EMBO/sd-character-level-ner huggingface dataset:
C Chromogenic assay performed on the medium of transfected cells to detect F8 activity levels reported as International Units/deciliter (IU/dl). Data are presented as mean ±SEM. Each dot within each group represent a different biological replicate (n): I + II n=3; I+II (Het.) n=3; I (N-int E) n=3; I (N-int B) n=3; II (C-int E) n=3; Neg n=4. Significant differences between groups were assessed using Kruskal-Wallis rank sum test Kruskal−Wallis, p value = 0.013. *indicates the significant difference between the I+II and the I (N-int E) groups: p value ≤ 0.05. ***indicates the significant difference between the I+II and the Neg groups: p value ≤0.001.
(B) Same overlap as in (A) for genes downregulated upon JNKi treatment during EMT and upregulated during normal EMT. Right panel displays RNA levels as in (A) for 10 transcription factors identified in this overlap.
I: Wild type, mps1-3, mps1-3 spc105-18, and mps1-3 GLC7-24 cells were synchronised in G1 with α-factor at 25°C and then released at 32°C in the presence of nocodazole (note that the presence of 3HA tags at the C-terminus of Mps1-3 slightly decreases the maximal temperature of suppression). Cells were collected after 90 minutes and fixed with formaldehyde for ChIP-seq analysis. ChIP sequence reads were normalised against sequence reads from corresponding input samples, and relative enrichment is plotted for chromosome III around the centromere (see the centromeric regions of all 16 yeast chromosomes in Fig. S5). Y‐axis shows enrichment values (linear scale, range is 0-10). Values below 1.5 are shown in grey, and values above 1.5 (i.e. sequences enriched in ChIP samples) are red coloured.
(H) Gene ontology (GO) analysis illustrates classes of proteins differing between CTNSWT and CTNS-/- cells (n = 3).
E Representative flow cytometry dot plots showing CD31+ Emcnhi and CD31+ Emcnlo EC populations in young and aged pancreas. Combo plot shows the population of CD31+ Emcnhi ECs in young and aged pancreas.
Relative luciferase activities of the -1650-Luc by the combination of MyoD and Ddx17 or Ddx17 mutant (K142R). Bars indicate the average of two independent experiments, and open circles represent the values of each experiment.
(A) Schematic representation of the experimental setting used for the MSU-gout model. Mice were injected i.a with 100 µg of monosodium urate (MSU) crystals into the knee. After 3 h, mice were treated intraperitonially (i.p.) with VHHmASC, VHH NP-1 as unrelated nanobody (both 5 mg kg-1), or vehicle (PBS).
(B-C) IP of YFP-hSgo1 from cells stably expressing the hSgo1 WT, 3A, and 4A using different salt conditions (50mM NaCl (B) or 150 mM (C)) followed by immunoblotting of indicated proteins and quantification by LiCor. Representative blots are shown. B56α signals were normalized to YFP and plotted. Error bars represent SD (n=3 for B and n=4 for C).
(A-B) Representative confocal projections of the whole pancreas (dashed lines) of 35-day-old Tg(ins:H2B-GFP);Tg(ins:Flag-NTR) transgenics, with or without Tg(bactin:igfbp1a), that were subjected to β-cell ablation between day 30-31 and then allowed to regenerate for 4 days. Scale bars represent 100 μm. (C) Body length of control and Tg(bactin:igfbp1a) zebrafish; P<0.0001. (D-H) Quantification of β-cell regeneration was automated with an ImageJ script. (D) Insulin-positive area per zebrafish. (E) Relative insulin-positive area per body length; P<0.01. (F) The percentage of the pancreas area that was insulin-positive was significantly larger in Tg(bactin:igfbp1a) than in controls; P<0.0001. (G) The total number of recorded units of adjacent ins:H2B-GFP+ pixels (units ranging from single β cells to β-cell clusters) did not differ between control and Tg(bactin:igfbp1a) zebrafish. (H) The size of recorded ins:H2B-GFP+ units was on average larger in Tg(bactin:igfbp1a) than in controls; P=0.039. n=26 in the control group, n=27 in the Tg(bactin:igfbp1a) group.
A-C) Representative images of FOXO1 localization upon scaffolds administration. Scale bars are 10 µm D) Quantifications of nuclear FOXO1 shown as percent of cells with nuclear FOXO1 stain, 100 cells were counted per sample.
Stepwise diffusion of FtsZ-Alexa 488 into FtsZ·SlmA·SBS condensates (FtsZ labeled with Alexa 647) at the indicated times in seconds (time zero, beginning of visualization for those particular condensates) in 100 g/L PEG. Scale bars: 4 μm.
DRP-1 is localized to the lumen of autophagic vesicles. Immunogold staining of 293 cells expressing HA-DRP-1 reveals a specific staining of DRP-1 in the lumen of double membrane autophagosomes containing cytoplasmic material (A and B) in autophagosomes containing organelles and vacuoles (C) and inside the body of autolysosomes containing digested matter (D). The gold particles do not overlap with the phagocytosed organelles in C or the lysosomes in D.
(c-e) Changes in lysosomal positioning induced by kinesin- or small GTPase-family members (c,d) correlate with changes in mTORC1 activity (e). HeLa cells were transfected with overexpression constructs (OE) or with siRNA as shown, followed by immunofluorescence (c,d) or by immunoblotting (e) analyses. Values are means ± s.e.m. of three independent experiments carried out in triplicate. All comparisons are with the control within each treatment condition, *P0.05, ***P0.005 Student's t-test; n.s. not significant. Uncropped images of blots are shown in Supplementary Fig. S7.
E. The percentage numbers of cells (Fig 7C) in G1, S or G2/M phase were analyzed by FlowJo 7.6 software. Data shown are mean ± SD (n = 3).
(K) CSAG2 Δ37 fails to promote anchorage-independent growth of H460 cells. Soft agar colony formation assays were performed in CSAG2-negative H460 cells stably expressing CSAG2 wild-type or CSAG2 Δ37 mutant (n=3 biological replicates). Data are represented as the mean ± SD.
(D) GST pull down assay. 3μg recombinant GST-T1B protein which immobilized on glutathione Sepharose beads was incubated with the cell lysates that obtained by adding 1ml lysis buffer to the HEK293T cells in 10 cm cell culture dish with a final protein concentration around 1μg/μl, after 4 hrs incubation, washed beads with cell lysis buffer five times and subjected to SDS-PAGE for immunoblotting with anti-TAK1.
(C) Quantification of the intracellular levels of transcripts for the SARS-CoV-2 N and SARS-CoV-2 E genes in the AT and endothelial layers of infected LoCs at 1 dpi (n=3 biological replicates) relative to expression of the eukaryotic housekeeping gene GAPDH. Data information: In all plots, the bars represent the mean value, and the error bars represent the standard deviation
A GST pulldown assay was performed to monitor the interaction between 6×His tag-fused VAPB_ΔTM and GST-fused PTPIP51_TPR (or GST-fused PTPIP51_ΔTM). VAPB_ΔTM pulled down by PTPIP51_ΔTM is marked with an asterisk and highlighted with a red arrow.
(C) The construct encoding Flag-Pdia4 and that expressing Myc/Flag-tagged Ndufs3 (top) or p22phox (bottom) were co-transfected into 293T cells. Total lysates of the cells were incubated with anti-Myc (left) or anti-Pdia4 (right) antibodies plus protein G beads. Their total lysates (TL) and immunoprecipitates (IP) underwent immunoblotting analysis anti-Flag antibody.
Evaluation of lung micrometastases using HE and vimentin-stained lung sections upon antiangiogenic therapies in Ren13BM and Ren28. proportion of mice with 0, 1, 2 or > 3 metastases (mets) per lungs (*p < 0.05 by Mann-Whitney test) are shown.
Effect of Okadaic acid (OA; 100nM), the PP2A inhibitor, on Ago2 phosphorylation The amount of phosphorylated Ago2 was measured in OA treated cells before and after LPS stimulation. The amount of Tyr phosphorylated Ago2 was measured by densitometric quantification of western blot data upon normalization against immunoprecipitated Ago2 amount (B).
MARK4 siRNA-mediated silencing increases the tubulin cytoskeletal area (A). (A) Data shown are representative of experiments performed in triplicate. Bar graph represents the average ± SEM of n ≥ 50 per technical replicate with 3 technical replicates per conditions.
(B) Model. IRF2BP1 is a SUMO-dependent transcriptional repressor of immediate early genes (IEGs). Transcription of IEGs is repressed by SUMOylated IRF2BP1, which binds to its proximal promoter. EGF receptor signaling yields at least two signals to induce IEG expression, one of which is the transient deSUMOylation of IRF2BP1.
The biomass objective function (BOF) was defined using the BOFdat software (Lachance et al, 2019a) and experimental data from Matteau et al. (Matteau et al, 2020). The stoichiometric coefficients for the major cellular macromolecules were generated with BOFdat Step1 (left), the inorganic ions and coenzymes with BOFdat Step2 (middle) and the remaining components with BOFdat Step3 (right), which identifies the metabolites with the greatest impact on the BOF gene essentiality prediction accuracy
(D) Percentage of phospho-S6 positive cells in the RGC layer 2 weeks after delivery of AAV-Cre-GFP or AAV-GFP.
H LAMP1-positive organelles were manually quantified for containing a p62-filled or empty lumen. A total of 50-60 LAMP1-positive organelles were analyzed in each experiment. Data are presented as mean ± SD (n=3 independent experiments) with paired t-test values
H, I, Accumulation of NoV RNA1 was determined by RT-qPCR in NoVWT-infected BALB/c suckling mice at 1 (H) or 3 dpi (I). n=5~7 per group. Data are shown as mean±SD. ****indicates p<0.0001 by student's t test.
(h) Western blot analysis of HeLa cells treated with indicated combinations of control siRNA or siRNA targeting GEMIN3, GEMIN4 and ATG5. Western blot analysis of CLN3 and DCP1A are used to demonstrate equal loading of wells.
(C) Bisulfite sequencing analyses of the miR-124 promoter. Each CpG site is indicated, and the methylation status of two different regions are shown. Open and filled circles represent unmethylated and methylated CpG sites, respectively. The percentage of methylated CpGs among total number of CpGs is also shown.
E. In vitro FRET-FLIM measurement of the PlexA-FRET Biosensor shows that the PlexA ectodomain undergoes a conformational change upon treatment with Sema1b resulting in more open conformation. The boxcharts represent the average lifetime. Box limits indicate the 25th and 75th percentiles, centred lines show the median, squares represent sample means, whiskers extend 1.5-fold the interquartile range from the 25th and 75th percentiles, p-value was calculated by one-way analysis of variance (ANOVA). ***P<0.001.
protein (D), and phosphorylation levels of Ser455 (E) in Acly in HSCs after the administration of 5-FU.
B | 3 days post transduction the surface expression of IgM/IgD (dot plots, top), IgD and CD23 (histograms, bottom) was measured by flow cytometry and compared between EV- and FoxO1-A3-transduced cells. Fluorescence minus one (FMO) stainings, lacking α-IgD or α-CD23 antibodies respectively, served as controls (ctrl). Bar diagrams below flow cytometry data display the percentages of IgD+ cells (n = 12; left) and MFI of CD23 (as relative units, RU), normalized to the MFI measured in the respective EV transduced cells; n = 12; middle). Fcer2 transcript levels were measured by qRT-PCR (right, n = 4). Mean ±SD, symbols indicate data from individual mice. Statistical significance of IgD expression was determined by applying the Wilcoxon matched-pairs signed rank test for CD23 and by applying the one sample two-tailed t-test for Fcer2 expression.
A-I Glucose metabolic parameters were assessed following 5 days of treatment of DIO male mice with vehicle (white), liraglutide (10 nmol/kg) (gray), RM-493 (3.6 μmol/kg) (black), or liraglutide (10 nmol/kg) and RM-493 (3.6 μmol/kg) (checkered). (D) fasted insulin levels,. Data represent means ± SEM;n = 8 in (A-H); *P < 0.05, **P < 0.01, ***P < 0.001.
C. Western blot analysis of the protein levels of MEF2C and GAPDH in the hippocampus of VPA-treated mice (n = 9) and saline-treated mice (n = 10).
Diagram depicting CRISPR/cas9-mediated deletion of the full coding sequence of ap2-o3 in the 17XNL and ap2-o3::6HA strains respectively, generating the Δap2-o3 and ap2-o3::6HA;Δap2-o3 mutants.
(A) Native MS spectrum of 30 µM SPOP28-359 confirms that SPOP self-associates through addition of dimers. The increase in mass indicates that the dimer is the stable building block within the assemblies.
D Ten-fold serial dilutions of cells and subsequent colony formation on the indicated plates, where expression of wild type GALp-CDC42 is either induced in the presence of Gal or repressed in Dex. Note how mutation of the wild type Cdc42 (KKSKK) to MMSMM is lethal (see blue box), whereas appending the Bem1 BC-1 motif to this cdc42 mutant restores viability (red box).
(b) Fixed acini were co-stained with Amylase (granules) and LAMP1 (lysosomes) and the fold overlap was calculated from 14 and 11 images obtained from 3 wild-type and 3 Trpml1-/- mice, respectively.
B) Chemical structure of rac5c. See Appendix Supplementary Methods for detail on compound synthesis and characterisation.
D. The 7SK RNA levels in these two clones were detected by qRT-PCR before and after the DOX treatment and normalized to the GAPDH mRNA levels. The error bars represent mean ± SD from three independent experiments.
(C, D) Immuno-blots showing secretion profile of Hcp-1 (associated with T6SS-1) and Hcp-2 (associated with T6SS-2) proteins, using protein specific peptide antibody in different NGJ1 strains. The T6SS-1- mutant was defective in Hcp-1 secretion (due to polar effect of plasmid integration, synthesis was also prevented) but proficient in Hcp-2 secretion. On the other hand, the T6SS-2- mutant was defective in secretion of Hcp-2 (although the protein was synthesized) but proficient in secretion of Hcp-1.
C. The indicated Flag-AMOTL2 WT or mutant proteins were subjected to an in vivo ubiquitination assay in 293T cells.
(E and G) ChIP-qPCR showing increased enrichment of ERG binding sites at Mpl or F2r loci following STAT5 knock-down (E) or stimulation with TPO (G).
B,C) Expression levels of the cluster markers increasing in WI compared to NI according to (A) during the progression of the immune response to wasp infestation. Collections were carried out at t0 (time of infestation, L2), 24 h (early L3), 48 h (mid L3) and 72 h (WL) after wasp infestation (n=3). The time line is on the x-axis and the normalised expression levels on the y-axis. The expression levels were normalised to the levels at t0. The dotted lines indicate t0 relative level (=1). The markers that do not display strong variability during the timeline are presented in (B) and the ones showing a strong up-regulation are in (C).
(A) Knockdown of UHMK1 blocked NCOA3 binding to ATF4. SGC7901 cells were treated as indicated. Co-IP was carried out with mouse immunoglobulin G (IgG) or anti-NCOA3 antibody. Then Western blotting was performed.
(G) Quantification of the fraction of cells with PIDD1 localized at the mature mother centriole. Experiments were performed in PLK4Dox monoclonal knockout cells. Data acquired across n = 3 biological replicates. Mean ± s.e.m.
(B and C) Growth and viability of wild type, phm8 and pnp1/urh1 strains in starvation.
(C) Schematic illustration of suggested model of Cdc55 regulation in the hyperosmotic stress response, with grey arrows signifying hypothetical relationships.
(c) Western blot against PDK1 and HIF1α in WT and Pink1 KO MEF transfected with siHif1α (or its siControl); ß-actin was used as loading control.
B. Body weight in YFO and AFO. Data information: Data are presented in the box plot or pie chart format. The central band in each box represents the median; boxes indicate the middle quartiles, and whiskers extend to the minimum and maximum values. *p<0.05, determined using Student's or Welch t-test.
Figure 7. Contrasting models for histone chaperoning during nuclear import of H3.1 and H4. In the dimer import model, H3.1 and H4 form a heterodimer soon after synthesis in the cytosol. This heterodimer is bound by the chaperones NASP, ASF1, RbAp46 and HAT1, which further associate with IPO4 before translocation to the nucleus. In the monomer import model, H3 and H4 monomers are bound by Importin-β proteins before translocation to the nucleus, wherein they form a heterodimer and associate with the core histone chaperoning machinery. Additional cytosolic factors may also transiently interact with the monomeric histones. Expanded View Figure Legends
LSM images of cross-sections through the heart of an adult Prox1-CreERT2;Ilk+/+ mouse (referred to as "Adult Control") and Prox1-CreERT2;Ilk∆/∆ mouse (referred to as "Adult ILK K.O.") showing the outer lateral region of the left ventricle (LV) Overall cardiac lymph vessel and blood vessel density in heart sections as determined by Lyve1-positive and CD31-positive area (normalised to total analysed myocardial area), respectively (n = 4 control and n = 5 ILK K.O. mice)
Quantification of the number of Ctrl (left panel) and 7/8KO (right panel) RPE-FUCCI cells with scr or sicyclin F that completed mitosis after HU release. For each condition, 100 cells were monitored by live cell imaging. Each cell was followed until it successfully finished mitosis and divided into two daughter cells for a maximum of 24 hours. Log-rank tests were performed to analyze the statistical significance.
Relative expression of selected cluster-specific genes in each cluster. High-density bar charts showed the distribution of the normalized expression levels of genes.
SUNCR1 protein expression in the gastrocnemius from sedentary or post-running mice (n=4).
(f) Cells from a were assessed for the L/R ratio of reformation tubules in a blind fashion after starvation and quantified. 25 cells were counted. The average L/R is indicated above each column.
Model for CST in protecting reversal forks stability. Upon fork stalling, the stalled fork is reversed by SMARCAL1, ZRANB3, or others. CST binds to ssDNA (5' overhang) at reversed forks to directly block MRE11 access and may also recruit RAD51. Without CST, nascent-strand DNA is degraded by MRE11, leading to the generation of excessive ssDNA and genome instability.
Luciferase signal driven by MDK-promoter transduced into SK-Mel-147 cells treated with vehicle (v) or BO-110 (BO) as indicated in Materials and Methods. Results were normalized to vehicle control. Data correspond to the mean ± SD of four biological replicates. Statistical significance was determined by ANOVA.
(H) Phenotypic classification of nuclear morphology after Cdca5 deletion and proliferation for 5 to 7 days. Size bar, 10 µm; error bars denote s.e.m.; n > 500 cells per condition.
Dot plot showing the correlation between the normalized density of indicated TEs per TAD (x-axis) and changes in inter-TAD interactions upon Piwi-KD (y-axis). Trend lines are in red. Spearman's rank correlation rho is indicated along with the p-value (algorithm AS 89).
Aminoacid and nucleotide sequences of the Nsmce2‐mutant allele. The SUMO ligase‐inactivating mutation used C185S; H187A (SD), which is the same originally described in yeast (Andrews et al, ) and which has been used as a SUMOylation‐deficient model in multiple studies. The nucleotide sequence derives directly from sequencing DNA from Nsmce2SD/SDmice.
(H) Left: Representative immunohistochemistry pictures of phosphorylated FAK on tyrosine (Y) 397 and of CD206 in serial sections of human PDAC tissues. Scale bar: 200µm Middle: Correlation plot between fibroblastic pY397 FAK score and CD45 or CD206+ cell number within human PDAC samples. Fibroblastic pY397 FAK score and percentage of CD206 positive cell quantifications were performed on a 47 patient cohort based on IHC staining. Spearman r = 0.4145, p=0.0019. Right: Percentage of CD206 positive cells in PDAC patient expressing either low or high fibroblastic FAK activity score.
(C) Split‐GFP analysis inatg8Δ cells. Cells expressing GFP halves were grown for 4 h in galactose medium, and scored for presence of fluorescence (−, no signal; +, fluorescent signal). Peroxisomes in cells expressing GFP-C‐Atg36 plus Pex3-GFP‐N were identified by mating with pex19Δ cells expressing HcRed-PTS1. Multiple fluorescent images were acquired in Z‐axis and flattened into a single image. Bright‐field image is a single plane. Bar, 5 μm.
In vivo effect 24 h after hydrodynamic injection of B mice with plasmids expressing miR-511 (grey, n = 19), miR-CTR (black, n = 19) or PBS (black, n = 8). Liver TNFR1 protein levels (left panel) were measured by ELISA. Twenty-four hours after plasmid injection, mice were injected with 25 μg TNF. All mice pretreated with miR-511 (grey, n = 12) survived, while 50% of the mice pretreated with miR-CTR (■, black, n = 12) or PBS (●, black, n = 12) died from TNF injection (middle panel). Twenty-four hours after injection of TNF, body temperatures of mice pretreated with miR-511 were significantly higher than those of the miR-CTR and PBS groups (right panel) (all groups n = 10).
(a) Confocal microscopy of wild-type and Nod1-deficient GFP-LC3-expressing MEFs infected for 2 h with wild-type S. flexneri M90T-RFP. (b) Quantification of the colocalization of GFP-LC3 signals with bacteria in a.
Clusters of Scgb1a1 lineage-labeled cells from 10XGenomics 3' single-cell RNA-sequencing (scRNA-seq) analysis visualized by Uniform Manifold Approximation and Projection (UMAP), assigned by specific colors at day 5 and 14 post tamoxifen treatment. The number of cells in the individual cluster is depicted in the figure.
Luciferase assay with T-binding elements (TBEs) around the indicated loci as shown in (A) and Fig EV3E. Relative luciferase activities of sorted cell fractions are shown with SDs. (three independent experiments with two technical replicates).
(C) Impaired PGAM5 processing in depolarized Oma1-/- mitochondria lacking PARL. Processing of L-PGAM5 to S-PGAM5 was examined as in (A) after 2 h in wild type (WT) and Oma1-/- mitochondria in the presence or absence of CCCP (20 µM, 2 h), which were depleted of PARL by siRNA as indicated. * unspecific cross-reaction.
(I) The dynamics of the biological process in muscle regeneration and the participating cell types. Genes were assigned to five groups (C1-5) based on highest time point of TR. OR indicates the specificity of participation to the biological processes.
A. GAPDH smFISH and IF analysis using anti-G3BP antibody (G3BP) and anti-Dcp1b antibody (DCP1) in A549 cells (RL-WT) or A549 RL-KO cells either mock transfected (mock) or transfected with poly(I:C) (PIC) for 5 hours. Scale bar 10 microns. B. Graph of the fraction of G3BP foci with different volumes in PIC treated RL-WT and RL-KO cells. C. Number of DCP1 foci per cell in PIC treated RL-WT and RL-KO cells relative to the number in mock treated cells. D. Average volume of individual Dcp1 foci in mock and PIC treated RL-WT and RL-KO cells.
(H) Jurkat TAg T cells transfected with cMyc vector or cMyc-p38IP were stimulated with 10μg/ml anti-CD3 for the indicated times, and then were lysed and immunoprecipitated with anti-TAK1 antibody and immunoblotted with anti-K63Ub, anti-cMyc and anti-TAK1 antibodies. Lysates were blotted with the indicated antibodies, and actin served as the loading control.
F. Absence of STING does not significantly decrease basal ISG expression. RT-qPCR of RNA extracted from hearts from Sting+/+ (n=3) and Sting-/- (n=5) three-month old mice. (E, F) Each data point represents the mean of technical triplicates from one mouse. Error bars, SEM. * = p<0.05, Mann-Whitney U test.
(Q-T) At larval stages, W07G4.5::GFP forms aggregates in intestinal cells (Q and R). These aggregates disappear upon RNAi knockdown of let-363 (S and T). (U-X) W07G4.5::GFP aggregates accumulate in intestinal cells in epg-7 mutant larvae (U and V). These aggregates disappear when let-363 is simultaneously depleted (W and X). (Y and Z) In atg-3 mutants, W07G4.5::GFP aggregates accumulate in intestinal cells (Y) and persist after RNAi knockdown of let-363 (Z).
(B) fixed for immunofluorescence analysis using anti-ERGIC-53 antibodies, or GFP fluorescence. In A, the asterisk indicates nonspecific band; in B and C, asterisk indicates cells that did not show a fragmented ERGIC-53.
(B) Oxygen consumption (VO2), (C) carbon dioxide production (VCO2) in 10‐month (mo)‐old chow diet (RD)‐fed control (Con) and knock out (KO) mice (n=4).