EMBO/sd-character-level-ner huggingface dataset:
E Interaction network generated from the interactome analysis of the 49 potential TORC1-dependent proteins conserved among fission yeast, budding yeast and human, based on collated annotations from the STRING database. Interactions between proteins were scored based on both functional and physical interactions from experimental, text mining and database sources only. Connections were drawn upon reaching a minimum interaction score of 0.4, and the lines were weighted to indicate the relative strength of the annotated interactions. The resultant network of the 28 connected proteins were functionally categorised based on their GO biological processes as annotated on PomBase, and represented by the following colours respectively: cytoplasmic translation (GO:0002181) and ribosome biogenesis (GO:0042254) in green, mRNA metabolism (GO:0016071) and transcription (GO:0006351) in purple, vesicle-mediated transport (GO:0016192) in yellow and actin cytoskeleton organisation (GO:0030036) in brown. Grey nodes indicate proteins that were not assigned to the highlighted functional categories. Proteins that were identified as common in both phosphoproteomics studies are denoted by the darker hues of the respective colour categories, and the nodes of essential proteins are outlined in white (9/28)
(I) The Y699F mutant increased the percentage of cells expressing high levels of CD41 and CD61. Bars represent means ± SD from three independent experiments.
Immunoblotting analysis of expression of micropeptide CIP2A-BP and β-actin in TNBC cells cultured with or without TGF-β.
G) Protein decay analysis of HP1 interaction-defective Setdb1 mutant. mESC lines stably expressing 3xFlag-Setdb1 or 3xFlag-Setdb1-3A were treated with CHX and MG132 for the indicated times. Stacked bar plots show the summarized protein amounts of Setdb1 (right). Data represented as mean ± SD (n = 4, biological replicates). **p < 0.01 (Tukey's honestly significant difference test).
C Number of tumours in the DMBA-treated mice at 8 weeks of age (n=3). Dots represent tumours having a range size of 0-10, 10-40 or >40 mm2 in an individual mouse.
(b) mRNA and protein production and degradation rates for SESN1 fitted under oscillatory dynamics were used to predict SESN1 protein expression under rising dynamics.
(F) Rac1 activity assay (N = 3). (G) Quantification of Rac1 activity levels in (F).
E: Median shift in the CF of the area and F (33.8 (22.5/42.2) s; N=45 biological replicates), the area and the LimE-GFP intensity (-11.2 (-19.6/ -10.3) s; N=21 biological replicates), and the area and the GFP-myo intensity (52.5 (41.3/62.8) s; N=11 biological replicates).
Statistical analysis of Pc and stx double mutant stxd77;; pcXT109 sleep profile compared with controls. number of sleep bouts (From left to right mean±SEM: 19.67±0.5610, n=77; 15.91±0.6843, n=80; 21.79±0.8670, n=41; 21.20±0.9624, n=43; 12.69±0.5957, n=77; 11.58±0.5415, n=80; 13.31±0.7201, n=41; 11.34±1.001, n=43).
Schematic indicating the volumes measured to calculate the normalized fluorescence recovery of a locus relative to the entire nucleus.
Immunofluorescent staining of SARS-CoV-2 infected differentiated bronchioalveolar-like cultures. Nucleoprotein (NP) stains viral capsid (red), which colocalized with SFTPC Scale bars indicate 50 μm.
TNFR1 protein levels in serum and tissues of different mouse groups (n = 4-13). TNFR1 protein levels were measured by ELISA and compared to B, the levels of which were set as 100% for each tissue. From left to right: B mice (black), TNFR1+/- mice (grey), (BxS) F1 mice (grey), S mice (grey); B.S-chr6-BB (black), B.S-chr6-SS (green) and B.S-chr6-BS (grey).
A. Molecular dynamics simulations of native (R4) or variant (K4 and N4) nucleolin GAR-derived peptides interacting with an idealized phospholipid bilayer (posphatidylcholine (PC): phosphatidylserine (PS), 4:1) in water. Amino acid sequences of peptides are shown above. Shaded area - standard deviations of three independent runs, each 50 ns long. Mean values are indicated by colored lines and overlay of these is shown on the right.
(E) Binding of BRD4 and PolII and distribution of histone marks (H3K27ac and H3K9ac) on BRD4 dependent and independent genes (from -5kb of TSS to +5kb of transcription end site (TES)) in UT and LPS treated WT and KO macrophages. Normalized ChIP-seq signals (rpm/bp) are shown on the Y axis. Arrows show reduced signals in Brd4 KO macrophages.
B) Different expression of inflammasome-related genes (abs(fold change) > 1.5, p < 0.05, Benjamini- Hochberg adjusted) in PD-1-/- vs. wild type microglia. C) Different expression of complement system-related genes (abs(fold change) > 1.5, p < 0.05, Benjamini-Hochberg adjusted) in PD-1-/- vs. wild type microglia.
A: Illustration of possible complex formation involving Dam1c, Bim1 and Ndc80c. After addition of Ndc80c to pre-formed Dam1c-Bim1 complex in solution two possible outcomes are expected. Either Dam1c and Ndc80c form a complex including Bim1 or Bim1 is replaced upon binding of Ndc80c.
D. qPCR assay for several synaptic genes (LRKK2, Cadm3 and Slc6a11) confirms reinstatement of gene expression with anti-miR-mix (n = 5-7, Kruskal-wallis test).
(a) Western blot showing EGFP-HDQ71-induced degeneration of rod photoreceptors at 9 d.p.f. as indicated by the decrease in the abundance of of monomeric (∼36 kDa) and dimeric (∼72 kDa) rhodopsin. Rhodopsin expression is further reduced by 3 μM (±)-Bay K8644, and recovered upon treatment with 3 μM verapamil, 100 μM 2′5′ddA, 3 μM clonidine and 1 μM calpastatin. No general toxicity to the zebrafish at these concentrations was observed. (b) Expression of EGFP-HDQ71 significantly reduces the levels of rhodopsin expression when compared to wild-type (WT) nontransgenic controls. This effect is further abrogated by 3 μM (±)-Bay K8644, whereas 3 μM verapamil, 100 μM 2′5′ddA, 3 μM clonidine and 1 μM calpastatin all protected against rod photoreceptor degeneration. Error bars show s.e.m.
C) Bacterial viability of three Gram-negative strains after exposure to buffer, 10% human serum or C5b6MAC. Buffer and serum conditions are the same as Fig. 1E.
(E) Aggregation of CD16:7-263-281 promotes its own degradation. 293 cells were transfected with the indicated constructs, aggregated and lysed for western blotting. Shown are overexposed anti‐CD16 WBs.
(E) LMP1 interaction with ANT1 in vitro. GST-ANT1 expressed in bacteria was incubated with a Flag-LMP1 protein and the proteins were subjected to Western blot analysis.
(H) Mitochondrial membrane potential is required for efficient import of Mcp3 precursor into mitochondria. Isolated mitochondria were incubated with radiolabelled Mcp3 in the presence or absence of CCCP. After import mitochondria were incubated with PK as in (G) and analysed by SDS-PAGE and autoradiography. I, 20% of radiolabelled precursor protein used in each import reaction; The arrowhead marks an additional band of the size of the cleaved N-terminus of Mcp3.
(A) Capillary-based protein detection (Jess) of antibodies against SARS-CoV-2 antigens in convalescent sera.
Hierarchical clustering of preadipocyte clonal cell line gene expression using Ward's agglomeration.
(D) Fluorescence images of NDP52 KD and control cells expressing mCherry-LC3 and MTS-TagBFP. Arrows indicate mCherry-LC3 puncta colocalized with MTS-TagBFP. Scale bars, 10 µm. Boxed areas in images are shown in the next panels on the right. Images are representative of four independent experiments
(H) Representative images (n=3) of CHME3 expressing Flag-CLIP170 or Flag-CLIP170ΔCAPgly stained for Flag and Tyr-MTs. Scale bar, 10 μm.
(C) Loss of CHD1 leads to increased sensitivity to PARP inhibition. Control or CHD1-depleted BPH1 cells were treated with the indicated concentrations of the PARP inhibitor olaparib and surviving fractions were measured by counting colonies after 3 weeks. Data represented as mean values (n=3, ± SD, p-value=0.0003, ANOVA, ***p ≤ 0.001).
Candicidal function of neutrophils depend on SOCE. (H) Coculture of Cd11b+Gr-1+ neutrophils from WT, Stim1fl/flMx1Cre and Stim1fl/flStim2fl/flMx1Cre mice with C.albicans in vitro for 0, 30, 60 and 90 min (MOI 0.5). Percentages of live C.albicans isolated from neutrophils that were lysed at the indicated time points. Data are the mean ± SEM from 6 mice per genotype and 3 independent repeat experiments.
E) Barplots showing qRT-PCR gene expression levels (mean +/- S.D.) of PTEN, FNDC3B, and STAM genes in control, 4hr and 24hr actinomycin D treated K562 cells. p-value: two-tailed t-test, (*** p < 0.05). The results represent data from 3 technical replicates from 3 independent biological preparations.
S100A8 and S100A9 expression were determined by western blotting of lysates from MoLC, MoDC and MoDC treated with TGF-β for 24h or from cell lines as indicated. Loading controls were done with GAPDH or actin antibodies. Human primary cells results are representative of three donors and the experiment shown is representative of three (n=3).
(J) Model for RQC-coupled (NGDRQC+) and -uncoupled (NGDRQC-) endonucleolytic cleavages in the R(CGN)12 reporter mRNA. Endonucleolytic cleavage sites are depicted corresponding to panel I.
Heterofibrils containing mCHERRY- RIPK3387‑518 and YPet‑ZBP1170‑355 Pearson's correlation coefficients measured from two confocal images of the indicated protein mixtures.
C, D Analysis of the half-life of β-globin reporters. Samples were collected at the indicated time points, and the mRNA levels of the HBB reporters were monitored by qRT-PCR and normalized to POLR2J and ACTB reference genes. The values shown are the average fold-change (mean ± SEM) from three independent experiments relative to the first time point.
Percentage of chromosome loss of indicated mutants. Data information: χ2 test is used to determine the p-value and number of colonies tested per mutant is indicated in Appendix Table S1.
Tlr7wt/wt female mice (n=6) and Tlr7-Y1025D mutant Tlr7ki/wt female mice (n=6) and Tlr7ki/ki female mice (n=5) were treated with indicated dose of IMQ for 4 days. D Quantitative PCR analysis of mRNA encoding IL-23/IL-17A axis cytokines and other psoriasis-related cytokines in the dorsal skin. Results were normalized to Gapdh expression. Data information: Data are represented mean ± SEM. P values are determined by two-tailed Mann-Whitney U test *P<0.05, **P<0.01.
(e-h) Progression of rod death determined by the reduction of the ONL was visualized by hematoxylin and eosin staining.
(C, D) Quantification of MDVs, defined as TOM20+ve/PDH-ve, (C) or PDH+ve/TOM20-ve (D) per cell under steady-state conditions were performed (n = 32-52 cells per condition from 3 independent experiments).
A) ADAR1-knockout HEK293 cells (clone 1) were modified with a lentiviral-based inducible system to express FLAG-LGP2 WT or a FLAG-LGP2 RNA binding mutant (K138E/R490E/K634E, denoted as "KRK mutant") in a doxycycline-regulated manner. Cells were treated 72h with doxycycline (dox). Protein lysates were analyzed by SDS-PAGE and immunoblotting using the indicated antibodies (n=3). iEV = inducible empty vector; iLGP2 = inducible LGP2.
+/- inhibitors: anti-MyD88 peptide inhibitor, anti-mouse TLR2 antibody, or lipopolysaccharide (LPS)-RS, an antagonist of TLR4 in (D)
(C) Wild-type, Afdn-KO and Afdn-KO with re-expression FLAG-tagged WT I-Afadin or a non-phosphorylable form (S1795A) stimulated with vehicle or insulin (n=4) for Immunoblotting.
(D) Oxygen consumption rates in A- and T-strains (ratio of means=0.65, p=0.0002, Welch's T-test, 3 biological replicates, each measured in technical duplicates). Data information: Vertical bars show the mean of the data. Error bars and shaded areas in all cases denote standard deviation. Significance keys: * p<0.05, *** p<0.0005 (Welch's t-test).
B Structure of pLvx-scFV-sfGFP-JARID1A. The scFV-sfGFP-catalytic domain of JARID1A was sub-cloned into a lentiviral vector. The distance between the 5' and 3' Long Terminal Repeats in the vector is 8.5 kb. The components of the plasmids are as follows: , RRE, rev response element; cPPT, central polypurine tract; pCMV IE, immediate early cytomegalovirus promoter; scFV, single chain variable fragment; sfGFP, super folder GFP; JARID1A; catalytic domain of JARID1A; GB1, solubility tag protein; NLS, nuclear localization signal; WPRE, woodchuck hepatitis virus (WHP) posttranscriptional regulatory element.
D, E. Mice were infected with PR8 and treated with equivalent doses of IFNα or IFNλ or Veh Ctrl at days 2, 4 and 5 post infection; survival and weight loss was monitored (D, data pooled from 4 independent experiments, n=12-29) (data representative of two independent experiments, n=3-5).
Treatment with BO-110 of human patient-derived xenografts (PDX) implanted in Vegfr3Luc nu/nu. 42 days after implantation (when systemic luciferase was detected), animals were randomized for treatment with vehicle (V) or with 0.8 mg/kg BO-110 (BO, twice per week), and luciferase emission was acquired at the indicated times. Scale, p/s/cm2/sr (x106).
F Quantification of peripheral ER structures in untreated WT and UPR-deficient ∆hac1 cells (SSY2228, 2331), overexpressing ICE2 from plasmid pSS761 where indicated. Bars are the mean percentage of cell cortex covered by tubules (purple) or sheets (green), n = 3 biological replicates. Upper error bars are s.e.m. for the sum of tubules and sheets, lower error bars are s.e.m. for sheets. Asterisks indicate statistical significance compared with the corresponding value in WT cells, as judged by a two-tailed Student's t-test assuming equal variance. **, P < 0.01.
Cumulative probability plots of mEPSCs amplitude (500 events per cell) and representative examples of mEPSCs (left panel) recorded from brain slices of S and SD mice. (B) Control neurons (Ctrl/S n=8 cells/4 mice, Ctrl/SD n=8 cells/4 mice)
STAT3 phosphorylation as assessed by Western blotting (B, D) of the indicated ABC-DLBCL and GCB-DLBCL cell lines, with and without 1h of exposure to 50ng/ml hIL-6 (B,D). STAT3 expression levels are shown as Western blot control.
16-days old MCF10A spheroids grown in matrigel/collagen mix were stimulated for 24h with either macrophage-conditioned or control medium in presence of amlexanox. Amlexanox reduces the number of spheroids with invasive protrusions. Error bars represent mean ± SEM from 8 independent experiments (n=2 per condition, at least 15 spheroids each from at least 2 fields of view). Macrophage donors are indicated as D1-D25. M1D - M1 differentiated, M1A - M1 activated, M2D - M2 differentiated, M2A - M2 activated macrophages.
E, Embryo tetraploid complementation assays with un-induced iPSCs, miiPSCs or wild-type ESCs (n=3 clones per condition). Pictures on the right show a representative example of a viable "all-miiPSC" mouse (black) generated from miiPSCs and litters obtained from "all-miiPSC" adult mice, which efficiently contributed to germline transmission.
F) Localization of transfected Myc-tagged wild-type and mutant (P160L) β1-tubulin in Nthy cells. Immunostaining with anti-Myc antibody (in green) and microtubule cytoskeleton stained with α-tubulin antibody (in red). Note that β1-tubulin -P160L is found throughout the cytoplasm showing puncta appearance, whereas wild-type β1-tubulin colocalizes with the microtubules
(c) Each compound also reduced TDP43A315T-EGFP levels (DMSO, n = 983; FPZ, n = 550; MTM, n = 542; NCP, n = 493).
C) Northern blot quantification of mature piRNA 21UR-1 levels in wild-type, prg-1 (n4357), mut-7 (mj253) and rpb-9 (mj261) animals.
J-M mPS-PI staining of stem cell niche in the indicated genotypes at 5 DAG. Blue arrows indicate the QC, and red arrows indiate the CSCs. The numbers denote total number of scored samples, with same phenotypes showing in (J-M). Scale bars: 10 μm. N Quantification of the CSC layer in the indicated genotypes at 5 DAG. Data information In (N), data represent mean ± SD of three independent replicates. **P < 0.01, *P < 0.05 (Student's t-test).
B, Body weight of chow- and HFD-fed mice. Data represent the mean (+/- 95% confidence) from 8 animals (n = 8). The unpaired t test was used to verify the statistical significance. P = 0.0005 Data information: In the figure, A.U. = arbitrary units.
D. Knockdown of β5 subunit of proteasome in macrophages promotes the expression of proinflammatory factors. RNA was extracted from Raw264.7 (shGFP or shPsmb5) and the expression of Il-1β and Il-6 were quantified through RT-qPCR. The data are means ± SD of three independent experiments. *p < 0.05, ***p < 0.001 (student's t-test).
(a) Immunoelectron microscopy analysis of HeLa cells transfected with Flag-Dvl2 under nutrient-rich or starvation conditions. The arrowheads indicate Flag-Dvl2. Scale bars, 1 μm (left); 250 nm (right).
A, B Volcano plots showing significantly changed proteins in KO hepatocytes relative to WT in basal (A) and HBSS (B) conditions.
(B). Giemsa staining of freshly isolated human neutrophils from a healthy donor incubated with iRBCs harboring late stages P. falciparum parasites (black arrows).
(H) FTMT mRNA expression was quantified for Huh7 cells by real-time RT-PCR before and after DFP (1.0 mM) treatment with or without SP1 knockdown by siRNA (n=5, biological replicates). mRNA expression of FTMT level was normalized to GAPDH. The central horizontal bar and the error bards indicate mean ± SD. The Tukey's honestly significant test was used for statistical analysis. NC: negative control siRNA, **: P<0.01.
(F) Quantification of loaded MCM in p53-WT and KO RPE1 cells treated with palbociclib (1.25uM) for 1 or 7 days followed by drug washout for 8 hrs after 1 day of arrest) or 24 hrs after 7 days of arrest to capture cell in early S phase. To quantify loaded MCM, soluble MCM was pre-extracted from cells and the amount of the remaining DNA-loaded MCM was analysed by flow cytometry (see Figure Appendix Figure S4 for representative FACS profiles). DNA content was measured with DAPI, and DNA synthesis was measured using a 30-minute EdU pulse. The amount of DNA-loaded MCM in early S phase cells was compared to untreated control cells. The measured fluorescent intensity, each sample was divided by the background intensity of an identically treated but unstained control. The resulting ratios were normalized to WT control cells. Graphs display mean date +/- SD from 3 experimental repeats. Significance determined by one-way ANOVA followed by Tukey's multiple comparisons test (** p = 0.001, **** p < 0.0001).
Immunoblot for Transferrin receptor (TfR) levels in the indicated fibroblasts under basal and serum-starved conditions.
B, C. 293T cells were transfected with the indicated DNAs and immunoprecipitated with an anti-Flag antibody or pulled down with streptavidin-binding beads.
IFNB1 response in HEK293 cells stimulated with transfected plasmid DNA. Mean ± SEM of n=3 independent experiments.
BMDMs were costimulated with TNF (100 ng/ml) and TAK1i (125 nM) for 4 h in the presence or absence of KCl (50 mM). Where indicated, cells were pre-incubated with MCC950 (10 μM) 20-30 min prior to TNF/TAK1i stimulation.
C. Representative images of PC6 cells overexpressing Miro1 K572R or Miro1 WT together with EYFP-Parkin. K572R mutant induces Parkin translocation similar to WT in basal conditions but not after treatment with A&O (both 7.5 µM) for 3 hours. Note the spatial heterogeneity values shown in the images
(B) Scheme representing the LMX1A, NURR1, PBX1 and TH/PITX3 domains in the embryonic VM at E11.5-12.5.
B Model calibration with integrated pAKT, ppERK and pS6 data upon inhibitor treatment and 5 U/ml Epo stimulation of mCFU-E, 32D-EpoR and BaF3-EpoR cells. Area under curve from time-resolved, quantitative immunoblotting data was calculated and is represented by filled circles. Error bars represent standard deviation estimated by an error model. Solid lines represent model trajectories.
D. Bar plots from isoform specific RT-qPCR analysis showing average fold change (y-axis) of PTC+ and PTC- isoforms from genes indicated on the bottom in WT and the two UPF3B mutant cells identified in the legend on the top right. For each isoform, levels in mutant cells are compared to the levels in WT cells (set to 1).
3 and retinoic acid induce p19ink4d expression. Expression of p19ink4d messenger RNA by reverse transcription-PCR (A) or protein by western blotting (B) was carried out on extracts of cells treated with 3 (1,25D3) or retinoic acid (RA), as indicated.
Addition of polyA RNA, PEG (PEG8000), or both induces the de-mixing of Tau at physiological concentrations (5 μM Tau in 25 mM HEPES, 1 mM DTT, pH 7.4). Scale bars=10 μm.
D Representative IF costaining with GAP43 and BrdU antibodies in the MOE of the NC and miR-200b/a KD mice injected with BrdU at 3 d. The white arrows indicate the cells positive for both GAP43 and BrdU. D' is shown at higher magnification of the boxed region, as three channel merged images (left image) and the separated channel (middle and right images). D: Scale bars, 20 μm; D': Scale bars, 2 μm. E Quantification of the ratio of the number of BrdU+ GAP43+ cells and the number of total GAP43+ cells in the MOE of the NC and miR-200b/a KD mice injected with BrdU at 3 d (n=3 mice each group; data represent the mean±SEM; ****p<0.0001; Student's t-test).
A HT-29 cells were transfected with two individual siRNA for PANX1, or scramble non-specific (NS) siRNA for 72 hours. Cells were pre-treated with 10 μM QVD-OPh (Q) together with 5 μM Birinapant (S), prior stimulation with 10 ng.mL-1 of TNFα (T), as indicated. Western blotting for hallmarks of necroptosis, as indicated. The arrowhead indicates MLKL cleaved fragment. Molecular weight markers (Mr) are shown.
Quantitative analysis showing robust association of Rheb with depolarized mitochondria within axons treated with CCCP. The percentages of mitochondria targeted by Rheb or Rheb-SSVM in the presence or absence of CCCP were quantified, respectively
Detection of the newly synthesized proteins in QARS (shQARS) or GARS (shGARS) knockdown cells and the control cells stably overexpressing mascRNA (mascRNA) or expressing the scrambled RNA (Scramble). Left, biotin detection of the labeled nascent proteins; right, coomassie staining of total proteins.   Quantification of the labeled nascent protein levels in Panel M.
(F) Immunoblot analyses with anti-phospho-S6K and anti-phospho-S6 antibodies show that NO donors activated mTORC1 in HeLa cells.
(f) A diagram of the BrdU labeling time point in electroporation experiments. (g) Immunostaining of BrdU. White arrows represent BrdU GFP double-positive cells. (h) Percentage of BrdU and GFP double-positive cells in GFP-positive cells n=3 brains for each group Data information: Error bars represent the means ± S.E.M. Two tailed unpaired T-tests were used to analyze the data, n.s. (no significant difference), p<0.05(*), p<0.01(**), p<0.001(***). Scale bar: f) 25 μm
(C) Protein levels of KLF10 examined by western blots (left) and its expression was normalized to the β-actin (right). n=3. Results represent three independent experiments. Data information: * P <0.05, ** P <0.01-. Results are shown as mean ± SD. Student's t test
(c) Rheb GTPase activity assays were performed by co-immunoprecipitating TSC heterodimers from HEK293 cells expressing Flag-TSC1 and TSC2-TSC2 wild type, Flag-TSC2 mutants or the Flag-TSC2 GAP mutant (L1624P), for the indicated times.
(A) Representative confocal images of eye cryosections immunostained with anti-Ezrin (green) and anti-ZO-1 (red) antibodies from 2-month-old WT mice sacrificed 3h after light on at 10 AM (diurnal condition - LIGHT) and 3h after light off at 10 PM (nocturnal condition - DARK), nuclei were counterstained with DAPI (blue). Enlarged boxes highlight Ezrin staining in both basal infoldings (BI) and apical extension (AE) of the RPE. At least n = 6 mice per group. Scale bar 10 μm. Data information: (RPE) Retinal Pigment Epithelium; (OS) outer segment; (ONL) outer nuclear layer; (BI) RPE basal infoldings (AE) RPE apical extensions.
Impact of Ctcflos KD on mitochondrial biogenesis. (R) Microscopic images of Mito Tracker stained brite adipocytes (Mito tracker (blue); DNA staining by DAPI (green); phase contrast (PC) (gray))
Quantitative data showing the ratio of SA-β-gal positive cells in the control and LATS2-knockout hOSE-MXIV, hOSE-YAP and hOSE-YAPS127A cells at the seventh passage.