EMBO/sd-character-level-ner huggingface dataset:
Tumors formed by SCC13 Act cells were treated ex vivo for 6h with follistatin (FST) (50 ng/ml) and/or SMIFH2 (10 μM), or with activin A (20 ng/ml) and stained for Ki67. N=3 tumor explants, n=4 histological sections.
F Live imaging of MCCs shows the inability of Ccdc108 mutant proteins lacking the seven amino acid IFT interaction domain to localize to cilia. Embryos expressing GFP tagged Ccdc108 mutant proteins (green) and Cetn4-RFP (purple) were imaged at stage 27.
D, After 1 day LDL depletion in 5 % LPDS, cells were loaded with 50 μg/ml LDL for the indicated times and intracellular cholesterol was detected with D4H as in C by confocal microscopy. CM, complete medium. Dashed lines indicate cell outlines. E, Quantification of D. Mean ± SD, n = 25-26 cells pooled from 2 independent experiments.
(a) A HeLa cell expressing KR-dMito (red), EGFP-DFCP1 (green) and EBFP2-parkin (cyan) were illuminated with 559 nm at the white dotted circle region, leading to the generation of a long parkin-labelled mitochondria tubule (right, magnified view of the light-activated region) for autophagic turnover (white arrow). Scale bars, 10 μm.
(C( Dab2 promotes cleavage of K63-linked polyubiquitin chains on Akt in vivo. Akt was immunoprecipitated from the soluble fraction of muscles expressing shLacz or Dab2-DN from fed and fasted mice using a specific antibody. Mouse IgG was used as a control for non-specific binding. Protein precipitates were subjected to immunoblotting with an antibody against K63-linked polyubiquitin conjugates.
(D) Heatmap of protein ratios (Δach1 versus WT, log2 scale) corresponding to indicated genes. Data were obtained from mass spectrometric analyses of acetylated proteins enriched by IP similar to (C, 1 mg/ml protein). Extracts from stable-isotope (SILAC)-labeled cells were mixed prior to IP (prelysate), and mean SILAC-protein ratios after IP were normalized to ratios of prelysates to correct for changes in general protein abundance. Two biological replicates were performed (Rep. 1 and Rep. 2) with a regression coefficient of 0.76 of observed protein ratios. Heatmap represents identified proteins with reproducible 1.5-fold upregulation (red color) or downregulation (green color).
For each of the four panels, the heatmaps on the left indicate the Pearson correlation of proteins with viral load in severe survivors and severe fatalities, the heatmap on the right indicate the significant pathways enriched by proteins positively or negatively correlated with viral load in severe survivors and severe fatalities (Fisher-exact test, p <0.05).
Figure 1. Symmetry breaking of Min protein patterns in vivo. A. Schematic showing Min protein patterns in a defined geometry originating from 1) a dynamic instability arising from an equilibrium state, or 2) dynamic transitions from a pre-existing pattern associated with cell growth. Green and red particles represent MinD and MinE proteins, respectively. The green gradient depicts the MinD concentration gradient.
Representative IF images showing the expression of YAP, p-S6, and ATF4 in serial sections of 3D organoids derived from secretory cells in indicated culture conditions. Tomato (for Scgb1a1 lineage, red), YAP (green), p-S6 (white), ATF4 (magenta), and DAPI (blue). Scale bars, 100μm.
Hypoxia activated TEAD activity (8x GTIIC-luc reporter) but this was reduced by GPRC5A depletion. A representative triplicate experiment is shown (n=3).
Wild-type (WT) and YF-eNOS (YF) mice were treated with vehicle (Veh) or angiotensin II (AII, 1.44 mg/kg/day) for up to 28 days. 3-Nitrotyrosine (3-NT) levels in lungs from WT and YF mice treated with vehicle (Veh) or AII (AII) for 28 days; n=7-9 mice per group (2-way ANOVA and Bonferroni).
Relative mRNA levels of immune related genes in Vgll4-knockdown A549 cells by qRT-PCR analysis
C HeLa cells transfected the indicated GFP-FBXO2 mutants (green) were infected with WT GAS for 4 h; scale bar, 10 μm. percentages of each FBXO2 mutants localized to GAS (C).
A In vivo suppressive function of WT and Traf6fl/flFoxp3Cre+ Tregs. Tregs from the indicated mice (CD45.2+) were isolated by FACS, as were naïve (CD62Lhigh/CD25-) CD4+ responder T cells from congenically distinct (CD45.1+) donor mice. Tregs and Tresponders were mixed at a 1:5 (2x105:10x105) ratio before injection into Rag2-/- mice. 7 days later, spleens were harvested, and the relative frequencies and absolute numbers of each transferred cell populations were determined by flow cytometry.
(C) Diagram of KUP9 gene structure. The T-DNA insertion site in the kup9-1 mutant and the mutant site in the kup9-2 mutant are indicated by the triangle and arrow, respectively. The filled boxes and lines represent exons and introns, respectively.
(A) Knockdown of SIRT1 abolished CSAG2-mediated decrease in ac-p53 K382. CSAG2 over-expressing HCT116 were transfected with SIRT1 siRNA for 72 hr before doxorubicin/TSA treatment for 6 hr. Cell lysates were blotted for the indicated proteins.
(d) Impaired inactivation of TORC1 in response to eIF4A knockdown is most apparent upon partial depletion of amino acids, caused by removal of amino acid subsets. After 5 days of knockdown, S2 cells were treated for 30 min with either complete Schneider's medium (+aa), Schneider's medium lacking all amino acids (-aa) or various subsets of amino acids, as indicated (where EAA "essential amino acids" = H,I,L,K,M,T,W,V). Error bars: std dev. n=3 biological replicates.
Bar graph showing the percentage of secretory, DATP, and AT1 cell clusters in control and Lats1/2 dKO lungs at day 5 and 14 post tamoxifen treatment.
H, Schematic of FAK-regulated PI(4,5) P2 generation on endosomes via PIPKIγ, modified from (Nader et al., 2016).
B Graphs show the quantification of different parameters in mice striatal interneurons (Ctip2-/NeuN+). N = 4 for both genotypes. An average of 5,000 nuclei was analysed for each sample. Representative images are shown. Scale bar 7 μm.
A. Left panel; HeLa cells were co-transfected with GFP-MBP (control), GFP-SIM1 or GFP-SIM1-mut (AGO interaction defective) along with RL-control or RL-3xbulge. Firefly luciferase was used as transfection control. Dual luciferase assay was performed. RL/FL luminescence ration was plotted after normalization with GFP-control. Data are presented as mean SD (n = 3), P‐value was calculated using Student's t‐test.
(C) Overall survival analysis using GEPIA datasets (log-rank test; the solid line represents the survival curve, while the dashed line represents the 95% confidence interval).
E-G. Detailed views of UBE2N contact patches A (E), contact B (F) and contact C (G). Key residues involved in interactions between MvcA (core domain: green, insertion domain: yellow, tail domain: blue) and UBE2N (cyan) are labeled and shown as sticks. Leu330 of MvcA is labeled in red stick in F and yellow stick in the bottom right panel, which shows it interacting with a nonpolar pocket of UBE2N (shown in electrostatic surface). Hydrogen bonds are shown as dashed lines.
(D) qPCR estimated mtDNA copy number in WHS and control cells. Values are expressed relative to control cells (C1-C3). Data are expressed as means ± SEM of n=3 independent experiments
(B) In vivo pull-down of HA-tagged SUMM2 by FLAG-tagged CRCK3 kinase domain. KD represents a truncation of SUMM3 with only the kinase domain (amino acid 201-510).FLAG-tagged full-length or truncated CRCK3 and HA-tagged SUMM2 proteins were transiently expressed in N. bethamiana by agro-infiltration. FLAG-tagged CRCK3 proteins were immunoprecipitated with anti-FLAG conjugated beads (Sigma) and detected by Western blot using anti-FLAG antibody. HA-tagged SUMM2 protein co-immunoprecipitated with FLAG-tagged CRCK3 was detected by Western blot using anti-HA antibody. Similar results were obtained in two independent experiments.
(a) Immunoblot for htt or p62 from total APHs (T) and their corresponding membranes (Mbr) and matrices (Mtx) isolated from livers of wild-type htt (18Q) and 111Q-htt mutant huntingtin knock-in mice (111Q). Left, representative immunoblots. Right, distribution of htt and p62 between Mbr and Mtx calculated by densitometric quantification in six such immunoblots. AV, autophagic vacuoles. Mean + s.d. *P 0.05 compared to wild-type values.
A Representative image of E18.5 coronal cortical sections stained for layer V marker Ctip2 (red) from Kcc2lox/lox embryos electroporated in utero at E14.5 with plasmid constructs encoding EGFP or EGFP+Cre (Cre). Upper boundary of layer V indicted with dotted line. EGFP signal is shown as green pseudocolor. DAPI staining (blue) marks cell nuclei. Sp, subplate; IZ, intermediate zone. Scale bar = 50 µm. B Number of EGFP+Cre neurons migrating above (II-IV) and below (V-VI/IZ-SVZ) the upper border of layer V normalized to respective data from embryos electroporated with EGFP alone. Statistical significance was determined using one-way ANOVA with Holm-Sidak's post hoc test, ***P < 0.001 to EGFP. Data are presented as mean ± S.E.M., n (EGFP +Cre) = 8 embryos; n (EGFP) = 8 embryos.
Western blot analyses of EV preparations. (F) EVs isolated under glutamine-depleted conditions were immunocaptured with anti-CD81 antibodies coupled to magnetic beads. All or most CD63 and CD81 appears to be pulled down, but less than 10% of Rab11a and Cav-1 is captured. NTA analysis suggests about 10% of all particles are pulled down with this approach.
(D) qPCR validations of circSLC8A1 and SLC8A1 mRNA changes in the SN, T-test p*=0.025. n=18 for CT and 24 for PD, x defines mean values.
A Schematic representation of Matrin3 with its domains in the wild‐type construct (WT) and the mutants used in overexpression, mPRI which has corresponding domain deleted in each one of the mutants, mPRI where the PRI motif is mutated from GILGPPP to GAAAPPA, ΔZ1 where the first zinc finger is deleted, ΔRRM where both the RRM domains are deleted and ΔZ2 where the second zinc finger is deleted.
(E) Enrichment plots from GSEA performed using LIVER-ID TFs as the gene set and transcriptomic changes induced by acute ERS in MPH (upper panel) or mouse liver (lower panel) as the ranked gene list.
USP36 interacts with Ubc9 in cells. H1299 cell transfected with the indicated plasmids were subjected to co-IP with anti-Flag antibody followed by IB.
H. Representative H3K27me3 and EZH2 immunofluorescence images and box plots (minimum, first quartile, median, third quartile and maximum) showing decreased H3K27me3 levels but increased total EZH2 levels in TGFβ1-injured AECs in co-culture with MCs (n = 5 biological replicates with >50 cells per experiment, scale bars 50 µm, *p < 0.05, unpaired t-test).
(A) Interaction between endogenous PAQR3 and the components of VPS34 complex in HEK293T cells. The cell lysates were used for immunoprecipitation (IP) and immunoblotting (IB) with the antibodies as indicated.
C) Exposure to stress conditions does not increase Tf2 transcript levels further in fft2Δ fft3Δ cells. Transcription fold change as in Figure 1D, but relative to act1 transcription and to transcription in the same culture immediately prior to stress, as measured by qPCR. Error bars represent standard deviation of reverse transcriptions of biological duplicates
B, AltFUS endogenous expression in HEK293 cells using a siRNA targeting FUS mRNA as negative control and over-expression of altFUS CDS as positive control (representative image from n=3). For the mock, siCTRL and siFUS conditions, 100 μg of total protein was loaded, when only 15 μg of total proteins was loaded for the altFUS over-expression condition.
F - Schematic view of the outcome of TG2 activation in infection. The increase in TG2 expression and activity in cells infected with C. trachomatis results in the up-regulation of the expression of glucose transporters. Increasing quantities of glucose are thus imported in the host cytoplasm and redirected to the vacuole, where they fuel bacterial growth. Parallel to this transcriptional outcome, the transamidating activity of TG2 targets the host enzyme GFPT, thereby boosting the hexosamine biosynthesis pathway. The bacteria consume the resulting UDP-GlcNAc, or an intermediate along this pathway, in particular to sustain bacterial division.
A-B Canonical pathways (A, DRG, and B, spinal cord) identified by IPA are ranked by P (-log10P). Positive and negative z-scores (in the spinal cord) indicate up-regulation or down-regulation, respectively, according to the color scale. Bar colors correspond to significant activation (orange), deactivation (blue), or no change (gray) in pathway regulation.
A Whole cell extracts (WCE) were prepared from the indicated strains, immunoprecipitated (IP) with anti-GFP antibody and subjected to western blotting with anti-V5-Pk (Serotec) and anti-GFP (Life Technologies) antibodies. Data are representative of three independent biological repeats.B As for A.
(C) Enrichment of defense-related genes in the Gmlmm1-1 mutant. The Gmlmm1-1 and WT plants (aged 2 weeks) were subjected to RNA-seq analysis. The genes that were highly expressed in Gmlmm1-1 compared with the WT (2-fold changes) are presented. The enrichment (%) of the GO terms indicated is presented, and the p-values are calculated by Fisher's tests. Detailed data are shown in the source data.
(ai) Western blot analysis of tubulin, LC3-I and LC3-II in zebrafish larvae where ATG7 was downregulated, as indicated. (ii) Western blot analysis of CALM-HA, actin and LC3-II in zebrafishlarvae where CALM-HA was expressed, as indicated. The larvae were treated with ammonium chloride (NH4Cl), as indicated. (SE, short exposure; LE, longer exposure). Quantification of LC3-II/actin ratio is shown. Data are representative of three independent experiments and shown as mean ±s.d. (*P0.05; two-tailed t-test).
Overexpression of TBK1 or TRIF induces ACE2 expression.TBK1 is an essential activator of RNA-sensing pathway. HEK293 cells were cultured in 24-well plates. 24 hrs later, plasmids as shown above were transfected into HEK293 cells. 36 hrs after transfection, total RNA was isolation for subsequent RT-qPCR analysis. Results in each panel are representative of three independent experiments.
C. DRIP peak heights in wild type and primpol DT40 normalised to Drosophila S2 spike-in. n (wild type) = 41445; n (primpol) = 48648. D. Correlation of normalised DRIP peak heights in the overlapping peaks between wild type and primpol. Blue line = 1:1 correlation; red line = linear regression through data. Data information: P values calculated with Mann-Whitney U test. In violin plots, bar = median; box = interquartile range (IQR); whiskers = upper and lower inner fences (1st / 3rd quartile + 1.5*IQR).
B. Cell lines generated from WT, null, and mutant p53 esophagi were assessed by Western blot analysis for p53 protein expression. Relative intensity densitometry of Rab11-FIP1 results are shown at the bottom.
(c) Widefield immunofluorescence images showing early endosomes (EEA1) and Golgi (golgin-97) in UOK257 and UOK257-2 cells. Scale bar = 10μm.
F: Image of group of NTH/GFP sporozoites stained with MitoTracker Red CMXRos, showing distinct subcellular positions of apicoplasts (green) and mitochondria (red). Scale bar = 10μm.
(A) The T cell clone 20-4/A4 recognizes an epitope derived from the NeoR protein in the context of HLA‐DP3. MHC class II expression on RCC1.24‐NeoR cells following IFN‐γ treatment confers recognition by 20-4/A4. This recognition is almost completely blocked by the HLA‐DP‐specific antibody B7/21. EBV‐B cells transfected with pINCO‐NeoR are able to present endogenous NeoR on MHC class II. As exemplified by the cell lines EBV‐B1.11 (HLA‐DP3) and EBV‐B1.25 (HLA‐DP4), recognition by 20-4/A4 is dependent on HLA‐DP3 expression. Bacterially expressed NeoR protein and a synthetic peptide encompassing amino acids NeoR216-229 served as controls.
C. Proliferation of melanoma cells over indicated times after treatment with siASNS, siSLC7A5, or both.
E Flg22-induced MAPK activation was analyzed by immunoblots with α-pMAPK. Experiments (B) - (E) were performed three times with similar results.
(H) Clonogenic assay +/- PLX4032 (150 nM), +/- GDC-0973 (5 nM) treatment for 10 days. The graphs represent the mean number of colonies (± SD) in 3 independent experiments (Student's t-test). (I) Number of weeks of chronic exposure to PLX4032 before emergence of resistance in control or ZEB1-expressing cells (n=3, Student's t-test).
B Quantification of motility as a measure for toxicity. Displayed is the mean ± SEM (N = 4) of body bends/30s of animals expressing the indicated transgenes or harboring the indicated mutations. Statistical analysis was done using one-way ANOVA with Dunnett's multiple comparison test. *** p ≤ 0.001. Co-expression of the hsp-110 hairpins exposed the ts mutant phenotype at the permissive temperate of 15°C, resulting in a significant increase in movement defects. All strains contain the sid-1(pk3321) allele.
The expression of the IL-6Rα (CD126) and signaling chains (gp130) was assessed by flow cytometry (A) on a panel of DLBCL cell lines. ABC- and GCB-DLBCL cell lines are color-coded in red and green; RC-K8 are depicted in grey, as their subtype is a matter of debate
Mad1 kinetochore levels in the indicated conditions normalized to level of CREST in HeLa cells. Cells were fixed at 45 min after releasing from RO3306 arrest into nocodazole. Bar indicates mean and standard error of mean is shown by line. At least 200 kinetochores from 10 cells were analyzed and representative result from at least 2 independent experiments is shown.
Confocal z-projections of dpr12∆50-81 heterozygous (A, n=15; C, n=10; E, n=10) and homozygous brains (B, n=8; D, n=18; F, n=24) expressing mCD8-GFP (CD8) driven by (E, F) R18H09-Gal4 (MBONγ4>γ1γ2 -Gal4). The greyscale channels are sub-z-projections comprised of slices restricted to the γ-lobe region. White dashed line demarcates the γ-lobe. Bottom: Cartoons schematizing MB lobe structure and innervation by specific PAM-DANs or MBON.
A. Rapamycin suppresses TLR3-stimulated IFNβ protein production in cultured macrophages: RAW264.7 macrophages were pre-treated with rapamycin [20 ng/mL] (30 min), Ku-0063794 [1 μM] (30 min), or amlexanox [50 μM] (2 hr.) and stimulated -/+poly (I:C) [30 μg/ml] for 6 hr. The secretion of IFNβ was measured by ELISA. Results represent the mean +/- SD of quadruplicate samples from one experiment. *p=.0009 relative to +Poly(I:C) by paired t-test (two-tailed).
B Theoretical calculation of the number of NEAT1_2 transcripts versus the length of the A blocks (represented by the number of segments) of spherical paraspeckles in the steady state. The parameters used for the calculations are shown in the Materials and Methods.
d, Quantification of autophagic activity of wild-type and Δapg12 cells by alkaline phosphatase (ALP) assay before (black bars) and after (white bars) nitrogen starvation for 4 h. Error bars indicate s.d. of three independent experiments.
A: Acyl-rac captured hydroxylamine-cleavable, acylate PIKfyve from mouse brains. Control: TRAPα, a non-acylated protein. Input: 10% of lysate.
(E and F) ARPE-19 cells were cotransfected with plasmids expressing TFEB-GFP together with inactive (E) or active Rag heterodimers (F). Cells were then incubated with 250 nM Torin-1 for 1 h (E) or starved in serum- and amino acid-free medium for 3 h (F). Anti-GST antibodies were used to detect Rag proteins. Arrows point to cells that do not express Rag heterodimers.
Fis1 knockdown prevents DFP-induced mitophagic autolysosomes. Nsi or Fis1i together with mito-pHfluorin were transfected into HeLa cells in the absence or presence of DFP (24 h), which were analysed using the mito-pHfluorin construct 72 h post-transfection (Red: mCherry-A or puncta indicating occurrences of mitophagy marked by white arrows; Green: SEP-A; Yellow: mitochondria labelled by mCherry-SEP-A; Blue: Fis1; Scale bar, 10 μm; n=25 cells per condition from three individual experiments; *** p<0.001; unpaired-t test).
Western blotting of samples after ectopic overexpression of HBP1 (B) alone, or together with WDR26 or GID4 in HEK-293T cells. HBP1 levels were monitored after treatment of MG132 or DMSO for 10-12 h (n=3).
G. Immunoblot analysis of secreted PGRN and ApoE (ApoEmed) in conditioned media and PGRN, ApoE, CLEC7A, P2RY12 and TREM2 in lysates of BV2 wild type (Grnwt) and PGRN deficient (Grnmut) cells. Soluble amyloid precursor protein (APPs) and calnexin were used as a loading control.
XBP-1S expression was determined by IHC in two different cohorts of human prostatectomy samples.Representative pictures of benign and tumor samples.
Western blot analysis of Flag-RNF8 denaturing-IP in HEK293 cells showing hyper-ubiquitination of RNF8 after proteasome inhibition (MG132, 10µM for 6h).
IL-1R signaling during rod degeneration was inhibited by intravitreal injections of recombinant IL-1 receptor antagonist, anakinra (from P20-22 to P26-27) in one eye of each rd10 animal, while the contralateral eye was injected with PBS as a control. Upper panels show representative retinal sections from control PBS-injected and IL-1RA-injected eyes from the same animal. ONL atrophy in control eyes was more advanced compared to IL-1RA-injected eyes, with greater mean ONL thickness and lower mean density of TUNEL+ ONL nuclei in IL-1RA-injected eyes (lower panels) (n = 15 animals; measurements in IL-1RA-injected eyes normalized to contralateral control eyes, paired t-test). Scale bar, 25 μm.
Schematic view showing the truncated mutants and ML/AA mutant of cyclin F (Left). HEK cells were transfected with indicated constructs and co-immunoprecipitation was performed using Flag resin (Right).
D Quantitative analysis of CD31 expression in FI, CI, PI and PI+MVF in % of FI (n = 3). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.
Bar-plots show the distance of multiple-tethered (O) and docked (P) SVs from presynaptic density (PD), 0-100 nm: MP-SV pool (dark blue); 100-500 nm: peripheral SV pool (light blue). Upon stimulation, multiple-tethered and docked SVs are localized significantly closer to the PD in OtofPga/Pga. P-values for (O) and (P) are calculated by Wilcoxon Rank test, * p < 0.05, *** p < 0.001, ns p > 0.05 and Ø inconclusive statistics because occurrence of docked SVs in wild-type resting condition is extremely rare. Multiple-tethered SVs, wild-type: inhib, n = 3 SVs; rest, n = 13 SVs; stim, n = 3 SVs; OtofPga/Pga: inhib, n = 21 SVs; rest, n = 34 SVs; stim, n = 16 SVs; docked SVs, wild-type: inhib, n = 2 SVs; rest, n = 1 SVs; stim, n = 7 SVs; OtofPga/Pga: inhib, n = 20 SVs; rest, n = 4 SVs; stim, n = 18 SVs.
(c) Size and number of endogenous ATG12 vesicles in VAMP2-knockdown HeLa cells in starvation condition. Confocal pictures are shown with arrows indicating ATG12 vesicles. Data are representative of three independent experiments and shown as mean ±s.d. for the size of ATG12 vesicle. (n≥100 vesicles; *P0.05; based two-tailed t-test). Scale bars, 5 μm.
F) Control and experimental peptides selected from peptide array-based in vitro kinase assay (see Fig EV2 for full details).
E) HeLa cells were transfected as in A), labelled with the indicated antibodies and imaged by SIM microscope. Scale bar in large panels, 5 μm; in small panels, 1 μm.
Stopped-flow time courses for translocon insertion of TM1 of EmrD (black) and EmrD(-) (blue) with mRNA constructs of varying chain length (50 to 135 aa).The FRET acceptor (Atto655) was placed at the N-terminus of the nascent peptide, the donor (Atto488) at position 111 (donor-in) of SecY. The results of global fitting are indicated (red lines).
(J) RT-qPCR analyses of selected ERS UP and LIVER-ID TF genes monitoring expression changes induced by 4h ERS in MPH pre-treated or not for 30min with 10µM PP2 (3 independent experiments). Mean Log2 FC ERS/Control are shown. The bar graph shows means ± SD (standard deviations). Two-way ANOVA with Bonferroni's post-hoc test was used to assess statistical significance, *P < 0.05.