EMBO/sd-character-level-ner huggingface dataset:
(G) Heart cross-sections were stained with FITC-WGA (Wheat germ agglutinin) to visualize cell membranes of cardiomyocytes. Scale bar: 20 μm. (H) Respective cell areas measured by Image J software and represented by box plots for each animal (six per genotype). Boxes represent the 25th and the 75th percentile with median represented by the black line in the box. The whiskers depict the minimum and the maximum value. P value <0.05 (mixed model approach) was considered significant.
(K) Insets showing representative γ-Tubulin (green) and Phospho-Vimentin (red) IF of the cortical VZ surface to evaluate the orientation of the cleavage plane of dividing aRGs. Pie charts show the percentage of vertical (green), oblique (yellow) and horizontal (red) division planes of mitotic figures in the E12.5 lateral pallium of animals with different genotypes, as indicated. n ≥ 2 brains per genotype. Data information: Nuclei (blue) were stained with DAPI. Data are represented as means ± SEM. 2-way ANOVA ; *P<0.05, **P<0.01, ***P<0.001). cale bars: 50µm.
(A) oxygen consumption rate (OCR) of mouse brown adipocytes treated with MPC inhibitor CHC (2 mM) or UK5099 (2 µM), n=6-7 biological repeats.
F Plasma levels of cardiac stress biomarkers: brain natriuretic peptide (BNP) (F1) and cardiac troponin I (cTnI) (F2) following isoproterenol treatment in mdx NaCl (n=5), surviving mdx (n=8), mdx/CD38-/- NaCl (n=5) and mdx/CD38-/- (n=8) mice. Data information: in duplicate After normality and variance comparison tests, significance was assessed using F2 Kruskal-Wallis followed by Mann-Whitney tests; F1: ANOVA followed by Student's/ Welch's t-tests; Values are expressed as means ± SEM. Significance: *p<0.05, **p<0.01, ***p<0.001.
Expected FRET changes during co-translational insertion of an N-out membrane protein. The FRET acceptor (Atto655, red star) was placed at the N-terminus of the nascent chain, the FRET donor (Atto488, yellow star) at one of two positions in SecY (see panel B).
(F) Table indicating the methylation-related genes (PRC2 members and KDM6 demethylase) differentially express between IκBα WT and KO EphB2-high sorted cells (RNA-seq).
(A) Amino acid sequence alignment of Sox4 GSK3 phospho-motif from mouse, rat, human and chimp. Mouse serine 316 (S316) (highlighted in green) and S315 (highlighted in yellow) predicted by PhosphoSitePlus to be phosphorylated. For S316 mutant, serine 316 mutated to alanine and for S316all mutant all highlighted serines mutated to alanine. Red highlight indicates proline residue following mutated serine.
E. Enriched pathways of up- and downregulated genes across the trisomic ES cell lines identified by KEGG pathway analysis.
Transcriptome-wide changes in the cells subjected to CoCl2 treatment, HIF1A-AS2 or ADAR1 knockdown were profiled by RNA-Sequencing. For genes that undergo up-regulation upon CoCl2 treatment (n = 505), overall expression profiles of the different cell groups are represented by the heatmap. The expression values (represented by normalized read counts) were displayed in shades of red or blue (linear scale) relative to the means of all corresponding values within individual experimental groups. Clusters of genes (based on unsupervised hierarchical clustering) are indicated and denoted by their experimental types/conditions.
(A) Rh1>lacZ+H2B-RFP exhibited nuclearRFP expression in the R1-6 photoreceptors (red). (B) Rh1>lacZ+Shits1 maintained at 29°C for 14 days resulted in lamina vacuolization. (C) Pan-Rh7>H2B-RFP exhibited expression in R7 (arrow) and R8 (arrowhead) (red). (D) Pan-Rh7>Shits1 incubated at 29°C for 14 days did not exhibit lamina degeneration. (E) Lamina monopolar (L) neurons (red) were selectively labeled by the Ln-GAL4 driven H2B-RFP with repo-GAL80. (F) Ln>Shits1, repoGAL80 shifted to 29°C for 14 days did not exhibit lamina degeneration. (G) R1-6 photoreceptors were killed in Rh1ts>lacZ+Hid shifted to 29°C for 14 days. Rh1ts indicates tubGAL80ts; Rh1-GAL4. Degeneration was induced in the lamina in addition to the retina. (H) rdgC306/+ mutant exposed to constant light for 14 days exhibited degeneration in the retina, as well as the lamina. DAPI: nuclei (white in A-H). (I, K) Rh1>lacZ+Shits1 at 29°C for 4 days exhibited vacuoles in the electron dense cytoplasm of epithelialglia or near the glianucleus. Arrow: vacuole with internal debris. Arrowhead: large vacuole. (J) Lamina cartridge of Rh1>lacZ+H2B-RFP. N indicates glialnuclei. (L) The percentage of the vacuole area in the lamina at 29°C for 14 days was examined. All P-values were calculated using one-way ANOVA with Tukey's post-test. Scale bar: 20 μm.
Upon binding of IL-17 to IL-17RA and IL-17RC, 6 molecules of ACT1 are recruited, creating docking site for trimeric TRAF6. TRAF6-created K63-polyubiquitin linkages promote activation of signaling pathways, but also trigger recruitment of TBK1 and IKKε kinases to IL-17RSC. Both kinases then phosphorylate ACT1 in disordered region of the protein. This leads to a spatial separation of TRAF6-binding sites present on ACT1, decreased avidity for TRAF6 and its release from IL-17RSC, ultimately leading to inhibition of signaling. In addition, TBK1/IKKε enable recruitment of TRAF2 in kinase-activity independent manner to promote stabilization of mRNA of target cytokines.
(c) HeLa cells were treated with H2O or 10 μM ROCK1 inhibitor, Y27632, for 8 h. Cells were then cultured in high glucose (0 h) or starved for in HBSS nutrient-free media for 6 h. One hour before collection, cells were incubated in dimethylsulphoxide (control) or 0.1 μM bafilomycin-A1. Whole cell lysates were resolved by SDS-PAGE and were analysed by western blotting with indicated antibodies.
(G) MEFs were infected with control or PAQR3-expressing lentivirus. Then a quantitative immunodepletion assay was performed with increasing amounts of the indicated antibodies. Supernatants of MEF lysates after immunodepletion (Post-IP) were examined to determine the level of VPS34 complex proteins.
(D) Model for ALYREF promoting histone mRNA 3'-end processing and nuclear export.
Representative confocal images of the pGRF2::GRF2:GFP translational fusion in WT or hyl1 backgrounds.
(A) Schematic of the ANKRD26 domain identified as PIDD1 interactor by yeast-two-hybrid screen. PMID = PIDD1 Minimal Interaction Domain; CCDC144C-like = Coiled-Coil Domain similar to CCDC144C; DUF: Domain of Unknown Function.
E Goss morphology of E10.5 ATRA-treated and untreated mice embryos. The ATRA-treated embryo exhibits an open neural tube (indicated by white arrows) compared to littermate controls. Scale bar: 500 μm.
A. Multiple alignment of a predicted Apc1-loop500 domain of vertebrate APC/Cs. The sequences corresponding to residues 515-584 in Xenopus tropicalis Apc1 are shown. A putative B56 binding region is coloured in green. Hs; Homo sapiens human, Pt; Pan troglodytes chimpanzee, Mm; Mus musculus mouse, Gg; Gallus gallus chicken, Xt; Xenopus tropicalis frog.
(B) Identification of critical amino acids for GFP-LC3 activation and colocalization with the endocytosed chimera. JAR cells were transfected with the indicated CD16:7-263-281 mutants and GFP-LC3A, aggregated and stained for the endocytosed chimera (red). Preparations were scored by blindly counting the number of red vesicles (chimera) and green vesicles (GFP-LC3A) per cell, as well as the number of red vesicles colocalizing with green ones. The percentage of green vesicles colocalizing with red ones was close to 100% for all mutants, that is, virtually no GFP-LC3A vesicles were unrelated to endocytosed chimera (not shown). At least 50 cells were scored per experimental point. The experiment was repeated three times. The graph shows the number of GFP-LC3A vesicles per cell expressed as the percentage of the value obtained for the wild−type chimera (left axis), and the percentage of chimera vesicles labelled with GFP-LC3A (right axis). Data are expressed as means ±s.d. of the triplicates. Asterisks indicate significant differences with respect to wild−type values (paired Student's t−test; P<0.01).
Left: Representative images of cells were transfected with super-folder GFP (sfGFP) treated with 250ng/mL Tunicamycin (Tm), 50nM Thapsigargin (Tg) and 250ng/mL Brefeldin-A (BFA) for 24 hours. Right: Quantification of the microscopy images of cells expressing ER-targeted sfGFP and the cytosolically localized mCherry. Data values are the mean ± SD of technical replicates (n=10) from 3 independent experiments (****p<0.0001). One-way ANOVA was applied for the statistical analysis through the GraphPad Prism 9 software. Scale bar 15μm.
H1299+shBRCA2DOX cells were grown for 4 days in the presence or absence of DOX and subsequently treated with 10 μM pyridostatin (PDS) for 1, 2 or 3 days. Whole-cell extracts were immunoblotted as indicated. KAP1 and IRF3 phosphorylation sites are shown in red. SMC1 and GAPDH were used as loading controls.
MED1 signals on MED4 puncta normalized to nuclear MED1 signals. MED1 signal intensity on each MED4 punctum was individually plotted.
(A) Drug administration protocol for intravital microscopy (IVM) experiments. Male, 10 week old C57BL/6 mice (n=3/group) were pretreated with vehicle or mixed inhibitor (Daminiozed+GSKJ4, 50 mg/kg each) at 16 hrs and 1 hr prior to TNF-α treatment. Inflammation was induced by an intraperitoneal injection of TNF-α (5 μg/mouse) and IVM was performed 4 hrs later.
D. Immunofluorescence of collagen matrix sections co-stained for MMP10 and DAPI. Scale bar = 20 µm.
C Immunoblot for exon 19 containing ApoER2 (top) and total ApoER2 (bottom). β-actin was used as loading control.D Quantification of ApoER2 protein isoforms shown in C (mean s.e.m., student's t-test).
Semi-quantitative RT-PCR validation of the purity of HSATIII lncRNAs. Purified RNAs at each step in A were validated by semi-quantitative RT-PCR. ChIRP using control oligonucleotide was performed as negative control (lane 3). U1 snRNA was examined as an nSB-localized non-HSATIII RNA. RT(-) samples (lanes 6-10) were used as negative controls for PCR without reverse transcription. Input: 10%.
B-D Time-dose-response plots indicating changes in RPPA measurements for pERK(Thr202/Tyr204) versus pAKT(Ser473) for two selected cell lines (C32 and WM115) after exposure to PLX4720. Mean values of four biological replicates are shown. Protein levels represent log2 fold change of each signal (at a specific dose and time) relative to a DMSO-treated control.
Experimental design for ES to EpiL cell differentiation of Nanogtg cells and two independent clones (Nanogtg;dTal1del#1 and Nanogtg;dTal1del#2) where the binding site for NANOG distal to Tal1 has been deleted (left). On the right, relative expression of Tal1 determined by RT-qPCR for each ES cell line (ESC; n=9 for all three lines) and EpiL cells without (EpiLC; Nanogtg and Nanogtg;dTal1del#1, n=8; Nanogtg;dTal1del#2, n=6) or with dox treatment (EpiLC +dox; n=9 for all three lines). The genotype of the cell lines is indicated below. Values were normalized to Nanogtg ESC. *P < 0.05, **P < 0.01, ns = not significant; ANOVA with Fisher post-test. Horizontal line represents mean values and error bars standard error of the mean (SEM).
(F) TGFβ Luciferase reporter assay of control or fibronectin silenced MCF10A-pIND20-HPN pL6-TGFβ1 (SRE) TGFβ1 reporter cells, with (DOX+) and without (DOX-) hepsin overexpression. (N=6 biological repeats; Y-axis shows fold change in Relative Light Units (RLU)).
Protein degradation in indicated yeast strains monitored by pulse-chase experiments for FLAG-Sbh2 Values for each time point are reported as means ± standard deviation n = 3 for FLAG-Sbh2
Gene Ontology (GO) analysis of genes harboring METTL14 arginine methylation-dependent m6A sites. Statistical analysis was performed using Hypergeometric test. The p-value for the enrichment of each biological process (GO term) is shown.
(i) Quantification of three independent experiments in triplicate. *P=0.026; other results non-significant by 2-tailed Student's t-test.
(B) Relative BE as a function of stimulus location, referring to the apical-most μLED evoking a response. The black line indicates the tonotopic axis as expected based on literature values, dashed lines indicate the regression line of individual (blue; correlation coefficient r = 0.33, p = 0.00066) and blockwise (purple; correlation coefficient r = 0.58, p = 1.96*10-7) oCI stimulation. Black markers indicate the data shown in panel A. Negative values can appear if the STC in response to a more basal emitter as compared to the apical-most emitter have a more dorsal BE.
F) Predicted contribution of microglial expression of each of the top18 genes to the observed bulk RNA-seq expression data, based on linear regression (see Materials & Methods). For 16/18 genes the microglial expression contributes significantly and 67% or more to the observed expression from the bulk RNA-seq. ***= Benjamini-Yuketieli-adjusted p-value (padj) <0.001; **= padj<0.01; *= padj<0.05.
(F, G) Impact of autophagy‐relevant proteins and of the TAK1‐IKK signalling axis on GFP-LC3 aggregation induced by the depletion of TAB2 or TAB3. HeLa cells stably expressing GFP-LC3 were transfected with siUNR or with siRNAs targeting the indicated proteins, alone or in combination, and 48 h later GFP-LC3VAC cells were quantified (mean values±s.d., n=4; *P0.01 versus siUNR‐transfected cells).
(A) Yeast two-hybrid analysis identified that Su(H) is the only Notch signaling key component that interacts with HP1c, while lamin mated with T-antigen was used as negative control and p53 mated with T-antigen as positive control. The interactions between HP1c and Su(H) were confirmed in both orientations. (BD: binding domain, AD: activation domain, QDO/X/A: Quadruple dropout medium: SD/-Ade/-His/-Leu/-Trp supplemented with X-a-Gal and Aureobasidin A).
E - HeLa cells were transfected with control siRNA or two siRNAs against HIF-1α. Two days later, cells were infected with C. trachomatis L2 (MOI=1) for 48 h. The indicated transcripts were measured by real-time RT-PCR and normalized to actin transcripts. The data are presented as relative mRNA levels compared to uninfected cells and shown as the mean ± SD. Each experiment was performed in duplicate and repeated three times. P-values of Student's ratio-paired t-test are indicated when <0.05.
(A-E) iPOND assays in Hela cells. Experiment schematic (top) and resulting immunoblots (bottom) are shown in (A, B, D) and quantifications are shown in (C, E) with antibodies used for immunoblots indicated throughout.B, C MMS22L dynamics at stalled replication forks. Quantification shows average relative abundance of indicated proteins detected in immunoblots, n = 3 except of time-point 5 h, n = 1; error bars, SEM.
qPCR quantification of retinal marker expression in PAX6D KO cells treated with control shRNA lentivirus and WNT8B shRNA lentivirus (n=3 biological replicates for each group).
(a-c) Slices through defocus cryo-tomograms of the endpiece in pig (a), horse (b), and mouse (c) sperm. Insets show digital zooms (black boxes) and subtomogram averages (white boxes) of microtubule tips. Note the presence of a plug (arrowhead) extending into the lumen.
(B) pho8Δ60pho13Δatg1Δ cells expressing wild‐type (wt), kinase‐dead (kd), Atg1‐VE (VE) or ‐EYE (EYE) mutants or an empty plasmid were grown to mid log phase and starved for 4 h in SD‐N medium. Pho8Δ60‐specific alkaline phosphatase (ALP) activity (nmol/min/mg) was measured in three independent experiments as described in 'Materials and methods', and plotted as relative ALP activity with standard deviation (s.d.) compared to the wild‐type controls.
(c) ATG4B depletion does not increase autophagic flux in serum-fed cells. Immunoblots for indicated proteins in lysates from scr or siATG4B NIH/3T3 cells in presence/absence of lysosomal inhibitors, ammonium chloride and leupeptin (Inh) for 2 h. Scale bars, 1 μm. Bars represent mean±s.e.m., n=3.
Representative quantitative analysis showing that overexpression of Snapin, but not Snapin-L99K, a Snapin
E 3D images of OHCnuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 µM PFT-α, 10 µM CDDP or 10 µM CDDP in combination with 100 µM PFT-α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar=5 µm.F Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions (n=50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One-way ANOVA test followed by post hoc Tukey's test (***P ≤ 0.0007, CDDPvs. control).
A At 22 days after stratification (DAS), leaf series of the LOF lines were made and the rosette area was calculated as the sum of the area of all individual leaves (n = 10 plants). The rosette area is presented relative to the corresponding wild type.
A. Percentage of tumor-infiltrating T cells, Treg and NK cells were identified by flow cytometry from CT26 tumors as indicated. Each spot represents one mouse. * P < 0.05; * * P < 0.01 by Student's t-tests.
(b-d) Microarray analysis. 16HBE cells were stably infected with pQCXIP (control) or pQCXIP expressing DN HRas. Control cells were treated with DMSO, GSK1120212 (500nM), or SCH772984 (1µM) for 4 days. RNA was isolated and analysed using an Illumina gene array; n=3 independent samples were prepared for each condition. (b) Venn diagram representing genes downregulated by >1.6-fold versus control, with an unadjusted p-value <0.05. (c) Relative expression levels of 33 genes downregulated by DN HRas, MEK and ERK inhibition, expressed as % of DMSO control. (d) Relative expression levels of EMP1. Error bars denote mean ± SEM, dots indicate individual data points. **, p < 0.002 (DN Ras = 0.0019, ERKi = 0.0016); ****, p <0.0001.
(B) Principle of inducible peroxisome-trafficking assay. COS-7 cells were transfected with truncated motor constructs of kinesins fused with FRB and GFP (summarized in (A)) and peroxisomes labeled with PEX-mRFP-FKBP. Upon addition of rapalog, kinesin motors are recruited to peroxisomes, and kinesin transporting features can be measured as peroxisome displacement.
H) Representative image of a HeLa nucleus after FISH with Chr17 centromeric probe (green). The distance of the FISH signals from the nucleus periphery was calculated as follows: the distance from the centre of the nucleus to the periphery (d1) and the distance from the centre of the nucleus to the FISH signal (d2) were measured. (scale bar 5 μm).
(g) Detection of mitochondrial O2·− using the mitochondrial-specific probe MitoSox in MEF incubated in the absence (−) or in the presence (+) of the plasma membrane permeable GSH-EE, or by expressing mitochondrial-tagged forms of glutamate-cysteine ligase, (+mitoGCL; empty vector, pIRES2-EGFP, denoted as −) or catalase (+ mitoCAT; empty vector denoted as −), shows effective mitochondrial ROS removal.
(H) COCO injections (P1) do not result in apoptosis in P5 retinas. Scale bar, 40 μm. (I) Quantification of apoptotic cells in control and COCO-injected mice (n=3).
B Bethesda assay performed on plasma samples mice injected with AAV-CodopV3; on the plasma of animals injected with AAV-N6 intein n=3 and the plasma of animals injected with AAV-CodopN6 intein n=2; plasma of a wild-type animal was used as a control. The dotted line indicates the threshold above which anti F8-antibodies are considered inhibitors.
A Expression of RBM47 was induced by DENV infection in 293T, HFF, HUVEC, and THP-1 cells. Cells were infected with DENV-2 at an MOI of 1 for 12 or 24 h. The expression of RBM47 mRNA (12 and 24 h post infection, hpi.) and protein (24 hpi.) were compared between virus-infected and non-infected cells (PBS). The PCR results are represented as the means ± SD of n = 3 biological replicates. Data information: Data are representative of n = 3 independent experiments. NS, non-significant; * P ≤ 0.05, **P ≤ 0.01, and ***P ≤ 0.001 (Student's t-test).
(B) Immunoblot analysis of PPARγ in nuclear fraction. On the right, quantification of PPARγ normalized to p84 is shown. Average of donor mice [19] and 4 experimental replicates per time-point, per group of recipient mice. (Two-way ANOVA, post hoc Holm-Sidak comparisons *p<0.05).
(F) Extracted proteins from Huh7 cells expressing the recombinant proteins as indicated were mixed with anti-GFP-coupled magnetic beads and immunoblotted with anti-mCherry and anti-GFP antibodies. Co-immunoprecipitation revealed a specific interaction of NCOA4-mCherry with FTMT-GFP or FTMTD57A-GFP, which has a substitution of alanine (A) for aspartic acid (D) at position 57 in the FTMT mitochondrial leader sequence (lanes 1 and 3).
of hM3D (Gq) DREADD receptors expressed within the MPOA by CNO rescues main aspects of maternal behavior in Shank2−/− mice. in the MPOA by CNO rescues main aspects of maternal behavior inShank2−/− mice.
E Whole cell respiration following treatment for 5 days with dsRNA against the genes indicated.
representative FACS histograms and bar graphs show total PPARγ protein levels relative to WT controls (J) Data shown in bar graphs are mean fluorescence intensity of indicated protein expression in PKCδ cKO HSPCs subsets relative to WT controls (n=4-6 mice per genotype per target). Data information: The statistical significance of difference was assessed using Two-tailed Student's unpaired t-test analysis for comparison of control and PKCδ cKO HSPCs. All data are presented as mean± SEM., *p<0.05, **p<0.001.
(c) Levels of PERK protein were assessed by western blotting in HeLa cells treated with 10 μM purmorphamine for 24 h. Actin was used as a protein loading control.
E: Images of ookinetes of parasite lines NTH∆PP showing dispersed NTH∆PP::GFP fluorescence; LAP3/mCherry showing focal LAP3::mCherry fluorescence in crystalloids; Cross (carrying modified alleles encoding NTH∆PP::GFP and LAP3::mCherry), showing dispersed LAP3::mCherry fluorescence. Arrow marks pigment cluster associated with crystalloids. Scale bar = 5μm.
(B) WI-26 fibroblasts were transfected with the indicated HA-tagged enzymes were lysed, immunoprecipitated with anti-HA antibody or control IgG and were analysed by western blotting for interaction by immunoblotting with the indicated antibodies.
(I) Patient samples from METABRIC dataset classified as TNBCs were assigned to the groups "PTEN-low" when falling in the lower quartile for PTEN expression, "PTEN-mut" when harbouring a non-synonymous mutation on PTEN gene, "PTEN-WT" in all other cases. Comparison of the expression of EGFR between the PTEN low or mut and the PTEN-WT groups. Data presented in a box and whisker plot with the central band indicating the median, the upper and lower extremes of the box or hinge being the third and first quartiles respectively and the whiskers extending to the most extreme data values Mean ± SD. P value calculated by unpaired t-test.
(E MDA-MB-468 were treated with serial dilutions of gefitinib (E) in the presence of vehicle, AZD8186 (0.25 μM), GDC0941 (0.25 μM) or MK2206 (0.45 μM), as indicated. Cell viability was measured after 4 days and normalised within each of the PI3K pathway inhibitor-treated condition to the viability in the absence of gefitinib Average ± SD of triplicates and representative of two independent experiments.
B Recombinant expression and purification of Nbs using immobilized metal affinity chromatography (IMAC) and size exclusion chromatography (SEC). Coomassie staining of 2 µg of purified Nbs is shown.
I. PRMT6 is necessary for AMPK-induced SIRT7 hypomethylation. Flag-tagged SIRT7 was stably expressed in scramble control MEF cells or cells expressing two independent shRNAs targeting Prmt6 (#1 and #2). Cells were cultured with or without glucose for 12 hrs. R388 methylation of immunopurified SIRT7 was determined by western blot
(E) Histology of the hepatocellular carcinoma using H&E staining in STAM mice fed a high-fat diet. The boxed area is enlarged on the right (x40 in left panel and x400 in right panel). The tumor has increased cell density, an increased ratio of nucleus to cytoplasm, and thickened trabeculae Scale bar: 100 μm.