EMBO/sd-character-level-ner huggingface dataset:
(A) Clusters of genes, whose expression changes towards the hepatocyte fate, upon removal of R-spondin 1 and noggin from the organoid culture media (Table EV5). The number of genes and the names of selected genes in each cluster are indicated. Gene expression levels (log2 scale) are shown for non-differentiated (N) and differentiated (D) gallbladder-derived organoids (GO), gallbladder tissue (GT) and liver tissue (LT). Upreg, upregulated; Downreg, downregulated.
C Knockdown of dhhc2 expression. Upper panel shows the promoter swap strategy applied in TTS strain, generating the dhhc2kd mutant with endogenous dhhc2 promoter replaced with clag promoter. Western blot confirming decreased expression of DHHC2 in dhhc2kd zygotes. Three replicates performed.
A-C Exponentially growing cell cultures were arrested in G1 with α-factor (αf) and released in YEPD supplemented with CPT (50 μM) (B) Quantitative analysis of Rad53 phosphorylation was performed by calculating the ratio of band intensities for slowly-migrating bands to the total amount of protein. Plotted values are the mean values with error bars denoting SD (n = 3). Statistical analysis: Student"s t-test.; ns, not significant; **, P< 0.01; ***, P< 0.001; ****, P< 0.0001
(G) Quantification of the band intensities of (D, E and F). The intensities of the phosphorylation bands were calculated using Image J software. The individual data points were shown (n=2 biological replicates).
(d,e) Mature miR-29a (n=3/4 mice for each age; one-way ANOVA, p<0.0001; post hoc Tukey's test ***p<0.001, ****p<0.0001, ns not significant) and Dnmt3a expression level (normalized to P10) at different ages measured by qPCR (n=3/4 mice for each age; one-way ANOVA, p<0.0001; post hoc Tukey's test: *p<0.05, **p<0.01, ****p<0.0001, ns not significant). One way ANOVA p-values are reported. Error bars represent ±SEM. f) Scatter plot showing correlation of miR-29a and Dnmt3a levels in the visual cortex display a strong negative correlation (Pearson correlation: r=-0.817, p<0.001). Each circle represents data from a single animal.
B HeLa cells were treated with Drp1 siRNA for 72 h, and then infected with x-light Shigella mCherry for 4 h 40 min for quantitative confocal microscopy. IPTG was added 30 min prior to fixation, and then samples were labelled with antibody for SEPT7. Graph represents mean % ± SEM of Shigella responding to IPTG outside (-) or inside (+) SEPT7 cages from 3 independent experiments. Student's t-test, *** = p<0.001.
(B) PY79 (WT) and ET42 (ΔdltA, PIPTG-sigX) cells, grown in the presence of IPTG, were infected with SPP1 (1:1 MOI) for 10 min. Next, phage adsorption was monitored before and after cell dilution (x100 fold). Percentage of phage adsorption was calculated as follows: (P0-P1) x100/P0, where P0 is the initial phage input in the lysate (PFU/ml), and P1 is the titer of free phages (PFU/ml) 10 min after infection. Shown are average values and SD of 5 biological repeats.
A Oxygen consumption rate of female mice fed a diet with 0.0075% Rosi for 2.5 weeks, determined by indirect calorimetry and normalized to body weight (n=9/10). Grey bars represent the dark phase
C qPCR analysis of lnc-SMaRT RNA expression in C2C12 cells undergoing differentiation at the indicated time points. The RNA expression levels in qPCR analyses were normalized against GAPDH mRNA and expressed as relative quantities with respect to GM samples set to a value of 1. Data are presented as the mean ± s.e.m. of three biological replicates (dots).
(A) Schematic of genetic perturbations to σV circuit. Second copies of σV components were added under the control of the PsigV promoter. ? = PsigV-sigV (2xsigV), PsigV-sigVrsiV (2xsigV-rsiV), or PsigV-rsiV (2xrsiV).
E) Immunofluorescence analysis of TRAF6 recruitment to the PVM of HFFs infected for 3 h with RH, Pru and PruΔgra15 strains. On the right-hand side, a representative fluorescent image is shown of TRAF6 recruitment to the PVM where Toxoplasma Pru strain expresses GFP, DNA was stained with Hoechst 33258. Scale bar is 10 µm. n=3 for all the strains. The antibody against TRAF6 was purchased from Abnova (Appendix Table S2).
(D) A model summarizing our hypothesis on the way that Lam6 functions to regulate contact site communication. In normal cells, where all contact sites are intact, Lam6 is found mostly in ERMES contact sites, and to a lesser extent in vCLAMP and NVJ. However, in case a contact site is lost, the Lam6 proteins that were localized to this contact become free to associate with the other contact sites, thus signaling that they must expand. Raising Lam6 levels in any other way in a contact site therefore would cause an expansion of this contact site.
(C) Side view z-projection of cartwheels containing the central hub and several CIDs from a mature centriole. Central hub, CH; cartwheel inner densities, CID. Scale bar, 20 nm.
(A,B) Western blotting analyses of the levels of autophagy-related proteins in BAT from mice at the normal temperature (30℃) or at 4℃ for 72 h (A). Expression of the indicated proteins was analyzed before and after 72 h cold exposure (4℃) (B).
Male APP23 mice (age at baseline: 12-14 months old) were dosed with CNP520 in food pellets for 6 months: Low dose 0.03 g CNP520/kg food, corresponding to a daily oral dose of 4 mg/kg; high dose 0.3 g/kg food, corresponding to a daily oral dose of 40 mg/kg. (B) Total cortical plaque area (normalized to total sample area (*10−2), stained with antibody NT-12.
(E) iMEFgt/gt stably expressing Cherry-STING were infected with parental MCMV or MCMV m152stop (MOI 0.5). Live cell imaging was performed and STING translocation quantified 120 min and 180 min post stimulation. Data shown is one representative of two independent experiments.
D Schematic of the screen layout, sgRNAs were cloned into the pBA439 backbone and introduced into Hoxb8-FL cells via lentiviral infection. Cells were cultured for either 2 or 4 days, followed by sorting for cells carrying sgRNA constructs (BFP+) into small pools and subsequent small-scale RNA-Seq analysis.
(B) The cross-sectional NfL levels also reflected longitudinal disease progression, as quantified by the annual SARA score change (available for 35 subjects). Boxes show the ranges between lower and upper quartiles, the central bands show the medians, and the whiskers show data within 1.5∙IQR of the median, with dots representing outliers. Subjects with high disease progression (annual SARA score increase ≥0.71 points/year, n=18, median split) had significantly higher serum levels of NfL than subjects with low disease progression
(c) HeLa cells stably expressing GFP-mRFP-LC3 (ref. 17) were transfected for 5 days with two rounds of control or clathrin heavy chain siRNA, during which they were either left untreated (UT) or treated with bafilomycin A1 (BafA1) for the last 15 h. Cells were then fixed and analysed on a Cellomics ArrayScan system. Quantification of autophagic vacuoles (AV) or autolysosomes (AL) per cell in the different conditions is shown in the graph. Asterisk, P 0.01; n.s., not significant. n = 2,000 cells.
DIV21 neurons were co-exposed to fixed concentration of Fib-Tau (0.36nM, 60min, ATTO550 labelled, red) and increasing concentrations (given in monomer-equivalent) of Aβ fibrils [in total 5-experiments were performed with either ATTO647 labeled Aβ or unlabeled Aβ fibrils A concentration-dependent increase in the binding and clustering of Aβ fibrils is seen. One-Way ANOVA with Dunnett's post-hoc test was performed to compare the different condition to the reference condition (100nM).The number of images analyzed is 18, 50, 50, 50, 25 in (D), from left to right. The data originate from 3 to 4 independent experiments. Data information: Box-plot represents: median, interquartile range and 10-90% distribution, Mann-Whitney-test is performed, n=40 images from 4-experiments, Scale bars, 5µm. *p<0.05, ***p<0.001; ns= not significant.
F. Immunoblots show the levels of BLM, TOP3A, RMI1, RMI2 and PrimPol after TOP3A, RMI1 and RMI2 downregulation in WT and BLM KO cells. Ponceau-S is shown as loading control.
A. Double immunofluorescence staining of amyloid plaques (6E10) and ITPKB in AD prefrontal cortex. Scale bar, 50 μm. Arrowheads indicate ITPKB immunopositivity.
(A) Simulations display heterogeneous σV activation after lysozyme stress (N=100). Dashed vertical line marks point of stress addition (parameter L changed from 0 to 1) in simulation.
(E) TFR1 mRNA levels in the liver of mice subjected to iron deprivation by feeding with an iron deficient diet (IDD) combined to a phlebotomy (PHL) (n=5-6); Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.
K. Carfilzomib activates NF-κB promoter in Raw264.7 cells. Raw264.7 cells were pretreated with or without IL-4 (20 ng/mL) for 24 hours, NF-κB reporter and TK were co-transfected for overnight, then stimulated by DMSO or Carfilzomib (1 μM) for 12 hours before luciferase assay performed. The data are means ± SD of three independent experiments. **p < 0.01 (student's t-test).
b t-SNE plot displaying local enrichment of phospho-sites corresponding to known substrates associated with the specified kinase. Dot transparency is scaled according to the P-value corresponding to the local enrichment of the annotation term
E. 10-fold serial dilutions of chm7Δapq12Δ strains grown at the indicated temperatures with either an empty pRS416 plasmid (-) or those expressing the indicated Chm7 constructs (pRS416-HA-CHM7, pRS416-HA-chm7-NTD, pRS416-HA-chm7-CTD). See Appendix Figure S2A for protein levels.
(E, F) MCF10A cells were treated separately (or not) with Latrunculin B (E) and by serum starvation (F) and LATS1 immune complexes and lysates were probed by western blotting for vinculin, LATS1, and TRIP6. Quantification of LATS1-TRIP6-vinculin binding is shown. (Mean ± SD; n=3; *P≤0.05, **P≤0.01, ***P≤0.001, T-test).
(C) Analysis of the senescence-associated β-galactosidase (SA-β-gal) activity in control and subject fibroblasts, overexpressing or not an EGFP-tagged version of the wild-type SLC25A46. Hydrolysis of X-gal results in the accumulation of a distinctive blue color in senescent cells. (D) Quantification of the senescence-associated β-galactosidase (SA-β-gal) activity in each of the experimental condition described in (C). In each condition, 200 cells were analysed. Percentage of positive blue cells corresponding to senescent cells was calculated. Experiments were done in independent triplicates. Error bars represent mean +/- SEM and p-values were calculated using a t-test.
A Protein and genetic structure including the different gephyrin domains and genomic location of the gene with an indication of the different exons. The position of the mutation identified in this study is indicated on the protein level, affecting the E-domain and on the genomic level, affecting exon 12.
Oxygen consumption measurements in control and TIMM50 mutant fibroblasts grown in glucose or galactose. Values of basal and maximal respiration along with ATP-production dependent, proton leak respiration and spare capacity are shown. Data are shown as mean ± SD, n = 4 biological replicates; ∗p < 0.05, ∗∗p < 0.01, ∗*∗p < 0.001 grouping both controls together.
(A-D) Components of the mitochondrial protein import machinery and selected proteins related to this process of control (143B, solid lines, grey bars) and ρ0 cells (dashed lines, colored and dark-grey bars). A and B, components of the translocase of the outer membrane (TOM) machinery (TOM avg.: average of TOMM40, TOMM22, TOMM5, TOMM6, TOMM7); C, components of the trans­locase of the inner membrane (TIM) machinery (TIM22 avg.: TIMM22, AGK, TIMM10B; TIM23 avg.: TIMM23, TIMM17A, TIMM17B); D, components of the TIM23-associated TIMM21 assembly machinery (left panel) and its association with prohibitin (PHB) and components of the mitochondrial quality control system (right panel). Plots and gene names are in corresponding colors, except for TIMM44 and TIMM50 (no migration profiles shown). In (A-C) data are presented as mean ± SD (n=4). *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 (Student's t-test).
Huh7 cells were infected with HCV (strain Jc1) using 30 TCID50/cell and 48 h later cells were fixed and processed for fluorescence microscopy. In case of samples shown in panels B-D, cells were first transfected with expression constructs specified in the left of each panel and 24 h later cells were infected as described above. Samples were analyzed with a Nikon TE2000-E inverted confocal microscope at 60× magnification. (A)-(D) Colocalization of HCV proteins specified in the top of each panel with protein disulphide isomerase (PDI; an ER marker), GFP-Rab21 (marker for early endosomes), GFP-Rab7 (marker for late endosomes) or βCOP-YFP (marker for COP I vesicles). The upper panels represent a low magnification overview; boxed areas are shown as enlargement in the corresponding panel below. The nucleus was stained with DAPI (blue). Scale bars represent 10 µm (top panels) and 2 µm (lower panels). The quantification of the degree of colocalization (Pearson's correlation coefficient) is given at the top of the enlarged pictures.
Representative confocal micrographs of Venus-LUZP1-expressing LUZP1 KO (REV) Eph4 cells in the apical plane. Scale bar, 10 μm.
B, Multiplexed activation of Ascl1, Lmx1a, NeuroD1 and of Ascl1, Lmx1a, Nr4a2 in primary astrocytic cultures. n=3, representative experiment from 2-3 independent experiments, 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.
B Representative pictures of different CTCs from the initial CellSearch® analysis of the metastatic breast cancer patient who gave rise to the breast CTC line. The detected tumor cells display clear keratin and DAPI staining, CD45-negativity as well as lack of, or very weak (4, 8), ERBB2 expression. Cells of small (about 5 µm in diameter, 1, 2) and large size (larger than 10µm in diameter, 2,3) were detected. While some CTCs displayed dot-like perinuclear keratin signals (1, 2), the majority showed diffuse keratin staining. Additionally, CTC clusters of 4-8 cells were present (5, 6). Some CTCs showed multiple/lobed nuclei (4, 7, 8).
TLR8 agonists inhibit HIV replication.Macrophages were incubated with (A) ssRNA40 or (B) CL097 for 24 h before infection with HIV for 3 h. Cells were then washed and incubated with ssRNA40 or CL097 for 10 d. Extracellular release of HIV p24 antigen into the cell supernatant at days 0, 3, 5, 7, 10 was detected by ELISA. Results are reported as mean ± s.e.m., n = 5. * p<0.05.
B. The predicted PUB domain in the N-terminus of SPATA2 interacts with CYLD, but not with LUBAC or other TNF-RSC components. GFP-SPATA2 and the indicated deletion mutants were purified from A549 cells that were stimulated with TNF-α for 15 minutes, and the enriched proteins were quantified using SILAC-based MS.
Lower subdomain of the shoulder, shown in ribbon (main) or surface representation (inset), with the arm, hook and paddle colored in shades of blue.
A Effect of mycolactone on v-abl pro-B cell viability after 24 and 48 h of mycolactone treatment, as measured by exposure of Annexin V and incorporation of PI. Data are Mean % of live, apoptotic and dead cells from technical duplicates , relative to total cells. Data information: Data shown are representative of experiments performed with two independent v-abl cell clones, with similar results.
A putative interaction surface of the ISX/BRD4 complex was presented through structural modeling.
(C) Body weight changes of the experimental mice during the experimental paradigm. Data represent the mean± SEM of n=8 mice per group; ****P < 0.0001, two-way ANOVA.
D Quantification of western blot (n=3 mice per genotype). Data information: , data are presented as histograms showing the mean ± SEM. ***, P≤0.001; *, P≤0.05 (Student's t-test).
(D) Training latency in the Barnes maze test of 6 month old wild type, 5XFAD and 5XFAD/p75NTR mutant mice, as indicated. Histograms show mean latency in seconds to find the platform hole ± SEM in 4 consecutive training sessions. Bar color codes are as in panel (A). *, P<0.05 vs. 5xFAD; #, P<0.05 vs. wild type, 5xFAD/ΔDD or 5xFAD/C259A (two-way ANOVA followed by post hoc test). N=14 (wild type and 5xFAD/ΔDD), 10 (5xFAD, (5xFAD/KO and 5xFAD/C259A) mice per genotype, respectively.
Intracellular caspase-3 activity measured in freshly isolated platelets using the chromophore Ac-DEVD-pNA. Experiments performed in a minimum of n=6 samples per group. Values expressed as Mean ± SEM. (caspase-3 activity ; *p=0.0157)
F) HeLa cells were co-transfected with unrelated oligonucleotides as a negative control (siCTR) and empty vector (EV) or 3'UTR siRNA TFG siRNA together with EV or HA-TFGwtLIR or TFGmutLIR3 plasmids, expressed at near endogenous levels. Protein extracts were analysed by WB to detect ULK1, TFG, and ACTIN as indicated. Densitometry analysis of ULK1 over ACTIN is shown (right). Data are mean value ± SEM. Statistical analysis was performed by one-way ANOVA followed by Dunnett's multiple comparison test. *, P<0.05; **, P<0.01, ns, not significant. (n=4 independent experiments).
(B) HEK293A cells were pretreated with 10 μM anisomycin for 30 min, or UV irradiation for 3 min followed by a 40‐min recovery, before incubation in EBSS for 2 h. Images were analysed as in Figure 2E. Bars=5 μm. Data are represented as mean±s.e.m. of 60 cells, EBSS mock versus EBSS anisomycin (*P=0.0142); EBSS mock versus EBSS UV (*P=0.0150); Student's t‐test.
C Interaction of peripheral stalks EG1 and 2 with the catalytic hexamer. The peripheral stalks are bound to the top of the B subunits via their C-termini (boxed). The electron density (contoured at 1.2 σ) for the C-terminal domains of EG1 and EG2 is shown in the panels to the left and right.D The structure of autoinhibited ScV1rotated 90° around the vertical from the view shown in panel A to highlight peripheral stalks EG2 and EG3. Note the bent appearance of EG3 compared to EG2 along with the presence of a partially unstructured region known as the "bulge" in subunit G (indicated with an arrow). The box shows electron density (contoured at 1.2 σ) for the EG3 N-termini contacting the C-terminal domain of the A subunit of a closed catalytic site (see asterisk). The horizontal lines on the structure indicate the sections shown in panels E (upper two lines) and F (lower two lines).
HCT116 cells were serum-starved for 24 h (d) and the cytosolic lysate was extracted for co-immunoprecipitation with anti-FoxO1, followed by probing with anti-Atg7
Macroscopic and histological analysis of the lungs of nude mice injected with MDA-MB-231 cells and CIP2A-BP or svCIP2A-BP via tail vein; lung metastatic nodules were visualized 8 weeks post-transplantation (5 mice per group). Right panel is the quantification of pulmonary metastases.
Figure 9. Diagram summarizes how breast cancer cells acquire their enhanced malignancy through TDLNs. TDLNs play a pivotal role in promoting breast cancer cells for distant organ metastasis. Breast cancer cells move to TDLNs where Tregs are elevated and secreted TGF-β1 to up-regulate Il-17rb expression in cancer cells (A).
Albumin-cre mice were crossed with KLF10flox/flox to generate hepatocyte-specific KLF10 knockout mice (KLF10hep-/-). Then, 8-week-old male KLF10hep-/- mice and KLF10flox/flox were treated with WD/CCl4 for 12 weeks. KLF10flox/flox mice were used as the control (Ctrl). n=5 per group. (C) Body weights. Data information: * P <0.05, ** P <0.01, *** P <0.001. Results are shown as mean ± SD. Student's t test
qRT-PCR analysis of mRNA levels of Skp2, Aurka, Dll1, and Hey1 in control cells and those treated with the indicated inhibitors. Error bars represent SEM (n = 3).
(A and B) Summary of candidate secretory autophagy cargos, identified by quantitative proteomics based on isobaric tandem mass tags (listed in Table EV1) and sorted by cellular compartments in (A) or presence/absence of leader signal peptide in (B).
Illustration of SILAC phosphoproteomics workflow. Flp‐In T‐Rex HEK293 cells stably expressing FLAG alone were cultured in unlabelled (R0K0) medium, kinase‐inactive (KI; D384A) PINK1‐FLAG cells were "medium" (R6K4) labelled, and wild‐type (WT) PINK1‐FLAG cells were "heavy" (R10K8) labelled using SILAC media containing the respective isotopes. All conditions were treated with 10 μM CCCP for 3 h and subjected to membrane fractionation. Four biological replicates of the samples were mixed in a 1:1:1 ratio, digested and fractionated by HILIC. Phosphopeptides from these fractions were enriched by TiO2 chromatography and analysed by quantitative mass spectrometry on an Orbitrap Velos Pro mass spectrometer. Data were analysed by MaxQuant and Perseus software packages.
C) The asymmetric loading of dynein into astral MTs emanating from the daughter SPB is affected in cdc14-1 and spc110S36-91A cells during the DNA damage response. Dynein distribution on astral MTs emerging from each SPB was scored by using Dyn1-GFP in strains containing Spc110-RFP. Graph represents the percentage ± SD of cells grouped into three categories depending on the pattern of dynein distribution on astral MTs: Type1, Dynein is exclusively loaded on astral MTs emerging from the daughter SPB; Type 2, Dynein is equally loaded on astral MTs emanating from both SPBs; Type 3, Dynein is absent from astral MTs. At least 100 cells from three independent experiments were scored. A representative picture showing the three patterns is included. Scale bar: 3μm.
F HEK293 cells were transfected with TAp73α along with ΔNp73β. PUMA mRNA was measured by qRT-PCR analyses. Bars indicate mean ± s.d. (n = 3).
RD SAMHD1-HA cell lines were treated with dimethyl sulfoxide (DMSO) or 10 μM MG132 for 12 h prior to harvest and subjected to IB with tubulin as a loading control.
Phenotypic analysis. Wild-type, uvr8, and rup1 rup2 seedlings were grown in 1/2 MS with or without UV-B (1 W/m2) for 2 weeks. Images are shown in (A); scale bars = 5 mm.
(d,e) The sequential state III oxygen consumption rate of heart isolated mitochondria was assessed using the Seahorse XF24 Analyser. With the initial presence of 5 μg mitochondria per well, 0.5 mM NADH and 4 μM FCCP, injections were performed as follows: port A, 50 μl of 20 μM rotenone (2 μM final); port B, 55 μl of 100 mM succinate (10 mM final); port C, 60 μl of 40 μM antimycin A (4 μM final); port D, 65 μl of 100 mM ascorbate plus 1 mM TMPD (10 μM and 100 μM final, respectively). Representative results of aged littermates are shown (d) and oxygen consumption by each complex was calculated from four independent experiments, five replicates per sample, and four samples per experiment (n=8 per group, e).
B Dose response curves for viability of parental cells (in red) or selected clones (in black) upon treatment with NFR for 48h. The green dashed box highlight concentration in the physiologically relevant range. Curves are mean ± s.e.m. of 3 independent experiments performed in triplicate. P values were calculated using 2way ANOVA analysis of variance between parental cells and each individual clone. Bar graph represents the EC50 (half maximal effective concentration) of the dose responses. Data are mean ± s.e.m. of 3 independent experiments performed in triplicate. P values were calculated using 1way ANOVA analysis of variance (P value in red) followed by Dunnett's multiple comparison tests. *P value ≤ 0.05, ** P value ≤ 0.01.