EMBO/sd-character-level-ner huggingface dataset:
e, HeLa cells treated with the indicated siRNAs were infected with S. Typhimurium and stained for NDP52 at the indicated time points. Fluorescent bacteria were counted by microscopy at the indicated time points. Graphs, representing at least two independent repeats, show mean and s.d. of duplicate coverslips for which >200 bacteria were counted. *P  0.05, Student's t-test. Scale bar, 10 µm.
A, B NB-3-Fc-coated bead aggregation assay (A). BSA-coated beads as a negative control (B).
D. Distribution of DNase-seq reads around the transcription start sites (TSS) of the mESC-specific SATS (left) and common (right) isoforms in three mESC lines (Ese14, Zhbtc4 and Escj7S) and three somatic cell lines (Nih3t3, Mel and fibroblast).
F-I. Colocalization of SKIP and HOPS complex with TBC1D15 as a function of HOPS subunit over-expression. F/H. Mander's overlap between F. SKIP or H. eVPS18 and endogenous TBC1D15, n≥5 images (2≥ cells per image) analysed per condition from 2 independent experiments, significance: one-way ANOVA test (relative to EV), ** p<0.01, *** p<0.001, ns: not significant. G/I. Mander's overlap between G. SKIP or I. eVPS11 and endogenous TBC1D15 as a function VPS18 overabundance, with or without FIS1 depletion (siFIS1), n≥3 images (2≥ cells per image) analysed per condition from 2 or more independent experiments.
A. WISH of dll4(upper) and notch1b(lower) in control injected embryos (left), evi1 morphants (middle) and evi1 morphant transgenic Tg(Hsp70l:vegfaa;myl7:eGFP) embryos at 32 hpf after heat-shock induction at 20 hpf (right).
F Quantification of protein reduction and western blot of lysates from a representative experiment of edited cells. Target protein levels from all biological replicates were normalized to MATRIN3. Each point represents a trial (n = 4). Bars indicate mean ± SD. Significance was determined compared to NT using two-tailed Student's t-tests. Data information: *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001.
Mice survival (i) are comparable between three treatments: DSS+DT (N=12), only DSS (N=8) or only DT (N=3). Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05, ** P≤0.01.
Quantification of fluorescence intensity of β -TUBULIN positive spindle fibers. Quantification of mean fluorescence intensity of β -TUBULIN positive spindle.
C Western blot analysis of 1D-BNGE of mitoplasts extracted from the indicated cell lines. Fully assembled COX migrating at 200 kDa was immunovisualized with antibodies recognizing MT-CO1 and MT-CO2. The presence of the assembly intermediates 'MITRAC' and 'S3' was also detected (arrows)
C Changes (log2 fold) in transcript expression (left) of select immune-related genes in U2OS mock or MLLT6 knockout cells treated with or without IFN-γ and total protein levels measured by immunoblotting (right). Numbers indicate band intensities normalized to GAPDH.
a, Phase partitioning of Apg8. Wild-type and Δapg4Δapg8 cells producing Apg8FG and Δapg7 cells were subjected to phase partitioning (see Methods).
Although PPM1H phosphatase is likely to be dimeric in cells, a 1:1 complex is shown for simplicity. The switch 2 helix is red and the phosphate site is yellow. The flap domain (305-414) encodes the primary specificity for phosphorylated Rabs while the anchor (33-79) contributes to folding of the enzyme. The β-motif (green, residues 480-496) is also indicated. The conserved loop motif (386-396) with a central Leu392 residue may couple substrate binding to catalysis.
J Ductal hyperplasia as quantified by the surface area covered by CK19 positive ducts in (D) is reduced in Sox9-null mice compared to control following BDL. All mice were treated with tamoxifen (Tam) which did not induce ectopic expression of SOX9 in non-fibrotic livers (Figure 2A, E and Appendix Figure S3). All experiments are n≥5 as indicated. Two-tailed unpaired t-test was used for statistical analysis. Data in bar charts show means ± s.e.m. P values indicated.
(A) Twelve weeks-old wild-type and cardiac specific Atg7 knockout (Atg7cKO) mice were injected with corn oil (vehicle control, Ctr) or 3,4-DC 24 h before surgery and subjected to 3 h prolonged ischemia. Representative images of left ventricular (LV) myocardial sections after alcian blue and triphenyltetrazolium chloride (TTC) staining are depicted. Scale bar equals 1 mm.
(A) Immunofluorescence images of RPE1 cells cultured in normal serum medium, and stained with antibodies against ENKD1 and Centrin and DAPI. Scale bar, 1 µm.
(h) Immunohistochemical staining of ATF4 in HCC and adjacent non-neoplastic areas from patients. Tumor tissues showed a higher expression of ATF4. Scale bar, 100μm. (i) Quantification of ATF4-positive cells in tumor and non-tumor samples showed that HCC tumors present higher ATF4 levels. Data are shown as mean ± standard deviation (SD). Statistical significance was calculated using unpaired t-test. (j) Representative images of immuno-histochemical staining of ATF4 and SLC7A11 proteins in HCC samples from patients. Scale bars, 50μm.
(d) siATG4B cells display increased nuclear LC3-II. Images for LC3-II (red) in scr or siATG4B NIH/3T3 cells in presence/absence of EGF (10 min). Scale bar, 5 μm. Bars represent mean±s.e.m. ***P0.001 compared with scr; Student's t-test, 60 cells from n=2.
(a) Confocal immunofluorescence microscopy images of HeLa cells transfected with Rab34-dsRED-Mito, FLCN-GFP and HA-FNIP2. White arrows highlight FLCN-GFP/HA-FNIP2 co-localisation distinct from Rab34-mitochondria/FLCN-GFP localisation. Scale bar = 10μm.
H Summary data for CHLA15/CHLA20 and SKNBE1/SKNBE2C showing relative cytochrome c release when pre-incubated with GW4869 to inhibit ceramide generation, compared with untreated cells. Data information: All data points from two (CHLA15) or three (SKNBE1) biological replicates are depicted in H. Statistical analyses were performed using an unpaired two-sided Student's t-test, with significance p<0.05 (trend, p<0.10).
(B) Mitochondrial fragmentation within the field of view shown in (A) results in increased mitochondrial numbers.
(d) Individual metabolites in ALA/LA and AA pathways significantly altered in both MSUS and PLMS. Numbers represent fold change according to a heat scale (right).
D. hPBT cells were transfected with LC3-cherry and treated as indicated. 30min after AICD induction cells were fixed and stained with TUNEL and DAPI. Representative reconstructions of confocal z-stacks of the LC3-Cherry fluorescence and single stacks for DAPI are shown. Scale bar, 5μm.E. Statistical analysis of the autophagy in cells treated as in (D) is shown. Data represent mean ± SE of three independent experiments (n = 20 cells per condition in each experiment).
(E) Histogram displaying the SILAC ratios (log2) of stress-induced phosphorylation sites that are induced in setup cdc55Δ in two separate experiments. The blue histogram shows the distribution of fold-changes when IGO1 and IGO2 are deleted and cells are exposed to hyperosmotic stress (setup SR igo1∆igo2∆). The orange histogram shows the distribution of fold-changes after deletion of CDC55 and upon exposure to hyperosmotic stress (setup SR cdc55∆). The same set of sites was compared between the two experiments.
ANAC032expression is induced by pathogen-derived signals. ANAC032 represses MYC2and PDF1.2A, but stimulates JAZ repressors thereby reducing JA/COR signalling. COR-mediated stomatal-reopening and thus bacterial re-entry into host cells is negatively affected by ANAC032 possibly through the MYC2-ANAC019/55/72 transcriptional cascade. Simultaneously, ANAC032 activates PR1gene expression and SA signalling by direct transcriptional repression of NIMIN1. Lines ending in arrows and Ts indicate positive and negative interactions, respectively.
D KCC4 and SIRT7 protein levels in kidneys from control mice or mice with metabolic acidosis. Values are the mean ± SEM.
Quantification by micro-CT of total tumor volume per mouse in (D) CB-839-, or vehicle-treated KP mice after infection with control sgTom or sgNf1.3 at 8, 12, 16, and 20 weeks post-infection. Vehicle-treated KP mice are the same control group for (D)
(a) WT and Pgam5 KO MEFs evaluated by TEM. The black arrows indicate mitochondria; (b) TEM analysis after 12 h CCCP treatment; black arrowheads indicate DMS. Inset shows a DMS with an encapsulated mitochondrion. The black arrows indicate mitochondria. Scale bar=0.5 micron;
PSAT1 expression was assessed semi-quantitatively using a 0-3 grade scale ("0": no staining; "1": weak; "2": moderate; "3": strong) on human breast cancer sections using immunohistochemistry. Representative images according to the PSAT1 staining grade are shown. Scale bar: 50 ­μm.
(B) HCT-116 ATG9A-HA KI cells with overexpressed GFP only, VenusC-ATG101-3X FLAG only, VenusN-ATG13-Myc only, VenusN-ATG13 Δ2AA only or both Venus N and C halves together were subjected to immunoprecipitation with GFP-trap nano body resin. Immunoblotted for indicated proteins.
Eight-week-old male WT and DOCK5-/- mice were fed a standard diet (SD) or high-fat diet ( HFD) for 3 months. Cumulative body weight.
Example of one experiment representing quantification of noise by aperiodic lengthscale in one CTRL versus one MBSm embryo; bars indicate mean with 95% confidence intervals.
(B) Antibody-uptake assays in parental or knockout FAM21, VARP and VPS29 cells. Cells were stained with an Alexa488 conjugated anti-mouse antibody. Arrowheads point to endosomal tubules. Data information: (B) scale bars represent 20µm
(c) The dark grey circle shows the percentage of proteins identified from all three purifications; the grey circle shows the percentage of proteins identified from two of the three experiments.
(D) Mei4 and Mcp5 proteins are produced in mitotically growing red1Δ cells. Protein extracts of mitotic wild‐type and red1Δ cells expressing Mei4‐HA and Mcp5‐myc were resolved on a polyacrylamide gel and then analysed by western blotting using anti‐HA (top panels) and anti‐myc (bottom panels) antibodies. Cdc2 was monitored as a loading control.
A-G. Statistical analysis of absolute number of total nucleated splenocytes, splenic B- and T-cells, and indicated mature B cell subsets in WT and KO mice. Results represent the data pooled from at least two independent experiments and numbers represent biological replicates for each group (A: (WT) n = 16, (KO) n = 17; B (B-cells): (WT) n = 16, (KO) n = 17; B (T-cells): (WT) n = 8, (KO) n = 9; C-E: (WT) n = 9, (KO) n = 9; F: (WT) n = 6, (KO) n = 6; G: (WT) n = 9, (KO) n = 9).
(N) Western blot analysis with cell lysates of THP-1 control or IRGM knockdown cells, untransfected or transfected with, heat-killed whole CHIKV or CHIKV viral RNA and probed with the indicated antibodies.
F. Representative images show a micronucleus or the main nucleus containing the Y chromosome (red) detected by FISH in no-doxycycline or doxycycline treated cells respectively. Chromosome X is shown in green. Scale bar represents 5 µm.
D, Cell viability as in C, measured 5 days after IR (1-10 Gy, fold vs. vehicle-treated cells, mock). *: t-test, p<0.03.
b, MEFs were generated from day 12.5embryos of Atg16l1 mutant mice, and western blot analysis was used to detect the a and b isoforms of ATG16L1 from whole-cell lysates
(B) Model of the intact monopolin complex. Four copies of Csm1 (blue) and two of Lrs4 (green) form the core 'V'-shaped kinetochore-binding complex (Corbett et al, 2010). Each dimer of Csm1 binds one Mam1 (orange) (Corbett Harrison, 2012), which in turn recruits one copy of Hrr25 (blue/green). Thirty-one residues of Mam1 (192-222) separate the protein's Hrr25-binding and Csm1-binding domains, which when fully extended could reach as far as ~120 Å.
(a) Δ133p53α expression is induced by cycloheximide (CHX). MRC-5 fibroblasts (at population doubling levels (PDLs) 51) were treated with CHX (25 μg ml−1) for indicated time periods and examined in immunoblot for Δ133p53α and full-length p53. β-actin was a loading control for normalization. The relative expression levels of Δ133p53α and full-length p53 are shown below the images.
F, HCT116 cells treated with 10 µM MPA for increasing time were analyzed by Western blots for the indicated proteins. α-tubulin was used as a loading control.
ApoE-/- (-/-) and ApoEYF (YF) mice were subjected to partial ligation of the left carotid artery (LCA) and given a cholesterol-rich diet. The right, non-ligated artery (RCA) was used as a control. 3-nitrotyrosine (3NT, green) levels in the RCA and LCA 2 days after ligation. CD31 (red) was included to label endothelial cells. n=5 mice per group (2-way ANOVA and Bonferroni). Scale bars: 50 µm.
E, Multiplexed activation of Ascl1/Lmx1a/NeuroD1, Ascl1/Lmx1a/Nr4a2 and Ascl1/ Lmx1a/ Nr4a2/Pitx3/FoxA2 in primary astrocytic cells. n=2-3 biological replicates, one representative run is shown, additional data in supplement. Activation levels are depicted as fold change between cells transfected with and without sgRNAs. All levels were normalized to β-Actin. Error bars represent mean ± SD between technical replicates.
Bioinformatic prediction of IGF2R and CD20 cross-reactivity. Cartoon representation of the IGF2R domain 11- CD20 (lime) complex obtained from docking simulations and residues involved in hydrophobic interactions are shown in stick format (b).
Mean decay distance of the second harmonic generation (SHG) signal emitted by human PDAC-associated collagen. Mean decay distance is represented by boxplots showing the second and third quartile of the data with the whiskers indicating the maximum and minimum data points. Outliers are indicated by individual markers. Stage T3 tumors have a higher collagen mean decay distance score compared with Stage T2 tumors (P = 0.02). Lymph node-positive tumors have a higher collagen mean decay distance score vs. lymph node-negative tumors (P = 0.047). Tumors showing vascular invasion have a higher collagen mean decay distance score than non-vascular invasive tumors (P = 0.037).
(E) Double label immunogold transmission electron microscopic images for LC3β (12μnm particles) and p22phox (18 nm particles) showing a p22phox‐positive single membrane cytoplasmic vesicle (D) and a p22phox‐, LC3β‐positive vacuole (E). Bars=200μnm.
A) Representative blood smears of patients with TUBB1 mutations (P1 and P3 homozygous for p.P160L, P4 heterozygous for p.Y106X, and P6 and P7 heterozygous for c.35delG) after May-Grünwald Giemsa staining. Variable platelet size in patients was observed with all three mutations with presence of macroplatelets (arrows)
(E) Electron microcopy images of control and Miro1CKO brains showing the ultrastructure of the mitochondrial compartment. The mitochondrial units in Miro1CKO cells are enlarged and show altered cristae structure at 4 months of age. This process is progressive as mitochondrial structures appear larger and with reduced intramitochondrial complexity at 12 months of age.
(E) U2OS cells stably expressing FLAG-tagged TIP60WT, TIP60S90A or empty vector (vec) were treated with 2 µM SNS-032 (SNS) for 3 hours as indicated. The nucleus was fractionated into nucleoplasm and chromatin. Both fractions were analysed by Western blotting
Flow cytometry of intracellular FOXP3 staining (right) or isotype control (left) in human CD4+CD25-CD45RA+ naïve T cells transduced with control retrovirus (Min) or retrovirus encoding hC/EBPβ and cultured for 2 d under conditions as indicated. Representative experiments are shown in the left panel and pooled data with mean±s.e.m are shown on the right. Histograms are gated for CD4+NGFR+. Statistical analysis was performed using unpaired two-tailed t test. (*p<0.05; ns, not significant)
(a) THPN induces the dissipation of ΔΨm in both time- and dose-dependent manners. The compromised ΔΨm is shifted to the right upon THPN treatment in flow cytometry. '-' represents vehicle treatment only.
(G, H) HeLa cells were infected by PAQR3 knockdown or overexpression lentivirus together with their respective control virus. After GS for 1 h, the cell lysates were harvested for IB.
C. Representative currents of PC2_F604P and PC2_AA mutants in the divalent ion-free bath solution, which contains 100 mM Na+.
A. MCF10A cells expressing shRNA against AMOTL2 were complemented with shRNA-resistant Flag-AMOTL2 WT or the K347/408R mutant. The indicated cells were harvested and analyzed by Western blotting for the indicated proteins.
(A) Volcano plot represents DVL3 transcriptional targets identified by RNA-seq in MDA-MB-468 cells (NTC vs. shB DVL3 and EV vs. DVL3-WT, upper panel), and in MCF7 cells (NTC vs. shB DVL3 and EV vs. DVL3-WT, lower panel). In the upper panel, the green dots represent significant downregulated genes, the red dots represent significant upregulated genes and the orange dots represent DVL3-ChIP hits in MDA-MB-468 cells. In the lower panel, the blue dots represent significant downregulated genes, the red dots represent significant upregulated genes and the orange dots represent DVL3-ChIP hits in MCF7 cells. Gene expression levels were quantified using Fisher's Exact Test Signal Search in the DNASTAR ArrayStar software package.
D. Effects of LINC00115 knockdown on ZEB1, vimentin, and E-cadherin protein expression. Data information: data are representative of three independent experiments. Error bars, ± SD. **,
E) The "top 18" GWAS genes are prioritized by finding the intersection of genes within the APPtg-Blue module (n=4236), AD GWAS genes with p<0.001 in Marioni et al. (Marioni et al, 2018) (n=314) and significantly differentially expressed genes in the age*genotype comparison of APPtg mice (n=798), using the SuperExactTest (Wang et al, 2015).
A-L) Serum starved HUVECs were stimulated with designed scaffolds normalized to 18 nM of F-domains for 15 minutes and analyzed by immunoblotting for pAKT (S473), pERK1/2 (T202/Y204), and pFAK (Y397) phosphorylation. A, E, I) pAKT, B, F, J) pERK1/2, and C, G, K) pFAK phosphorylation levels are quantified and normalized to Icos-cage signaling levels. Appendix Figure S1B shows the detection of two bands expected for pERK1/2. Representative immunoblot gels of cells stimulated with or without scaffolds at 18 nM of F-domain: D) helical bundles, H) trimeric and tetrameric homo-oligomers and tetrahedral nanocages, L) Icosahedral nanocages and trimeric subunit.
(D) Genomic location of the top matches (red rectangles) of the mouse c-Maf binding profile (shown at the top) and of the MARE sequence identified by (Ho et al, 1996). Motif search was performed within 2 types of regions (purple rectangles): 1) The promoters of IL-4, IL-5 and IL-13, and 2) within open chromatin regions identified in 2 replicates of lung ILC2s or lung Th2 cells (dark blue tracks). The ATAC sequencing data (shown as bigwig coverage tracks) was retrieved from GEO (GSE77695). For each match of the c-Maf binding motif, numbers in parentheses indicate the log-likelihood ratio score and the raw p-value calculated by the FIMO tool. The transcripts of each gene are shown at the bottom of each panel. Mouse genome = mm9 and Integrative Genomics Viewer = v.2.8.0
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. Human pan T cell RNA was isolated and cell culture supernatant was sampled. D mRNA expression of CD8+ cytokines IFNγ, PRF1, TNFα, GZMB and CTLA4 in stimulated human T cells relative to internal controls, n=15/14/10/14/9 biological replicates. Data information: Data depicted as mean ± SEM (protein data) and box plots with median, twenty-fifth and seventy-fifth percentiles and range (all other). Dots indicating individual values. *p<0.05, **p<0.01, ***p<0.001, paired t-test/ Wilcoxon matched-pairs signed rank test, as appropriate.
cfu quantificatio of intracellular Shigella in HeLa cells pre-treated wit anysomycin in the absence or presence of the p38 inhibitor SB203580, and corresponding controls
D The locomotor activity of the miR-200b/a KD mice was similar to that of the NC mice (NC: n=13 mice, miR-200b/a knockdown: n=15 mice; data represent the mean±SEM; p=0.5030; Student's t-test).
GUS staining of 4-d-old homozygous CBF1p:GUS transgenic seedlings grown at 22°C in D or continuous W, R, FR, and B light. Scale bar = 1 mm.
K HEK-293T cells were transfected with the indicated plasmids and then treated with MG132 for 10 h. Cell lysates were immunoprecipitated using anti-Flag antibody and then subjected to immunoblotting.
(H, I) Purified ACTR2 or VASP was phosphorylated in vitro by NIK or PKA and subsequently used in a phosphatase assay with His-PTENε or without purified PTENε protein as a control, followed by immunoblotting with antibodies against p-ACTR2 (Thr237 and Thr238) and p-VASP (Ser157). Purified proteins (PTENε, PKA, NIK, ACTR, and VASP) were detected by anti-His antibody (ZSGB-BIO, TA-02).
C. Average amplitude of mEPSCs (pA) for both control (white bars) and naspm treated (black bars) neurons under each of the conditions, TTX, TTX + DHPG, and TTX + DHPG + 2APB/dantrolene. TTX, n = 26; TTX + naspm, n = 17; TTX + DHPG, n = 18; TTX + DHPG + naspm, n = 23; TTX + DHPG + 2APB/dan, n = 32; TTX + DHPG + 2APB/dan + naspm, n = 36, p < 0.005, ANOVA. D. Average frequency of mEPSC (Hz) for both control (white bars) and naspm treated (black bars) neurons under each of the conditions, TTX, TTX + DHPG, and TTX + DHPG + 2APB/dantrolene. TTX, n = 26; TTX + naspm, n = 12; TTX + DHPG, n = 18; TTX + DHPG + naspm, n = 23; TTX + DHPG + 2APB/dan, n = 32; TTX + DHPG + 2APB/dan + naspm, n = 36, p < 0.0001, ANOVA.
F) Bar graph comparing average peroxisomal area of Control, GFPMiro1 and GFPMiro2 overexpressing WT MEFs (n=60 cells per condition over three independent experiments). Data information: Calculation of statistical significance in F) was a one-way ANOVA with Newman-Keuls post-hoc. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM. Scale bar is 10 μm. Scale bar in zooms is 5 μm.
J, Total proteins were extracted from the hindlimb muscle tissue of NoVWT-infected BALB/c suckling mice to measure the viral coat protein (CP) and B2 protein by Western blotting. Staining of β-actin was used as a loading control.
(B) Complexome profiles of the cI assembly factor NDUFAF2 in WT (blue) and ∆4-CYB (red) mitochondria The represented values are the mean ± SEM of the two reciprocal labeling experiments.
(B) Western Blotting of SKOV3-Empty "E" and SKOV3-OPCML "O" cells pre incubated with either no drug (DMSO only control), 1.09 μM R428, or 2.84 μM R428 for an hour and stimulated with Gas6 for the indicated times. GAPDH was used as loading control
(D) ChIP assays with -MSK1 and -ERK2. Precipitated DNA was analysed by PCR for the presence of sequences corresponding to the BCAS1 and KRT23 genes. * P-value < 0.05.
B) Western blot analysis of FUS levels under control knockdown (lanes 1, 4, 7), FUS knockdown (FUS KD; lanes 2, 5, 8), and FUS rescue (lanes 3, 6, 9). HeLa cell extracts were subjected to SDS-PAGE and western blotting with anti-FUS antibodies (green) and anti-FLAG (red, upper part). The yellow signal in the upper part is due to the overlay of the red and the green channels. Tyrosine tubulin was detected as loading control (red, lower part).
Immunohistochemistrystaining for TBL1 in paraffin-embedded tissue sections of wild-type or p48+/Cre; Kras+/LSL-G12Dmice. 1, 2: healthy tissue with acini, islet of Langerhans, and duct (zoom-in in panel 2) showing occasional weak nuclearstaining. 3, 4: PanIN-1 lesions with nuclearstaining. 5, 6: PanIN-2 lesions with nuclearstaining. 7, 8: PanIN-3 lesion with nuclearstaining. 9-12: invasive pancreatic ductal adenocarcinoma cells with nuclear and occasional faint cytoplasmicstaining. Scale bars: 100 μm. Images are representative of 32 wild-type and 29 p48+/Cre; Kras+/LSL-G12Dmice.