EMBO/sd-character-level-ner huggingface dataset:
(c) Immunoblot of Cx43 IP in MEFs from WT or Atg5−/− mice grown in serum-supplemented media.
E Microtubule regrowth assay was performed on NHF, Lowe 1676 and Lowe 3265 cells with 20 μM nocodazole for 2 h on ice, followed by rinse with PBS, and addition of pre-warmed medium to induce microtubule regrowth. Cells were then immunostained with anti-α-tubulin and anti-γ-tubulin antibodies at the indicated time point after addition of pre-warmed medium. The magnified view shows the cytoplasmic microtubules organization center. Scale bar, 10 μm. F Quantitative analyses of focused microtubule arrays numbers at γ-tubulin (microtubule organizing center, MTOC) measured in the experiments shown in E. n = 3 per group in which 30 cells were counted per condition per experiment. D Data information: data are presented as mean ± SEM. * ≤ 0.05, ** ≤ 0.01, calculated by two-way ANOVA, multiple comparisons.
Relative responses of KP mice tumors treated with (G) AOA, or vehicle starting from week 8 post-infection and measured until week 20. Relative response = average tumor volume with treatment / average tumor volume with vehicle.
(B) The supernatant (S200) and pellet (P200) fractions were collected after centrifugation at 5,000 g for 5 min. The P200 fraction was resuspended in 10% Ficoll, and vacuoles were isolated by flotation through 4% Ficoll. V, vacuole; I, 4/10% Ficoll interface; P, gradient pellet. Proteins were detected by Western blotting. The positions of prAPI, mAPI, and mPrA are indicated.
C. Representative images and analysis of AIF accumulation in the nuclei of PC3 DKO2/3 and PC3 DKO2/3+1 cells, 24 h after treatment with 100, 200 or 400 μM H2O2. Data information: Nuclei were visualized by DAPI staining. Arrowheads: AIF translocated to nuclei. Untreated control cells are shown on the left. Right panels, AIF-positive nuclei were counted from pictures taken from three independent fields in two independent experiments. Means ±SD are plotted. PC3: *** p<0.0001 compared to untreated cells of each genotype as assessed by Student's t-test. Scale bars, 10μm.
E) WT and USP7 KO keratinocyte were treated with MG132 at 10μM for 6 hours, then subjected to immunoprecipitation using anti-ubiquitin antibody. Precipitated product was analyzed by immunoblotting with IKKα antibody. Band intensity was determined by densitometry and shown as bar graphs. Statistical analysis is conducted using unpaired Student's t-test. Error bar represents S.D. (standard deviation). N=3 (biological replicates). **, p<0.01. Kd: kilodalton for molecular weight markers.
C) HeLa C1 cells transiently transfected with RISC free control siRNA or siRNA duplexes directed against TRAPPC8 or RAB1A and B (knockdown confirmed by immunoblot analysis), were treated with D/D solubiliser for the indicated time periods, trypsinised, fixed and their GFP content analysed by flow cytometry. The line graph shows the GFP fluorescence as a percentage of t=0, ± s.e.m. from three independent experiments.
C Percent of mouse weight after GVHD induction with IV injection of mitocepted PBMC or control PBMC cells (n=3, with a total of 25 mice per group). Control group in grey, were untreated mice (n=6 mice). * p<0.05 by Mann Whitney t-test.
(A) MEFs were then infected with retroviral vectors encoding the indicated B-Raf proteins. Giemsa staining revealed transformed and hyper-proliferated cells by dark purple colour. (B) Quantification of Focus formation potential of the B-Raf mutants used in (A). n = 3, mean + SEM, t-test, *** p < 0.001.
(A) RNA-seq of MCF7 and MDA-MB-231 transfected with miR-515-5p revealed the down-regulation of five transcripts, NRAS, FZD4, CDC42BPA, PIK3C2B and MARK4.
Effects of KYA1797K and PTD-BBR on RAS degradation IB assay of MT-HCT116 or SW48 cells treated with indicated conditions for 24 and 96 hr, respectively
Muscle sections (30μm) were cut from snap frozen tissue of 20-month old GA149 mice (Tgx GA149) or wild type controls. Immunohistochemical staining was performed to assess synaptic protein levels in proximity to NMJs. Sections were immunostained for SV2 or Synaptophysin, and counterstained with neurofilament. A) Left Panels: Representative images show SV2 levels (green) in proximity to α-bungarotoxin positive NMJs (red) in wild type animals (top) versus GA149 animals (bottom). Right Panels: Representative images show SV2 levels (green) overlapping with neurofilament (blue) at synaptic terminals approaching muscle in wild type animals (top) versus GA149 animals (bottom).
D End-point RT-PCR analysis for selected marker genes (n = 3 biological replicates).
C) Significance values from GSEA using combined STAT3 gene sets identified in B. Each treatment group is compared to tumor-bearing control (cachexia) transcriptomes.
The effect of kinase inhibitors on EDN induced cell migration of UACC257 cells was analysed using a scratch assay. Scratches were made in UACC257 monolayers. Serum was removed and cells were treated with PBS or 100 nM EDN in combination with DMSO or kinase inhibitors at 0.1 μM or 1 μM in triplicates. A Example pictures showing the effect of EDN on migration. Cell free areas are delimited by blue lines. Migration was quantified as the change in cell free area between 0 h and 48 h. B The four inhibitors that were effective at 1 µM are shown in detail, i.e. every point corresponds to one well. C Abundance of E-Cadherin (normalized to GAPDH and Actin) was assessed by LC-SRM after 48 h treatment with EDN or kinase inhibitors at 1 µM. Only the single inhibitor which could reverse EDN induced E-Cadherin repression is shown. * p < 0.05 two-sided unpaired t-test.
(A) Schematic displays uORF/oORF configurations for reporter experiments. GFP reporters contained variable uORF configurations: no uORFs, 1 uORF, 3 uORFs, 1 oORF, or 1 uORF in weak initiation context. TLS length (104nt) and polyA tail length (60A) was constant across all reporters, and TLS sequence differed only by single nucleotide changes at each uORF start codon (or two single nucleotide changes in the weak context reporter). Constructs (100pg) were coinjected with dsRed (150pg) into 1-cell-stage embryos and quantified at 24hpf.
Representative current clamp traces from the IC of control and Cdc50a cKO mice; +100 pA (upper) and +400 pA (lower) currents were injected into control mice (left) and Cdc50a cKO mice (right) for 500 ms.
B. ﻿Two-dimensional UMAP representation of single-cell RNA-seq 1151>Ama-RNAi dataset colored by cell type, including 51 tracheal, 3,107 epithelial and 180 myoblast cells.
(C-I) 4T1-injected or EMT6-injected mice were sacrificed at the indicated week after initial injection. Collagenase-digested specimens from the primary tumors or inguinal LN tissues were cultured in culture dish for cancer cell enrichment. The detailed process is described in the methods section. After several days selection/culture, viable 4T1PT, 4T1LN, EMT6PT, and EMT6LN cells were used for the following assays:(D and E) Tumorigenesis assays were determined in BALB/c mice (n = 3 mice per group) orthotopically injected with 5x102 4T1PT or 4T1LN cells. Tumor mass (D) and tumor weight (E) were measured on day 28. Scale bar: 1 cm.Data information: In (A-G), all experimental data were verified in at least two independent experiments. All values are presented as mean or mean ± SD.
(b) Binding between eIF4A and NAT1 is regulated by amino acid availability in a TORC1-independent fashion. Co-immunoprecipitation of tagged eIF4A and NAT1 in control Kc167 cells, or cells treated with medium lacking amino acids or supplemented with 20 nM rapamycin for indicated times. Representative of 3 biological replicates.
D Model of EGR2-OST1 modulation of cold stress responses in Arabidopsis. At warm temperature (22°C), EGR2 can be modified by myristoylation, which allows it to recognize OST1 and inhibit its activity to ensure plant growth. Under cold stress (4°C), the interaction of NMT1 and EGR2 is decreased, thereby causing the accumulation of unmyristoylated EGR2, which shows reduced interaction with OST1 and disrupts the interaction of EGR2-OST1 as well. This ultimately leads to activating OST1 protein kinases and enhancing plant freezing tolerance. Clade A PP2Cs, such as ABI1, also partially contributes to regulating OST1 activity in response to cold stress. EGR2-M and u-EGR2 represent myristoylated and unmyristoylated EGR2, respectively.
B. Schematic diagram of domain structure of Sig1R, coded by SIGMAR1. Amino acid sequence misplaced by L95fs mutation is shown by a red rectangle. Note that both of ALS-causative mutations (L95fs, E102Q; highlighted with red arrows) are located near the ligand-binding motif. In addition, recently identified mutations that cause distal hereditary motor neuropathy (dHMN), E138Q, E150K and a splice-site mutation resulting in in-frame deletion of 20 amino acids (Δ31-50), are indicated by green arrows.
(J) IF analysis of developing intestines from E12.5 to E17.5 with the indicated antibodies. Scale bars, 25 μm.
A-C) Gene ontology analysis for rhythmic proteins was carried out using Gene ontology enrichment analysis and visualisation Significantly rhythmic WT proteins were compared against background (all proteins identified in the experiment), and the top non-overlapping GO Biological Process terms shown, sorted according to FDR q-value. Fold enrichment is annotated on each bar (A). The same GO analysis was carried out comparing proteins rhythmic that were rhythmic in CKO cells (B) and for proteins that were rhythmic across both genotypes (C).
(O) Co-immunoprecipitation between NFATc1 and PA28γ in HEK293T cells cotransfected with WT HA-SIRT7 or an enzyme-dead mutant (H187Y).
C. Differential analysis between healthy donors (CTR, n=8) and COVID-19 (COVID, n=7). The heatmap represents arcsine-square-root transformed cell frequencies that were subsequently normalized per cluster (rows) to mean of zero and standard deviation of one. The color of the heat varies from blue, indicating relative under-representation, to red indicating relative over-representation. Bar and numbers at the right indicate significant differentially abundant clusters (green) and adjusted p values (Differential analysis performed by diffcyt package present in the Catalyst package). The statistical analyses was done using GLMM (according to the actual guidelines) and all p-values were Bonferroni corrected. Clusters were sorted according to the adjusted p values, so that the cluster at the top shows the most significant abundance changes between the two conditions. D. Boxes and whiskers plots representing maximum, minimum, median value, 25 and 75 percentile of different subpopulations of monocytes in healthy donors (CTR, n=8) and COVID-19 patients (COVID, n=7).
B, C The average replication rate ± SEM (B) and the average fork distance ± SEM (C) in the indicated folate concentrations at 14 and 21 days. At least 115 DNA fibers were analyzed at each concentration and at each time point to determine the average replication rate. At least 71 replication forks were analyzed at each concentration and at each time point to determine the average fork distance.
(C) Histological images of colonic tissues from control (n=10) and cKO (n=10) mice at indicated timepoints after DSS treatment. The Panels with non DSS are identical to Panels in Fig EV1F. Scale bar: 100 μm.
Comparison of the spleen weight Each symbol represents an individual mouse. Small horizontal lines indicate the mean (error bars, s.e.m)
Representative bioluminescence imaging (BLI) pictures of mice transplanted with AE9+Nras AML cells. Day 0 indicates the start of combination therapy with cytarabine (AraC) + doxorubicin (Doxo).
(a) mRNA and protein production and degradation rates for SESN1 under oscillatory p53 dynamics were fit as described in (Fig 3a).
(C) Flow-cytometric analysis of Pax5 protein expression by intracellular Pax5 staining of lymph node B220+CD19+ B cells from a Pax5+/+ mouse (grey filled) and B220lowCD19+ B-ALL cells from a 10-week-old Pax5Jak2/+ tumor mouse (black). The full-length Pax5 protein was detected with an antibody that recognizes C-terminal Pax5 sequences that are absent in the Pax5-Jak2 protein.
B) Transgene transcript length is not affected in rpb-9 (mj261) mutants. Scheme of the gfp unspliced transcript showing the positions of RT-qPCR primers (top) and pairwise ratios (3′ to 5′) of unspliced gfp amounts along the transcript as indicated by the primer pairs (bottom). (n=3, error bars represent SD). ns= not significant (two-tailed t-test).
A) Negatively selected primary NK cells purified from PBMCs of three healthy donors were tested for activation markers using flow cytometry. NK cells were incubated with immobilized IgG (mepolizumab, Mpz), soluble IC (Mpz:IL-5 = 1:1), soluble Mpz or soluble IL-5 (all at 200 nM, 106 cells). Incubation with PMA and Ionomycin (Iono) served as a positive control. Incubation with medium alone served as a negative control. Each dot represents one donor measured in technical duplicates. Error bars = SD. One-way ANOVA (Tukey); *p<0.05, ****p<0.0001.
(C) NET-seq data at the YDR261C locus with a novel DNC transcript. Annotations as in (B)
E-H - Details of rosettes (large arrows in E; dashed lines in F-H) from Irs2+Gfp-overexpressing E14.5 embryos immunostained as indicated. Small arrows indicate apical mitoses, arrowheads indicate basal mitoses (F,G) and Par3+ apical surface at the centre of rosettes (H), dotted lines indicate apical surface, dashed lines indicate basal side of rosettes. Inset in (H) is at the same scale.
Active RAB13 (RAB13-GTP) was pulled-down using MICAL-L1 RBD-GST from the indicated PMO-treated cells The amount of endogenous RAB13 was measured by quantitative Western and relative levels of active RAB13 are plotted. n=8 (D), n=4 (E). Bars: mean ± s.e.m..
Bar graphs showing the reversal potentials of PC1-CTF/PC2_AA and the indicated mutants tested in bath solutions containing 100 mM of the indicated ions. Two PC1 and two PC2 mutations caused dramatic changes in the reversal potential for almost all tested ions (B), indicating that these amino acids are essential for ion permeability. Statistical significance between reversal potentials of all pore mutants and that of the PC1-CTF/PC2_AA channel are indicated. Oocyte numbers are indicated in parentheses. Data are presented as mean ± SD (n.s.: not significant, **P < 0.01, ***P < 0.001, Student's t-test).
A In organello import of the precursors of TFAM and AAC1 into isolated mitochondria from control and TIMM50 mutant fibroblasts in the absence or presence of the uncoupler FCCP. The radiolabeled precursors were incubated with isolated mitochondria for the indicated times followed by trypsin treatment only in the case of AAC1. Coomassie Blue (CB) staining was used as loading control and the radiolabeled protein (TNT) as reference for quantification. The position of the precursor (empty arrowheads) and the mature protein (filled arrowhead) are also shown. Western blot for TIMM50 is shown as cell line control. B Quantification of TFAM and AAC1 import from control and TIMM50 mutant fibroblasts expressed as fraction of the input radiolabeled precursor converted into mature protein and normalized to Coomassie Blue signal. Data are shown as mean ± SD, n = 3 biological replicates; ∗p < 0.05, ∗∗p < 0.01, ∗*∗p < 0.001 grouping both controls together.
(I) Analysis of Pearson correlation coefficients (PCC) of CEP55 vs. MYC transcriptional activity in breast cancer TCGA tumor data with R=0.4157, p<0.0001.
A) Laminin α5 in the basement membrane supports strong adhesion of endothelial cells via β1 integrins, which ensures the correct cortical tension and stabilizes VE-cadherin at cell-to-cell junctions, required for a normal shear response. B) In the absence of laminin α5, the strength of endothelial cell adhesion is significantly reduced, leading to reduced cortical stiffness, less VE-cadherin at cell-to-cell junctions and correlated higher number of recycling VE-cadherin molecules, and a reduced shear response. Blue denotes recycling VE-cadherin- positive vesicles.
E Representative images of the mEOS-cdc42 mutants signal (cyan) after inducing the expression of GAL1p-CDC42 in the presence of Gal or repressing it in the presence of Dex. The cells in the blue and red boxes correspond to the cells in the blue and red box in panel (D). Images are average fluorescence intensity projections in which black and white pixels have been inverted.
(A) Myeloid cell-type distribution. The bar plots show the relative contribution (% of cells out of total) of custom cell-type classification labels within each experimental condition. (B) Lymphoid cell-type distribution. The bar plots show the relative contribution (% of cells out of total) of custom cell-type classification labels within each experimental condition.
C Maximal cytochrome c release for all DX/REL pairs with ≥3 biological replicates); box-whisker plots summarize data (box 25%-75%; belt=median; dot=mean; whiskers=minimum and maximum values). Statistical analyses were performed using an unpaired two-sided Student's t-test, with significance p<0.05 (trend p<0.10). Cyto c, cytochrome c
(G-J) Ts65Dn has learning and memory defects, but Ts65Dn/DSCR1+/- mouse clearly rescues learning and memory defects to control levels. Values are shown as mean ± SEM, and tested for statistical significance by one-way ANOVA followed by Bonferroni post hoc test. N = 8 (control), 5 (Ts65Dn), 10 (Ts65Dn/DSCR1+/-) animals, *P< 0.001 (G, H). *P< 0.05 (I), **P< 0.01 (I). (J) Open-field analysis shows no defects in movement of tested animals. Values are shown as mean ± SEM, N = 6 (control), 5 (Ts65Dn), 3 (Ts65Dn/DSCR1+/-) animals.
B. Double-luciferase detection of small peptides that affect BMP4 transcription (Data are shown as mean ± SEM, n =3 independent experiments, ** p < 0.01, **** p < 0.0001, one-way ANOVA).
Effect of PP2A knock-down on Ago2 phosphorylation and its miRNA association. Cellular miRNA levels (K, left panel mean +/- s.e.m., n=3) and Ago2 associated miRNAs content in cells treated with siCon or siPP2A were measured using qRT-PCR and plotted (K, right panel, mean+/- s.e.m., n=3).
(B) The efficacy of the same drugs in human Airway Chips infected with CoV-2pp. Chloroquine, Arbidol, toremifene, clomiphene, amodiaquine, Verapamil, and Amiodarone were delivered into apical and basal channels of the chip at their respective Cmax in human blood, and ne day later chips were infected with CoV-2pp while in the continued presence of the drugs for 2 more days. The epithelium from the chips were collected for detection of viral pol gene by qRT-PCR; viral entry in untreated chips was set as 100%. *, P < 0.05; **, P < 0.01; ***, P < 0.001.
(a) At 16 h post-transfection with GST, GST-K-α2 or GST-K-α4 along with Flag-vFLIP (top) or Flag-cFLIPL (bottom), HEK293T cells were used for GST pulldown, followed by immunoblotting (IB) with anti-Flag or anti-FLIP antibody. Whole-cell lysates (WCLs) were used for IB with anti-GST, anti-Flag or anti-FLIP antibody.
Experiments were performed using murine BMDMs. (D) Intra-phagosomal proteolysis in WT and inhibitor-treated BMDMs (n = 4 wells) was monitored as in Fig 1B. BMDMs were pre-treated with 0.1 μM PD0325901 (10 min) to inhibit MEK1, pre-treated with 1 μM VX-745 (1 h) to inhibit p38α and pre-treated with 10 μM C34 (1 h) to inhibit TPL-2. (E). Intra-phagosomal acidification in WT and inhibitor-treated BMDMs (see (D) for conditions) was assayed as in Fig 1C (n = 4 wells). Data information: One representative experiment out of three shown. Error bars and shaded areas represent SEM. **** P < 0.0001. Paired Mann-Whitney t-test; all differences relative to WT are ****.
(D-F) Cell viabilities (D), cell death mechanisms (E), or Mtb growth rates (F) of Mtb-infected Socs6-/- BMDMs that were transfected with plasmids expressing Myc-RIPK3 or Myc-RIPK3 K51A mutant as indicated. Z-VAD treatment concentration was 20 μM and the treatment time was 24 hours. Data are shown as the mean ± s.e.m. of n = 3 biological replicates.
D. The site of interaction of the motif3 of veal2 (CLM) with the Prkcbb protein indicates that it lies in a previously known DAG binding site. Both RNA (pink) and protein (purple) structures are shown as ribbon models. The distances between nucleotides of motif-3 of veal2 and the 2 amino acids of Prkcbb are given in Å units.
G, H. U1 Grx1-roGFP2 cells were supplemented with BSO (G) or GSH (H) for 16 h to deplete or replenish GSH, respectively. Following this, cells were treated with Vs for 15 min, exposed to H2O2, and the ratiometric response was measured.
H Regulation of the ITSN-DENND2B interaction. In the absence of phosphorylation, DENND2B binds the SH3A (A) domain of ITSN. Phosphorylation of DENND2B by PKD occurs on Ser-30 residue within the first proline-rich domain (PRD). Phosphorylation of Ser-30 recruits 14-3-3 which outcompetes ITSN binding.
E. Morphology and quantification of FIJs-treated CMs undergoing cytokinesis by H3P and Aurora kinase B (AURKB) staining.
(D) HuR western blot in middle right panel confirmed the presence of HuR and the truncated version of it in the immunoprecipitated materials. A representative domain picture of HuR and HuRΔIII are shown in the upper panel. Relative levels of HuR bound miR-122 were determined by qRT-PCR (mean+/- s.e.m., n=3) (middle left panel). Amount of miR-122 recovered from the immunoprecipitated materials were normalized against the amount of HuR or HuRΔIII present in the Immunoprecipitated materials. Ago2 western blot confirmed its presence in the FLAG beads used in the assay while Ago2 was not detected in HuR immunoprecipitated materials (bottom panel).
(E-F) Expression of CSAG1 (E) and CSAG2 (F) in normal adjacent (blue) or tumor tissue (red) from TCGA RNA-Seq data. N.D. represents normal adjacent is not available. Data visualized by firebrowse. Number of biological replicates are as follows: ACC 41, BLCA 307, BRCA 524, CESC 175, CHOL 11, COAD 153, COADREAD 232, DLBC 36, ESCA 121, HNSC 416, KICH 46, KIPAN 515, KIRC 411, KIRP 58, LAML 7, LGG 528, LUAD 301, LUSC 400, MESO 31, OV 183, PCPG 70, PRAD 204, READ 79, SARC 156, SKCM 422, STAD 288, STES 409, TGCT 126, THCA 408, THYM 75, UCEC 306, and UCS 37. Central band indicates median, boxes define 25 and 75 percentiles, and whiskers define 5 and 95 percentiles.
(B) Experimental scheme of dual labelling of DNA fibers in shWRNIP1WT, shWRNIP1 and shWRNIP1T294A cells. Cells were pulse-labelled with CldU, and then subjected to a pulse-labelling with IdU.(C) Analysis of replication fork velocity (fork speed) in the cells under unperturbed conditions. The length of the green tracks were measured. Mean values are represented as horizontal black lines (ns, not significant; Student's t-test).
(E) FRAP analysis of TFEB-GFP‐positive lysosomes from control MEFs (blue) or MEFs treated with Torin 1 (red). Each data point represents mean±s.d. from five independent spots.
(G) Upper panel: computational algorithms using PROMO and JASPAR predicted that two putative KBEs were harbored in ΔQP region (position -400 to +200). QP, QKI-5 promoter; KBE, KLF6 binding element. Lower panel: anti-KLF6 ChIP was conducted in A549 cells and followed by PCR and gel-staining to confirm the presence of QKI-5 promoter sequence containing KBE1 (position -346 to -336) or KBE2 (position +21 to +31). The input and anti-IgG antibody were used as positive and negative controls, respectively.
(D) Western blot analysis for Lin28a in cortex of E15 WT and hFOXM1-cKI mice. β-actin was detected as loading control.
I Tau expression in worm lysates, as detected using the human tau-specific antibody HT7.
(A) Kinetic SHP099 modulation of p-STAT3 (Tyr705) and p-ERK1/2 (Thr202/Tyr204) in endothelial and B16F10 cells; SHP099: 5μM HUVEC; 20μM BMEC and B16F10; representative immunoblotting of 3-5 experiments; h: hours. (B) Quantification of band intensities in panel (a); p-STAT3/STAT3 and p-ERK1/2/ERK1/2.
Fluorescence stainings for YAP (green), F-actin (magenta) and with the nuclear marker DAPI (blue) of primary hepatocyte cultures treated with DMSO (control), Y27, deoxycholic acid (DCA) or DCA+Y27 for ~18 h. Indicated areas (dashed rectangle) are shown as magnifications in insets.