EMBO/sd-character-level-ner huggingface dataset:
(A) Xbp1 splicing analysis (left panel) and quantification (right panel) of bone marrow-derived macrophages (BMDM) cultured in conditioned medium (CM) of Rv-treated DLD1 and SKOV3 cells or respective control medium (culture medium of cancer cells not treated with Rv), and CM of fused B16 melanoma cells or their nonfused parental cells.
D. Age of disease onset as measured by a decrease of 5% or more in forelimb grip strength (not significant by log rank analysis).
E,F lsy‐6 mutants show defects in ASEL fate specification and do not express the ASEL‐specific reporter lim‐6pro::GFP.
Immunolabeling of lamin-B1 and nuclear pore complexes (NPC) shows the location of CYT and NE Tau in relation to the nuclear envelope in seeded HEK sensor cells. White arrows and boxes show position and width of cross-sectional profiles shown in (D). Scale bar=10 μm. Cross sectional profiles show the localization of Tau (green) in CYT accumulations adjacent to the nucleus in the cytosol, and the colocalization of NE Tau with lamin (pink) and NPCs (blue). Notably, CYT-1 also contains NPC signal. Dashed vertical lines indicate x-positions of highest intensity values for respective intensity profiles.
Graph of flow cytometry data shows the percentage of cells in given cell‐cycle phases 48h after transfection with plasmids encoding scrambled siRNA or siRNA specific for CDK1. Graph represents the mean of three independent experiments. All data represent the mean ± SEM from three independent experiments. Student's t-test analysis was performed, with *p≤0.05 and **p≤0.01.
(G) Nitric oxide (NO) levels in the culture media of cells relative to the IFNγ/TNFα control 24h after treatment Data information: All quantifications are of three independent experiments (n = 3) and error bars represent the SEM For panels E through G, p-values were calculated using the Student"s t-test. *, p < 0.05; **, p < 0.01 from DMSO controls; ††, p < 0.01 from IFNγ/TNFα treated controls
(H-I) Lifespan assay of (H) wt and (I) gas-1(fc21) vs gas-1(fc21); cest-2.2 O/E nematodes grown on control and fat-5 RNAi bacteria. Data information: , the median lifespan ± SEM across replicates is reported underneath the graphs, and additional information (e.g., n numbers) Certain lifespans were run at the same time, but representative figures were split for the sake of clarity
(E) Venn diagram showing the genes commonly upregulated in YAP signature 1 and in BCCs, well-differentiated and EMT-containing SCCs
A Structure of TAB2 NZF (red) in complex with Lys63 diUb (cyan) [pdb‐id 2wwz (Kulathu et al, )]. Ser65 for both Ub moieties is shown as spheres and highlighted with a blue circle.
V. cholerae ΔvrrA ΔmicV strains carrying the indicated reporter plasmids (x-axis) and either an empty vector control (pCtr), the pMicV, or the pVrrA plasmid, were cultivated in M9 and GFP fluorescence was measured. Fluorescence of the control strains was set to 1. The target genes were classified according to (B): regulated by both sRNAs
K. The relative number of EBV copies in C666 cells transfected with the YTHDF1-specific siRNAs (siY1-1 and siY1-2) or the siNC control was quantified using qPCR. At 24 h after siRNA transfection, the EBV copies were quantified The mean value of EBV copies in the siNC cells was normalized to 1.
I BiP mRNA levels in primary stellate cells isolated from mouse liver and then treated with or without TGFβ ± 4μ8C. * P = 0,008, n = 3.
(C) Sashimi plots as shown in Figure 2A (without conservation score) for decay-inducing AS events upon cold (At-SCL33, left) or warm temperature (At-SR34, right). Data shown represent, from top to bottom, warm-dark, warm-light, cold-dark and cold-light conditions as indicated on the right of the plots.
(D) Probabilities of HP2 closure from the integrated densities (Mean ± SD from 1000 bootstrap samples). Statistical significance was tested by comparing bootstrapped confidence intervals (*, 95% confidence intervals do not overlap).
E Number of CD41+ megakaryocyte colonies from patient samples after 4D7 treatment. CD34+ from patients with myelofibrosis with CALRdel52 or CALRins5 were plated on collagen-based matrix in presence of 20 µg/mL 4D7 or IgG control (n=3 biological replicates). Data information: Unpaired students t-test used to determine statistical significance Bars represent standard deviations *, P = 0.05 - 0.01, **, P = 0.01 - 0.001, ***, P = 0.001 - 0.0001, ****, P <0.0001, n.s, not significant.
F, G. Effect of 4-OHT administration on intestinal organoids of different genotypes kept in the presence (undifferentiated) or absence (differentiated) of R-spondin-1. F. The viability of organoids assessed by the resorufin assay. Mean ± SD, n = 3 wells per mouse. P < 0.05 are shown (unpaired t-test). Organoids were isolated from two mice of each genotype. G. IF images of intestinal organoids from Ssrp1fl/fl; CreERT2+/+ mice kept in the presence or absence of R-Spondin-1. The organoids were stained with antibodies to LGR5 and SSRP1 and counterstained with Hoechst (DNA).
N Hcy-treated eggs exhibited NTDs phenotypes at embryonic stage 8 (E8). A normal embryo (a) and neural tube defect phenotypes (b, c) are shown. Exencephaly (white arrows) and spina bifida (blue arrows) are indicated. Scale bar: 500 μm.
(E) Lifetime analysis of CCPs which are positive for EGFP-Dyn2WT or EGFP-Dyn2S619L with or without siRNA-mediated specific knockdown of endogenous Dyn2.
(C) Cell lysates prepared from HeLa cells were solubilized with Triton X‐100 and incubated with protein A‐immobilized anti‐Beclin (lane 2) or anti‐PtdIns 3‐kinase antibodies (lane 4). As controls, preimmune sera of the respective antibodies (lanes 1 and 3) were used. Retained proteins were separated by SDS-PAGE and detected by immunoblotting with anti‐PtdIns 3‐kinase (upper panels) and anti‐Beclin (lower panels) antibodies.
F, G Confocal images showing the basal region of cochlear explants treated with either culture medium alone or containing 10 µM CDDP for 1 (F) or 2 (G) days. Hair cells were identified using Myosin 7A (red), phosphatidylserine sites on the cell membrane surface were detected using fluorochrome-labeled Annexin V (green in F), and apoptotic DNA fragmentation was identified using a TUNEL apoptosis kit (green in G). The white arrow heads indicate cell surface Annexin V-positive labeling (lower left) and TUNEL-positive nuclei (lower right). Scale bar=15 µm.
Western blot showing rescue of Mta123∆ ES cells by ectopic expression of Mta1, Mta2 or Mta3 from a transgene (TG). Total RNA Polymerase II acts as a loading control (αRNAPII). For all western blots molecular weight is indicated at left in kDa.
(A) Representative images of wt and egl‐1 mutant embryos, bearing the plgg−1DsRED
E) Syntaxin 5 knock down induces mislocalization of GnT-V similar to SPPL2c overexpression Cells ectopically expressing GnT-V were treated either with non-specific siRNA (siCtr) or with siRNA targeting Syntaxin 5 (siStx5). GnT-V was visualized in immunofluorescence using anti-V5 antibody targeting its C-terminal tag and either BIP was co-stained as ER marker protein or TGN46 as Golgi marker protein. Scale bar 5 µm.
(C-D) The effect of stable knockdown CSAG2 in HCT116 (C) or A375 (D) were determined for anchorage-independent growth in soft agar colony formation assays for 14 days. The number of colonies was quantified and is shown. Data are represented as the mean ± SD, n=3 biological replicates.
(I) Relative anti-Y-Ae MFI in CRISPR-targeted B cells normalized to HEL-only immunized mice. N = 10 immunized mice across 3 experiments. Data show mean ± SEM.
(F) p47(E86K, E88K) does not bind to FTCD. GST-tagged p47wt/mutant (0.50 μg) was incubated with the indicated His-tagged proteins (p97, 1.0 μg; FTCD, 0.75 μg). The blots were probed with antibodies to p97, FTCD and GST.
F. Cytoscape visualization of the protein network resulting from HDAC3 interactome and H3K9ac ChIPseq and RNAseq upon SNA. The signalling network was created by combining the protein interactome of HDAC3 and H3K9ac dependent genes with increased gene expression upon SNA. HDAC3 is in red at the center of the network. The line thickness is proportional to the interaction score. Highlighted in orange circles are the validated pathways and targets via IHC (Figure 6) or ChIP-qPCR (EV Figure 4), regeneration associated genes (RAG) are highlighted in orange triangles.
(D)-(E) Candidate modifiers. Upper panels: Scatter plots associating the expression of the GCD (SMN1) vs. identified PMs in healthy GTEx muscle tissues (left panels) and spinal cord tissues (right panels); the expression of SMN1 (X-axis) vs. that of the negative DPM modifiers (D) U2AF1 and (E) HNRNPA0. Bottom Panels: Boxplots associating the expression of the identified DPMs in case-control studies; the expression of (D) U2AF1 and (E) HNRNPA0 in SMA and in healthy control muscle (left panels) and spinal cord (middle panels) tissues. Right panels show the levels of these predicted modifiers in healthy muscle samples with low ratio of SMN2-FL to SMN2∆7 and those with high ratio of SMN2-FL to SMN2∆7. Data information: Empirical P-values significance is indicated for two thresholds (** is P-value<0.01 and *** is P-value<0.001, using the permutation test The P-values denoted in the upper panels of and E are for the hyper-geometric enrichment test. There are six control (blue) and eleven SMA biological replicates (red) from muscle tissues and four control (blue) and six SMA biological replicates (red) from spinal cord tissues. The Reads Per Kilobase Million (RPKM) measure was used in the GTEx dataset, and the Fragments Per Kilobase Million (FPKM) measure was used in the SMA case-control dataset.
Functional complementation of WT DHFR from an arabinose inducible pBAD plasmid rescues growth defects of mutant strains grown at 42°C (for WT, W133V and V75H+I155A strains) or at 40°C (for I91L+W133V and V75H+I91L+I155A) in M9 medium supplemented with amino acids.
B. HEK 293T cells were transfected with plasmids as indicated for 24 hr and treated with DMSO, thapsigargin (TH), ISRIB, or TH plus ISRIB for 2 hr followed by analysis of the protein level of CHOP, p-eIF2α, total eIF2α, Endou-Flag, and its variants using Western blot. The α-tubulin served as an internal control. Protein levels relative to each internal control were presented at each lane.
Comparisons of protein stability among wild-type protein and the mutants indicated on the right.
(F, G) Electron micrographs of NDP52 KD and control cells. Asterisks indicate mitochondria sequestered by autophagosomes (mitophagosomes, yellow dotted line). The ratios of mitophagosomes per mitochondrial area are shown in (G). Ten cells from three independent experiments were counted. Values are the means ± SD. *p < 0.05 compared with scrambled-oligo treated cells, determined with one-way ANOVA followed by the Student's t test
(A) Venn diagram showing overlap between virophagy-related genes in HeLa cells (Orvedahl et al., 2011) and ZIKV-infected hNSCs (Tang et al., 2016).
(F) PtenΔC/ΔC mice (P19-37) treated with Slc6a20a-ASO display unaltered mEPSC frequency and amplitude in CA1 pyramidal neurons, as compared with ASO-untreated PtenΔC/ΔC mice. Note that mEPSCs in WT mice are not affected by Slc6a20a-ASO treatment. (n = 13 neurons from 3 mice for WT-saline, 14 (2) for WT-ASO, 14 (3) for ΔC-saline, and 12 (3) for ΔC-ASO, ***P < 0.001, ns, not significant, two-way ANOVA with Bonferroni's test). The error bars represent SEM.
Mutant W133V was grown in amino acid supplemented M9 medium (M9+AA) for 4 hours at 42°C, and subsequently placed on M9 agar pads and their growth was monitored at room temperature. Shown are phase contrast images taken from different time points throughout the time-lapse experiment. Unlike cells experiencing TLD, an irreversible phenomenon, W133V DHFR cells recover and resume growth at low temperature.
A Combined IF and DNA FISH analysis of RAD54 (IF) and telomeres (FISH) in ALT and non-ALT cell lines. White arrows indicate RAD54 foci that colocalize with telomeres. Scale bars = 10 µm B Quantification of data in A. A cell was counted positive if it contained 1 or more colocalization event between RAD54 and the telomere. At least 100 cells were counted per cell line per repeat. For SaOS2, NOS, SJSA1, HeLa LT n = 3. For Cal72, U2OS, HuO9 n = 4. Values shown are mean±sd
Sw.71 (left panel) and HPC cells (right panel) were treated with IFNβ to detect ISG20 protein expression. (C) Sw.71 and HPC cells were treated with different doses of IFNβ (3, 30, 300 ng/ml) for 24 h and protein was collected for determining ISG20 protein expressions by western blot. Note the increase of ISG20 protein expression in a dose-dependent manner. β-actin served as a loading control. (
(D) UPLC-MS/MS analysis of 2'-O-methylation of m1G37_tRNAPhe(GAA), -G34A, -G34C and G34U after incubation with FTSJ1-WDR6. 2 μL of Gm (1 ng/mL), Am (1 ng/mL), Cm (1 ng/mL) and Um (5 ng/mL) standards were injected to UPLC-MS/MS as control. cps, counts per second.
E TaqMAN real-time PCR analysis of MdCAX3G expression in girdled Md/Mx and Md/Mb under Fe deficient and Fe replete conditions for 3 days.
(G) Preventing sumoylation of Lys-1034 compromises separase's ability to support DSB repair. The indicated variants were probed for their ability to functionally replace endogenous separase in HDR as described in figures 6A and 6B. Shown are averages (bars) of 3 independent experiments (dots) counting ≥ 100 cells each
B. Rev3l+/+ and Rev3l-/- MEFs were pulse-labelled with EdU for 15min, permeabilized, fixed and stained for EdU incorporation (green). S phase sub-stages from I to IV were evaluated by visual inspection of the cycling population (>300 EdU+ cells, top panel). Scale bar= 5 μm. Dot plots and pie charts show the relative proportion (percentage of total S) of each sub-stage from I to IV (middle and bottom panel, respectively). Each dot represents the mean of two technical replicates.
C IF for Ki67 (green) in iPHet and iPKO ESCs 5 days after treatment with 4‐OHT. White arrows mark Ki67‐positive ESCs. Red arrows mark Ki67‐negative ESCs. Scale bar, 20 μm.
(B) Time-lapse 3D-SIM imaging of sheath dynamics (TssB-sfGFP) in the absence of TslA in A. baumannii DSM30011. Data information: Scale bars and time intervals are indicated.
A. Wild-type (WT) and the indicated mutant strains were grown for 3 hr at the non-permissive temperature (36°C) to inactivate Mts3. Phosphatase-treated cell lysates were analyzed by western blot with anti-Sre2 serum and imaged using chemiluminescence. P and N denote Sre2 precursor and cleaved nuclear forms, respectively.
(C) Comparison of the activity of key metabolic enzymes between midlife flies grown at 18ºC and 25ºC. Midlife flies grown at 25ºC have lower CS and ATPCL activity to midlife flies at 25ºC. CS, citrate synthase; ATPCL, ATPcitrate lyase. N=9 midlife vs 6 cold midlife for CS and 7 midlife vs 6 cold midlife for ATPCL.
Quantification of HW/TL ratio (E), N=6 to 10 mice/group, in Tip30 Het or WT mice 2 weeks after TAC. Animals were treated with Narciclasine daily for 14 days after TAC as indicated.
C Sequence and ApoER2 target region of most active ASOs from (B). Exonic and intronic sequences are in capital and lower-case letters, respectively. Conserved nucleotides between human and mouse ApoER2 are shown in black, non-conserved nucleotides are red. Predicted, conserved binding sites for splicing factors are labeled as intronic splicing silencers (ISS1 and ISS2).
C) Schematic representation of purine degradation pathway with overlaid Molecule Activity Predictor (MAP) analysis showing increased purine degradation in age-1; gas-1 mutants and the consequent xanthine accumulation. Shades of red and green are proportional to fold change, whereas shades of blue and orange are proportional to the strength of the prediction, as calculated by IPA.
(A-H) 3D views of 232 x 232 μm2 fields of view of the AT (A, G) and endothelial layer (B, H) from infected LoCs reconstituted without macrophages at 1 (A, B) and 3 dpi (G, H). Orf1ab antisense RNA, S RNA, ACE2 mRNA, and nuclear staining with DAPI are false-colored pink, amber, spring green, and electric indigo, respectively. (C, D) Zooms corresponding to the region in (A) highlighted with white and yellow boxes, respectively. (C) An example of infection and intracellular replication in a cell with no detectable ACE2 expression (white arrow) as well as nuclear localization of viral RNA (white arrowhead). (D) An example of an uninfected cell with ACE2 mRNA expression (yellow arrow). (E, F) Zooms corresponding to the regions in (B) representing increased nucleic acid staining (hyperplasic) and normal levels of nucleic acid staining highlighted with white and yellow boxes, respectively. (E) Examples of infection of hyperplasic endothelial cells both with and without ACE2 expression (F) Examples of endothelial cell infection with no ACE2 expression, nuclear localization of viral RNA in an infected endothelial cell is indicated (white arrow).
Concentration of Prdx4 in supernatants of Prdx4 WT and KO BMDMs. Cells were primed with LPS (100 ng/ml) for 6 h, followed by pretreatment with 20 µM YVAD or DMSO as control for 30 min and stimulated with 5 mM ATP for 4 h or no further stimulation. Each bar represents a mean of n=3 mice, vertical lines indicate SD. **, p < 0.01; n.s. not significant (two-tailed t-test).
A. Growth curves for DT40 wild type, ddx11, timeless and ddx11/timeless cells, with and without 4 μM pyridostatin (PDS). Cells were seeded at 5 x104 cells/ml on day 0 and the viable cells were counted each 24 h for 4 days. Bars represent SD of two independent experiments performed in duplicate. Doubling times (DMSO): WT 13 hours, timeless 18 hours, ddx11 16 hours, ddx11/timeless 24 hours. Doubling times (PDS): WT 13.6 hours, timeless 27 hours, ddx11 25.7 hours, ddx11/timeless 47.5 hours.
F. Confocal fluorescence images of Proteostat (1:2000, red spots) and DAPI staining (blue), scale bar is 10µm. G. Quantitation of aggregates/cell in IGRs cell lines by immunofluorescence analysis, left panel; fluorescence gain of soluble proteins treated with Proteostat reagent, right panel. (T-test analysis, * = p-value<0.05, N=3 biological replicates, data are mean ±SD).
A-D Cells were infected at the indicated MOI. Viral replication (Left) and release (Right) were assessed by flow cytometry and RT-qPCR. A) Caco2/TC7 cells (MOI 0.01) B) Calu-3 cells (MOI 0.001) C) Vero cells (MOI 0,01) D) primary human airway epithelial cells (HAEC) virus release (Right) and infectious virus release (Left) (MOI 0.01). Data are mean ± SD of at least 3 independent experiments. Statistical analysis: Mixed-effect analysis or Two‐way ANOVA compared to D614G reference, ns: non‐significant, *P < 0. 05, ****P < 0.0001.
Sublingual infection of WT, Stim1fl/flVav-iCre and Stim1fl/flStim2fl/flVav-iCre mice with 2x107 CFU of C. albicans. (E) Frequencies of Cd11b+Gr1+ neutrophils in the tongues from the indicated mice at day 7 p.i. Bar graphs represent the mean ± SEM from 3 experiments and 9 WT, 7 Stim1fl/flVav-iCre, 8 Stim1fl/flStim2fl/flVav-iCre mice.
C Protease protection assay in mitochondria expressing Mpc1‐GFP, Mpc2‐GFP, or Mpc3‐GFP. Intact mitochondria (M), mitoplasts with a ruptured outer membrane after hypo‐osmotic swelling (Sw), or mitochondrial lysates with 0.5% Triton X‐100 (Tr) were treated with proteinase K (PK). Loading controls are Tom70 (outer membrane), Tim23 (inner membrane), and Mdh1 (matrix). GFP‐fused Mpc2 and Mpc3 are degraded in mitoplasts, whereas Mpc1‐GFP is not.
Staining for BRAFV600E with a mutant epitope-specific antibody confirmed the upregulation of BRAFV600E in R1, R2, and R5. Scale bar represents 100 μm.
(G) Venn diagram showing the overlap between MCF7 DVL3 ChIP-seq peaks and H3K27ac ChIP-Seq.
(H) HeLa cells treated with Dynasore were processed for immunogold labeling on cryosections and double labeled with ATG16L1 (10 nm) and mATG9 (15 nm). Scale bar, 100 nm.
A) Representative images of Caco-2 cysts transfected with control siRNA (siGlo) or siRNAs targeting ROCK1 and ROCK2, fixed and stained for prominin-1, F-actin (Phalloidin) and Nuclei (Hoechst). Confocal Z-sections of cysts are displayed. Arrowheads show non-protruding cells. Arrows point to protruding cells. White stars mark nuclei that are off-centered relative to the cyst's monolayer. Scale bars: 20 μm.
B) Close-up view shows helix-7 tilts away from the seed region in the MI-AA mutant.
Immunofluorescence staining of Oct4 in miRNA mimic transfected ESCs. 20 miRNAs decreased Oct4 expression and produced small and grossly differentiated cell colonies, 12 miRNAs mildly affected Oct4 expression, and 8 miRNAs improved Oct4 expression and yielded compact and undifferentiated cell colonies. Representative pictures are shown. Full data are shown in Supplementary Fig S3C.
Huh7.5 cells were transfected with the negative control siRNA (NC) or the Rubicon (Rb) siRNA for 48 hours and then infected with 1 m.o.i. of HCV. (C) Fluorescence imaging of RFP and GFP puncta in cells transfected with the control siRNA (top two panels) or the Rubicon siRNA (bottom two panels). Cells were fixed at 24 and 48 hours after HCV infection for the analysis. Boxed areas in merged images are enlarged and shown to the right. (D) Percentages of RFP puncta that were also positive for GFP in Huh7.5 cells treated with either the control siRNA or the Rubicon siRNA. The results represent the average of >50 cells.
(C) Flow cytometry analysis of Annexin A1 in 10C cells transfected with control siRNA (dotted black line) or CDH1-specific siRNA (dotted red line) followed by no treatment, or incubation with BSA (1000 µg/ml) or FadAc (1000 µg/ml) for 1 hr. C, untreated control. Data are mean values ± SD. The experiment was performed in triplicates and repeated twice. ***p<0.001 (two-way ANOVA).
Outline of endocytic cholesterol transport. After endocytosis by the LDL receptor, LDL are delivered to early and then late endosomes. Free cholesterol is released in late endosomes and then exported to its cellular destinations.
F-I. Behavrioural tests of Aβ(1-42) infusion mice. (G) Intracerebroventricular (i.c.v.) injection site brain schematic diagram.
C) Pulldown of overexpressed Pex19 in Cos7 cells with a Pex19 antibody shows interaction with full-length Miro1, but not Miro1 lacking the transmembrane domain.
C-F Eosinophils numbers in (C) blood, (D) BALF, (E) spleen and (F) BM of Dusp5+/+ Rag2-/- (open circles) and Dusp5-/- Rag2-/- (grey squares) mice 13 days following infection with N. brasiliensis. C, E and F are from the same experiment and are representative of three independent experiments. D is cumulative of 3 independent experiments.
E. Effect of net-1 mAb on induction of Granta-519 cells apoptosis, detected by TUNEL staining. Left panel: representative images are shown. TUNEL positive cells are labelled in red. Nuclei are counterstained in blue by Hoechst staining. Right panel: quantification of one representative experiment out of three performed is exposed. Results are presented as percentage of TUNEL-positive cells per field. *: p=0.04; two-sided Mann-Whitney U-test.
D, Localization of GFP-SnRK1α1 and GFP-SnRK1α2 in root cells of 5-d-old Arabidopsis WT and tsn1 tsn2 seedlings grown under 23°C (NS) or incubated at 39°C for 60 min (HS). Insets show enlarged areas inside dashed rectangles. Scale bars = 10 μm.
Loss of LRP6 phosphorylation in chondrocytes treated with the GRK2 inhibitor CMPD101. rat chondrosarcoma (RCS) cells (D) were treated with 20 µM CMPD101 overnight and then treated with 100 ng/ml Wnt3A for 1 hour. Note the less LRP6 phosphorylation (pS1490- and pT1572-LRP6) in cells treated with CMPD101. Mean ± SEM. Mann-Whitney U test; number of biological experiments is indicated.
b) A comparison of ATG5 sequences in different species demonstrates the presence of a conserved putative NES, similar to that present in Beclin 1. The sequence alignment was performed with Clustal W using sequence data obtained from GenBank. The characteristic leucines are indicated in red and the resulting sequence of ATG5-ΔNES, following mutation of three leucines within this motif, is shown. (c)