EMBO/sd-character-level-ner huggingface dataset:
(f) siRNA-targeting Ptch2 was transfected into HeLa cells stably expressing mRFP-GFP-LC3 and representative confocal microscopy images are shown. Scale bars represent 26 μm. Percentage of GFP-positive vesicles (autophagosomes), RFP-positive vesicles (total number of vesicles) or percentage of autolysosomes (calculated by subtracting numbers of GFP from RFP vesicles), quantified using a Cellomics array scan, was calculated relative to control siRNA-transfected cells. Although an increase in autophagosome biogenesis generally increases both the number of GFP+ vesicles and the number of GFP-/RFP+ vesicles as a result of an enhanced autophagy flux, defects in autophagosome degradation, such as in bafA1-treated cells, increase GFP+ vesicles but not GFP−/RFP+ structures, as GFP remains intact. Graph shows the mean value obtained from four independent experiments in triplicate and with control conditions set to 100. In all panels, unless indicated, graphs show mean values and error bars represent s.d. from a triplicate experiment representative of at least three independent experiments. Statistical analyses were performed by two-tail Student's t-test: **P0.01; *P0.05; NS, not significant.
(F) Quantification of spindle angles average in control cells and in cells depleted of CITK, ASPM or co-depleted of the two proteins (n ≥ 150 cells, in at least 3 independent experiments).
I Scatter dot-plot graph of the quantification of RAD51 foci in in 15 zygotene nuclei randomly selected from three different individuals of each genotype. Bars indicate mean and standard error and statistical significance was assessed with an unpaired two-tailed T-test function (****, p < 0.0001).
(B) Quantification (%) of explants presenting shoots after 21 days after incubation on SIM. Results were obtained from 3 independent experiments with at least 20 calli per condition. Bars marked with an asterisk (*) are statistically significant (P<0.05) according to the T -test.
HeLa cells stably expressing untagged TFGwtLIR or TFGmutLIR3 were transfected with 3'UTR TFG siRNA, starved for 1h, fixed, permeabilized and immunolabelled with ULK1 (red) alone or ULK1 (red) and ERGIC53 (green) (H). Hoechst was used to stain nuclei. analysed). Co-localization analyses (H) were performed by Jacop plugin. Values of Mander's coefficient for ULK1, expressed as percentage, are reported as mean ± SEM (bottom graph). (n=3 independent experiments, n=19 fields analysed) White arrowheads point at co-localization events between ULK1 and ERGIC. Statistical analyses were performed by unpaired Student's t‐test. **, P<0,01; ***, 0,001. Scale bar 5 μm.
A. Heatmap visualization of the expressions of selected nitric oxide (NO)-related genes.
(A) Schematic representation of the experimental design. The hybrid TX1072 mouse female ESC line was used, in which Xist can be induced from the endogenous B6 allele. Time course nChiP-seq for H4K20me1 was performed and compared to a published H3K27me3 dataset (GSE116480)(Zylicz et al., 2019).
Suppression of IFNγ-inducible PD-L1 expression by YAP5SA is compromised in miR-130a KO A549 cells. PD-L1 expression levels were analyzed by qRT-PCR in IFNγ-treated control or miR-130a KO A549 cells pre-transduced with lenti-YAP5SA virus
B Co-staining of SNX10-Flag and PIKfyve in Caco-2 cells transfected with SNX10-Flag. Scale bar: 20 μm.
D. Increased amounts of FoxM1 plasmids were transfected into 293T cells. After 36 hr, cells were treated with 50 ng/ml Wnt-3a for 6 hr. Cell lysates were then subjected to IP with β-catenin antibody, followed by IB with β-catenin, ICAT, FoxM1 or IgG antibodies.
(E) Meta-data analysis of published GRO-Seq and ChIP Seq data sets. Gro-Seq Minus (red/maroon) or Plus (purple/pink) RNA strand from Control or Nutlin -3a treated MCF7 cells was mapped to human 18q subtelomere. Histone H3K27ac, H3K4me1, and H3K4me3ChIP-Seq data sets from untreated MCF7 are also shown for these subtelomeric regions. Right panel shows a zoom in of approximately 1000bp (light blue on left panel) surrounding the p53 response element within the subtelomere.
B. Representative M-mode images from left ventricle from CamkIIδc TG and control mice. ESD: Left ventricle end systolic diameter, EDD: Left ventricle diastolic diameter.
B. GSEA demonstrates that down- or upregulated genes in Hnf1aaKO mice (downward or upward arrows) showed down- or upregulation, respectively, in gene lists ranked by differential expression in non-classical vs. classical PDAC molecular subtypes from the TCGA-PAAD study (Cancer Genome Atlas Research Network. Electronic address & Cancer Genome Atlas Research, 2017). All enrichments had GSEA FDR q values < 0.01.
(f) maximal glycolytic activity and (g) spare glycolytic capacity were calculated as in Appendix. Fig. S6.
G. Quantification of viability test. Since the UAS-Ama-RNAi[GD12733] transgene is inserted on Chromosome X the genotype of females is Mef2>Ama-RNAi whereas males are Mef2>+. Box plot showing the ratio of flies with genotype of interest (females) over control flies (males). The whiskers show 5-95 percentile, and the middle line the median. * p=0.014 (Mann-Whitney test, N≥6 independent biological replicates). Full genotypes are w, UAS-Dicer2;+; mCherry-RNAi/Mef2-GAL4 and w, UAS-Dicer2, UAS-Ama-RNAi[GD12733];+; Mef2-GAL4.
A Representative images of Bem1-GFP and the PS marker LactC2-GFP in wild type and cho1∆ cells. Images show average intensity projections of deconvolved z-stacks. Black and white pixels were inverted to improve contrast for display. B Frequency of cells displaying polarized Bem1-GFP signal in wild type and cho1∆ cells. Values are means ± SD, n > 100 cells in each of 3 independent experiments. Paired Student's t-tests were performed.
Examples of gene clusters obtained with hierarchical clustering of phenotype profiles composed of the 17 specific phenotype fractions. Phenotypes 1-17: [1] coat: increased patch number; [2] coat: aggregate; [3] vacuole: class E; [4] late endosome: condensed; [5] actin: bright patches; [6] late endosome: membrane; [7] actin: aggregate; [8] coat: decreased patch number; [9] actin: decreased patch number; [10] late endosome: fragmented; [11] coat: depolarized patches; [12] actin: depolarized patches; [13] vacuole: multilobed; [14] vacuole: fragmented; [15] vacuole: enlarged; [16] vacuole: class G; [17] vacuole
B. qPCR analysis of Ahr expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 4h as indicated. Ahr expression was normalized to Hprt1. Ahr expression among groups was normalized to Medium. n = 4 independent experiments; mean ± SEM; one-way ANOVA, Dunnett's multiple comparison test.
Western blot images of p53-/- MEFS with or without overexpression of eGFP-Trf1 WT or mutant alleles followed treatment with ERKi. Data are representative of n=2 biological replicates
C Detected fragments per million (FPM) for SPRR5 in control (siCtrl) as well as LINC00941 deficient (siLINC00941) epidermal tissue for all biological replicates on day 3 (D3) of differentiation as obtained by DeSeq2 (FC = fold change) (n = 4‑5 epidermal tissue cultures/knockdown group).
Bronchial epithelial (BEAS-2B) cells were challenged with PBS (as control) or with 2 µg/mL Poly(I:C) (PIC) or with influenza A/Scotland/20/74 (H3N2) virus (IAV) at MOI=1 for 4 h and treated or not with succinate (Suc) for 20 h. (e) A neuraminidase activity test was also applied in cells infected or not by IAV and treated or not with malonate (a succinate dehydrogenase inhibitor), in comparison with succinate. Data information: Data are represented as the mean ± SEM of e) independent experiments. Statistical analysis was performed using the Kruskal-Wallis test with Dunn's post-test (*P < 0.05).
G IF at E11.5 for PGCs (arrows) with MVH (red) and STELLA (green). Scale bar, 20 μm.
F Relative fold changes of C9orf72 variant RNA levels normalised to RPL13A, after 14-day 10 µM H89 treatment vs vehicle treatment (N=1 C9 patient line, four technical replicates). No significant changes were observed between H89 and vehicle for any of the isoforms (2-way ANOVA with Šídák's multiple comparisons test, all not significant, P>0.05). Data information: Error bars reported as ± SD. Not significant = P>0.05, *P<0.05, **P<0.01. T
C-F GlaB inhibits MB‐SCs' self‐renewal and proliferation. (C) Suspension of single MB‐SCs isolated from Ptch1+/−mice. MBs were cultured in stem cell medium to allow the formation of primary neurospheres. Primary neurospheres were dissociated and treated with increasing concentrations of GlaB or DMSO only. After 7 days of treatment, the number of secondary neurospheres derived from a known number of single cells was counted. The self‐renewal MB‐SCs' capability is expressed as percentage of neurosphere‐forming cells (left). Representative bright field images of tumor neurospheres after GlaB treatment are also shown (right).
(B) Formaldehyde fixed RFP+ UPEC were mixed with 10 µM Alexa-Fluor488-hGBP1F or -hGBP1FR584-586A supplemented with 2 mM GTP. Following 60 min of incubation hGBP1F-enclosed UPEC were quantified. Graphs depict mean ± SEM of combined data from three independent experiments. Significance was determined by unpaired t-test, two-tailed. ****, P ≤ 0.0001.
Structure of the RIPK1:RIPK3 RHIM core, prepared using PyMol Graphics System from PDB 5V7Z. The RIPK3 sequence is coloured in blue and RIPK1 is coloured in green. Tetrad residue side chains are shown as sticks; Tyr, Asn/Gln, Ser and Cys side chains are shown in wheat, red, grey and yellow, respectively. Core tetrad interactions across the opposing β‑sheets are indicated by the dotted box Model of M45:RIPK3 RHIM core, prepared by appropriate mutation of RIPK1. The M45 sequence is coloured in cyan and RIPK3 in blue. Tetrad residue side chains are shown as sticks; Tyr, Asn/Gln, Val and Cys side chains are shown in wheat, red, grey and yellow, respectively. Core tetrad interactions across the opposing sheets are indicated by the dotted box
Technical validation of 10 top DEGs in PD iPSC‐derived DAn as compared to controls (n = 14) identified by genome wide gene expression study (upper heat‐map) and validated by real‐time qPCR (lower heat‐map). Relative gene expression and statistical significances were calculated using the ΔΔCt method and GAPDH, ACTB, and PPIA as endogenous controls. Pearson correlation analysis between microarray and real‐time qPCR data showed a high degree of correlation (r 2 = 0.99, P = 7.7 × 10−7) (bottom graph). L2, LRRK2‐associated PD; s, sporadic PD.
D. (Left) Venn diagram of the significant proteins shared by both IGR and WM cell lines. (Right) Histograms representing the metastatic and primitive signatures H/M ratios.
C) Antibody staining for TEAD4 reveals a gradient of expression along the crypt-villus axis in both the small and large intestine, with uniformly high expression in colorectal adenomas, similar to SOX9.
Results summary (E) from Affymetrix CytoScanHD Arrays of 33 primary MPM cell lines (called MESO #) from Nantes, France (GEO dataset GSE134349). Red lines denote the KRAS locus on chromosome 12p12.1.
Cross-link connectivity map of SVgrG-Tle1H complex. The two proteins are represented as rectangles in which the residues number and known domains are indicated. Straight lines represent inter-molecular cross-links, while dotted lines represent intra-molecular cross-links. Only the cross-links identified in two independent experiments were considered. Raw and cured data are provided in Dataset EV1.
h, alpha-KG, released from octyl alpha-KG (800 µM), decreases state 3, but not state 4o or 3u (P = 0.997), respiration in mitochondria isolated from mouse liver. The respiratory control ratio is decreased in the octyl alpha-KG- (3.1 ± 0.6) versus vehicle-treated mitochondria (5.2 ± 1.0) (*P = 0.015; by t-test, two-tailed, two-sample unequal variance). Oligo, oligomycin; FCCP, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone; AA, antimycin A.
(A) The precursor form of wild-type COA7 is synthesized in the cytosol and imported into the mitochondrial intermembrane space by the MIA pathway, where it is involved in the respiratory chain biogenesis.
(G) Full-length Mcp3 precursor accumulates during import if IMP processing is abolished. Radiolabelled internally HA-tagged Mcp3 without (HA-Mcp3) or with mutation in the Imp1 cleavage site (D70G+HA) were incubated with mitochondria as in (F). After import samples were incubated with or without PK (20 µg/ml). Samples were analysed by SDS-PAGE and autoradiography.
WT and Vav-BCL2 derived E14.5 total bone marrow cells (C) were treated for up to 48h with different doses of CHK1i. Survival was assessed using Nicoletti staining and flow cytometry. Bars represent means ± S.E.M. (n=3 biological replicates per genotype).
Comparison of the 72-h measured relative viability AUC between two cell lines (C32 and WM1552C) treated with four RAF inhibitors and one MEK inhibitor.
Meta-gene plot showing average ISWI enrichment (y-axis = ChIP/Input) in clonal ISWI-3HA parasites at 12 hpi from 1.5 kb upstream of the translation start site ("Start") to 1.5 kb downstream of the translation stop site ("Stop") for genes that are down- (blue) or up-regulated (yellow) upon ISWI knockdown. One replicate was used for the ISWI ChIP-seq.
Protein to mRNA abundance plot for brain tissue. The slope of the regression line indicates that high abundance mRNAs give rise to more protein copies per mRNA than low abundance mRNAs.
GSEA pre-ranked analysis comparing the Mex3a-/- transcriptional profile against (E) the Mex3ahigh
A) Effects of RNF26 knockdown on virus-induced polyubiquitination of endogenous MITA. The THP-1-RNF26-RNAi or control cells (2×107) were infected with SeV or HSV-1 for the indicated time points or left uninfected. Cell lysates were subjected to IP under denatured conditions with anti-MITA and the immunoprecipitates were analyzed by immunoblots with anti-Ub(K48) (upper panel), anti-Ub(K63) (middle panel) or anti-MITA (lower panel). The whole cell lysates were analyzed by immunoblots with antibodies against the indicated proteins.
F, Depletion of Smurf2 reverses the shPTPN3-induced degradation of TβRI. HEK293T cells were transfected with expression plasmids for shPTPN3, shSmurf2 and HA-TβRI. 48 h post-transfection, cells were harvested for immunoblotting analysis. TβRI level was determined by Western blotting with the anti-HA antibody. Levels of other proteins were done by Western blotting with the indicated antibodies.
(L) In vitro kinase assay of purified Sox11WT and S244allS289all mutant using recombinant GSK3β protein and radiolabelled ATP. Experiment performed as in (K).
Confocal microscopy analysis of the subcellular localization of Axin1-GFP upon expression of WT or oncogenic RNF43 (R519X). Scale bars represent 10 μm. RNF43 is visualised by Flag-staining. Asterisks indicate RNF43-expressing cells.
(G-H) Immunoblots (G) and quantitative data (H, n=3) showing NFATc1 levels in HEK293T cells transfected with NFATc1-CA, with or without ectopic SIRT7, treated with MG132.
(F, G) The bur1-ΔC mutant exhibits a synthetic growth defect with vac17Δ. Quantification of colony size in tetrad dissection, relative to the average of WT colonies. A total of 25 full tetrads were analyzed. p-value determined with a one-way ANOVA and Tukey post hoc test. ** (p-value < 1 x 10-2), *** (p-value < 1 x 10-3). Red bar; average in each category. Error bar; standard deviation (SD).
Rate of whole-cell H2O2 (e) and mitochondrial O2·− (f) detection in WT and Pink1 KO MEF
qPCR validation of Lpl and Fabp4 expression in sorted ATM subsets from eWAT of ND- and HFD-treated (16 weeks) mice (n = 3 of 5 pooled mice each). Data are presented as mean ± SD. *P < 0.05; **P < 0.01, ***P < 0.001; ****P < 0.0001; ns: no significant difference. Representative FACS analysis of CD36 expression in ATM subsets from eWAT of HFD (16 weeks) mice (n = 4 mice).
(D) The response of a mitochondrial matrix-localized Grx1-roGFP2 probe, expressed in Δprx1 cells containing a plasmid encoding either wild-type Prx1, Prx1-P233stop or Prx1C91A to the addition of 1 mM exogenous H2O2. Cells had been pre-treated with either 10 mM H2O2 or with water as a control. For these experiments, cells were grown in SGal (-Leu, -Ura) medium and harvested at early exponential phase. OxD refers to the degree of sensor oxidation. Error bars represent the standard deviation (n = 3 biological replicates, with cells obtained from 3 independent cultures for every strain and probe combinations. For each biological replicate three technical replicates were performed).
Retinal isomerization in the rhodopsin dark state: E) WT, F) T94I and G) G90D rhodopsin, H) The fraction of 11-cis retinal is plotted as a function of time and fitted to a single exponential decay.
(D) Box plot shows a significant reduction in locomotor activity during the wake state under a low (light blue box) than a medium (dark blue box) intensity LD regime on the 5th, 6th and 7th dpf. (E) As in D for the rest state (dark phase). No difference in locomotor activity was detected. Data information: boxplot divides the data in quartiles: the box indicates the interquartile range, with the horizontal line in the box denoting the median of the data set, the whiskers extend to the minimum and maximum, and meet the box at the median of the lower (quartile 1) and median of the upper (quartile 3) half of the dataset. Black dots indicate biological replicates (n=18), the red dot indicates the mean, red error bars indicate the confidence interval (95%) and asterisks indicate significance (0.01<p(✱)<0.05, 0.001<p(✱✱)<0.01, p(✱✱✱)<0.001, ns = not significant).
(c) Mechanism by which C18-ceramide (Cer) induces lethal autophagy involves, at least in part, the lipidation of LC3B, forming LC3B-II (LC3-PE), and interaction of LC3B-II and ceramide on mitochondrial membranes upon Drp1-mediated mitochondrial fission, which targets autophagolysosomes to mitochondria for lethal mitophagy.
(b) Ratio of LC3-II to tubulin on knockdown (KD) of control, epsin, clathrin heavy chain, AP2 or AP1, with or without bafilomycin A1, quantified from three independent experiments (two for epsin) and represented in the graph. Asterisk, P 0.01; two asterisks, P 0.001; three asterisks, P 0.0001.
A schematic illustrating the effect of transcription speed on RNAPII stalling at promoter proximal regions. Accelerated RNAPII is prone to move out of stalling regions (centered at the position of the first nucleosome) at 5' end of genes, resulting in reduced promoter proximal stalling peaks in RNAPII profile by plaNET-seq.
A schematic illustration of p53's C-terminal modifications and described functional implications, including key regulatory enzymes.
Immunofluorescence micrographs showing the expression of ACE2 receptor (D) in the well-differentiated primary human lung airway epithelim on-chip (Post) versus the same cells prior to differentiation (Pre).
B. Thapsigargin (Tp, 1 µg/ml) increased Nox4 protein levels in H9c2 cells. n=4-6/group. *, significant compared to baseline.
D. RT-qPCR of Axin2 expression in bEnd.3 cells treated with serial dilutions of F4L5.13, NDP or isotype control for 24h. Data are presented as mean ± SEM, n=3.
F, G Immunoblots showing the levels of CBF1-myc proteins after exposure to white light. CBF1-myc seedlings were first grown at 22°C for 4 d in D, and then transferred to continuous W light for the indicated time periods within 1 h (F) or ranging from 1 h to 24 h (G). anti-HSP was used as a sample loading control. Numbers below the immunoblots indicate the relative band intensities of CBF1 or CBF1-myc normalized to those of loading control, respectively. The ratio of the first clear band was set to 100 for each blot.
A Scheme of the mouse intraductal xenograft (MIND) approach. Freshly isolated human breast tissue is dissociated to single cells, which are lentivirally transduced and injected into the milk ducts via the teat. In vivo growth is monitored by weekly luminescence measurements. At endpoint, xenografted mammary glands and blood are collected for further analyses.
G Immunoprecipitation analysis of acetylation of Myc-p97 in HEK293T cells transfected with Myc-p97 (WT, K663R or K651R) and then treated with additional NaCl (+34 mM) for 12 hrs. Data information: Data are representative of at least two biological replicates.
(F) Co‐immunoprecipitation of Beclin‐1 with‐WT and mutant (G138A) Bcl‐XL. Results are representative of at least three experiments yielding similar results.
Compacted chromosomal interaction domains (red and green) are connected by a domain boundary denoted as a blue line. (Top) High rates of transcription that produce a relatively long (> 2 kb) transcript (wavy orange lines) locally decompact the DNA, thereby creating a spatial gap between flanking loci. This spatial separation diminishes the long-range contacts that can occur within a fixed sphere (black dotted circle), leading to the domain boundaries visible by Hi-C analysis. High rates of transcription can also prevent supercoil diffusion, helping to limit DNA-DNA interactions on a shorter length scale (grey dotted circle). (Bottom) In the absence of transcription, DNA at a domain boundary (blue) will become more compacted, reducing the spatial separation between adjacent domains, and enabling supercoil diffusion, thereby promoting long- and short-range contacts, respectively.
F Luminescence derived from HEK293T transfected with GA-NLuc reporters WT or mutated and treated with H89 for 24 h. Mutational analysis of near-cognate CUG start codon from three biological replicates and four technical replicates, n = 12. Data are mean ± SEM. 2-way ANOVA followed by Dunnett's multiple comparisons test, *P = 0.0130 WT H89 vs WT DMSO, ****P<0.0001, CUG mutated H89 vs CUG mutated DMSO. Concentration used: 2.5 μM H89,
, Effect of LARP6 knockdown on Col1a1, mRNA expression in WT and CRTH2-/- fibroblasts. Fibroblasts were transfected with Si-LARP6 or scramble siRNA. After 48 h transfection, RNA was prepared for qRT-PCR analysis. GAPDH was used as housekeeping gene. *P < 0.05 vs WT, #P < 0.05 vs scramble (two-way ANOVA); n = 6 for all groups.
B. Fold change of the main PC and PE species in the lysosomal membranes of MDGI-silenced (shMDGI) and control (Scr) cells (Log2, by mol % data). Abbreviations: [Lipid class] [total number of acyl chain carbons]:[total number of double bonds in the chains]. A representative heatmap of two independent experiments is shown.
(E) Gene Set Enrichment Analysis comparing gene location of ΔNLef1 peaks and SG gene expression signature.
(A) SDS-PAGE analysis of the PPM1H(D288A): pRab8a complex in the presence of DSBU crosslinker. Control migration of proteins are on the left. NP, non-phosphorylated Rab8a; P, phosphorylated Rab8a. The migration of control and crosslinked proteins is marked on the right.
(C) Macrophages were pretreated with bafilomycin A1 (Baf A1), SID 26681509 (SID) or vehicle control before incubation with CL097 or ssRNA40 for 24 h before infection with HIV. Cells were then washed and incubated with TLR8 agonists and inhibitors for 10 d and ELISA performed for extracellular HIV p24 antigen release over 10 d. Results are reported as mean ± s.e.m., n = 5. * p<0.05; # p<0.001.
Overview of the experimental and analytical setup. ATAC-seq was performed on 35 AML samples comprising the mutational groups N: NPM1 mutated, F: FLT3-ITD, N/F: NPM1/FLT3-ITD, D/N/F: DNMT3A/NPM1/FLT3-ITD. Indicated colors represent GPR56 protein expression grouped into high (> 70% GPR56+ cells per sample, n=13), medium (30-70% GPR56+, n=5), and low (< 30% GPR56+, n=17), cytogenetic and molecular genetic characteristics, and gender. ATAC-seq data was subjected to the computational pipelines diffTF, diffBind, and GREAT. RNA-seq was performed on CB CD34+ cells after GPR56 knockdown and analyzed by DESeq2. The combined information was used to identify differential TF and signaling pathway activities up- and downstream of GPR56.
C) ELISA binding results of mAbs specific for hRSV F (left panels) or hMPV F (right panels) with the proteins indicated at left. mAbs specific of hRSV F bind epitopes of antigenic site II (Mota and 47F) or antigenic site IV (101F). mAs specific of hMPV F bind epitopes of antigenic site II (MF9, MF12, MF14 and MF15) or antigenic site IV (MF16).