EMBO/sd-character-level-ner huggingface dataset:
This figure compares conformation of aminoacyl residues of the two A-site substrates:A. ACC-PuromycinB. ACCA-Pro.To show position of the A-site substrates relative to the P-site, the model P-site substrate tRNA-Phe is shown as in the pre-attack complex of the ribosome (pdb id 1vy4). In both illustrations, the A site is viewed as through the peptide exit tunnel. In addition to S. cerevisiae residues numbering, E. coli numbering is shown in parenthesis. Comparison of the two structures shows that the side chain of the methyl-tyrosine is bound to the conserved hydrophobic A-site cleft, whereas the side chain of the proline residue penetrates the actual site of peptide bond formation where it may interfere with alignment of the reacting groups and proper positioning of the attacking electron pair of the α-amine.
Distribution of LV and HF at the mouse embryo stage E15.5 (A), E16.5 (B) and E17.5 (C). Maximum projection images of whole mount immunofluorescence analyses using LYVE1 (red) as lymphatic endothelial marker and counterstained with DAPI (blue). Red arrowheads denote HF placodes. n= 3 - 4 embryos. Scale bar, 50 μm.
(e) Immunoblots for LC3-II in UC and HD lymphoblasts treated or not treated with protease inhibitors. Right: LC3-II values and LC3-II flux. Extended study in Supplementary Figure 8a. Mean + s.d.; #P 0.05. Full-length blots in Supplementary Figure 20.
A. Oocyst development of concavin(-) parasites complemented with either the P. berghei gene or the P. falciparum orthologue fused to GFP. Data points represent individual midguts observed between d12-17 post infection of 3 independent cage feeds. Shown is the mean ± SEM. P-values are calculated using the Kruskal Wallis test followed by the Dunns multiple comparison test.
(E) U2OS cells stably expressing FLAG-TIP60WT, FLAG-TIP60S90A or empty vector (vec) were subjected to ChIP using anti-FLAG antibody. Immunoprecipitated DNA and input were subjected to quantitative real-time PCR using primers annealing in the myc locus about 50bp upstream (myc+50) or about 500 bp downstream (myc-500) of the transcription start site. Promoter occupancy of FLAG-TIP60WT or FLAG-TIP60S90A was determined as percent input in relation to FLAG -TIP60WT. The graphs and error bars represent mean and standard deviation of three individual experiments (one-way ANOVA, Bonferroni"s multiple comparison test, myc+50 WT vs. S90A p=0,0289, myc-500 WT vs. S90A p=0,0155 (*p < 0,05))
C Relative root length [% of control] of Col-0 (n=11-13 ), lrx3/4/5 (n=9-13 ) and fer-4 (n=11-12) after 3 days of RALF1 treatment. Statistical analyses were performed for each concentration using one-way ANOVA followed by Bonferroni post test (1 µM and 1.25 µM b: p < 0.001; 1.5 µM b: p < 0.05, c: p < 0.001). Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values. Representative experiment is shown.
(C-F) TFIIIB (Brf1-3HA) and RNAPIII (Rpc82-3HA) ChIP-qPCR was performed in asynchronous (async.) and after 2h in S phase +0.2 M HU. Enrichment was quantified at several tDNA loci. Data is expressed as percentage of input. ETC4 serves as a control locus which does not recruit RNAPIII. (D,F) Graph depicts the mean percentage of Brf1 or Rpc82 kept on chromatin after HU-treatment, calculated as a ratio HU/async in the indicated strain. Occupancy levels are derived from ChIP-qPCR values.
c, Dysfunctional CTLs detected in all five TNBC patients determined through scoring a T-cell exhaustion signature. UMAP featureplot of the exhaustion signature across all stromal and immune cells as in Fig. 1D.
Neonates were obtained by caesarean delivery. a, b, Successfully resuscitated pups were monitored in a humidified chamber without milk feeding (a) or with artificial milk feeding provided every 3-6 h through a tube inserted into the stomach (b).
(f) Representative western blot for NECAB2 showing knockdown efficiency. 1, scrambled non-targeting shRNA; 2, NECAB2 shRNA.
C Average chromatin accessibility (normalized read counts) of genes found in common and wild-type (WT, N=3) specific LADs for WT (N=3) and R6/1 (N=3) mice. Each point corresponds to the value from an individual sample. Data is shown as the mean ± S.E.M. Wilcoxon Mann Whitney test was used for statistical analysis. Exact P values are reported in Appendix Table S3.
(A) 293T cells were transfected with empty vector or HA-tagged wild type (WT) or deletion mutant (Δ654-828) ULK1 and subjected to immunoprecipitation with anti-HA antibody followed by immunoblotting with the indicated antibodies.
(D) Venn diagram of transcription factors in which the natural abundance of 13C and 15N and the ratio of 13C to 15N that were perturbed in their respective mutant alleles. Transcription factors are listed if the AGI or AGI:Salt Treatment linear model terms are statistically significant (P < 0.05) as determined by a two-way ANOVA from 3-5 biological replicates per genotype per condition.
Colorimetric HIV-1 RT activity assay using constant amount of HIV-1 RT (0.5ng) and performed with increasing amounts of immunopurified E2C and S100A9 eluates. Means ± SD colorimetric data obtained from duplicates of depicted independent experiments were normalized to E2C-containing conditions and shown on graphs. Each datapoint in the graph represents an independent experiment.
B-C The direct binding of p-CREB to human FST promoter was detected by ChIP-PCR (B) and ChIP-qPCR (C). c-Fos was used as positive control of p-CREB target gene. Normal IgG was used as negative control of ChIP. Data information the experiments were performed in triplicates, and the data were presented as mean ± SEM. **P<0.01, ***P<0.001 (Student's t-test).
B. Co-IP assays showing that CRY2, CIB1 and CO form a protein complex. Samples were prepared from 10-day-old WT or 35S:Myc-CIB1/35S:CO-Flag or 35S:Myc-CIB1/35S:CO-Flag /cry2-1 seedlings grown in LDs (16L/8D), and samples were collected at ZT16.
A Gene ontology enrichments for biological processes in the downregulated genes in the fat body following dsPiwi1 treatment. The heat map shows the gene ratio percentage and the number of differentially expressed genes for a given GO term/the number of all the locust genes for a given GO term.
(F). E level in the medium from adrenal chromaffin cell cultured with vehicle + NC, vehicle + siOXGR1, AKG (100 μM) + NC or AKG + siOXGR1 for 30 mins (n = 8 per group).
A Upper: Coomassie blue stained SDS-PAGE showing purified full-length myoVa (arrow) from HEK293T cells using a StrepTag-GFP-tag. Lower: Western blot of StrepTag-GFP-myoVa shows that myosin is associated with HEK293T-cell endogenous calmodulin (CaM) upon purification.
Two distinct surfaces are revealed on parkin upon binding of the UbcH7-Ub conjugate. Chemical shift perturbations were measured from 1H-15N TROSY spectra of 2H,13C,15N-labelled R0RBR parkin bound to unlabelled pUb in the absence and presence of one equivalent unlabelled UbcH7-Ub. Chemical shift perturbations (absence of signal, average shift + 1 SD) are modelled onto the surface of R0RBR bound to pUb (PDB 5N2W). The UbcH7-Ub binding site comprises the RING1 and IBR regions (magenta). An adjacent site composed of many buried residues was also observed (cyan) that results from E2-Ub binding but does not include the E2 binding site. Sections of the tether and linker regions not visible in the crystal structure were added using Modeller (Eswar et al, 2006) so that chemical shift changes for residues not observed in crystal structures could be mapped.
C Changes in food intake of mice in (A) during 10 weeks of HFD (cohort 1). n=9 for GFP (cage 1 = 5 mice; cage 2 = 4 mice) and n=8 for PLTP (cage 1 = 4 mice; cage 2 = 4 mice)
(G and H) In the presence or absence of TGF-β1, QKI-5-overexpressing A549 and H1299 cells were allowed to migrate through a polycarbonate membrane in Transwells. After 24 h, migrated cells were stained, photographed and counted in at least four random fields under a light microscope. Representative images (left) and the migrated cell numbers (right) were presented. (I and J) QKI-5-overexpressing A549 and H1299 cells were treated and allowed to invade through Matrigel-coated membrane in Transwells. Invasive cells were determined
D. Response of HyPer7 probes targeted to indicated compartments to treatment of mtDAO-expressing cell lines with 4 mM D-Ala (black, wild type; red, PRDX1 KO; blue, PRDX2 KO; cell generated with the piggyBAC system). Cells were grown in glucose-containing medium. Solid line represents average, points colored in the lighter version of the respective color are the corresponding ratios measured in individual cells. Data information As most of the data were not normal distributed, instead of a t-test, a Wilcoxon/Mann-Whitney-U-test was performed and samples were compared in pairs. *, p ≤ 0.05, **, p ≤ 0.01, ***, p ≤ 0.001
(E) Boxplot showing pairwise Pearson correlation between plus and minus strand transcription at bidirectional enhancers over cell lines. Only enhancers with observed bidirectional transcription in at least 5 cell lines and varying transcription over cell lines (coefficient of variation > 50%) were considered (n=715 Median, hinges, whiskers and notches are shown as in (B).
C. Michaelis-Menten plot with the variation of H2O2 (0-400 µM) in the presence of Vs (20 ng/µL), GSH (2 mM), NADPH (0.2 mM), GR (1.7 units) in phosphate buffer (100 mM, pH 7.4) at 25°C.
C Immunodetection of endogenous p97 after LLOMe treatment as in (A). Percentage of cells showing recruitment of p97 in three independent experiments (mean ± SD).
F Exponentially growing cell cultures were serially diluted (1:10) before being spotted out onto YEPD plates with or without CPT
ZR-75-1 and CAMA-1 cell lines were treated with 1 µM MK-2206 or 1 µM AZD5363, for indicated time periods. Cell lysates were subjected to (B) mRNA isolation followed by cDNA preparation. Real-time PCR was performed on cDNA samples using specific primers against SGK1, SGK2 and SGK3 isoforms. Relative mRNA levels were calculated using 2^(-deltadelta) Ct method using DMSO treated samples as calibrator.
(E) Macrophages were transduced with non-specific scrambled shRNA (shNS), or TLR8 shRNA (shTLR8) and analyzed for TLR8 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4.
(D) Boxplot of DNA methylation in the wild type, nrpe1, epcr1/2, and arid2/3/4 mutants. The hypo-DMRs identified in the nrpe1 mutant was defined as RdDM target loci. Asterisks indicate that DNA methylation is significantly (P<0.001) decreased in the mutants as determined by paired student t-test. Horizontal lines represent the median, and the bottom and top of the box represent the 25th and 75th percentile. The whiskers represent data range within 1.5× of the interquantile range.
F Cultured hippocampal neurons were field-stimulated with four trains of 200 APs (40 Hz, 5 s; 90 s gap between each train) (Stim) or left unstimulated (-), fixed and stained for MAP2, Synaptophysin (Syp), and PI(3) P. Arrows indicate PI(3) P puncta in synapses. Scale bar, 10 µm. PI(3) P puncta that do not overlap with neuronal soma and synapses belong to astrocytes in culture and are disregarded from the quantification.
Deficiency of VGLL4 reduces IRF2BP2 protein levels. Immunoblot analysis of A549 and LLC cell lysates transfected with siRNA for control and VGLL4
(A) Representative western blots of histone acetylation levels of HeLa cells lysed at indicated time points after UV irradiation (16 J/m2, left panel), α-amanitin (second panel, 100 µg/ml), THZ1 (third panel, 1 μM) or flavopiridol (right panel, 1 μM) treatment. Blots were stained with α-acetyl-lysine (top panel), α-histone H4 (middle panel) and α-tubulin (bottom panel)
(A) Classification of the protein-coding transcriptome in zebrafish, human, and mouse reveals that uORFs are widespread and translated. Transcripts containing at least one uORF are marked in purple, transcripts containing no uORFs but at least one oORF are marked in orange, and transcripts lacking both are grey. In zebrafish, 3 different translation thresholds were applied to classify translated uORFs, and each transcript then classified by its highest confidence uORF: Low confidence (dark pink): RPF RPKM >0; Medium confidence (light purple): ORFScore > 0; High confidence (dark purple): ORFScore > 6.044.
Representative images (I) and cfu quantification (J) of Listeria bound to HeLa cells pre-treated or not with arsenite followed by incubation with the bacteria for 20 min
(E) Amino acids 282-323 of TMEM59 lack LC3 activation potential. 293 cells were transfected with the shown chimeras, HA-LC3A or HA-LC3B and GST, and processed for western blotting against the indicated molecules. Control WBs of unaggregated samples are shown in the lower panels.
A. A schematic depicts the procedure of the establishment of PDX and drug administration.
(I) Scheme depicting eEF1A domains, their different binding patterns for GDP/GTP or eEF1B2 and the His-tagged eEF1A1 mutants. Western blot analysis of GST-pulldown assays with GST-TIP30 and the indicated His-tagged eEF1A1 mutants are shown.
(D) Doxycyclin (Dox)-inducible p53 H1299 cells were treated without (-) or with (+) Dox in media containing 10% serum or in serum free HBSS, and then subject to ChIP assay with control IgG or p53-specific Ab6 antibody. ChIP DNA was assayed by qPCR using primers specific for p53 binding site at p21 (top panel), p53-negative control IGX1A (middle panel), or p21 positive control (lower panel). Error bars represent SD, and * indicates p value < .05. p-values were determined by Student t-test.
HEK-293T cells were transfected with various combinations (above lanes) of plasmids encoding Myc-ABRO1 and Flag-tagged NLRP3 (WT), NLRP3 (S194D), or NLRP3 (S194A). Immunoblot analysis of Myc- and Flag-tagged proteins in cell lysates immunoprecipitated with anti-Flag M2 beads.
(A) PS1/2-/- MEF cells stably transduced with PS1 WT or PS1 L435F were analyzed for PS1 expression and APP processing by immunoblotting as in Fig 1A. Antibody 5E12 was used for the detection of the PS1 CTF.
(B) Auto-phosphorylation of recombinant HisMBP-MAP4K4 wild-type, no auto-phosphorylation in the kinase-inactive HisMBP-MAP4K4-D139A protein. The phosphorylation level was determined by Pro-Q Diamond phosphoprotein gel stain (upper panel), protein loading amounts were visualized by Coomassie G-250 staining (lower panel). The predicted molecular weight of HisMBP-MAP4K4 is 118.4 kDa.
B. Exogenous immunoprecipitation of PTENε with FLAG-tagged CDC42, ACTR2, VASP, and FSCN1. The plasmid expressing PTEN, PTENε, or mock carrying C-terminal S-tag and HA tag was co-transfected with FLAG-tagged CDC42, ACTR2, VASP, or FSCN1 plasmid in HEK293 cells separately. Cell lysates were incubated with S protein agarose followed by western blotting with antibodies against the FLAG tag and HA tag. G1-4 stand for immunoprecipitation group 1-4.
(F-H) Western blotting analyzed Il-17rb in shLacZ, shSmad2 (F)4T1 cells treated with recombinant TGF-β1 for 5 days.
(a) A549 cells were transiently transfected with adenovirus expressing GFP-Atg14L or GFP-Atg14LCAAX and subjected to starvation. The cells were fixed and stained with anti-Beclin-1 antibody. Higher magnification of the boxed areas is shown below.
A Diagram of the mating type loci in S. pombe. The position of the silencing reporter gene (kint2::ura4+) is shown. The target regions in the ChIP analysis are indicated by black bars above (kint2::ura4+) and below (cenH) in the diagram.
C. Kymograph profiles (left) highlighting that the photoactivated regions in prometaphase (upper panel) split and move towards both poles, whereas metaphase spindles (lower panel) flux uniformly towards individual poles (indicated by red dotted lines). Illustration of the photoactivated regions (right) in prometaphase and metaphase spindles, highlighting that interpolar MTs overlap over a broader region in early mitosis, becoming focused at the spindle equator in metaphase. Scale bar, 30 sec. D. Percentage of cells with parallel and antiparallel flux movements during prometaphase and metaphase. N (number of cells, number of independent experiments): prometaphase (23, 3), metaphase (22, 3).
E and F. mEPSCs in AII amacrine cells are largely triggered by Ca2+-influx via presynaptic L-type Ca2+-channels (E, representative mEPSCs traces recorded in regular [2 mM] or reduced extracellular Ca2+-concentration [0.3 mM], or in the presence of nimodipine [50 µM] in regular Ca2+; F, summary graphs of the mean mEPSC frequency and amplitude under the conditions described for E).
(B) T47D-MTVL cells transfected with control or BRM and BRG1 (B/B) siRNAs were induced or not with hormone, and subjected to ChIP assays with a-H1. Precipitated DNA was analysed by PCR for the presence of sequences corresponding to the BCAS1, KRT23, IGFBP5, VAMP1, CCDC173 and RAB3D genes. The histograms show the mean ± SD of 3 experiments performed in duplicate. * P-value < 0.05.
a, Polyclonal T-cell development in Atg5-/- to wild-type (WT), or wild-type to wild-type grafts. The top dot plots show CD4 and CD8 staining; the bottom dot plots show expression of CD25 and Foxp3 by CD4 SP thymocytes; n ≥ 5.
H,I. Immunofluorescence images (H) and quantifications (I) of Cyclin B1 and MAD1 kinetochore levels in control (MAD1-WT) or MAD1β HeLa cells (two independent clones: C13 or C24) treated with nocodazole.
B. The same total lysates as shown in (A) were assayed for the level of K48-linked polyubiquitin. Actin is shown as a reference. The levels of K48-linked polyubiquitin were quantified from multiple independent repeats. (means +/- SD, n = 5, numbers above the bars indicate p values calculated with the two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli).
a-l, The presence of ubiquitin-positive dots was examined by immunohistochemistry in several regions including cerebral cortex (a, b), cerebellum (c, d), hippocampus (e, f), hypothalamus (g, h), amygdala (i, j) and pontine nuclei (k, l) of Atg7flox/+; nestin-Cre and Atg7flox/flox; nestin-Cre mice. Note the presence of numerous ubiquitin dots in the amygdala and hypothalamus of the representative mutants. Scale bars, 50 µm.
SUMO4 were co-overexpressed with CHAF1A in HEK293T cells respectively. SIM imaging was performed for each combination.
(D) Polarized mitochondria stained with MitoTracker red (red arrowheads) were not labeled by Parkin. In contrast, damaged mitochondria marked by Parkin (green arrowheads) were not stained with MitoTracker red.
Expressing β-cat K49Q increased its nuclear translocation. HEK293 cells were transfected with eGFP-β-cat WT or K49Q for 48 h, and then β-cat protein level in different fractions was measured by Western blotting Data information: Data are expressed as mean ± SEM, *, P<0.05; **, P<0.01, ***, P<0.001 vs β-cat WT (C) Data were analyzed by Student's t test
A Activation of the NF-κB pathway by RIPK2 Lysine- and phosphosite mutants. RIPK2-deficient THP-1 cells reconstituted with wild-type RIPK2 or RIPK2 mutants were stimulated with L18-MDP, harvested at indicated time points and activation of the NF-κB pathway was analyzed by immunoblotting.
D, Cysteine phosphorylated PRL2 does not bind to CNNM3. Recombinant PRL2 was phosphorylated by treatment with OMFP and subjected to pull-down by the CBS-pair domain of CNNM3 as a GST fusion. Only unphosphorylated PRL2 was observed in the pull-down lanes while phosphorylated PRL2 was in the flow-through lanes.
Effects of thioperamide on cholesterol-dependent transcriptional regulation. The parental HeLa MZ cells, NPC1 KO cells or NPC2 KO cells were treated or not with thioperamide 10 μM for 18h. Total mRNA was extracted and both LDLR mRNA and HMG CoA reductase mRNA were quantified by RT-PCR. (n=3 independent experiments, error bars = SD, one-way ANOVA, *=p<0.05; **=p<0.005)
(F and G) Average plot (top) and heatmap (bottom) of H3K27ac reads in the cis-regulatory regions of genes belonging to the gene set "HALLMARK_MITOTIC_SPINDLE" (F) or "HALLMARK_G2M_CHECKPOINT" (G) in HSCs in the steady state or early phase.
(C) Cells from the end of the experiment described in (A) were fixed and processed for ChIP-Seq, using antibodies specific for phosphorylated Serine 5 in the C-Terminal Domain of the Pol II catalytic subunit Rpb1 (CTD-Ser5P). For each of the three indicated strains, the histograms represent the normalized read density (DNA sequence read count per million reads, or RPM), across a sample gene body.
WCE and FLAG-tag NS3 IP assay immunoblots of 293T transfected with BTV-NS3-FLAG plasmids and increasing amounts of Ubiquitin-HA plasmids, and probed (IB) for ubiquitin (HA), BTV-NS3 (FLAG) or GAPDH expression.
A Tethering assay using the F-Luc-HhR-poly(A) reporter and λN-HA-AGO1 (wild-type or pocket mutants) in S2 cells. A plasmid expressing R-Luc served as a transfection control. (A) F-Luc activity and mRNA levels were normalized to those of the R-Luc transfection control and set to 100% in cells expressing the λN-HA peptide. The panel shows mean values ± standard deviations from three independent experiments.
D Chromatin accessibility as assessed by the number of ATAC peaks identified in the sorted populations of normal thymic T-cell precursors and in T-ALLs, respectively (n=10/19 patients have two biological replicates, n=9/19 patients have one replicate). Horizontal lines of the box plot indicate the median, lower and upper limits of each box correspond to the first and third quartiles (the 25th and 75th percentiles) and the lower and upper whiskers extend from min to max; pval=4.4e-08 (Kruskal-Wallis Test).
C: Cal27 and JHU029 cells were transfected with control or mimic miR-7 and relative expression of ELDR was analyzed by qRT-PCR. 18S rRNA was used as an internal control. n = 2 biological replicates; n= 3 technical replicates. Data are represented as the mean ± SD,
A Molecular structure of the HIV-PI Nelfinavir (NFR) and schematic representation of the protocol used to generate NFR resistant clones. HeLa cells were maintained with 10μM NFR. After 15 days, few clones proliferating in the constant presence of 10μM NFR in the culture medium were selected and expended for further analysis.
Expressing Tau-k18(-) or Tau-2CA abolished its anti-apoptotic function. N2a cells, transfected with eGFP-Vec, or eGFP-Tau40, or eGFP-Tau-k18(-), or Tau-2CA for 48 h, were then treated with 0.5 μM STP for 4 h followed by co-staining with c-cas-3 (red) The apoptotic rate (E) was presented as the ratio of yellow (c-casp-3 and GFP co-stained) to green (the total GFP-expressing cells) staining. Data information: Data are expressed as mean ± SEM, *, P<0.05; **, P<0.01, ***, P<0.001 vs Tau plus STP Data were analyzed by one-way ANOVA.
(E) Immunoblotting against the GFP or the GAPDH of proteins extracted from HEK293 cells transfected with either a wild type or mutant (AGG into CGG) construct containing 80 G4C2 repeats embedded in sense C9ORF72 fused to the GFP in the GR frame.
(G) The frequencies of CD150+CD48- and CD48+ fractions within lineage-EPCR+ after HSCs in the late phase were cultured for 4 days with or without A-485 (1 μM), an inhibitor of histone acetyltransferase.
Effect of MB on the proliferation of WT CTLs, PD-1KO CTLs. Splenic cells were stained with 5 μM of CFSE and seeded into aCD3/aCD28 coated 96-well plates. 10 μg/ml of PD-L1 were administered in media. Cell proliferation were checked by monitoring dilution of CFSE 48 hours after CD3/CD28 stimulation by gating on CD8 positive population through FACS analysis. WT: splenic cell from wildtype C57BL/J mice. PD-1KO: splenic cell from PD-1 knockout mice.   Statistical results of (A)   Data information: Data are representative of three independent experiments. Unpaired t-test; Error bars denote s.e.m. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001