EMBO/sd-character-level-ner huggingface dataset:
C. On the left side, a schematic overview of Oct4 and its mutants used for iPSC generation. POUS and POUHD are shown as green bars connected by the linker. Sites mutated to the respective Oct6 residues and Oct6 linker are denoted in orange, and the mutation in the Sox-Oct interface is in black. The efficiency of these constructs for iPSC generation from MEFs is depicted as the absolute number of GFP-positive colonies on the right. Error bars represents standard deviations of biological replicates (n=3) and differences between selected samples were compared using ANOVA (p-values: Oct4WTxOct47D,22K p = 6.9e-3; Oct4WTxOct4LinkO6 p = 7.3e-4; Oct4WTxOct4151M p = 1.2e-2; Oct4151MxOct4LinkO6,151M p = 1.1e-2; Oct4LinkO6,151M xOct47D,22K,LinkO6,151M p = 7.1e-3) (*** p < 0.001, ** p < 0.01, * p < 0.05).
WT cells and the indicated mutants were left untreated (0 min) or were treated with cycloheximide (CHX) to block protein synthesis for 90 min and 180 min at 26°C or at non-permissive temperature (37°C) where indicated. Total cell lysates were analyzed by SDS-PAGE and Western blotting with the indicated antibodies. (C) SEC13 WT and sec13-4 cells were preincubated for 30 minutes at 37°C before CHX was added.
(B) The experiment as described in (A) was repeated twice with U2OS cells and twice with Ba/F3 cells and the blots were quantified. Each dot represents the ration of FLAG-TiIP60 to H4 in the chromatin fraction of altogether four individual experiments as shown in (A)
A Western blot of lysed transgenic nematodes that express the UbG76V-GFP and mRFP reporters in the hypodermis at the L4+48h stage, probed with antibodies recognizing GFP or actin as a loading control. The position of molecular weight markers is shown on the left of each blot. The position of UbG76V-GFP protein, as well as UbG76V-GFP with the indicated number of additional ubiquitin moieties, based on molecular weight, is indicated to the right of each blot. Twenty animals were loaded per lane for each indicated genotype.
(D) ESCs as in (B) were engineered to express H3K27me3-mintbody (SNAP/JF646) and H4K20me1-mintbody (mCherry). Cells were cultured in the absence of LIF for 2 days. Time-lapse images for 12 z-plane confocal stack were acquired every 1 h. Maximum intensity projection images are shown with elapse time (hh:mm). Arrowheads mark Xi. Scale bar = 10 μm
Non-canonical pathway for cysteine biosynthesis in Mtb. MoeZ transfers sulfur from a yet unknown source to the C-terminus of CysO to form thiocarboxylated CysO (CysO-SH). CysM, a non-canonical cysteine synthase, utilizes O-phospho-L-serine (OPS) and CysO-SH as substrates to generate CysO-cysteine adduct, which is cleaved by a protease Mec, to release cysteine and regenerate CysO(Burns et al., 2005).
B. Representative confocal microscopy images of living cells treated for 5 days with dsRNA against the indicated genes and stained with both MitoTracker Green and LysoTracker Red. The scale bar is 10 μm.
(A) Standard replication assay on undamaged (UD), 8-oxoguanine (8oxoG), and thymine glycol (Tg) templates in the absence of TLS components.
D. Quantification of apoptotic HSPCs at the indicted time points after 5-FU treatment of control and cKO mice (n=6 per genotype). Data information: Data presented as mean ± SEM. The statistical significance was assessed using repeated-measures two-way ANOVAs by two-tailed Student's unpaired t-test analysis (D and E). *p<0.05, **p<0.01 and ***p<0.001.
(F-H) circ LMP2Ain specific probe and detected by real-time PCR (F) and RT-PCR (H). The relative levels of 5 miRNA candidates were detected by real-time PCR (G) and RT-PCR (H). GAPDH was used as a negative control.
Representative Western blot of full length and cleaved caspase‐3 levels in control and Dgcr8Δ/Δ cells following 5−6 hours of differentiation (n = 2).
(h) A rescue experiment using a specific mutated FoxO1 plasmid to validate the activity of FoxO1 in the induction of autophagy in HCT116 cells in the presence or absence of serum, with or without E64 and pepstatin A.
B. Split-effector construct design. Data information: Npu: Nostoc punctiforme, Ssp: Synechocystis sp., CDS: coding sequence. BASCs: bronchioalveolar stem cells, BADJ: bronchioalveolar duct junction, NLS: nuclear localization signal.
(A) Endogenous Beclin 1 is ubiquitinated through K63 linkage during the process of autophagy. EBSS cells starved in EBSS for the indicated times were lysed and immunoprecipitated with anti‐Beclin 1 antibody. Immunoprecipitates were dissociated with 1% SDS and re‐immunoprecipitated with anti‐Beclin 1 antibody, followed by immunoblotting with antibody specific for lysine 63‐linked poly‐ubiquitin chains (anti‐K63‐Ub). (
IHC representative images (left) and quantification (right) the expression of CD31 (D) from primary tumour; scale bar, 100 μm.
(B) Recombinant proteins were mixed, as indicated, and incubated as above. The reactions were stopped, subjected to SDS-PAGE and stained with Coomassie Blue.
(A) Representative micrograph of an eye from day 7 after glutamate intoxication, from a mouse that was i.v.-injected with monocytes, showing monocyte localization to the SRS after this mode of application, and indicating a potential homing route for the cells (IL-10, red; CX3CR1-GFP, green).
(G-I) Representative confocal micrographs of Brucella-infected control cells at 24 hr p.i. triple-stained for HA-Sec61α (a marker for rough ER; green), B. abortus (red), and Lamp2 (a marker for endosomes/lysosomes; blue) (G). An expression construct for HA-Sec61α was co-transfected with scramble siRNA. The infected cell is outlined with white dashed lines. Scale bars are 10 μm. Magnifications of the boxed areas 'a' and 'b' are shown in (H) and (I), respectively. Large vacuoles adjacent to replicating bacteria were stained for both Sec61α and Lamp2 (H). B. abortus was co-stained with Sec61α but not with Lamp2 (I).
(C) NIH-3T3 cells stably expressing Flag-NEMO were mock infected or infected with MCMV-M45-HA or MCMV-ΔM45 at an MOI of 7. Seven hpi, cells were fixed and analyzed as described for panel B.
(A) Body temperature before (Basal) and during cold exposure (n=7-8) in 10‐month (mo)‐old chow diet (RD)‐fed control (Con) and knock out (KO) mice
B, C Comparison of relative fold changes between RNA-seq and qRT-PCR results for rpoE and mclA mutants (B) and the rpoE and the addition of corticosteroid to wild-type H. influenzae (C). All qRT-PCR results were normalized using the Cts obtained for the 16S rRNA amplifications run in the same plate. The relative levels of gene transcripts are determined from standard curves. Values given are the mean and standard deviation of triplicate measurements (three biological and three technical replicates).
(A) Red1 dots co‐localize with cleavage factor, Pcf11; the canonical poly(A) polymerase, Pla1; a nuclear exosome subunit, Rrp6; and a nuclear poly(A)‐binding protein, Pab2. Microscopic images of strains expressing both Red1‐tdTomato and either Pcf11‐, Pla1‐, Rrp6‐, or Pab2‐GFP are shown. Bars, 2 μm.
HEK-293 cells expressing the NanoBiT-Gq protein and indicated B2R constructs were treated different concentrations of bradykinin, and ligand-induced change in luminescent signal was measured. Concentration-response curves were plotted using GraphPad Prism to calculate pEC50 (top) and Emax(bottom) values included in the graph. Data represent mean±SEM of three independent experiments with each performed in duplicate, and normalized with respect to the luminescence signal under basal (no-agonist treatment) condition (treated as 1).
(E) Merlin-depleted LN229 cells stably transduced with empty vector, Flag-tagged wild-type (WT) Merlin, or its K396R mutant were subjected to immunoprecipitation with a Flag antibody followed by western blotting.
F Pie chart illustrates major classes of gene ontology terms enriched in gene lists upregulated in CT+ and RA+ CMs.
(C) Left panel: RNA-Microarray analysis comparing PC3 cells transfected with siCLU versus siSCR and Kinexus phosphokinome microarray analysis comparing LNCaP-transfected with siCLU versus siSCR. Target genes expression is shown as fold change relative to siSCR, p ≤0.05 by an unpaired t-test for all the genes listed. Central panel: Venn diagram to graphically illustrate the overlap of mRNA and proteins involved in the regulation of mitosis in both transcriptome and phosphokinome analysis. The comparison of these 2 experiments shows modification of 4 mitosis regulators. Right panel: Western blot validating the expression levels of target proteins.
(D) Gene expression analysis showing fold induction levels (Log2) of selected genes comparing BY4741 wild-type and STE5p-NAT4 strains under NCR (2% glucose) and CR (0.1% glucose) conditions. Expression levels were normalized to TAF10, whose expression remains unchanged.
Immunofluorescence analysis of ZW10 and Mad1 upon depletion of Rod. Scale bar, 5 μm.
D. Schematic representation of human REV3L and truncated constructs. Conserved domains between yeast and human REV3L are in black blue (the N-terminal domain, 1-333 aa) and in green (the catalytic domain, 2276-3130 aa), the REV7 interacting domains are in red (1880-2001 aa). A large region in royal blue not found in yeast protein is almost exclusively encoded by exon 14. All the truncated constructs lack the NTD domain and were fused to GFP. MEFs cells were transiently transfected with various GFP-REV3L constructs and fixed with 4% formaldehyde. The distribution of the GFP-REV3L mutants was detected by autofluorescence and nuclei were visualized using DAPI staining. Scale bar= 5 μm
TFEB silencing reduced human EC morphogenesis. Representative images of tube-like-structure of scr-shRNA and sh-TFEB human ECs stained with phalloidin-555. Bar graph indicates the percentage of phalloidin+ area in sh-TFEB and scr-shRNA ECs (scale bars: 0.25 mm; n=6, mean±SEM; ***p<0.0001 versus scr-shRNA by Student's t-test).
c Proliferation of OT-I Cas9-EGFP CD8+ T cells transfected with EGFP or with ITSN2 sgRNA activated for 48 h with N4 peptide MHC tetramers (0.01-0.1 nM) in the presence or absence of soluble anti-CD28 antibody or with PMA and ionomycin (PMA/Iono) or with IL-7. Data are presented as mean ± standard deviation (SD) from four proliferative measures of two independent sgEGFP and sgITSN2 transfections. Data are representative of three independent experiments.
Expression levels of IFNβ concentration in the media (B) upon HNRNPC silencing in the cells with lentiviral shRNA-mediated stable knock-down of DDX58 or IFIH1. Each sample has 3 replicates. Error bars represent mean ± SD.
(G) p97 binds to FTCD in Golgi membranes. Salt-washed Golgi membranes were incubated with either GST-tagged p97wt or p97(V722k, E724K). The isolated membranes were solubilized, and then GST-tagged p97wt/mutants and their binding proteins were recovered with glutathione-beads. The bound proteins were assayed by Western blotting with antibodies to FTCD and GST.
ChIP-seq on liver derived from mice which were subjected to hypoxia (6h and 24h), followed by DEX (10 mg/kg) injection and 2h later sacrificed for liver isolation. (E) Examples of specific GR DNA-binding peaks, associated with the DEX-induced gene Slc22a5 in hypoxia (6h and 24h).
J, High magnification fluorescent image of differentiated astrocytes. Scale bar: 20 µm. K, Astrocytes from KO cultures covered a larger area than WT astrocytes. Data points represent means of individual cultures (n > 30 astrocytes per culture). Depicted are data points per sample with genotype means ± SEM.
B to D. Determination of anti-HBV efficacy and safety of treated mice by measuring their body weight (C).
(C) APP (green) distribution within enlarged Rab5QL-GFP endosomes (magenta) in dendrites of siCD2AP- or siControl-treated neurons expressing APP-RFP and Rab5QL-GFP upon DAPT treatment, analysed by spinning-disk confocal microscopy. Scale bar, 10 µm. White squares indicate a Rab5QL-positive endosome magnified on the right. Scale bar, 1 µm.(D) Qualitative analysis of APP distribution between the lumen and the membrane of Rab5QL-endosomes (n=4, NsiControl=45 (774 endosomes), NsiCD2AP=52 (888 endosomes); *P=0.0368 siCD2AP vs. siControl, t-test, mean ± SEM).
Schematic diagram of the 3" end of the Prdm1ihCd2 allele (Minnich et al., 2016). The frt-flanked IRES-hCd2 (ihCD2) reporter gene, which was linked to a 258-bp long terminal repeat (LTR) sequence of the Moloney murine leukemia virus (MoMLV, green), was inserted between the stop codon and 3" UTR of the Prdm1 gene. C-terminal sequences of exon 8 contained in-frame tag sequences encoding the Flag and V5 epitopes, two TEV protease cleavage sites and a biotin acceptor sequence. The inserted MoMLV enhancer sequence is shown below together with its regulatory elements (Speck et al., 1990). GRE, glucocorticoid response element; LV, leukemia virus factor-binding site; NF1, nuclear factor 1; polyadenylatio
B. RIP-Seq of PRKCB in HUVECs identified a candidate lncRNA with significant q-value (0.002) and high expression.
A, U2OS, HeLa and HEK293 cells were transfected with Flag-tagged wild type (wt) or mutant (RG, RF, RK) p14ARF-containing plasmids. Overexpression was analyzed by immunoblotting using α-Flag (exogenous p14ARF proteins) and α-β-TUBULIN (loading control) antibodies (A). As visualized here, p14ARF with the Flag-epitope tagged reproducibly showed a clear migration difference between wt and mutant p14ARF proteins, with the mutants (especially the RK mutant) migrating slowlier than wt protein in the SDS-PAGE. The staining signals of the p14ARF bands were densitometrically quantified and normalized to the respective β-TUBULIN signal, as specified by the numbers below the blots, with the protein signals of p14ARF wt set to 1.
(H) USP1 removes polyubiquitin chains linked to K8 on Akt. Akt was immunoprecipitated from the soluble fraction of TA muscles transfected with USP1(C90S) , HA-Akt(K8R) or control from fasted mice, and protein precipitates were analyzed by immunoblotting with anti-Akt antibody. Mouse IgG was used as a control for non-specific binding. Right: Densitometric measurements of presented blots. Data is presented as the ratio between ubiquitinated Akt to total Akt in each lane (n=2).
C. DFM at 96 h APF stained with Phalloidin (red), anti-Kettin (green) and DAPI (blue). Anterior up, dorsal right. DFM are numbered in white as in (Lawrence, 1982). D. IFM at 96 h APF, transverse section (top) stained with anti-PS-integrin (green), Phalloidin (red) and DAPI (blue), dorsal up; sagittal section (bottom) stained with anti-Kettin (green), Phalloidin (red) and DAPI (blue), anterior up, dorsal right.
(k) Top, RT-qPCR analysis of miR-16 or let-7a levels in AGO2 immunoprecipitates from DMSO- and BAF-treated HeLa cells. Error bars represent s.e.m. Bottom, a representative western blot of AGO2 immunoprecipitates used in one replicate of these experiments. Uncropped images of blots are shown in Supplementary Fig. S3.
(C) qRT-PCR analysis of Asn AAC and Leu CUG codon tag reporter mRNAs at 6 hpf relative to 2 hpf in mock-injected and AnsB-overexpressing embryos. Data information: bar charts show the average of three independent biological replicates. Error bars show SD. Individual data points are shown as dots. P-values were calculated using two-sided Student's t-test.
E A potential model for the Shigellaseptin cage and actin tail assembly pathways. Based on our findings we propose that (i) mitochondria promote septin cage assembly for antibacterial autophagy or (ii) Shigella fragment mitochondria to counteract septin cage entrapment. Depending on the fragmentation of mitochondria by IcsA, Shigella will be compartmentalised in septin cages or spread cell-to-cell via actin-based motility.
(C) HEK293T cells co-transfected with HA-tagged p38IP together with cMyc-tagged TAK1 (open arrow) or ub-TAK1 (solid arrow) were lysed and immunoprecipitated with anti-cMyc, and then immunoblotted with the indicated antibodies. Asterisk indicates non-specific bands. The relative intensity of the IP bands was quantified by densitometry and is presented in the right.
E HeLa cells were treated but fixed after additional 2 h of chase. Samples were stained for Galectin-3 (Gal3) to detect damaged lysosomes, and LC3B as marker for autophagosomes. Note the reduction of LC3B colocalization with Gal3 indicating impaired autophagosome formation. Arrows indicate colocalizing or non-colocalizing vesicles. Scale bars: 20 µm, 5 µm for inlays.
(B) Structured illumination microscopy image of perimCherry/cytoGFP E. coli confirming localization of mCherry (red) in the periplasm and GFP (green) in the cytosol. Scale bar = 3 µm.
F and G Representative IHC staining of neutrophils in small (early time points) (F) and large (late time points) (G) tumours. Scale bar 100 µm (upper panel) and 10 µm (lower panel). Arrows show neutrophils.
(J, K) U2OS cells were treated with 3,4-DC in the presence or absence of dichloroacetate (DCA), α-ketoisocaproic acid (KIC), or L-leucine (Leu). GFP-LC3 dots were quantified in (J). Acetylation staining was performed as previously described, and acetylation intensity in the cytoplasm was measured in (K). Data are means ± SD (*** = p < 0.001 versus DMSO/Ctr; ##=p<0.01, ###=p<0.001 versus 3,4-DC/Ctr).
(I) Basal OCR in Flp-In 293 HA-GFP or Flp-In 293 HA-IKKε cells treated with doxycycline (50 ng/ml) in combination with dichloroacetate (DCA) for 16 hours, measured using Oroboros high resolution respirometry.
(A-D) Neocortex of mouseE13.5embryos was in utero electroporated with a plasmid encoding, under constitutive promoters, Cas9_T2A_PaprikaRFP and gRNA targeting either LacZ (Control, Con) or Tbr2 (Tbr2), followed by analysis at E15.5.(A) Electroporated area showing the effects of Cas9 expression (revealed by PaprikaRFPDAPI, magenta) together with either control gRNA (top) or gTbr2 (bottom) on aRGCs expression (green, immunofluorescence); blue, Cas9staining. Boxes indicate areas shown at higher magnification in the insets (45 x 45 μm). Dotted lines indicate nuclei of progeny of electroporated Cas9; note the presence of Tbr2 immunoreactivity in the control (top) and its absence upon Cas9/gTbr2 plasmid electroporation (bottom). Scale bars, 20 μm.
Representative images of small intestine organoids from WT and G3Terc-/- mice incubated with or without APE1 inhibitor (CRT0044876, 10μM) treatment. Arrows indicate the crypt-like structure in organoid cultures (A). Quantification of organoid number (per well) and size (in 104 μm2) (n=3-4 mice per genotype/treatment) (B-C).
786-0 cells expressing WT or enzymatically dead (ED) GDH1 were transfected with siNC or siRNF213 for 48 hours and then were treated with or without aa starvation for 12 hours. The intracellular level of αKG was measured using an αKG determination kit and normalized to 786-0 cells expressing WT GDH1 transfected with siNC under normal culture conditions. Unpaired t-test was used (B). Data information: The data are represented as the means ± SEM of three independent experiments (N.S.: not significant; *p < 0.05; **p < 0.01; ***p < 0.001).
(C) QC cell observation using the QC marker line ProWOX5:GFP. Seeds were germinated on HK medium for 4 d, then the seedlings were transferred to LK or HK medium with or without NAA (100 nM) for 96 h. Scale bar, 10 μm.
Kymographs of TssB1 and TssA1PA dynamics. TssA1PA localizes exclusively at sheath initiation site (B-E), disappears after contraction (C,D) or remains in place for longer timeframe (C,E). TssA1PA signal appears in neighboring cell shortly after T6SS attack (B,C).
A. Glutamate content in the culture medium ([Glu]e) from either hTauAT (n=10 culture inserts containing 6 slices each) or control slices (n=5-12 culture inserts) analyzed at DIV 5, 10, 20 and 25. Glutamate content from medium cultured with hTauAT slices is shown in percent of control at each time point. Increased levels were observed between DIV 5 and DIV 20. At DIV 25 glutamate levels already declined to control levels. One-way ANOVA followed by Tukey's post-hoc test *p<0.05; **p<0.01 ***p<0.001.B. Lactate dehydrogenase (LDH) release (a measure of cytotoxicity) analyzed in hTauAT (n=17-19 culture inserts containing 6 slices each) or control slices (n=15-16 culture inserts) at DIV 5, 10, 20 and 25. LDH release of hTauAT slices is shown in percent of control at each time point. A pronounced increase (~25%) in LDH release was observed due to hTauAT expression starting at DIV 10 but not at DIV 5 One-way ANOVA: *p<0.05; **p<0.01 and ***p<0.001.
(B) Top list of FAM210A-interacting proteins in IP-MS (immunoprecipitation-mass spectrometry) analysis. PSM: peptide spectrum match.
(i) HEK 293T cells were transfected with empty vector or Flag-FMRP, and lysates were subjected to m7GTP-agarose pull-down as in (C)
C, D. Metaplots (left) of mean values per bin centered on all TSS, TSS not bound by GFP-UBR7, and GFP-UBR7 bound TSS. Dot plots (right) represent H3K4me3 (Antibody 1) from parental 293T cells (C) or loss of H3K4me3 in UBR7KO versus parental cells (D). Box limits represent 25th and 75th percentiles. Whiskers extend to 1.5x the interquartile range. Outliers are represented as black dots. A Kruskal-Wallis multiple comparisons test with Dunn post-hoc test was used to calculate Benjamini-Hochberg adjusted p-values (italics). Values p<0.05 are pictured. Experiment was performed with two independent anti-H3K4me3 antibodies
Z ambulatory activity of 9-week-old male mice as measured over 24 hr (n=4 males per group).
Cyclin E-expressing BJ cells were grown for 7 days with and without folate. Fork distance distribution (Kb). The color code is as in (A). Empty vector (n = 78); CycE (n = 79); empty vector −folate (n = 71); CycE −folate (n = 80).
(B) WT PEMs were incubated with Akt inhibitor AKTV/triciribine (10 µm) for 30 minutes before infection with S. typhimurium strain ΔinvG for 5 hours. Lysates were immunoblotted with the indicated antibodies. (
(B) MCF10A cells were stimulated with EGF (10 ng/ml) for up to eight hours. At the indicated time points, cells were harvested, RNA was isolated and used to determine expression levels of specific lncRNAs and mRNAs, using the SurePrint microarray platform (from Agilent). The heatmaps depict lncRNAs (left) and mRNAs (right) for which a >1.5-fold (lncRNAs) or a >2-fold (mRNA) change in expression was observed in at least one of the time points, compared to un-stimulated cells (time zero). Note that each row of the heatmap represents an individual lncRNAs/mRNAs, and values (see color scale at the bottom) indicate the log2 ratio of RNA levels between each time point and time zero.
(B) M-Track proximity assay of Cdc55 fused to the protA-H3-HA prey-tag and Gis1, respectively Rph1, tagged with the HKMT bait-tag expressed in a rim15∆ strain background. Background signal intensity was defined using a strain expressing only Cdc55-protA-H3-HA and no tagged bait protein (noHKMT). Positive control: Nup2-HKMT, CDC55-protA-H3HA. me3: antibody recognizing me3K9H3; HA: 12CA5 antibody
(F) Western blot analysis with lysates of control or IRGM+/- HT-29 cells or Flag-IRGM complemented IRGM+/- HT-29 cells with indicated antibodies of viral restriction factors.
E) Inner membrane damage of three Gram-negative strains exposed to buffer, 10% serum or C5b6MAC. Buffer and serum conditions are the same as Fig. 1D.
(b) Generation of endogenous C18- and C18:1-ceramides in response to wild-type CerS1 and mutant CerS1 induction was measured by LC/MS/MS.
C. Representative confocal double immunofluorescence images displaying GFAP (green) and Iba1 (red) distribution in the middle corpus callosum of septostriatal sections of control mice (a-c), and of mice fed with cuprizone for 5 weeks in the absence (d-f) or in the presence of D-Asp (g-i). Scale bars in a-i: 50 μm. (j-k) Quantification of GFAP+ and Iba1+ cells in the middle corpus callosum of septostriatal sections of control mice and of mice fed with cuprizone for 5 weeks in the absence or in the presence of D-Asp. Data were normalized to the total cell number (Hoechst signal) and expressed as percentage of controls Data information The values represent the means ± S.E.M. Level of significance was determined by using i C, j-k, one-way ANOVA P<0.0001 followed by Bonferroni post hoc test, *P<0.05 versus control, ^P<0.05 versus cpz (n=4 mice for each group