EMBO/sd-character-level-ner huggingface dataset:
Controlled cell migration of 3 representative cells in PA-Rac1 assay. White spot: 440 nm laser spot; Green area: the original position of the cell; Red area: the current position of the cell; Yellow area: the overlapped area. Scale bar: 10 μm.
D, E Representative APs of VM and AM at 1 Hz in response to (D) IKur block by 4-AP and (E) IK,ACh activation by CCh. AP parameters are shown in Supplementary Table S5.
B) Representative AP from LQT2corr-, LQT2N996I-, LQT1corr-, and LQT1R190Q-CMs paced at 1 Hz, under baseline conditions (black) and after application of increasing concentrations of LUF7346 (colour-code is shown).
(a,b) dUTX directly interacts with ecdysone receptor (EcR/Usp). (b) Immunoprecipitation (IP) of EcR and dUTX in SL2 cells. Cells were transfected with HA-dUTX and the cell lysates were immunoprecipitated using anti-HA or a control IgG isotype antibody. The immunoprecipitates were analysed by western blotting using the anti-EcR and anti-HA antibodies.
(b) DLD parental or NCOA4−/− cells were incubated in the presence or absence of DFX and the levels of FTH and FTL were determined.
KGN cells were transfected with 200 nM of scrambled control or FOXL2-specific siRNAs for 24 h. Then, KGN cells were further transfected with 20 nM of control miRNA, miR-1236, control anti-miRNA, or anti-miR-1236. The proportion of annexin-V-positive apoptotic cells (A and B) were analyzed by flow cytometry. The data are presented as the mean ± SEM of three independent experiments. Different letters denote statistically significant differences (p < 0.0001; Student-Newman-Keuls test).
Western blot for representatives of all five respiratory complexes in control and TIMM50 mutant fibroblasts grown in glucose or galactose. Two biological replicates are shown for each cell line and condition. Significant changes in protein levels in TIMM50 mutant fibroblasts compared to controls have been boxed in red.
TOPflash reporter assays in HEK293T cells stimulated with either control, Wnt3a, Wnt3a and RSPO1-4 conditioned media, or by transfection with the indicated constructs. Where indicated, cells were co-transfected with the indicated siRNAs.
Quantification of the vector dose reaching orthotopic GBM in mice upon intravenous administration of 5x1010 TU of RGD4C/AAVP vector. The vector amount, in tumors, was expressed as TU/g tumor tissue. Data shown are representative of two experiments, n=5.
(B) Comparison of the self-interaction of FAM134B mono-phosphorylation mutants using co-IP.
Immunofluorescent staining of SARS-CoV-2 infected differentiated small airway cultures. Nucleoprotein (NP) stains viral capsid (red), which colocalized with the ciliated cell marker AcTUB Phalloidin was included to stain actin Scale bars indicate 50 μm.
(J) Similar to panel F, bacterial killing by PBneutrophils was evaluated 3 and 16 hr post-infection and in heart.
D-E. Late recruited proteins do not follow the same recruitment pattern in the MKI67 KO cells compared to WT HeLa cells. White arrows indicate where protein aggregates can be seen. D. DENND4A (HPA065343). Median overlapKO = 0.671, median overlapWT = 0.803 (P = 1.02x10-4) and median Pearson correlationKO = -0.224, median Pearson correlationWT = 0.236 (P = 1.91x10-5). E. NOL12 (HPA003547). Median overlapKO = 0.468, median overlapWT = 0.820 (P = 1.01x10-17) and median Pearson correlationKO = -0.318, median Pearson correlationWT = 0.381 (P = 1.81x10-10). White arrow indicates metaphase cell. Data information: Protein of interest is shown in green and DAPI in blue. Scale bar 10 μm. For the colocalization analysis data; biological replicate 1 highlighted in grey and biological replicate 2 in green. Both the overlap and Pearson correlation between DAPI/Protein staining was measured and a two-tailed unpaired Wilcoxon test was used. Box limits mark 1st and 3rd quantile, whiskers the 1.5x interquartile range and center line the median.
Diagram showing the procedure of shNfatc1 virus infection at the early stage of reprogramming. RT-qPCR analysis of Nfatc1 expression in MEFs infected with shNC and shNfatc1 viruses. n = 3.
H: Postoperative in vivo GI transit measurement in mice treated with ambroxol or vehicle.
D-E. Two orthogonal views of the partially open SARS-CoV-2 S trimer cryoEM map (one SB domain is open). F. Atomic model of the closed SARS-CoV-2 S trimer in the same orientation as in panel D. The glycans were omitted for clarity.
E Quantification experiment showing the percentage of SPLICSL dots positive for HK2 in HeLa cells (n=10 cells analyzed from three independent experiments; mean±SD).
(C) Expression analysis of Pogz by western blot in mouse embryonic fibroblasts (MEFs) generated from E12.5 embryos with the indicated genotype. NIH3T3 cells were used as a comparison. Gadph was used a loading control.
(c) Δ133p53α is colocalized with LC3B upon autophagy induction. MRC-5 fibroblasts with FLAG-Δ133p53α under starved conditions (as in a) were co-immunostained with anti-FLAG antibody (Δ133p53α, green) and anti-LC3B antibody (red). Two representative sets of images, including DAPI and merged images, are shown. Scale bars, 10 μm. (d) Quantitative analysis of Δ133p53α-LC3B colocalization. The number of colocalized signals out of total number of Δ133p53α signals or out of total number of LC3B signals was counted in 26 cells. Data (percent colocalization) are mean±s.d. Almost all Δ133p53α signals were colocalized with LC3B, while ~80% of LC3B signals were colocalized with Δ133p53α.
Box-and-whisker plots showing quantification of association between the indicated protein and Golgi elements Top and bottom ends of the boxes represent 75th and 25th percentiles, and whiskers represent 90th and 10th percentiles. The median is depicted with a solid line. Individual Golgi elements from at least 14 cells were delineated (>500 elements/experiment) and the intensity of each protein spot associated with each Golgi element was measured. Data were collected from two independent experiments and normalized to WT mean.
C) Representative images of human adenocarcinoma explants after 2 days in 3D collagen-I gel, in non-treated (NT) or ROCK inhibitors treated-conditions (+Y27632) and (+H1152) and stained for the apical pole (Ezrin), F-actin (Phalloidin) and nuclei (DAPI). Boxed regions of NT, +Y27632, and +H1152 explants are shown at high magnification. Arrowheads point to non-protruding cells. Arrows point to protruding cells. White stars show nuclei that engage in protrusions. Scale bars: 20μm. D Explants displaying (D) lumens from 10 patients were quantified and results presented as percentage of total explants. Over 50 explants were counted per condition (duplicate) and per patient(Means ± SEM). P values were calculated using unpaired t-test (****p<0.0001 , n.s : non significant).
Volcano plot showing that 2756 genes are differentially regulated between THY-Tau22 and WT mice during learning. The log2(Fold-Change) was estimated by DESeq2. FDR<0.05 and |log2 Fold Change| > 0.2. Red dots correspond to genes with adjusted p-value <0.05. Numbers in the corners represent the number of down-regulated (left) and up-regulated (right) genes. C Heatmap representing expression of z-score of the 2756 deregulated genes in all experimental conditions. Color-coding was performed according to the z-score of the normalized reads counts divided by gene length. Clustering was performed using the Unweighted Pair Group Method with Arithmetic mean method and the Pearson"s distance. Groups: WT VEH_HC (n=3), WT VEH (n=2); TAU VEH (n=2); TAU MOL
Human WAS patient CD4+T cells- APC conjugates display synapse symmetry defects similar to those observed in mouse WASP-/- CD4+ T cells. CD4+T cells purified from healthy controls or WAS patients were incubated with superantigen loaded HUVEC cells for 5' (APC; see 'Methods') and imaged using confocal microscopy. Each image represents a maximum intensity projection of the synaptic area. Graph in the middle shows values normalized to the mean value of the 'Healthy' case. In the case of 'actin' and 'actin foci', n= 87 for healthy and n= 63 for WAS; in the case of pCasL, n=56 for healthy and n= 21 for WAS; for 'AR' graph, n= 88 for healthy and n= 63 for WAS case. P values; ***P <0.001; n.s. P=0.09, as determined by using Mann-Whitney two-tailed test between populations of cells within the same experiment.
(I) Proteostasis disruption by hsf-1 knockdown does not increase exopher production. n = 60 and 55; N = 2.
(A) UCSC genome browser view of normalized TT-seq coverage on the plus and minus strand at the TAL1 locus (hg38; chr1:47,194,268-47,242,880; (Kent et al., 2002)) in the leukemia cell lines Jurkat and K562. For better visualization, TT-seq coverage is cut at 200 (purple lines). eRNAs are shown between the plus and minus strand. Red line indicates the short 12 bp insertion in Jurkat cells, introducing novel binding sites for the transcription factor MYB
A. Schematic of SLAMseq workflow. Cells were pretreated for 30 min with LSD1 inhibitor (100 nM GSK-LSD1) and newly synthesized RNA was subsequently labelled for 1 or 6h with 4-thiouridine (4sU). RNA was extracted and alkylated and subjected to 3'-sequencing.
LSK (Lin- Sca1+ cKit+) cells of the indicated genotypes were isolated by cell sorting from the fetal liver at embryonic day E13.5 or the bone marrow of adult mice and treated for 48h with PF-477736 [1.5 μM]. Survival was assessed using AnnexinV-staining and flow cytometry. Bars represent means ± S.E.M. from n=6 wild type and n=3 Vav-BCL2 fetal liver LSK cells (left) and n=3 bone marrow LSK cells (right).
Addition of human or mouse recombinant ASM to human melanoma or B16F10 cells, respectively, results in binding of ASM to the tumorcell surfaces as determined by flow cytometry. Cytochalasin B was added to control for internalization of added ASM.
A. Detergent-solubilized yeast extracts from cells containing chromosomal Flag-tagged rbd2 or rbd2-G246R in rbd2Δ background were prepared, and proteins associated with Rbd2-Flag were immunopurified using anti-Flag magnetic beads. Equal amount of total (lanes 1-3) along with 25x bound fractions (lanes 4-6) were analyzed by western blot with anti-Cdc48 serum and anti-FlagIgG.
(F) Kaplan-Meier survival analysis of Pax5Jak2/+ (black) and control Pax5+/+ (grey) mice. n, number of mice analyzed. A P value of < 0.0001 was determined for the survival curves by statistical analysis with the log-rank (Mantel-Cox) test.
A) The first screen was carried out using HEK293T cells transfected with the ERMIT bait/prey, system, the XBP1 splicing reporter and the siRNA library (n = 5). The counter screen was carried out using the same experimental setup without the ERMIT bait/prey system (n = 4).
F. Coverage plot of H3K27me3 from naïve B cells (Frangini et al., 2013) and H3K79me2 (from WT activated and naïve B cells) flanking 4 kb around transcriptional start sites (TSS) for genes upregulated in KO (KO Gain) or non-differential Expression Matched genes. Coverage was calculated as reads per genomic content cutoff at the 0.995th quantile and rescaled to a maximum of 1. Black boxes indicate the relavant B cell population for comparing the distribution of H3K27me3 and H3K79me2 for the indicated gene sets obtained from the differential gene expression analysis of Dot1L-proficient and deficient B cells.
D MitoSox fluorescence following treatment for 1-3 days with dsRNA against the genes indicated.
Fig. 6 Lack of lipid droplets inhibits starvation-induced formation of autophagosomes. (A, H) WT pep4∆ (pep4∆) (A,B), tag∆ste∆ pep4∆ (tag∆ste∆pep4∆)(C,D), ste∆ pep4∆ (ste∆pep4∆)(E,F) and tag∆ pep4∆ (tag∆pep4∆) (G,H) cells were grown to an exponential phase in YPD before being starved in SD-N for 2 h, and were then processed for electron microscopy. H is a magnification of the box in panel G. Magnification of proliferating ER in a tag∆ste∆ (H1246) cell is shown in (I) Asterisks indicate autophagic bodies. N, nucleus; PM, plasma membrane; CW, cell wall; ER, endoplasmic reticulum; M, mitochondrion; V, vacuole; #, trehalose; F, ER proliferation. Scale bars: 1 µm (A-H) and 200 nm (I). (J) Average number of autophagic bodies per cell section was determined by counting 100 randomly selected cell profiles. Error bars represent standard deviations fromcounting of the three grids. ***P < 0.001 (Student's t-test). SD-N,nitrogen-starvation medium; WT, wild type YPD, complete medium.
(G) Raf-1 RBD GST-pull-down assays confirmed that shcircFNTA can decease KRAS activity in UMUC3 cells (upper panel), and oecircFNTA can increase KRAS activity in J82 cells (lower panel).
The macrophages from Atx∆ΜΕ/∆ΜΕ and Atx+/+ mice were stimulated by LPS [20 ng/mL, 20 min : The cell lysates were subjected to immunoblotting analysis with antibodies as indicated. Regular ERK1/2, were used for a loading control. Presented are the representative image from at least three independent experiments.
B WT and 4KR mutant MLKL were inducibly expressed in Mlkl-/- MDFs by doxycycline for 6 hrs and cells were untreated (UT) or treated with TSI, followed by UBA-pull down. Representative of three independent experiments.
(a-b) Atoh1+ progenitors show stem cell capacity during normal homeostasis and regeneration. At early stages of recovery, d10-12, Atoh1+ cells lineage trace the colonic crypt (N=4 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50μm Data are represented as mean ± SD analyzed using two-way ANOVA with Sidak's multiple comparisons test *P≤0.05, ***P≤0.001.
(A, B) Effect of stable expression of PPM1D in PPM1D−/−MEFs. PPM1D−/−MEFs and PPM1D-transfected PPM1D−/−MEFs were treated with etoposide (10 µM), and the expression of each protein was examined by western blotting. (B) Semiquantitative analyses of protein expression in (A) (n = 3; mean ±  SD). *p < 0.05, **p < 0.01, NS: not significant.
(C) Increased cell death resulting from A3A expression along with depletion of CCT. U2OS-A3A cells were depleted of CCT4 by siRNA, treated with dox, or combination. Cell death was measured by staining cells with fluorescent labeled calcein AM (live) and DNA (dead) stains. Bar chart shows quantitation of FACS results averaged over three biological replicates. Statistical analysis was performed using a paired two-tailed t test, n=3; error bars, SEM.
A-C Nurr1 and Foxa2protein levels in mDA neurons decrease in vitro after long-term culture (B and C).Nurr1 and Foxa2protein levels were also quantified in cultured mDA neurons over 6-34 days in vitro by Western blotting (B)
E |Elevated hFwe-Lose expression in nasal swab probes predicts patients' disease outcome. Box plots show an increased expression of hFwe-Lose in nasal swabs of patients, who were hospitalized or died, versus patients who were not hospitalised, for retrospective (training; n = 203) and prospective (validation; n = 80) patients' cohorts. Two-sided Student's t-test was performed, and p-values are presented on the plot. The vertical axis represents hFwe-Lose expression normalized to the mean of non-hospitalized patients. The color refers to the COVID-19 disease outcome prediction: gray for not hospitalised, blue for hospitalised and red for deceased patients. In the retrospective cohort, the outcome prediction was 84% correct in predicting non-hospitalisation; 63% correct in prediction of hospitalisation; 100% correct in death prediction. In the prospective cohort, the outcome prediction was 100% correct in predicting non-hospitalisation; 72% correct in prediction of hospitalisation; 55% correct in death prediction (45% of deceased patients were predicted to be "only" hospitalised; none of deceased patients had "not hospitalised" prediction). Two-sided Student's t-tests were performed (compared to non-hospitalised patients), and p-values are presented on the plot. The central band shows the median, the box indicates the interquartile range, the whiskers extend to the most extreme points within the 1.5-fold distance of the interquartile range above and below the box.
H Quantitative RT-PCR detection of miR-34a-5p levels in PDGFRα+ cells, sorted by FACS from the lungs of either wild-type (34awt/wt) mouse pups, or mouse pups in which miR-34a expression in Pdgfra‑expressing cells (34ai∆PC/i∆PC) at P5 (n = 4 animals for each group).
B. Confocal images of tsA201 cells expressing PI4KIIα-GFP. Cells were treated with either vehicle (control), U18, or U18 and PF for 24h prior imaging. Bottom panels show an enlarged view of the enzyme in a perinuclear area. C. Quantification of PI4KIIα-GFP mean fluorescence intensity in Golgi normalized to the cytoplasm. Control: n=12; U18: n=14; U18+PF: n=12. D, E. Same as (B, C) but in tsA-201 cells transfected with PI4KIIIβ-GFP. Control: n=18, U18: n=22, U18+PF: n=23.
(V) CD8+ T cell suppression by normoxic and hypoxic IL10 macrophages treated with glufosinate (20µM), rapamycin and a combination of both for 24 h (n=4). Proliferation was evaluated by reading radioactivity as cpm (counts per minute), after incubation with 1 μCi / well tritiated thymidine. The proliferation of T cells cultured without macrophages was used as control.
C, D: correlations between apoM and HDL-C (C) and albumin (D). Data information: Scatter plots and fitted regression line are shown in each figure. Each apoM measurement was run in triplicate, and performed at least twice in independent assays. Pearson correlation was performed for statistical analysis. Exact p values or ****p < 0.0001 are reported in the figure.
D. Kaplan-Meier survival curve of bone marrow engraftment model of TF-1 TpoR CALRdel61 cells showing improved survival of mice treated with 4D7 compared with IgG control commencing 1 week after tail vein injection (n=5 mice per treatment). Data information: For all survival curves the log-rank Mantel-Cox test P value is shown.
(A) HEK293 cells were transfected with ATF3 shRNA or vector (pLKO1), treated with 50 nM MG132, and then subjected to immunoblotting.
Intensity plot across the white dotted line in tPH-CynA-KikGR expressing cell before and after Wortmannin treatment in (A).
F, Co-immunoprecipitation to determine the serine phosphorylation sites in human HIF2α responsible for its binding to USP33. Ectopic GFP-tagged USP33 along with HA-tagged wild type HIF2α or HIF2α mutants with indicated serine to alanine point mutations were expressed in 293T cells. Cell lysates were subjected to immunoprecipitation with anti-USP33 antibodies Co-immunoprecipitated products were immunoblotted with the indicated antibodies. The S484A mutation largely attenuated the interaction of HIF2α with USP33, indicating that the serine 484 site in HIF2α was the most important phosphorylation site for the interaction between HIF2α and USP33.
(C-I) BMDMs were primed with LPS for 4 h and then treated with LicoB for 1 h, prior to stimulation with nigericin for 45 min or ATP for 1 h. Western blot analyses of pro-caspase-1 (p45), pro-IL-1β, NLRP3, and ASC (the arrow indicates ASC in the whole cell lysate (WCL); activated caspase-1 (p20) and cleaved IL-1β (p17) in the culture supernatants (SN) of BMDMs (C, G). Caspase-1 activity (D, H), IL-1β secretion (E, I), and LDH release (F, J) in the SN were measured. Coomassie Blue staining was used as the supernatant loading control, while lamin B was used as the lysate loading control.
(I) Normalized peptide abundance for glycoproteins from hCAFs treated or not with FAK-I.
(C and D) siRNA loss of FUS does not affect ER-mitochondria associations or alter expression of VAPB, PTPIP51 or mitofusin-2 (MFN2) in NSC34 cells. (D) representative electron microscopy of ER-mitochondria associations in control (CTRL) and FUS siRNA treated cells. Arrowheads with loops show regions of association. Scale bar=200 nm. Data analysed by unpaired t-test. N=27-28 cells and 193-202 mitochondria.
(A) Schematic depiction of the S6 protein (red) in the context of bacterial ribosome (after PDB:6WD0, left) and yeast mitochondrial ribosome (after PDB:5MRC, right) highlighting the position of the N-terminus of S6 (red arrow, only shown on the left image). Proteins homologous between bacterial and yeast structures are shown in orange, mitochondria-specific protein mS26 in teal and rRNA in grey.
(F) ANT1 interaction with LMP1 is dependent on its domain 2 in 293T cells. ANT1 and LMP1 domain architecture and schematic representation of its respective deletion constructs used in this study in 293T cells. IP/IB was used to detect the interaction between Flag-tagged LMP1 and Myc-tagged ANT1 mutants. IP of cell lysates using a Flag or Myc antibody.
F. Representative silver-stained gels of in vitro GST-pulldown of GST or GST-Sir3SaID and Sae2C purified peptides. Control: Sae2C (300 ng, lane 4).
(A) Immunofluorescence microscopy staining of Fst1 (green) and α-SMA (red) in NRCFbs at 24 hours after recombinant TGF-β1 (10ng/ml) stimulation. Nuclei were stained by DAPI. Scale bar indicates 50μm.
Blood glucose levels (F) or area under the curve (AUC, (G)) during an oral glucose tolerance test performed in the same mice as in (E).
C Assembly intermediates/dead end assembly products in mitochondria from Subject 3 according to data from complexome profiling. Assembled subunits are highlighted in surface view within cryo-EM structure (PDB: 6g2j) (Agip et al., 2018).
(C) Graph showing the number of neurospheres per P100 cell plate, at different steps, as indicated. While Nr2f1 KO neurospheres (orange line) proliferate for a longer time compared to WT ones (blue line), the loss of one Pax6 allele (gray line) almost restores normal proliferation rate and exhaustion time. Complete Pax6 loss is not compatible with stem cell renewal (yellow line). n ≥ 3 culture wells from n = 2 independent batches. Data information: Data are represented as means ± SEM. 2-way ANOVA ; *P<0.05, **P<0.01, ***P<0.001).
A. Schematic diagrams of codon optimized (lacking extensive G4C2 repeat) plasmids expressing N-terminally EGFP fused 89 repeats of either poly-GR, poly-PR or poly-GA under the control of CMV promoter.
Figure 3c. Outline of formation and activation of DNA replication complexes in G1/S phase. Origin recognition, pre-replication and pre-initiation complexes are depicted; Genes dependent on CDK12 kinase activity (log2 fold-change<-0.85; p<0.01) are shown in red.
(C) Pathogenic CARD14 mutation enhances MALT1-dependent CARD14-induced IL-8 expression in human primary keratinocytes. Cells were transfected with scrambled (scr) or MALT1-targeting siRNA as indicated, 48 h later followed by transfection with CARD14 wild-type (WT), CARD14(G117S) or CARD14(E138A) as indicated. TNF treatment was used as a control. After 24 h, IL-8 concentration in the cell supernatant was analyzed via ELISA. Values are the mean of triplicates ± s.e. Expression levels of MALT1 and CARD14 variants is verified by immunoblotting (bottom panel).
(A-C) Chronological lifespan (CLS) analyses in SC 2% glucose medium of wild-type (WT) cells compared to Δach1 (C) cells (see also Figure S3). Survival was determined by colony-forming capacity (clonogenicity). Data represent means ± SEM (n = 4) of a representative aging experiment.(D-F) Propidium iodide (PI)-positive cells analyzed by flow cytometry to quantify age-induced cell death of experiments shown in (A)-(C). Data represent means ± SEM (n = 4) (see also Figure S4).(G-I) Extracellular acetate assessed from crude culture supernatants obtained at indicated time points of experiments shown in (A)-(C). Data represent means ± SEM (n = 4).∗p < 0.05 and ∗∗∗p < 0.001.
A. Conformational change of Tau detected by ALZ-50 antibody immunoreactivity in stratum lucidum (asterisks) of area CA3 and somata in stratum pyramidale (arrowheads).
(B) In vitro proteolysis assay using N‐terminal tail‐deleted HsAtg4B. LC3-GST was incubated with either wild‐type or N‐terminally truncated HsAtg4B and was subjected to SDS–PAGE analysis.
A The effect of the IRE1α inhibitor 4μ8C on TGFβ-induced skin fibrosis in C57BL/6 mice as measured by the percentage of sirius red areas in the hypodermis. Ctrl (n = 6); Ctrl + 4μ8C (n = 5); TGFβ (n = 8); TGFβ + 4μ8C (n = 8). * P = 0,046.B Representative skin tissue sections stained with sirius red for collagen (top) and αSMA (bottom). Scale bars = 50 μm.C Percentage αSMA-positive cells in the hypodermis of mice from the experimental setup in A. * P = 0,024.