EMBO/sd-character-level-ner huggingface dataset:
A-F, Representative FM4-64-stained Arabidopsis roots (grey) expressing pWOX5::mVenus-NLS (green) in Col, plt2, plt3 and plt2, plt3 double mutant background in longitudinal (A-D), or transversal (E-F) optical sections. E', F', Analysis of representative images in (E) and (F) in Imaris to detect and count individual expressing nuclei. E'', F'', Overlay of 10 roots (biological replicates) showing the area of detected fluorescence (high levels in red, low levels in blue) in Col and plt2, plt3 double mutant roots. G, Number of nuclei (biological replicates) expressing pWOX5::mVenus-NLS in Col and plt2, plt3 double mutant roots summarized in box and scatter plots. H, Area of WOX5 expression in µm2 in Col and plt2, plt3 double mutant roots summarized in box and scatter plots. G, H Box = 25-75 % of percentile, whisker = 1.5 interquartile range, − = median, □ = mean value, = minimum/maximum. (G, H) Kruskal-Wallis ANOVA analysis with subsequent Dunns test (G) or one-way ANOVA and post-hoc Holm-Sidak multiple comparisons test was used to test for statistical significance (H). Asterisks indicate statistically significant differences (α = 0.01). Number of analysed roots (n) (biological replicates) is indicated for each genotype and results from three technical replicates per genotype. Scale bars represent 10 µm; NLS = nuclear localisation signal.
(F) CSAG2 Δ37 mutant that does not bind SIRT1 does not enhance SIRT1 activity in vitro. In vitro SIRT1 activity towards p53 ac-K382 peptide was determined in the presence of GST, GST-CSAG2 or GST-CSAG2 38-127, n=3 biological replicates.
C. Cdc20-5A efficiently binds to the B56 binding site mutant APC/C. The purified recombinant WT APC/C or Apc1-loop500 mutant APC/C (1-L557A/V560A) was incubated with WT Cdc20 or non-phosphorylatable Cdc20 mutant (5A) in ∆APC∆Cdc20 anaphase extract at 23˚C for 55 min. The APC/C was recovered with Apc3 monoclonal antibody (AF3.1) beads and the bound proteins were analysed by SDS-PAGE and immunoblotting with indicated antibodies. D. Quantification of C. The intensities of WT APC/C control were arbitrarily set to 1.0. Error bars, s.e.m. from three independent experiments.
Relative HDX differences from (A) are mapped to the structure of pParkin:pUb and UbcH7-Ub complex. Regions where HDX is faster in the pParkin:pUb:UbcH7-Ub complex at the one minute time point are indicated in red while those regions in blue exchange more slowly using a similar the gradient as Fig. 1. Based on HDX and NMR experiments (C, D) the pUbl domain is shown oriented towards the RING0 domain (dashed arrow, top). The increased HDX for RING2(Rcat) and RING0 suggests the RING2(Rcat) domain has a weaker interaction with the RING0/RING1 domains upon UbcH7~Ub binding (dashed arrow, bottom). Regions shown in grey are peptides that were not mapped.
Th cells (CD4+) were purified using magnetic beads from spleen and lymph nodes of 4-5-weeks-old mice. The cells were stimulated with anti-CD3 and anti-CD28 antibodies, beneath a trans-well with 0.4μm pore containing 25-30 worms. The Control wells contained only unused schistosomal-medium.
(A) SCOC is required for autophagy in HEK293 cells. Anti‐ULK1, ‐Actin and ‐LC3 blot after siRNA treatment in HEK293 cells in FM, ES or EL. Representative blot; quantification of LC3II/actin of averaged duplicates; error bars represent s.e.m. (n=3). Significance was determined using a two‐tailed paired t‐test: RF EL versus siSCOC‐03 EL, *P=0.0419.
C. Schematic depicting the infection and interferon addition to evaluate ISG15 induction following SARS-CoV-2 and astrovirus infection.
Entry of MLV pseudotyped with SARS-CoV-2 S or SARS-CoV-2 Sfur/mut in BHK cells transiently transfected with hACE2. The experiments were carried out in triplicate with two independent pseudovirus preparations and a representative experiment is shown.
(A) A schematic representation of the heterogeneity within a neuronal population for HSV-1 reactivation following inhibition of the canonical AKT-mTORC1 signalling pathway. Dark blue neurons signifies cells undergoing "Successful" (productive) reactivation with Gadd45b localized in the cytoplasm (nuclear exclusion); light blue neurons shows cells remaining in the latent state with Gadd45b localized to both nuclear and cytoplasmic compartments; white-labelled cells with dark blue nuclear puncta signifies "Unsuccessful" (abortive) reactivation with Gadd45b localized to nuclear foci/puncta; and white-labelled neurons represent uninfected cells with low-level Gadd45b localized to both nuclear and cytoplasmic compartments.
(C) Averaged spike responses obtained from multi-electrode array recordings shown as PSTH of 4, 8 and 2 cells respectively of three different macaques (580 nm; 1.24 × 1017 photons cm-2 s-1). PSTHs are presented as mean ± SEM (dashed lines, calculated over responding cells). Raster plots of a representative cell from each individual macaque are shown below (10 stimulus-repetitions).
A) Cyclin B2 knock-out and induced degradation by immunoblotting. Indicated cell lines were analysed 24 hours after mock or Dox/IAA/Asv (DIA) treatment using the indicated antibodies to confirm homozygous gene tagging and efficiency of protein degradation. (
Linear regression plot of in vitro limiting dilution assay (LDA) for control (shc) or shMALT1 seq#1 and seq#2 transduced GSC#9. Data are representative of n=2. Knockdown efficiency was verified at day 3 by western-blot using anti-MALT1 antibodies. GAPDH served as a loading control.
Adherence of GBS A909 to human CEACAM1 (CC1)-, CEACAM3 (CC3)-, CEACAM5 (CC5)-, CEACAM6 (CC6)- or CEACAM8 (CC8)-expressing, or an empty vector control, HeLa transfectants at MOI of 10 for 30 mins. Mean and SD for n = 4 independent replicates are shown.
(E) Quantification of free cholesterol levels (FC) analyzed by lipidomics after subcellular fractionation to obtain MAM from the indicated cells. Lipid units are represented as molar mass over total moles of lipids analyzed (mol%). Graphs represent percentage over controls. Dashed line represents control levels. One-way ANOVA. (n=4; * p< 0.05)
C. Hierarchical clustering heat map of differentially expressed genes in the hearts of 7- and 12- week old wa3 mice in comparison to WT.
(F) Budding yeast Spt5N and Spt5N-3A were expressed as fusions to Protein A in budding yeast cells. Cell extracts were treated with DNase as indicated, to release nucleosomal histone complexes from chromatin, before immunoprecipitation (IP) of Spt5N / Spt5N-3A on magnetic beads coated with IgG. The bound proteins were eluted and then analysed by mass spectrometry (the panel indicates the detected spectral counts).
Profiles of the converted red fluorescence at the back remain almost symmetric over time. The dotted line represents the axis of symmetry of the intensity profile of the photoconverted fluorophores at t = 0.
(A) Heat map visualization of top 30 differentially regulated mRNA transcripts. Color represents significant down- (blue) or up-regulated (red) mRNA expressed as a log2 fold change relative to vehicle corrected for the false discovery rate.
Northern blotting of mascRNA and 5S rRNA in the lysates of HEK cells before and after FBS starvation.
Mammary organoids were isolated from 19-20 weeks old C57Bl/6 mice on normal (ND) or high fat diet (HFD) (n=3). Organoids were cultured in collagen for 2 days after which the number of invasive protrusions per each organoid was determined microscopically. Amlexanox reduces the number of invasive protrusions in organoids isolated from mice on G) ND or H) HFD. Error bars represent mean ± SD from 3 independent experiments where 30 organoids were counted per each mouse (labelled with a different symbol shape).
f, Fibroblast cells from patients with Scheie syndrome (GM01256) or healthy controls starved and blotted with indicated antibodies. g, Cells in f imaged. Lysosome size classified by Image-ProPlus (IPP) software.
(f) Left: Representative images (Bright field; DAPI, nuclei; CDH5, endothelial cells; CXCL12) of aortic sections from chow diet-fed and LIDPAD mice (scale bar, 40 μm). Boxed regions were further magnified (scale bar, 30 µm). Arrows point at aortic endothelial cells. AW: Aortic wall; L: lumen. Right: Box-whisker plot of CXCL12 fluorescent intensity in the aortic vascular endothelia. CXCL12 fluorescent intensity for each delimitated endothelial region is represented as individual data points on the plot. Box-whisker plots indicate median (middle line), 25th, 75th percentile (box) and the lowest/ highest data points (whiskers). Chow diet-fed (n = 3) and LIDPAD diet-fed (n = 3) mice were analysed, with 10-20 delimitated endothelial regions per mouse analysed for image quantification.
(b) The Ulk1 S317/777A mutant is compromised in LC3 lipidation in response to glucose starvation. ULK1MEFs were cultured in MEFs-free medium for the indicated times. LC3-II level was determined by western blotting and the LC3-II accumulation was normalized by α-tubulin and quantified (bottom, n = 3, mean ± s.d.). A representative western blot was shown. The LC3 antibody used in this experiment seemed to preferentially recognise the lipid-modified form of LC3-II, which migrated faster on the gel.
Wild type C57BL/6 mice were injected with anti-G-CSF antibody alone or in combination with anti-IL-6 antibody one hour prior to CoPP treatment; the injections were repeated daily for 5 days and mice were sacrificed 6 hours after the last CoPP injection. CD45+ cells, granulocytes and HSC numbers in PB measured by flow cytometry.
(D) NKX2.2-shRNA or control plasmid was electroporated into the brains of E13.5 embryos. At E16.5, the brains were harvested to investigate the cell distribution. Date information: Representative images from at least three independent experiments.
(E) Proposed model for the centrosome-dependent PIDDosome activation upon different stimuli. The centrosome constitutively acts as PIDD1 centralizer. A local increase in PIDD1 concentration (achieved either by centrosome clustering or upon p53 activation) triggers PIDDosome activation. In ANKRD26-deficient cells, the inability of the centrosome to generate a local increase in PIDD1 concentration hinders the activation of the complex in response to both stimuli.
Parkin-mediated ubiquitination recruits p62 and HDAC6. MEFs were transfected with WT, A240R, and T415N mutant GFP-parkin followed by CCCP treatment for 8 h. Cells were double immunostained with cytochrome c (red) and p62 antibody (blue) in A, and cytochrome c (red) and HDAC6 antibody in C. Arrows indicate mitochondrial aggregates. (B and D) The average percentages of p62- or HDAC6-positive mitochondrial aggregates from three independent experiments are presented with standard deviation as error bar.
B COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h and stained for the indicated proteins. Scale bars, 10 μm.
H Left: Kymographs of Magic Red cathepsin B substrate-labeled degradative lysosomes in the proximal dendrites of neurons infected with shSc and shLAMTOR1. Scale bar, 5 µm. Right: Quantitative analysis of vesicular movement from kymographs (N = 16 neurons from 3 independent experiments). Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by Mann-Whitney U test
E. ETC-159 treatment of HPAF-II orthotopic xenografts reduces the expression and protein levels of multiple HR and FA pathway genes. (E) Tumor lysates from HPAF-II xenografts treated with vehicle or ETC-159 for 8 or 56 hours were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. Each lane represents an individual tumor.
F-K. Enzastaurin treatment rescues hemorrhage phenotype in veal2gib005Δ8/+ zebrafish embryos indicated by rescue of the vascular integrity defects in veal2gib005Δ8/+. Arrowheads show the presence of hemorrhage due to the vascular integrity defects. Experiment was repeated in biological replicates and total no of embryos scored are mentioned on figure. (F-I) Magnification-5X, Scale bar-100μm, (J-K) Magnification-20X, Scale bars-50μm.
A, B MARS (A) and MARS2 (B) mRNA expression levels were measured by real-time PCR in blood samples with 2 and 3-4 copies. Relative expression levels were normalized to GAPDH levels, and data were quantified relative to the mRNA expression levels of 2 copy samples. Data are presented as the mean ± SEM. *P ≤ 0.05, **P ≤ 0.01. Unpaired Student's t test
Kaplan-Meier overall survival curves for TNBC patients with high or low micropeptide CIP2A-BP expression in Suzhou cohort (discovery set, n = 112) and Guangzhou cohort (validation set, n = 105).
(C) Confocal images of dLGN after AAV2 injection. The dLGN was outlined with the dotted line. MCherry reveals axons and synapses of AAV2-infected RGCs. Left scale bar, 50 µm. Right scale bar, 5 µm.
(D, E) Representative confocal micrographs of control (upper panels), Yip1A-knockdown (middle panels), and IRE1-knockdown (lower panels) cells double-stained for Lamp2 (a marker for late endosomes/lysosomes; green) and B. abortus (red) at 24 hr p.i. BCVs co-localized with Lamp2 are indicated by arrowheads. The infected cells are outlined with white dashed lines. Scale bars are 10 μm. The percentage of Lamp2-positive BCVs was determined, and is shown in the line graph (E).
A) z-stacks were acquired from FM4-64 labeled vacuoles in wildtype cells (BJ3505), using a spinning disc microscope (step size 200 nm). 3D reconstructions from these stacks reveal a peripherally located fusion pore. Scale bar 2 µm.
Automated microinjection was performed on organotypic slices of mouse E14.5 - E15.5 dorsal telencephalon using a solution containing Dextran-A555 (not shown) and Alexa488 (green). Slices were fixed after microinjection (n = 71 cells total) and were stained for Tbr2 (white, H-J). (A-C) Representative examples of a non-coupled cell (A, cartoon on the right), a 2-cell cluster (B, cartoon on the right) and a 5-cell cluster (C, cartoon on the right). The asterisks indicate the Dx-A555-positive, microinjected cell. Percentage of microinjected cells found in a coupled cluster (coupled, green). Cluster size, expressed as % of total. Distribution of coupled cells expressed as the distance from the ventricular surface (0 µm = ventricle surface. Distribution of coupled cells divided into 11 bins and expressed as % of total. the images on the left are maximum intensity projections (MIP) of 18, 17, 23, 12 and 30-focal planes, respectively
D. HeLa cells were transfected with Nup358 siRNA (siNup358) or Nup214 siRNA (siNup214). Western blot (WB) indicates the extent of Nup358 depletion and the level of Dcp1a.
C Plasmin cleaves VN at the 45RG peptide bond. Urea purified VN was incubated with plasmin (substrate/enzyme ratio: 10:1 w/w) for 2 h at 37°C and the reactions were analysed by MALDI-TOF mass spectrometry.
E, F. HUWE1 co-precipitates with PCNA in anti-PCNA immunoprecipitation from extracts of MCF7 (E) and 8988T (F) cells, showing that the HUWE1-PCNA interaction can be detected in different cell lines.
(g) Subcellular fractionation of TSC2−/− MEFs transfected with Flag-TSC2 wild type, or Flag-TSC2 mutants (RQ or RQ-9NT). β-integrin and catalase were used as subcellular markers for membrane and peroxisome fractions, respectively. WCE, whole-cell extract. The arrow indicates the position of overexpressed Flag-TSC2.
Promoter activity of CDKN1A (E) and MDM2 (F) were quantified in Set8 knock-down cells before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after DNA damage (10 Gy IR). Left panel: The percentage of cells with active TSS, subdivided into populations with strong (> 75% of TSS, solid colors) and weak (<75% of TSS, shaded colors) activity, is shown as stacked bar graphs, the mean fraction of active promoters is indicated above each bar. Right panel: Distributions of calculated transcription rates at active TSS are presented for each time point as probability density estimates (PDF, see Data Visualization section). We measured a higher fraction of active promoters upon damage compared to A549 wild type cells (Figure 3), while transcription rates remained unchanged.
Prediction of enhancers in the genomic loci of mtDNA maintenance genes, 100 kb upstream of the analyzed gene, found in human-mouse and human-rat comparisons. EEL score for individual elements: red bars. Protein coding genes upstream from mtDNA maintenance genes are shown with black lines under each locus (picture not in scale). POLG shows three highly conserved elements in a gene-poor region. TWNK shows one distant element, with several genes between the element and the gene, suggesting the element not be a specific regulator for TWNK. Abbreviations: TWNK, Twinkle mtDNA helicase; POLG, DNA polymerase gamma, catalytic subunit; POLG2, DNA polymerase gamma, accessory subunit; SSBP1, single stranded DNA binding protein 1; TFAM, mitochondrial transcription factor A.
A The transcript levels of SlHAK20 in TS-670 and three independent SlHAK20Hap1-YFP transgenic lines grown under normal growth conditions.
i, Schematic of shortening phases by overexpression of cyclin D. Cyclin D was overexpressed in RPE cells and the durations of each phase were quantified for a full cell cycle.
Mice received the indicated compound for 3 consecutive days and lung ILCs were analyzed by flow cytometry the following day. Expression of ST2, KLRG1 and c-Maf was assessed in ILC2s. (D) the percentage of ST2+ KLRG1+, ST2-KLRG1+, ST2+KLRG1-, ST2-KLRG1- ILC2s (2way ANOVA, interaction: F(12,56)=13.82, p<0.0001)) Each symbol represents one individual biological replicate. Bars represent mean ± SEM.
D A typical phase-plane trajectory of the state in STEN, where the initial inhibition level (r0) and threshold (th) are marked. The inset kymograph shows a typical STEN.
Human peripheral blood mononuclear cells (PBMCs) were cultivated for 48h in RPMI containing 80mg/dl glucose (NC) and supplemented with 10mM beta-hydroxybutyrate (BHB). T cell stimulation was performed through CD3/CD28 Dynabeads at a bead:cell ratio of 1:8. I T memory cell differentiation protocol: Following initial incubation and stimulation, CD4+/CD8+ T cells were isolated via magnetic cell separation and cultivated with 50 U/ml IL2 and 25 ng/ml IL15 for an additional 72 hours.
D. CYP26C1 and SHOX are members of the retinoic acid pathway. Vitamin A, retinol (ROL), enters the cell and is oxidized to retinaldehyde (RAL). RAL is then oxidized to retinoic acid (RA). RA can enter the nucleus and regulate the expression of its targets. CYP26C1 controls RA intracellular levels by oxidizing this molecule in more hydrosoluble retinoid molecules like 4'-hydroxy-retinoic acid (4'-OH-RA), which can be readily excreted. High levels of RA downregulate SHOX expression.
C. Blood glucose levels for insulin tolerance test of control (n=10) and Rbpji∆EC (n=7) mice. Data represent mean ± SEM, unpaired t-test.
(e) Quantification of ACT1-CUP1 mRNA levels. Spliced ACT1-CUP1 mRNA levels were calculated relative to U6 in each lane. The quantification was based on three independent experiments.
A. Structural views suggesting that Mdm12 might have a preference for certain phospholipids. The surface representation of Mdm12 positioned around the binding site for the head group of PE is shown with charge distribution (left) and the sequence conservation (right) in the same orientation. Surface electrostatics and sequence conservation were calculated using an APBS program [31] with the nonlinear Poisson-Boltzmann equation and contoured at ±3kT/e, and ConSurf website (consurf.tau.ac.il) [32] with 34 different yeast orthologs, respectively. The ribbon diagram shown in the middle indicates the overall orientation of Mdm12.
qRT-PCR results showing the enrichment of seven miRNAs in Ago1x immunoprecipitate relative to that in Ago1 immunoprecipitate in HeLa cells. Bars show mean of three experiments ± S.E.
Western blot for p53, p53 pS15, and vinc in HCT116 silenced for PHD1 with two different constructs (constructs 1 and 2) upon exposure to 300 μM 5-FU for 8 h.
(A) HOIP, HOIL-1L, and SHARPIN co-localize with Htt-Q97 aggregates. SH-SY5Y cells co-expressing Htt-Q25-GFP or Htt-Q97-GFP (green) and HOIP, HOIL-1L, SHARPIN, or HHARI (red); DAPI (blue). Scale bar, 10 µm.
(C) Zwilch interacts very prominently with only one of the two ROD protomers, sandwiched between the N-terminal β-propeller and residue 850. A few interactions also link Zwilch to the C-terminal region of the second protomer.
D Calculated LuC ratios for the indicated protein pairs. The positive control proteins PA-NL and PA-mCit-NL and the interacting proteins NL-BCL2L1 and PA-mCit-BAD show high LuC ratios.
(C and D) Relative expression levels normalized to WT of (D) mitochondrial chaperones, proteases and TFAM in 3 - 4 week old mice (n = 3 - 4).
Comparison of the level of 1-h pERK inhibition between two cell lines (C32 and WM1552C) treated with four RAF inhibitors and one MEK inhibitor.
(C) Graph relative to Notch3 expression in MuSCs isolated from 1.5 month old mdx mice treated either with vehicle (CTR) or TSA (TSA), and in EVs derived from FAPs (EVs-FAPs) isolated from 1.5 month old mdx mice treated either with vehicle (CTR) or TSA (TSA) (n=3). Star (*) indicates statistical analysis by Tukey test relative to mdx vehicle treated mdx mice (CTR); *p<0,05;. hash (#) means significance compared to EVs-FAPs CTR, ##p<0,01. § indicates significance by Anova test; §§ p>0,01.
L EFS in a CNS orthotopic model in which drug sensitivity was observed. EFS is time of inoculation of tumor cells to event (defined by neurologic symptoms or weight loss).
E. Wild type cells were transformed with plasmids for the expression of the indicated proteins. Q97-GFPnF is a non-fluorescent version of Q97-GFP. Close proximity of the two split GFP parts results in fluorescence which was visualized by microscopy. Shown are mean values and standard deviations of three replicates. Bar, 5 µm.
(e,f) Bar graph showing normalized liver weights (mean ± s.d. for n = 10 mice per group ***P≤0.001; e) and total lipid content in mice with the indicated genotype (mean ± s.d. for n = 5 mice per group; ***P≤0.001; NS, not significant; f). Mice injected with an empty HDAd virus behaved as wild-type untreated mice; therefore, data are not represented in the figure.
D, MCF10A WT cells were pretreated with DMSO or AZD6738(250 nM) for 2 hours, and then irradiated with 20 Gy, and cells were harvested at indicated time points for immunoblotting.
D) HEK293A and VPS15 KOs were stained for p62 (green), ATG9 (red) and LAMP1 (blue).
A. The vgrG genetic modules of the tested A. tumefaciens strains. Genes are color coded according to the predicted function or results of functional assays [24]. The vgrG-associated genes are v1-v6 for 12D1, v1-v9 for 1D1108, v1-v7 for 15955.
ELISA-based Quansys mouse chemokine assay was performed with Capan-1 (Cap), MiaPaCa-2 (Mia), Colo357 (Colo), and C5LM2 (C5) orthotopic tumor samples treated with saline (control) or 2G8 (n = 3/group) to detect mouse chemokine changes after treatment. Change of mouse IL-6 was shown.
(A) Western blotting of phospho-Thr389-p70S6K (pS6K), total p70S6K (S6K), phospho-Ser235/236-S6 (pS6) and total S6. Quantification represents the pS6K/S6K (n = 3) and pS6/S6 (n = 4) ratios relative to the non-treated (NT) control Data information: Error bars represent the SEM. Significance between means was first determined using ANOVA. Significance p-values were calculated using Fisher"s LSD. *, p < 0.05; **, p < 0.01 from NT controls; ††, p < 0.01 from IFNγ/TNFα treated controls
C Growth curves in WT1 and double mutant clone 1 cells treated with or without b-estradiol (n = 3, mean +/- SE).
b, Fluorescence microscopy of HeLa cells transfected with the indicated IpaJ mutants. The cis-Golgi (GM130, green) and F-actin (red) are shown. Scale bar, 10 µm.
Distributions of death times that result from simulations in (C, D), respectively. Fractional survival indicated after 24-hour time course simulation.
G. Overrepresentation of Aβ APRs in amyloid plaques of nonAD brains.(statistics: hypergeometric test with Bonferroni correction). * P ≤0.05, ** P≤0.01 The original data was taken from Xiong et al and included three biological replicates.
(E-G) Comparative inhibitory effects of GM3 16:0 on mTLR4/mMD-2 (E), mTLR4/hMD-2 (domain-swapped complex) (F), and hTLR4/hMD-2 (G) (n=3).