EMBO/sd-character-level-ner huggingface dataset:
C The table first row shows the number of genes significantly up or down regulated at 24 h of Dox treatment, subdivided in promoter-, intragenic-, intergenic-targets (± 50 kbp from TSS), and the rest. The following rows depict - for each gene class - mean (average) values of FPKM in cells treated or not with Dox for 24 h and the corresponding Δ FPKM and Fold change (Fc). Data are from 3 independent biological replicates.
F Similarly, ISCU1/2 expression was preserved in PECAM+ endothelial cells derived from mice treated with anti-miR-210 (N = 4/group), **P = 0.0016.
Two-photon imaging of these mice confirmed that propagating calcium waves were reduced by MRS2179 (APP/PS1-Stat3WT, n = 6 (4 female and 2 male) mice; APP/PS1-Stat3KO, n = 6 (2 female and 4 male) mice; age, 8 months; Mann-Whitney test).
B Immunoblot analysis of BHK cells infected with MuHV‐4 and MuHV‐4 [g‐KSHV‐TK] or uninfected cells using antibodies against phosphotyrosine (p‐Tyr), GFP, MuHV‐4 TK, ORF17 (capsid) and glycoprotein N.
(a) NRK cells stably expressing CFP-LC3; LAMP1-YFP were transfected with nonspecific (NS)- or AP4-RNAi and starved for 12 h. Scale bars, 5 μm. (b) Cells from a were assessed for enlarged autolysosomes in a blind fashion after starvation and quantified. n = 100 cells from three independent experiments. Error bars indicate the s.d.
Increased interaction of IRE1α K481R with BIM. Cells transfected with indicated vectors 24 hours prior to immunoprecipitation, followed by immunoblotting with indicated antibodies.
(C) Allele-specific expression ratios of X-linked genes are represented as heatmaps, with X-inactive genes in red (ratio ≤ 0.135), X-active genes in green (ratio > 0.135) and mono-allelic Xcas expression in blue (ratio between 0.5 and 1). Genes are ordered by genomic position and subdivided into three groups according to the timing of X-inactivation (early X-inactivation = early XCI, late X-inactivation = late XCI and Escapees).
(H) Immunofluorescence microscopy for changes in the localization and expression levels of EMT markers in epithelialNMuMG cells (d0) and cells treated with TGF-β for seven days in the presence of JNK inhibitor (d7 JNKi) or control (d7 DMSO). Staining was performed with antibodies against Fibronectin 1, with Phalloidin to visualize the actin cytoskeleton and against Paxillin to detect focal adhesion plaques. It is important to note that the untreated epithelial cells are highly proliferative and appear small in size, round in shape and adhere to surrounding cells whereas day 7 TGF- β-treated (mesenchymal) cells are much bigger in size, elongated in shape and detached from the nearby cells. Scale bar, 100 μm, 63X magnification.
The research strategy to dissect the role of RBPs in regulating exit-from-pluripotency. Firstly, we constructed individual RBP KO ES cells and examined their ability to exit from pluripotency through forming EB and random differentiation by LIF withdrawal assay.
(C) Colony-forming unit assays to increasing CPT concentrations of the same mutant combinations as in (B). Mean values ± SD are plotted. Four biological replicates have been performed.
Correlation of [68Ga]Pentixafor PET mean TBR and CXCR4 cell surface expression assessed by flow cytometry. n = 8 tumors were analyzed.
Confocal analysis of LC3B (green) in GSC#9 treated for16 hours with vehicle (DMSO) and MPZ (20 µM) with or without chloroquine (CQ, 20 µM). Nuclei (DAPI) are shown in blue. Scale bars: 10 μm.
C. ELISA of secreted IL6 concentrations of IL6-OPT, IL6-WT and IL6-DE from HEK293T cells transfected with plasmids bearing IL6-OPT, IL6-WT and IL6-DE. Data information: In (C), the data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A one-way ANOVA with Tukey's multiple comparisons was performed between samples where, p<0.01 (**) and p<0.001 (***).
(E) Western blot analysis of α-synuclein indicates the presence of some α-synuclein in the CM of neurons loaded with the fibrils, after 72h compared to control medium and to lysate of cells directly exposed to the fibrils. α-tubulin was used as loading control.
The relative abundance of each lipid class (mean ± SEM) within the set of six membrane lipids. n = 3 MS analyses of 4DO fat body samples for each genotype. ‡ symbols indicate a significant difference compared to w- expressing Luciferase RNAi, * symbols indicate a significant difference compared to dTorKO expressing luciferase RNAi. Note we only tested the effect of Lipin, Ctdnep1, and Nep1r1 RNAi when a lipid class significantly differed between w- and dTorKO. One-way ANOVA, Tukey's multiple comparisons test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 and ‡‡‡‡ p < 0.0001.
D In vitro substrate ubiquitylation assay for Doa10 variants with Ubc7 (left) and Ubc6 (right). Ubc7 reactions contained equimolar amounts of Cue1 and were performed with Ub(K48R). Top: representative immunoblot using a poly-clonal α-RNase A antibody; "no E3" reaction does not contain any S-Doa10, "no ATP" reaction does no contain ATP, but wild-type S-Doa10(94H). The RNase-Ub2 band co-migrates with a nonspecific band (#) common to all samples. Bottom: Quantification of RNase-Ub signals is shown. Values are reported as means ± standard deviation (n = 3). Significances for pairwise comparisons were determined by One-way ANOVA Test; * p < 0.05. For clarity, only significances related to the "no E3" control of a given E2 are shown. In addition, the reaction containing Ubc7 and S-Hrd1(400R) shows significantly more ubiquitylation than those with Ubc7 and other E3 variants.
(C, D) Dual and single colour kymographs showing that microtubule binding behaviour of p150 depends strongly on ionic strength: (C) In standard assay buffer, 10 nM Alexa647-p150 (green) accumulates at the plus end and on the GMPCPP-stabilised segment of a growing Atto565-microtubule (magenta).
MIP of cerebral vessels of 4dpf Tg(fli1aep:CAAX-eGFP) embryo (grey LUT; inverted). Higher magnification panel shows a kugel (arrowhead) protruding from the posterior mesencephalic central artery (PMCtA).
a, Flow cytometry analysis of cGFP and cDsRed following co-culture of Nrl.Gfp and DsRed cells (1:1) and analyzed at 3 DIC (N = 3 independent co-cultures with a technical triplicate), 7 DIC (N = 5), 21 DIC (N = 4); One-way ANOVA non-parametric, Kruskal Wallis;
D Quantification of H3P immunostaining in intact animals and at 48 hpa in control or TOR KD animals (n = 5-10).
(B) Analysis of altered mitochondrial gene expression resulted from our RNAseq showing that affected genes and their coding proteins carry a high numbers of glutamic acid and glutamine residues, in accordance to the mitochondrial translational defect.
(F) 2xFYVEFYCO1 does not colocalize with 2xFYVEHrs (left) and PXp40phox (right). HeLa cells were imaged 24 h after transfection with the indicated constructs. Bars, 10 µm.
A. SDS-PAGE analysis of the D391N DIS3L2-RNA complexes. RNAs were radioactively labeled at the 5' end and DIS3L2-bound RNAs were detected by autoradiography. The negative control was performed with HEK293T-Rex cells (Control)
(A) U2OS cells were transfected with a siRNA pool targeting human TIP60 (Dharmacon) or luciferase (Dharmacon). The nuclear lysates were analysed by Western blotting 24h after transfection
(b) Western Blot analysis of proIL1β. Relative abundance is the average of 3 independent experiments with different donors.
Wild type (WT) and TRIM21 knockout (KO) mice were infected with 10^5 FFU LCMV clone 13 (6 mice per group) and 2 mice were uninfected (UI). Kaplan-Meier survival were compared over 15 days post infection (pi).
K Quantitative analysis of islet cells in transplanted FI and PI+MVF per HPF (n = 70 each). Mean ± SD. Unpaired Student's t-test was used for statistical analysis. *P < 0.05 vs. FI.
(f) Left: Schematic of transendothelial migration assay with patient-derived BOECs and immune cells. Right: Transendothelial electric resistance (TEER) measurements of BOEC barrier tightness in the presence and absence of PBMCs and/or AMD3100. Box-whisker plots indicate median (middle line), 25th, 75th percentile (box) and the lowest/ highest data points (whiskers). ns, non-significant (t-test). Sample size is n = 5 patient samples, with 3 technical TEER readings recorded per sample.
(H) Full-length HOIL-1 AlphaFold structural prediction (AlphaFold Uniprot ID: Q9BYM8) with likely location of allosteric ubiquitin shown. The region shown in (G) is indicated.
C. SH-SY5Y neuroblastoma cells treated with non-targeting (Ctrl) or Rab1a siRNA were co-transfected with EGFP-LC3 (green) and empty vector (EV), Myc-C9orf72L or Myc-C9orf72S (red). As positive control EV transfected cells were treated for 3 h with Torin1 (250 nM). Autophagosomes were quantified as the number of EGFP-LC3 positive puncta per cell (Mean ± SEM; one-way ANOVA with Fisher's LSD test; ns, not significant; * P ≤ 0.05, *** P ≤ 0.001, **** P ≤ 0.0001; N (cells from 2 independent experiments) = Ctrl/EV: 102; Ctrl/EV/Torin1: 92; Ctrl/C9orf72L: 97; Ctrl/C9orf72S: 76; Rab1a/EV: 102; Rab1a/EV/Torin1: 107; Rab1a/C9orf72L: 101; Rab1a/C9orf72S: 87). Rab1a knockdown was confirmed by RT-qPCR (Appendix Fig S2). Scale bar = 10 µm.
Hematoxylin and eosin (H&E) staining of a human GBM tumour. The black square represents the approximate location of the field shown in G (left image). Serial sections were used for H&E and RNA-FISH. Scale bar: 300 µm.
(A) Schematic diagram of strategy employed to C-terminally tag PABPC1 in PABPC4KO HeLa cells using CRISPR-Cas9 mediated homology directed repair (HDR). Adapted from (Sheridan & Bentley, 2016). Homology arms flanked repair cassettes containing a DHFR sequence, preceded by a HA tag and separated from an antibiotic resistance gene (denoted as AbR and either Puro or Hygro) by a T2A cleavage site followed by a SV40 signal.
H. Scaled representation of SCRN1-associated proteins identified with pull-down assay followed by mass spectrometry analysis of purified BioGFP or BioGFP-SCRN1 from HEK293T cell lysates with adult rat brain extracts. All candidates showed >10 enrichment of PSM compared to control.
(E) Western blot of HeLa cells transfected with the indicated siRNAs and treated with Torin E64D/PepA. Data are representative of three independent experiments.
, Western blot analysis of Collagen Ⅰ and Ⅲ expression in heart tissues from control and F-CRTH2 KO mice 21 days after ISO challenge.
B Dose-response curves of CDDP-induced loss of OHCs (blue line) and IHCs (red line) in basal cochlear regions. Data are expressed as mean ± SEM (n=5 cochleae per condition and per time point).
Western blotting showing the overexpression of SRSF2 in 293T cells, which was co-transfected with NUMB reporters of WT, ∆M1 or ∆M2. ∆M1 or ∆M2 represents plasmid deleting corresponding binding site.
Intracellular total iron content (left) and Fe2+ to Fe3+ ratio (right) measured by CE-ICP-MS in normoxic B16-F10 cells (n=3). Data were analyzed using a one-way ANOVA with Tukey's multiple comparisons test.
B-C. The graphs show the average number of chromatid breaks per spread. In each experiment 30 chromosome spreads for each condition were analysed and three independent experiments were performed. Error bars represent SEM. Statistical significance assessed by student t test (** p˂0.01, *** p<0.001
(B), (C) and (D) represent different zone lengths, different zone cell numbers, and cell length of the indicated seedlings germinated and grown on LK or HK medium for 7 d. MEZ, meristem zone; EZ, elongation zone; MAZ, maturation zone. Data are means ± SE (n = 10-15, individual plants). Student's t-test (**P < 0.01) was used to analyze statistical significance, and "#" represents the control.
J-O Epifluorescence stereo microscopy of mammary glands harvested from 15‐day‐old Wnt4::GFP females either WT (n = 18) (J, M), ERα−/− (n = 4) (K, N), or PR−/− (n = 3) (L, O). dTomato expression (J-L); EGFP expression (M-O) is not abrogated in ERα−/− nor PR−/− epithelia. Arrowheads mark the main duct originating from the nipple. Scale bar: 50 μm.
RNAseq data from scaf1+/+ and scaf1-/- skeletal muscle for the indicated diet (standard diet scaf1+/+ and scaf1-/- n=4, double diet scaf1+/+ n=3, scaf1-/- n=4). (G) Heatmap of metabolic differentially regulated pathways in Gene Set Enrichment Analysis (GSEA) in the indicated comparisons.
D Representative images of confocal microscopy performed with PMA-differentiated THP-1 cells treated with IMQ (10 µg/ml) for indicated durations. Scale bar: 20 µm.
(D) Cartoon presentation of Dsc complex members and evolutionary conserved functional domains with human candidate genes that show the highest homology in the indicated domains.
(F) Dissection of NGDRQC+ and NGDRQC-: The carboxyl-terminal region of Hel2 is required for both NGD and RQC which is likely triggered on a disome unit (pale yellow). It contains the primarily stalled, leading ribosome followed the colliding ribosome. For NGDRQC+ cleavages occur on mRNA covered by the disome, whereby the leading ribosome undergoes RQC. In the mutant Hel2 lacking the C-terminus, an alternative NGD pathway takes place (NGDRQC-). Here, cleavages occur on mRNA covered by the ribosomes following the disome unit (blue) and the leading ribosome is not affected by RQC (grey).
H GFP fluorescence image of the Mx roots under different treatment. Nuclei were labeled using DAPI. Scale Bar: 100 μm.
Representative confocal z-stack images showing cFos (magenta)-positive neurons from control and Cdc50a cKO mice (CTX: cortex, HP: hippocampus, and IC: inferior colliculus). Scale bar, 20 μm. Bar graphs showing the relative area of cFos-positive cells in the brains of control and Cdc50a cKO mice (n = 5 for each group, **P = 0.0030, n.s., not significant).
(f) Midguts expressing GFP-Atg5 in enterocytes (larger nuclei) with an Atg7d4 loss-of-function clone cell (lacking RFP) at puparium formation. Representative images are shown.
(D) ATAC peaks overlapping with H3K27ac peaks detected in HSCs in each phase or CD48+ progenitor cells in the late phase after the administration of 5-FU were selected as cis-regulatory regions.
Microarray analysis of Ptgis, Tbxas1, Ptges2 and Ptgs1 expression from Gata6-WT and Gata6-KOmye pMɸ isolated from naïve mice. Data is shown as mean +/- SEM from three biological replicates. Statistical significance was determined using empirical Bayesian statistic corrected for false discovery rate by the Benjamin-Hochberg procedure.
(c) Substitution of arginine for lysine at position 47 significantly inhibits ubiquitylation of RALB. (
The inhibition of transcription was assessed for the negative and positive ICD hits identified with the predictive algorithm (Figure 1). U2OS cells were treated with the agents at concentrations corresponding to their IC60: 1 μM dactinomycin (DACT), 50 μM topotecan, 1 μM becatecarin, 0.5 μM trabectedin, 5 μM UCN-01, 30 μM mycophenolate mofetil, 30 μM nonoxynol-9, 25 μM dactolisib, 2.5 μM β-lapachone, 5 μM 5-fluorodeoxycytidine and 2 μM RH-1 for 1.5 h followed by 1 h with EU. The percentage of transcription inhibition was calculated and the coefficient of correlation (R) and associated p-value (p) between the percentage of inhibition and the theoretical ICD score was calculated using the Pearson method.
(D) Effects of RNF26 on IRF3 ubiquitination. The 293 cells (5×106) were transfected with Flag-IRF3 (5 µg) and RNF26 (1 µg) together with HA-Ub or its mutants (1 µg each). Eighteen hours after transfection, 3-MA (500 ng/mL) was added into culture medium for 4 hours to protect IRF3 from autophagosomal degradation during the experiment. The cell lysates were subjected to IP under denatured conditions with anti-Flag and the immunoprecipitates were analyzed by immunoblots with anti-HA (upper panels) or anti-Flag (lower panels). The whole cell lysates were analyzed by immunoblots with anti-Flag or anti-RNF26 as indicated.
Δapg5 cells were transformed with vector alone, wild-type APG5 or APG5K149R, and then immunoblotted with anti-HA (b)
F) Possibilities for FM4-64 transfer between the inner leaflets of two tethered vacuoles. Flipping between the trans-leaflets of a hemifusion structure; reversible flipping into the outer leaflet, establishing a minor pool that then transfers through the buffer or through the outer leaflet; or passage through a fusion pore.
(C) Localization of translocated VgpA (upper panel) and VgpAL10A (lower panel) during infection.
A α-Syn foci in WT cells might constitute active sites for propagon formation. Disaggregation in these sites generates smaller α-Syn fragments that are more toxic and more readily transferred to adjacent tissues. As they are also more seeding competent, this leads to an amplification of the aggregated material. The disaggregation of amyloid-type aggregates by the HSP70 system is an important part of a propagation cycle involving repeated fragmentation of larger fibrils to generate and amplify toxic seeding-competent particles. In contrast, the disaggregation of amorphous aggregates leads to the formation of smaller seeding-incompetent fragments, which are eventually completely dissociated. B. In HSP-110 KD animals, the disaggregation activity is impaired. Impaired fragmentation of amyloid-type aggregates leads to reduced foci formation, toxicity and spreading. In contrast, amorphous aggregates persist and increase over time.
(G) Immunoprecipitation with anti-Flag M2 affinity agarose gel and immunoblotting with anti-Vps34 antibody shows that AAA Myc-Bcl-2 decreased Flag-Beclin 1-hVps34 interaction in the presence (right panel) or absence (left panel) of DETA NONOate in HeLa cells transfected with hVps34 along with either empty Flag or Flag-Beclin 1, and with pcDNA3.1 or AAA Myc-Bcl-2. Graphical data denote mean ± SEM.
TDP-43 LCD phase separates in coarse-grained simulations with explicit solvent. Condensate of TDP-43 Wt LCD is shown, protein colored according to chain identity. Water omitted for clarity. Ions shown in cyan.
(D) Velocities of the moving particles calculated from the slopes of the kymographs. Data are shown as mean and SD from n = 49 moving particles of three independent cultures. ****, p < 0.0001; Unpaired t test.
Representative immunofluorescence images of HeLa cells treated with an indicated various drugs (E). Cells were extracted, fixed, and co-stained for Cyclin B2 (green), ACA (red), and DNA (blue).
I. Scatter plot of PKD phosphorylation in jejunum (normalized to GAPDH) vs. high density lipoprotein (HDL) of morbidly obese female patients. n=7.
D. The decrease of glucose and increase of lactate in culture medium were measured by ELISA assays in HepG2 cells, HAT1 KO HepG2 cells, and HAT1 KO HepG2 cells reconstituted with either wild type HAT1 or mutant HAT1 (T188A). N = 3 biological replicates. Data are presented as mean ± SD. Student's t-test, **P < 0.01.
6-week-old male CD36 wild-type (WT) or knockout mice (CD36KO) were administered with AAV-GFP (Ctrl) or AAV-KLF10 (KLF10OE) through tail vein injection, and then kept on WD/CCl4 for 12 weeks. n=5 per group. (F) Hepatic TG contents. Data information: * P <0.05, ** P <0.01, *** P <0.001. Results are shown as mean ± SD. 1-way ANOVA
F. Surface plasmon resonance sensorgrams of Nec-1 targeting tau (left), and the corresponding dissociation fitting curve from the saturated region (right) under various concentrations of Nec-1.
Immunofluorescence analysis of p62 (green) and ProteoStat Aggresome staining detection reagent (red) in KRIT1 wt and KRIT1-KO lung endothelial cells. The yellow signal in the merged images represents an overlapping spatial relationship between green and red fluorescence. Magnification in insets. Scale bar, 50 μm. The images are representative of four independent experiments.
E, F. Representative confocal images of mitochondrial fusion in Drp1-/- 293T polykaryons in cultures subjected to the PEG-based fusion assay in the presence or absence of endogenous hFis1. Drp1-/- cells stably expressing mitoGFP or mitoRFP were transfected with scrambled siRNA (control siRNA) or with hFis1-siRNA as indicated and then co-cultured and fused by PEG treatment. Left panel: control siRNA transfected; right panel: hFis1-siRNA transfected (E). Quantitative analysis of extent of mitochondrial fusion in individual hybrid cells was performed by the Pearson's correlation coefficient (PCC) in three independent experiments and summarized in (F).
(B) Pex11-GFP western blot showing pexophagy in WT cells grown 6 h in galactose medium (0) then switched to starvation medium for 1, 2 or 3 h as indicated. (W), WT (empty plasmid); (N), GAL1-mRFP-ATG36; (C), GAL1-ATG36-mRFP; (U), GAL1-ATG36. WT shows pexophagy by endogenous Atg36.
(C) Root length (averages ± SD, n ≥ 15) of Arabidopsis seedlings that were exposed to 100 nM Pep2. (*, p < 0.05 in two-tailed tests compared to the differences (± Pep2) from the corresponding values of bak1-3 plants. Two independent experiments were combined for statistical analysis.)
G ELISA analysis of the protein level of secreted IL-1β in supernatants of Ccdc50+/+ and Ccdc50-/- BMDMs (top panel) and BMDCs (bottom panel) treated as in (A-C) (n = 3 biological replicates). Data information: Data are representative of three biological replicates and are shown as the mean with SEM *P <0.05, **P < 0.01, ***P < 0.001; two-tailed unpaired Student's t-test.
D. Schematic illustration of proposed protective mechanism from Stx-induced apoptotic and inflammatory responses through inhibition of O-GlcNAcylation.
A-B HT‑29 cells were transfected with non-silencing control siRNA (sictr) or siRNAs against USP22 (siUSP22) for 48 h at 20 nM. After transfection, cells were treated with 20 µM zVAD.fmk, 0.5 µM BV6 and 1 ng/ml TNFα either for 6 h and analyzed by Western blotting (A) or for 18 h, and the percentage of PI-positive cells was assessed by fluorescence-based PI staining (B). Vinculin served as a loading control.
Sox2 and Oct4 mRNA levels upon overexpression of YPet-SOX2 or YPET-SOX2-delDBD (n=3). p-values: two-sided t-test with unequal variance.
L miR-150 mRNA levels in primary mouse skin fibroblasts treated as indicated with TGFβ and 4μ8C. * P = 0,00031 compared to untreated control, n = 3.
(E) GST pulldown assay using the indicated myosin VI constructs or GST alone (as control) and lysates from HEK293T cells transfected with Flag-OFD1 construct. IB was performed with anti-Flag antibody. Ponceau staining as indicated.
A putative interaction surface of the ISX/BRD4 complex was presented through structural modeling. The electrostatic surfaces are drawn either blue for positive or red for negative charge (e and f).
(C) Immunofluorescence microscopy. Wild type hepatocytes were infected with LacZ or NBR1 adenovirus for 48 hrs and then immunostained with anti-p62 and anti-NBR1 antibodies. Each inset is a magnified image. Bars: 20 µm. The number and size of p62-bodies were measured in more than 100 cells. Data are shown as means ± s.e. ***P < 0.001 as determined by Welch's t-test.
D) ChIP analysis of Atoh1 and Gfi1 loci using H3K27me3 specific antibody. The same crypts described in C were used. H3K27me3 levels were normalized on Histone H3 density (percentage of H3 signal). Graphs show mean ± SD.
(F) Graph shows the percentage of Pax6+ cells among GFP+ cells in enlarged SVZ (n = 5 each group; two-tailed unpaired t-test, control vs. hFOXM1, P<0.0001; mFoxm1vs. hFOXM1, P<0.000 1).
E Pie diagrams showing the grouping of neurons in the PVN (upper row) and in adjacent pre‐autonomic areas (lower row) cumulatively based on electrophysiological criteria listed in Supplementary Table S1. Secretagogin+ neurons typically belonged to Ia and IIa subtypes.
(C) Immunoblot analysis of BAT cells stimulated with 8-Br-cAMP for 5 minutes in the presence of Rapa, Torin or Wrtm for the indicated proteins.