5% of the total cell lysate.
GFP-Parkin stably expressing HeLa cells were treated and then subjected to PLA using antibodies against FLAG and PGAM5. During Stx17 knockdown, cells were transfected with a plasmid encoding FLAG-FUNDC1. Scale bar, 5 μm. Values are means ± SEM (n = 3). *P<0.05 and **P<0.01 as compared with Mock (+CCCP) by paired Student's t-test.
(C) Quantification of the number of GSCs per non-tumorous germarium, and of germaria with GSC tumors, in the indicated genotypes. The number of scored germaria (n) is indicated. The two-tailed Student's t test and the χ2 test were used in the left and right panels, respectively. *** p-value <0.001, ** p-value <0.01, * p-value <0.05.
F, Co-transplanted P3-4 Crx::Cre and P3-5 ROSAmT/mG donor photoreceptors into C57BL/6J recipient retinas show Cre reporter gene induction in donor cells located in the SRS 14 days post-transplantation.
a, Polychromasia (Wright-Giemsa stain, indicated by arrows) and increased reticulocytes (brilliant cresyl blue stain) revealed by staining blood smears from 6-week-old wild-type (WT) or Nix-/- mice (scale bar, 20 µm).
(B) 10.1 fibroblasts were mock infected or infected with wt MCMV or ΔM45 at an MOI of 5. Cells were left untreated or treated 30 min after infection with 10 mM NH4Cl to block lysosomal degradation of LC3-II. Cells were harvested at the indicated time points, and LC3-II levels in cell lysates were analyzed by immunoblotting using an LC3-II-specific antibody. LC3-II levels were quantified by densitometric analysis and normalized using the corresponding actin levels. Fold increases are shown relative to mock-infected cells.
While no changes were seen in morphological parameters of peri-plaque astrocytes, there was a significant increase in the process length of near-plaque microglia, indicating higher microglial complexity (Mann-Whitney test for all comparisons; APP/PS1-Stat3WT, n = 12 (6 female and 6 male) mice; APP/PS1-Stat3KO, n = 12 (7 female and 5 male) mice; age, 8 months).
(F) Dot plot showing over-represented Gene Ontology gene sets among genes upregulated in wildtype compared to c-Maf knocked-down ILC2s. The color scale depicts the adjusted p-value, while the size of the dots and x-axis depict the absolute number or the proportion of upregulated genes included in each gene set, respectively.
(i) HeLa cells were transfected for 2 days with the indicated siRNA or treated with 25 μM forskolin for 0.5 h and lysed. Equal amounts (50 μg) of proteins were separated by SDS-PAGE and immunoblotted using the indicated antibodies. Uncropped images of all blots in this figure are shown in Supplementary Fig. S8.
(F) Isothermal titration calorimetry (ITC) was used to test the binding affinity of αKG (1 mM) to recombinant KDM4A (0.05 mM) or KDM6A (0.05 mM) (left), and then statistical analysis was performed (right). The data are represented as the means ± SEM of three independent experiments. Unpaired t-test was used (N.S.: not significant).
C. UMAP (Uniform Manifold Approximation and Projection) dimension reduction representative of GATA6 regulon expression in MM011, MM029, MM047, MM074 and MM099 from Wouters dataset UMAP is colored according to the continuous GATA6 AUCell values (from 0 to 0.2).
At snRNA loci, Integrator generates snRNA 3′ ends leading to Pol II termination. ints-11 knockdown results in readthrough past termination sites and polyadenylation of snRNA transcripts. At motif-dependent piRNA loci, Pol II pauses ~28 nt and ~48 nt downstream of piRNA TSSs. ~28 nt short capped RNAs may be generated via direct dissociation of Pol II from chromatin at the ~28 nt pause site. When Pol II transcribes past the ~48 nt pause site, Integrator acts to cleave nascent precursors approximately when Pol II is at +58 from piRNA TSSs, generating ~38 nt short capped RNAs and ~20 nt degradation fragments. ints-11 knockdown does not lead to Pol II readthrough, suggesting that additional mechanisms prevent Pol II elongation at piRNA loci.
(B) Fresh BM mononuclear cells collected from AML patient were treated for up to 6 days. Proliferation was assessed at day 3 in parallel (section ii).
C Graph showing the percentages of MitoSOX red-positive Tsc2-deficient 105K cells treated for 24 hours with DMSO or drugs in vitro with 10% FBS complete medium (except for the condition without L-histidine). Clorgyline 1 μM, loratadine 100 nM, rasagiline 1 μM, and rapamycin 20 nM. Differences relative to rapamycin alone were determined by a two-sided t-test (DMSO P = 6x10-5, clorgyline P = 2x10-5, loratadine P = 6x10-4, rasagiline P = 4x10-5; combination with clorgyline P = 1x10-4, loratadine P = 3x10-5, and rasagiline P = 9x10-4; replicates/condition n = 5; assays n = 2). The bars indicate mean ± SD.
E, F. The relative amounts of indicated metabolites were quantified by ELISA assays in HepG2 cells, HAT1 KO HepG2 cells, and HAT1 KO HepG2 cells reconstituted with either wildtype HAT1 or mutant HAT1 (T188A). N = 3 biological replicates. Data are presented as mean ± SD. Student's t-test, **P < 0.01; ns, no significance.
(A) Male wt and PIDDosome-deficient mice were injected with 25 mg/kg DEN at the age of 15 days and their livers were analyzed 10 months later.
C) GSH/GSSG ratio quantification in HC and ACM C-MSC cultured in GM (n=8 biological replicates). Data information: mean ± SEM. * p<0.05, ** p<0.01.
D Codons translated by Q-tRNA are depleted in down-regulated proteins and increased in up-regulated proteins in both forward and reverse SILAC.
D. The effect of overexpression and interference of LncBMP4 on the proliferation of PGCs was detected by EDU proliferation assay. Scale bar: 100 µm (n = 3 independent experiments).
B N1E-115 cells stably expressing mSt-INPP5E (WT, D477N, ∆CAAX, or 295-644) treated with siControl or siINPP5E were cultured in growth medium with or without 125 nM Baf.A1 for 2 h, and then analyzed by immunoblot using anti-LC3 and anti-GAPDH antibodies. The mSt-INPP5Es used in this study were resistant to mouse siINPP5E because target sequence of the siRNA is different from the human correspondent sequence.C Quantitation of protein signal intensities from immunoblots in B, showing differences in LC3-II levels in the presence and absence of Baf.A1 following normalization to the control proteinGAPDH. Results represent means ± s.d. of three independent experiments. **, P < 0.01; *, P < 0.05.
(C) Cells as in (A) expressing GFP‐Atg8 were grown to mid log phase with starvation for 4 h in SD‐N medium. The processing of GFP‐Atg8 was analysed and quantified as in Figure 1I.
qRT-PCR detection of IFNB1 mRNA in scrambled (Scramble) or STING shRNA stably transfected (STING KD) THP-1 cells stimulated with ec-di-AMP (5 μg/ml) and ecGAMP (5 μg/ml) or transfected with ISD or poly(I:C).
(c) Locally weighted scatterplot smoothing fit of CG, CHG and CHH methylation levels in stem cells and non-stem cells plotted on TE length. + = stem cells; - = non-stem cells, E = nuclei from embryos, D7/14/35 = nuclei from 7/14/35 day-old plants, S7/14 = nuclei from 7/14 d-old above-ground seedlings.
E Western blot analysis of USP33 in HT1080 cells treated with NMS873 (10 μM) and additional NaCl (+34 mM) for 12 hrs. Data information: Data are representative of at least two biological replicates.
phosphorylation status of proteins involved in Ca2+ signaling in human, rat and mouse models of exercise.
Left panel: flag-tagged full-length HDAC1 was overexpressed with myc-tagged TDP-43 in HEK-293T cells; the cell lysates were immunoprecipitated for flag and immunoblotted for TDP-43 and flag. Right panel: myc-tagged TDP-43 was overexpressed with flag-tagged full-length HDAC1 in HEK-293T cells; the cell lysates were immunoprecipitated for myc and immunoblotted for flag and TDP-43.
(C) Reciprocal IP of (B). YFP-hSgo1 expression construct was transfected into cells stably expressing FLAG-B56α WT, R222E and 5A, followed by YFP IP and immunoblotting of indicated proteins. Representative blots are shown (top). B56α signals were normalized to YFP and plotted (bottom). Error bars represent SD (n=4).
D Western-blot analyses of total 4EBP1 protein and its phosphorylated form levels of RKO and IMT1-resistant RKO cells, two representative experiments are shown (Repl. 1 and 2). GAPDH is showed as loading control.
RT-qPCR analysis of Gldc, Cbs and Tdh expression in R406- and shSyk-treated cells (E) and FK506-, shPpp3ca- and shNfatc1-treated cells (F) on d8. n = 3.
Representative images (G) and cfu quantification (H) of bacteria bound to HeLa cells pre-treated or not with arsenite followed by incubation with Salmonella mutant strains ΔfliC, ΔfliC/pFliC or ΔflhC for 10 min
Effect of HK2-targeting on in vivo neoplastic growth. Intratumor administration (5 injections of 2 nmol peptide every 12 h) of either cl-HK2pep or HK2pep (F; CNT n=4; cl-HK2pep n=5; HK2pep n=5 mice) in Balb/c female mice. Data information: Throughout the Figure, cl-SCRpep or SCRpep are used as peptide negative control. In F, mean tumor volume±SD is reported; Student's t test ***p<0.001
(b) Filling the defects with inverted cone-shaped lipids inhibits lipidation. In vitro coupling reactions of GL1 were run on sonicated liposomes containing 30 mol% DOPE (2 mM total lipid) as in Fig. 1. To determine whether inverted cones influenced the reaction, increasing amounts of stearoyl-CoA were added immediately before initiating the reaction with ATP. Quantification is of n = 3 samples; error bars represent standard deviation. P values represent a comparison with samples without stearoyl-CoA. **P 0.1; *P 0.05.
Z-projection of HeLa cells expressing GFP-centrin1 pre-treated with DMSO or 0.2mM CK666 during prometaphase arrest and forced mitotic exit and stained with phalloidin for F-actin.
(C) Time-lapse 3D-SIM imaging of sheath dynamics (TssB1-sfGFP) of B. thailandensis E264. (D) Time-lapse 3D-SIM imaging of sheath dynamics (TssB1-sfGFP) of B. thailandensis E264 in the absence of tagM1. Data information: Yellow arrows indicate examples of contact-dependent sheath foci or paired sheath assemblies. Scale bars and time intervals are indicated.
G. mRNA levels of CTGF measured by real-time PCR in IGR37 treated with DMSO or NB-360 (T-test analysis, * = p-value<0.05, N=3 biological replicates, data are mean ±SD).
(I) Model for gene regulation by chromatin-associated IκBα. In brief, dynamic dissociation of IκBα from the chromatin at specific genetic loci promotes transcription of genes involved in stem cell maturation or differentiation (upper panel). Absence of dynamic binding (middle panel) or cells IκBα deficient (lower panels) fail to activate IκBα-dependent transcription thus imposing a differentiation/maturation blockage.
(F) RT-qPCR analysis of indicated genes was performed using RNA extracted from the duodenum of 5 and 8 weeks old control villin-Cre (n = 6) or villin-Cre x floxed IκBα mice (n = 6) both male and female. Expression is shown as fold change between littermates, paired t-test. SD shown. * p < 0.05 ** = P < 0.01.
(C) Relative proportion of DS9 cells expressing aggregates of Tau RD-YFP over a 50-hour period monitored by IncuCyte. DS9 cells were left untreated, the graph represents means of 3 independent experiments ±SD.
(C) dSTORM super-resolution analysis of the distal appendage markers FBF1 and ODF2 in control and myosin VI-depleted cells. To emphasise the symmetry of the structures, the signals from all nine appendages were averaged (bottom). Representative images are shown; scale bar, 200 nm.
(B) The central carbon metabolism pathways are illustrated along with the nodes branching out into amino acid precursor synthesis (green arrows). Glucose to acetate diauxie requires switching from the pathways facilitating glucose consumption (represented in blue) to those responsible for acetate consumption (represented in red). More details in Fig. EV1B.
(C) Immunoblot analysis of fibronectin, hepsin, and β-tubulin (loading control) in cell lysates from MCF10A-pIND20-HPN cells with (DOX+) or without (DOX-) hepsin overexpression. The graph shows the quantification of fibronectin levels.
F Cellular component separation assay showing that S1P was enriched in mitochondria. Biochemical fractionation of the whole cell lysate (WCL), cytosol (Cyto, tubulin), mitochondria (Mito, COX IV), lysosomes (Lyso, LAMP1), Golgi apparatus (Golgi, GM130), endoplasmic reticulum (ER, ERp72), and nucleus (Nue, Lamin B) from HaCaT cells.
(B) Representative western blot analyses of KB-AT-23 and antithrombin expression on plasma samples (n=4) collected from animals 27 weeks post-AAV injection. kDa, molecular weight marker.
C. Western blot analysis of ITPKB knock down in APPPS1hippocampus using an siRNA oligonucleotide against ITPKB. Sample size, n=6 per group. Values were normalized to control-injected group (Ctr) and presented as mean ± SEM.
B. V5-BirA*-AURKA is expressed at near endogenous levels in the stable line. HEK293T cells and HEK293T::V5BirA*-AURKA lysates were immunoblotted with antibodies against V5, AURKA and vinculin (loading control).
(F) Location of uS3 (K212) and uS10 (K6 and K8) ubiquitination sites. All ubiquitination sites are in the close spatial vicinity highlighted with red spheres. RACK1 proteins from both the leading and the colliding ribosome form the major head-to-head contact bringing together both C-terminal tails of uS3s as well as the N-termini of uS10s. For the uS10 ubiquitination sites, only an approximate position is shown as indicated by dashed lines since the uS10 N-termini containing K6 and K8 are invisible in the structure most likely due to flexibility.
F. Relative distribution of mitochondrial tRNA sequence reads obtained from the CRAC experiments using UV or 5-AzaC crosslinking with cells expressing the NSUN3-HisPrcFLAG (NSUN3) protein or control cells (FLAG). Only mt-tRNAs that were represented by more than 5% of all mt-tRNAs reads are labelled.
Hematoxylin and eosin sections of BAT from WT and CPEB2-KO female mice at 4 and 12 mo old. Scale bars, 1 mm
D. Schematic model showing the mechanism of EML4-GyrB foci formation. EML4-GyrB foci are formed by dynamic cross-linking interactions between the EML4 trimerization domain (TD) and dimerization of GyrB domain in the presence of coumermycin A1.
G) Designed F-domain scaffolds fall into Ang1- and Ang2-like classes. Color indicates highest (1) to lowest (0) pAKT, pERK1/2, and pFAK level which were column normalized. Cell migration level and vascular stability (48-hour timepoint) were also column normalized from highest to lowest.
ChEP analysis using EGFP (control)- or Piwi-KD OSCs. Signals with an adjusted p-value (Bonferroni test) of less than 0.05 are highlighted in red. The signals for Lam, LamC, and H1 are labelled within the plots.
(M, N) Mitochondrial respiration was measured in WT and MCK-KO soleus tissue after a bout of low-intensity exercise for 50 min under basal conditions and in response to 4 mM oligomycin (complex V inhibitor), 4 mM FCCP (uncoupler), or 4 mM each of rotenone and antimycin A (complex I inhibitor) (n = 8, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing). (O, P) Mitochondrial respiration was measured in Dnmt3a knocked down L6 myotubes which were transduced with lentiviral under basal conditions and in response to 4 mM oligomycin (complex V inhibitor), 4 mM FCCP (uncoupler), or 4 mM rotenone and antimycin A (complex I inhibitor) (n = 5, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).
(A) Isolated mitochondria were incubated with radiolabelled Mcp3 precursor protein for the indicated time periods. After import mitochondria were reisolated and analysed by SDS-PAGE and autoradiography. The arrowhead marks an additional band of the size of the cleaved N-terminus of Mcp3. p and m, precursor and mature forms, respectively.
(c) The abundance of H3K27me3 on the promoters of apoptosis and autophagy genes detected by ChIP. SL2 cells knocked down for dUTX were chromatin-immunoprecipitated with anti-H3K27me3 and anti-GFP (IgG control) antibodies following ecdysone treatment. Results are shown as the fold enrichment of % input compared with RNAi control.
Distribution of the plasma membrane reporter PH::GFP in cells where dynamin activity had been blocked using a temperature-sensitive allele of dynamin (shibirets in (E) it was inactivated ~15 minutes after the tube had begun to form.
(I) Iron concentration of mock, OTUD1 and OTUD1C320S tumors was assessed by Inductively Coupled Plasma Mass Spectrometry (n = 3 biological replicates, mean ± s.e.m., *P = 0.0237, **P = 0.0098, two-tailed unpaired Student's t-test).
(h) Midguts dissected from animals expressing Dts7, a dominant temperature-sensitive mutant of the β2 subunit of the proteasome, specifically in GFP-marked cells at puparium formation and analysed by fluorescence and differential interference contrast microscopy. Representative images are shown. (i) Cell size quantification (μm2) from h, n = 6 animal intestines per genotype with 1-5 cells measured per intestine. Quantification is shown as mean ± s.d. NS, not significant. Scale bars, 20 μm.
(D and E) HeLa cells transiently transfected with Strawberry-ATG16L1 were treated with YM-201636 (100 nM, 2 hr) in HBSS, then fixed and stained for endogenous WIPI-2. Bar, 10 μm. (E) Quantification of ATG16L1 and WIPI2 structures per cell, n = 20 cells (mean ± SEM; n = 3 independent experiments; ∗∗∗p < 0.001, t test).
(B) MeDIP-qPCR analysis to validate regions that are hypermethylated in Tet2Rank-/-; Tet3aRank+/- BMMs stimulated with RANKL for 2 days. (C) Gene expression of TET target candidates in BMMs stimulated with RANKL for 2 days.
C. Scatterplot of the additive versus dominant effect for each Chr 4 caQTL target locus. Points along the diagonal lines indicate dominant effects (red - caQTL targets found at the Riok3/Rmc1 locus.
C. Phosphorylation kinetics of T532, T539 and S558 on Apc1-loop500 of the endogenous APC/C in Xenopus egg extract. Endogenous APC/C was immunoprecipitated with Apc3 MAb (AF3.1) beads at the indicated time points after mitotic induction by adding non-degradable cyclin B, analysed by SDS-PAGE and immunoblotting with phospho-specific antibodies, pT532, pT539 and pS558. Quantification of Fig EV5A. The intensities at 45 min were arbitrarily set to 1.0. Error bars, SEM from three independent experiments.
H) Secreted protein measured in a cytokine array (RayBiotech) of a variety of inflammatory proteins in proliferating and senescent (10 days after 20Gy X-ray) Parkin-expressing MRC5 fibroblasts. Data are mean±S.E.M of n=3 independent experiments. Asterisks denote statistical significant P<0.05 One-way ANOVA.
a. (i) Cell subtype map of CA1 neurons in the hippocampus as annotated by JSTA. Scale bar is 500 micron. Distribution of CA1 subtypes in the hippocampus, computed by projecting cell centers to the lateral to medial axis. CA1 neuronal subtypes show a non-uniform distribution across the whole CA1 region. (ii) Smoothed histogram highlighting the density of CA1 subtypes across the CA1 region.
E-H Gametangiophores (E, G) and gametangia (F, H) of gMpFGMYB-S [Y] (E, F) and gMpFGMYB-L [Y] (G, H). Scale bars, 1 mm (E, G), 50 μm (F), 100 μm (H).
A Quantification of the average expression ± s.e.m. of Ptger1, Ptger2, Ptger3, Ptger4, and Ptgir mRNAs in whole-thickness lung, ileum or colon tissues or in jejunal spheroids cultured in stem cell (Stem), WAE (dmPGE2) or enterocyte (EP4i) medium (n = 3 independent experiments). Data are presented as fold change compared to lung tissue. n.d., not detected.
(G) Representative movement traces of the indicated mice used for quantification in (H) and (I).
RPE cells or RPE cells stably expressing the wild-type or mutant EGFP-FAM110A were transfected with control or two various FAM110A siRNAs and were analyzed by time-lapse microscopy. Plotted are means of the medians of the time from NEB to MAT ±SDs. A hundred cells were quantified per condition (n=3). Statistical significance was determined by ANOVA (**** p<0.0001, ** p<0.005).
A) Representative electron micrographs of entire boutons in wild type, hiw;wnd, and hiw;wnd, Elav-GAL4 > dNmnat RNAi NMJs.
E) The binding of MDM2 to the RB mRNA in H1299 cells as estimated using RNA CoIP. Cells were treated with doxorubicin (1 µM for 16 h) or DMSO.
(F) GST-NDP52 conjugated with glutathione-Sepharose resin was incubated with purified recombinant LC3 and MTPAP∆MTS∆C. The pulled down complex was subjected to western blotting. Data are representative of three independent experiments
(C-E) Overexpressing of exogenous SLFN11 in U2OS cells results in decreased HR-directed DNA repair. A U2OS DR-GFP cell line stably expressing Flag-tagged SLFN11 was generated (C-D). The resulting cells were electroporated with an I-SceI expression plasmid. 48 hr after electroporation, cells were harvested and assayed for GFP expression by FACS analysis. Error bars are s.d.; n=3. (E).
Correlation (Pearson) of CASP2 mRNA with transcript levels of Ki67 in the TCGA data set.
O Lentiviral-mediated endosialin knockdown (shEN) and control (CTL) in LX-2 cells (n = 3). Magnification 10×.
Heatmap representations of transcripts and protein accumulations for the RNA-protein pairs with rhythmic transcripts Distribution of phase difference between RNA-protein pairs for those with rhythmic transcripts
CRISPR/Cas9-based knockout of ERp18 in HEK293T cells expressing ATF6α. ERp18 levels in control (WT) and knockout (KO) cells were detected with an antibody to ERp18.
D Time-lapse imaging of liquid droplets fusion after mixing 10 μM cGAS-mCherry with 1 μM FAM-labeled dsDNA. Data information: Representative images are shown Error bars, mean with s.d. Scale bars, 5 μm (D)
Cideb-K128A fails to promote SREBP processing. Cideb-/- mice were injected with adenovirus expressing GFP, Flag-Cideb, or Flag-Cideb-K128A, and sacrificed 7 days after injection. Liver lysates were subjected to IB with the indicated antibodies following SDS-PAGE and quantification of IB data from 3 independent experiments. Data represent Mean ± SEM; **: p < 0.01, ***: p < 0.001, by 2-tailed Student's t test.
D. Log2 fold change of H3K4me3 level when comparing BXD75 or BXD87 to the parental genotype either at the location of the peak or based on the genotype at the QTL for all trans-caQTL for which the local genotype and QTL genotype differ (LOD score ≥ 7).
The cell lines were STLC-synchronized in mitosis, fixed, and stained with antibodies recognizing FAM83D (C) Representative images of mitotic cells are included. Scale bars, 20 µm.
K) Schematic drawing showing the resolved pH values and resulting gradients under respiratory and glycolytic conditions. The color gradient was generated following the ratiometric pH code used throughout the study.
Time-lapse confocal images of tPH-CynA-KikGR (green) expressing AX3 cells. Back cortical region of cell was photoconverted at time 0. Green fluorescence was converted to red. Front and back of the cell is shown, box showing the photoconverted region.