EMBO/sd-character-level-ner huggingface dataset:
(B) HEK293A cells were transfected with either tagged wild-type, T300A, or S278/T300A ATG16L1 in the presence or absence of ULK1. Cleavage of ATG16L1 was analyzed by WB. Levels of ATG16L1 cleavage were measured from 3 biological repeats (right panel). Data information: Unless otherwise indicated experiments were performed three times. Data are represented as mean ± standard deviation and p values were determined by Student's T-Test.
E) Trajectory plots comparing the trajectories of Cd59a, Chordc1, Hpgd, Ldhb, Lincred1, Myo6, Slc39a11 and Tlr1 in WT, mdx++ and mdx+- mice.
Body weight (C) of ChATfl/fl;LysM-Cre (n = 7 for ChATfl/fl, n = 8 for Cre ChATfl/fl;Cd4-Cre (n = 6 for ChATfl/fl and n = 7 for Cre ChATfl/fl;Mb1-Cre (n = 12 in C, n = 9 for ChATfl/fl, n = 8 for Cre and littermate ChATfl/fl mice housed at RT.
(D) Negative correlation between total RNA editing and circRNA abundance, correlation = -0.37, Correlation test p value = 0.0015.
(G) Scheme of the experiment. Twenty-two BALB/c mice were inoculated i.p. with 3.5x104 CT26-LUC cells and treated with either 800 μg BoxA or PBS 3 times a week, 10 times in total. Yellow arrows represent BLI imaging.
(B) The graph depicts quantification of CHIKV plaque assays (plaque-forming units/ml) in Vero cells performed from the culture supernatant of CHIKV (MOI 1, 24 h) infected HT-29 control and IRGM knockdown cell
Comparison of the Hallmark gene expression signature "TNFA_signaling via NFKB" in near-diploid (low aneuploidy) and highly-aneuploid (high aneuploidy) human cancer cell lines from the CCLE. *, p= 5e-08, empirical Bayes-moderated t-statistics. The y-axis represents the ssGSEA expression score. The grey line marks an ssGSEA score of 0, indicating the genes in the hallmark "TNFA_signaling via NFKB" geneset is not differentially regulated.
A ARChIP‐exo defines four types of high‐confidence agonist‐liganded ARBEs. Numbers indicate motif counts. The first two columns of each ARBE panel show normalized tags distribution over ARBEs on the forward (blue) and reverse (red) strands, separately. Forward strand refers to the motif‐containing strand. The aggregated tag density is shown at the top of the raw signal plots. The third column of each ARBE panel represents the bound motif sequences ordered as in the left two columns.
E: IGV tracks of rhabdoid tumor genes previously identified to be occupied by non-canonical SWI/SNF (Michel et al., 2018). ID3 and JUND3 decrease in H3K27ac occupancy and chromatin accessibility following exposure to mithramycin for 8-hours or 18-hours.
F. R388-methylated peptide, but not the unmodified peptide, blocks α-meSIRT7(R388) antibody. After incubation with unmodified peptide or R388-methylated peptide (R388me2a), α-meSIRT7(R388) antibody was used to detect immunopurified SIRT7
D, E. Distribution of the m6A peaks across the host transcripts (D) and EBV transcripts (E) was analyzed based on three independent PA-m6A-seq experiments. PA-m6A-seq assays were performed in CNE2EBV cells following EBV reactivation, which was induced using TPA and NaB.
Morphology of four-week-old soil-grown plants of Col-0, mekk1-5 ndr1, and two independent transgenic lines of SNIPER1 OE into mekk1-5 ndr1 background. Scale bar = 1 cm. The mekk1 ndr1 double mutant was used instead of the mekk1-5 single mutant is to overcome the sterility. SNIPER1 gene expression in the indicated plants as determined by RT-PCR. Error bars represent mean ± SD (n = 3). Two independent experiments were carried out with similar results. Quantification of H.a. Noco2 sporulation in the indicated genotypes 7 days post inoculation (dpi) with 105 spores per ml water. Error bars represent mean ± SD (n=4). Three independent experiments were carried out with similar results. Growth of P.s.m. ES4326 on four-week-old leaves of the indicated genotypes at 0 and 3 dpi with bacterial inoculum of OD600 = 0.001. mn stands for mekk1-5 ndr1 double mutant. Error bars represent mean ± SD (n=4). Three independent experiments were carried out with similar results.
Nucleoplasmic YTHDC1 (A) and WTAP (B) intensities upon HSATIII knockdown. Control and HSATIII knockdown cells after thermal stress exposure (42°C for 2 h and recovery for 1 h at 37°C) were stained by HSATIII-FISH and IF using anti-YTHDC1 or anti-WTAP antibodies. nSB and whole nuclear areas were defined by binarized images of HSATIII and DAPI, respectively. Box plots represent the average intensities of YTHDC1 and WTAP in the non-nSB nucleoplasm area of each nucleus. The first and third quartiles are the ends of the box, the median is indicated with a vertical line in the box, and the minimum and maximum except for the outliers are the ends of the whiskers. The outliers are indicated with open circles. The mean is indicated with X. P-value (Mann-Whitney U-test) is shown above (n=40). (B, D) Correlation between the intensity of YTHDC1 (B) or WTAP (D) in non-nSB nucleoplasm and the nSB occupancy in individual nuclei. nSB occupancy is the ratio of the nSB area to the whole nuclear area of each nucleus in (A) and (C). Pearson coefficient of correlation (R) and p-value are shown above (n=40).
(D) Complex I IGA (cI-IGA) analysis of digitonin-solubilized samples after inhibiting mitochondrial translation with doxycycline for 6 days (0h). After removing the drug and restoring synthesis of the mtDNA-encoded subunits, the cells were collected at the indicated times to follow the appearance of cI reactivity with time. The gels were incubated in the reaction mixture for 24 hours. SS = steady state. The asterisk indicates the presence of a high molecular weight cI-containing band of unknown nature
(E) Proliferation was measured in primary lung resident fibroblast isolated from either IPF lung or TGFα mice and treated with either control or AURKB siRNA. ****P < 0.00005, unpaired t-test, (n=9-11).
E. U1-Grx1-roGFP2 cells were pre-treated with Vs for 15 min, exposed to H2O2 for 2 min, and ratiometric response was measured.
D. WB analysis for Cx43 in samples derived by miRNAs pulldowns performed with whole lysates of HEK293Cx43+ cells and biotinylated miR-133b and miR-509-3p (n=5 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs.
c, Representative images of GFP-LC3 puncta (autophagosomes) in skeletal and cardiac muscle of GFP-LC3 wild-type and GFP-LC3BCL2 AAA mice before exercise, after 80 min exercise, or after 75% of maximal exercise capacity. Scale bar, 20 µm. d, Quantification of data (mean ± s.d. of 4 mice per experimental group) in c.
Heat map of differentially expressed genes between cancer and healthy tissue/organoids reveals upregulation of several HGSOC biomarkers and reduction of FT differentiation markers in the cancer samples. Differential expression determined by single-color microarray for 8 different patient samples was significant for all genes with p < 0.05 except for OVGP1 and TOP2A in organoids.
Cpd A enhances the anticancer activity of bendamustine. H1650 cells were treated with various doses of bendamustine with or without 40 μM Cpd A (nontoxic dose, see Fig1C and Supplementary Fig S2) for 48 h and subjected to MTT viability assays.
(D) FACS analysis of CD133 and GFAP using X08 GSCs and DFCs. Data are from representative experiments repeated at least three times.
c, Arrowheads indicate GFP-LC3+ SLAPs devoid of Lysotracker Red in cells infected for 4 h.
Gene ontology (GO) analysis of biological processes for transcriptionally upregulated genes (≥1.5-fold; adjusted p-value<0.05) after combined VPS4A+B silencing using the enrichGO function from clusterProfiler.
(a) The HDX values after 120 min of BakΔTM bound to ΔH5 nanodiscs are subtracted from the values with soluble BakΔTM and plotted against the amino acid sequence. α-helical secondary structure is indicated at the top.
Densities (cells/mm2) of VCAM1+ B1 cells in the adult V-SVZ. n=4, **p=0.002. Densities (units/mm2) of NSC units in the adult V-SVZ. n=4, **p=0.0022. Distribution of NSC units with different numbers of B1 cells. n=4, ****p<0.0001 (1 B1 cell/unit), **p=0.0025 (2 B1 cells/unit), **p=0.0063 (3 B1 cells/unit), *p=0.0385 (4 B1 cells/unit).
E. Sre1 cleavage assay was performed as in (C). G128V, A127D and A186T mutant strains were obtained from our previous mutagenesis screening (Stewart et al, 2012). Dsc5 serves as a loading control.
A. Survival frequencies after DSB induction at LYS2 locus in the indicated strains. Error bars indicate survival standard error (SEM) of at least three independent experiments. Data information: Significance was determined using 2-tailed, unpaired Student's t test. *P-value 0.01 to 0.05, significant; **P-value 0.001 to 0.01, very significant; ***P-value 0.0001 to 0.001, extremely significant; ****P < 0.0001, extremely significant; P ≥ 0.05, not significant (ns).
A Consensus sequence around m6A modified bases in the BREX‐containing B. subtilis genome. The modified base is marked by an arrow. Modifications were directly detected by DNA sequencing using the PacBio platform.
(G) The RNA reporter vector encodes F-luc as the primary reporter and R-luc on the same plasmid as the internal transfection control. The effect of tRNAPhe(GAA) in protein translation was revealed by a reporter assay. 6×TTC (Phe) or 6×TTT (Phe) were inserted after the PGK promoter region of F-luc as the positive reporter.
(i) Western blot analysis of a GFP-Trap immunoprecipitation experiment from HeLa cells showing that expression of HA-RILP promotes the association of GFP-Rab34 and HA-Rab7.
(A) The relative frequency of Gly in the final 50 residues of functional human proteins with different subcellular localizations. The number on each graph denotes the left-tailed p-value of the -1 residue. CT-inside and CT-outside represent membrane proteins with their C-termini facing the cytosol or extracellular space, respectively.
Thymocytes isolated from WT and Cd4cre A1fl/fl mice were stained with anti-CD4, anti-CD8 and anti-TCRβ antibodies and were gated by the high expression of TCRβ (TCRβhigh). Representative images are shown (D).
(A,B) HEK 293T cells transfected with denoted plasmids were (A) deprived of nutrients for 90 min, and then replenished with DMEM for 30 min or (B) stimulated with 50 ng/ml epidermal growth factor (EGF) for 30 min. The S6K immune complexes were analysed by immunoblot using appropriate antibodies (top three panels). Flag (ATG1α) blots were completed from the same cell lysates (bottom panel).
Bovine heart mitochondria were incubated at the indicated pH in absence or presence of 200 μM DPC, treated with 1% (w/v) digitonin and F-ATP synthase was immunoprecipitated with an anti-F-ATP synthase Ab followed by 15% SDS-PAGE. β subunit and CyPD content were detected by Western blotting. The ratio between CyPD and the corresponding β subunit is reported in the lower part of the panel, referring to pH 7.4 values as 100%. Data are an average ± s.e. of 3 independent experiments.
(h) Kinetics of the appearance H-2Db-gp33+ CD8+ T cells among peripheral blood mononuclear cells (PBMCs) after infection as in a (left); each line represents one mouse. Right, frequency of H-2Db-gp33+ CD8+ T cells remaining on day 15 relative to that on day 8, set as 100%.
Transmission electron microscopy (TEM) demonstrated the presence of anchoring fibrils (arrows) at the DEJ of the corrected epidermis (middle right panel) and in a normal human skin biopsy (left panel). Note the absence of anchoring fibrils in the RDEB epidermis (middle left panel). Detection of human COLVII by immunogold staining in the DEJ of corrected epidermis (right panel). Scale bar: 250 nm.
Defective de novo miRNP formation in cells pre-treated with PP2A inhibitor. Ago2 associated (F) and total (G) miR-122 levels were measured by qRT-PCR and normalized against immuneprecipitated FH-Ago2 content and U6 RNA respectively. Values obtained upon 14 hrs of DOX treatment were considered as unit and relative values obtained upon 24 hrs of DOX treatment are plotted. All samples were treated for 24 hrs with LPS (mean+/- s.e.m., n=4).
(A) Graphs showing the inhibitory effects of chloroquine, arbidol, toremifene, clomiphene, amodiaquine, verapamil, and amiodarone when added at 0, 1, or 5 uM to Huh-7 cells infected with SARS-CoV-2pp for 72 h (black bars). The number of pseudoparticles in the infected cells was quantified by measuring luciferase activity; viral entry in untreated cells was set as 100%. VSVpp were tested in parallel to exclude toxic and nonspecific effects of the drugs tested (grey bars).
(B) In the CRH test, the secretion of these hormones is measured after CRH administration.
E Geranylgeranylation activity of WT GGTase-III and the indicated mutants (100 nM each). Cys195-farnesyl Ykt6ΔAIM (1 μM) and 3H-GGPP (1 μM) were used as substrates (mean ± SEM, n = 3).
Reduced weight gain in the adult. Error bars: SD; 2-way ANOVA p=0.0009; Sidak's multiple comparison test, **p <0.01. n=13-20 mice.
A schematic to show how the active (higher molecular mass) fraction was estimated from the distributions in (E), with a cutoff of 0.4 defined by the 0 min distribution and used to analyze the datasets.
Box-whisker plot shows the number of Rab5 cargos that finally reached the leading edge membrane during 120 s. (1 representative of 3 independent experiments and n= 23 cells). The ends of the whiskers are set at 10% and 90% of the entire population, ns, no significant difference, two-tailed Mann-Whitney.
B. The molecular brightness of different GFP tagged constructs was obtained with GFP monomer and GFP-GFP dimer as the brightness standard. Cells of strain yIO664 (SCC1-GFP) were analyzed throughout the cell cycle by PCH. To examine the effects of Wpl1, Pds5, and Eco1 on cohesin dimerization, the PCH analysis was repeated in strain yEB005 cells (SCC1-GFP WPL1∆), strain yEB002 cells (SCC1-GFP PDS5-AID), and yAM946 (SCC1-GFP ECO1-AID) in which Pds5-AID/Eco1-AID was depleted with auxin.
F) Effect of F-domain scaffolds on the vascular stability at 48- and 72-hour timepoint were assessed by taking the average of the number of nodes, meshes, and tubes and normalized to vehicle as log2 fold change. All experiments have at least three biological replicates except for Ang2, Tet1, Tet2, akC4, and Icos2 at 72-hour timepoint in tube formation assay that have two biological replicates.
A Overall view of the central cavity of the β subunit showing insertion of the C-terminal tail of Ykt6. PTAR1 is omitted for clarity. The Cys194-linked geranylgeranyl and Cys195-linked farnesyl moieties are shown in orange and purple, respectively. PPi, inorganic pyrophosphate.
(C) Extracellular acidification rate (ECAR) of npTh17 cells before and after addition of 25 mM glucose, 5 μM oligomycin and 100 mM 2-deoxy-D-glucose (2-DG). Seahorse graphs and bar graphs depicting glycolysis, glycolytic capacity and reserve the mean ± SEM from of 2-3 mice per genotype from one representative out of three independent experiments.
Average exocytosis level measured as ΔCm (G) and corresponding Ca2+‑current integrals (QCa2+) (H) in wild‑type (CD1B6F1: n=6 IHCs; B6: n=11 IHCs (B6 data replotted from Strenzke et al, 2016)), dual-AAV-TS transduced Otof-/- (n=8 IHCs), and non‑transduced (n=11 IHCs) Otof-/- IHCs. Transduced IHCs that showed eGFP expression, but had almost no exocytosis are depicted as dashed lines (not included into the average)
E, differences in CHIKV E2 protein expression between acute-phase and convalescent-phase samples per MetaHybridLouvain sub-community. Sub-communities are ordered by largest to smallest difference and filtered to sub-communities where the median of the channel means per sample was higher in the acute-phase samples at a significance threshold of FDR < 0.05. Sub-communities are named by their parent canonical community name plus an arbitrary number
Principal component analysis (PCA) of the DIA-MS phosphoproteomic data for the different stimuli separated by time points. Hierarchical clustering analysis of z-scored intensity values of significantly regulated (ANOVA, permutation-based FDR <0.05) phosphopeptides of the different time points. Column clustering hierarchy is indicated at the top. Row clusters for term enrichment analysis are color coded and indicated on the right.
(F) Representative presentation of increased RNA foci in C9orf72 carriers upon lentiviral-mediated hnRNPA3 knockdown. (G) Quantification of the number of RNA foci (fold change). 3 cases were analyzed. Single points indicate an average obtained from 29-30 cells per case. Color code labels values obtained in fibroblasts derived from the three individual patients. Two-tailed t-test. Mean ± SEM. Scale bar= 10 μm.
H Ptch1 mRNA expression levels (left panel) were determined by qRT-PCR in Daoy cells transfected with siRNA specific for Gli1 and Gli2 (siGli1/2) or a non‐specific control siRNA (siCtr) and treated for 24 h with GlaB or DMSO as a control. (right panel) The graph shows Gli1 and Gli2mRNA expression levels determined by qRT-PCR in Daoy cells transfected with siGli1/2 or siCtr. Results are expressed as fold repression relative to control, and data were normalized to GAPDH and HPRT expression.
(A,B) Time course of representative binding/unbinding events in EAAT1 and GltPh simulations, shown as the distance of the closest K+ to the respective site.
Recombinant S1 proteins of SARS-CoV-2 and SARS-CoV were incubated with 293T-ACE2 cells and subjected to FACS evaluation for binding.
(C) Molecular interaction between TSC2 and Rheb in the presence or absence of lactate in HA-Rheb-overexpressing HCT116 cells after serum deprivation overnight.
D, Explanted organ of Corti from an Otof+/+ mouse at P4 after two days in vitro (DIV2) at 37°C immunostained against otoferlin (magenta) and Vglut3 (green). Note the intense immunostaining of otoferlin at the plasma membrane. Scale bar 10 µm.E-J, Explanted organs of Corti from Otof-/- mice at P4 were transfected by GeneGun with otoferlin cDNA and eGFP and immunostained at DIV2.E, Example cell transfected with wild-type mouseotoferlin cDNA.F,G, Representative cells transfected with mouseotoferlin including the 20 amino acids of the RXR motif (see Fig EV4). Cells in G were incubated at 38.5°C for 30 min prior to fixation. The RXR-otoferlin transfected cells show a membrane localization of otoferlin surrounding the Vglut3 immunofluorescence/eGFP fluorescence at the basal pole of the cells (arrows), similar as in controls (A,B).H,J, Both the human RXR motif and the Ile515Thr mutation were introduced in mouse cDNA, and cells were incubated at 37°C (H) or for 30min at 38.5°C (J) before fixation. Here, green fluorescence surrounds the otoferlin immunofluorescence (arrows), suggesting loss of otoferlin from the plasma membrane.K, Quantification of the relative plasma membrane levels of otoferlin (as in Fig 1) revealed normal plasma membrane abundance when the human RXR motif was present, but a strong reduction for otoferlin with RXR and Ile515Thr (individual cells; mean ±SEM; t-test).
B. Lysates of HEK293T cells, transfected with the indicated plasmids, were subjected to boiling, followed by IP with the GFP antibody (PSMA2), followed by IB with the ubiquitin (DAKO) antibody (upper panel). Inputs were immunoblotted with the GFP or myc antibody (lower panels). Three independent blots were quantified and band intensity normalized to control average. (ANOVA, *p<0.05, **p<0.001, mean + s.e.m)
(B) Sequence alignment shows that most of the Sb-CCM1 suppressor mutants contain de novo amino acid changes and only two mutants have switched their residues from the S. bayanus sequence to the S. cerevisiae sequence (F294L and D400N). Letters beside the phylogenetic tree (in which the line lengths are not proportional to the evolutionary distances) indicate the amino acid state at the 400th residue and parentheses contain the codons encoding for the amino acids.
Early adhesion of PilE mutants as a function of piliation per bacterium normalized to that of pilESB.
qPCR quantification of PAX6 expression in Wildtype and PAX6 KO during retinal differentiation (n=3 biological replicates for each group).
(G) Quantification of the number of cells with nuclear TFEB from DMSO‐ and CQ‐treated fields in (E) and (F). In all fields, scale bars represent 10 μm. In all histograms, each value represents mean±s.d. from three independent fields with N=300.
(E) Stereo view of ADP binding to C. glabrata Hrr25 (formate structure; SO4- structure is equivalent, but the GxGxxG motif is disordered in that structure). All active-site residues shown in panels (D) and (E) are conserved between S. cerevisiae and C. glabrata Hrr25.
Figure 2. Overview of lysine-acetylated proteins in the light reactions (A)identified in this study in Arabidopsis. The classification of proteins into functional bins was performed using MapMan (Thimm et al, 2004). Color code: proteins not identified in the LC-MS/MS analyses (white), proteins without identified lysine-acetylated sites (grey), and proteins with one (yellow), two (orange), three (dark orange), or four or more acetylation sites (red). For the Calvin-Benson cycle, each box indicates a separate Arabidopsis AGI identifier as indicated in Dataset EV6. Cytb6f, Cytochrome b6f; FBPase, Fructose-1,6-Bisphosphatase; GAPDH, Gyceraldehyde-3-phosphate dehydrogenase; PGK, Phosphogycerate Kinase; PPE, Phosphopentose epimerase; PPI, Phosphopentose isomerase; PRK. Phosphoribulokinase, PSII, Photosystem II; PSI, Photosystem I; RuBisCO, Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase; SBPAse, Seduheptulose-1,7-Bisphosphatase; TPI, Triose Phosphate isomerase; TK, Transketolase. A template of the light-reaction schematic was kindly provided by Jon Nield and modified.
A) Outline of the SATAY screening procedure. Cells expressing plasmids containing the PE and PC synthesizing enzymes and a plasmid harboring the galactose inducible transposase (TPase) and a transposon (TN) disrupting the TRP1 gene were grown for ~56h in galactose-containing medium to induce transposition (step 1). Cells were inoculated in synthetic medium lacking tryptophan in either KennedyON or OFF conditions, grown for several generations (step 2) and harvested for DNA extraction and sequencing of transposon insertion sites (TNs) (step 3). TNs are mapped to the genome to identify genes that become required under certain rewired conditions (step 4). An illustrative example of TN insertions of four libraries visualized in the UCSC genome browser highlights a genetic requirement for DRS2 (green bar) in KennedyOFF conditions.
(B) Western blot from H1299 (p53-null) cells treated with siRNA Ku70 or control (ii), followed by transfections of RNA constructs depicted in (i). p53 protein levels from the WT and the ΔB2 reporters depicted in (i) normalized to firefly luciferase (transfection control reporter) (iii, n=3).
(A) A schematic view of the lncPSCA and PSCA loci. The risk-associated SNP rs2978980 is shown as the red vertical line. Data from the UCSC Genome Browser, including epigenetic marks for histone H3 lysine 27 acetylation (H3K27ac) are shown.
C, Representative electron microscopy (EM) pictures of CTL and THEM6 KO 22rv1 cells taken at low (left) and high (right) magnification. Red arrows point towards abnormal ER structure. Scale bar represents 500 nm.
B. qRT-PCR analysis of pro- (Nos2, Mcp1 and Tnfα) and anti- (Arg1, Fizz1, Il10, Il4rα and Tgfβ) inflammatory markers in GFP-CriptoMy-LOF and GFP-Control MPs at day 2 and 5 after injury. Data represent mean±SEM of relative mRNA level normalized with Gapdh (n≥4 biological replicates; ***P<0.001, Student's t-test).
E-H k-means clustering of significantly enriched proteins. Four major clusters were classified: chromatin binding, epigenetic modification, chromatin remodeling, ubiquitination and SUMOylation.
C, D. Projection on the principal components PC1, PC2 (C) and PC2, PC3 (D) of gene expression profiles during mESC differentiation.
D. Example of hematoxilin/eosin staining of brain coronal sections from mice sacrificed after 45 days of treatment with prazosin (PRZ) or vehicle. i: tumor infiltration. n: tumor necrosis. Scale bar = 2 mm. GBM44 GICs.
LCI assays showing that CBF1 interacted with phyA in living plant cells. Scale bar = 1 cm.