EMBO/sd-character-level-ner huggingface dataset:
Immuno-EM of p62-positive structures in Vps24- and Tsg101-depleted cells. Cryosections of HeLa cells transfected with Vps24 (A, C, and E) or Tsg101 (B, D, and F) siRNA were incubated with antibodies against p62 (15-nm protein A gold, 10-nm in D). Membrane-free p62-positive aggregates (C and D) or p62-positive structures contained within dense clusters of vesicular-tubular elements (A and B) were detected. Vesicles with early endosomal morphology (EE) or multivesicular appearance (MVB) associated with these clusters. We also observed p62 labeling in electron-dense structures sequestered within amphisomes in cell depleted of Vps24 (E) or Tsg101 (F). The amphisomes typically consist of an electron-dense p62 positive body (E and F, arrowhead), and a multivesicular endosomal structure (E and F, arrow). Bars, 200 nm.
(A) Schematic representation of the arginine-transamination reaction network than leads from arginine to succinate. Enzymatic reaction steps are indicated by arrows and annotated with corresponding enzyme commission (EC) numbers. Leftward facing dotted arrows represent ureohydrolase, rightward facing dashed arrows decarboxylases, downward-pointing solid arrows aminotransferases, and dashed and dotted arrows dehydrogenase enzyme reaction steps. The names of the metabolites are indicated above their chemical structures according to the following abbreviations: arginine (ARG), ornithine (ORN), 5-guanidino-2-oxo-pentanoate (GOP), agmatine (AGM), 5-amino-oxopentanoate (AOP), putrescine (PUT) , 4-guanidino-butyraldehyde (GBL), 4-aminobutyraldehyde (ABL), 4-guanidinobutanoate (GBA), 4-aminobutanoate (GABA), succinic semialdehyde (SSA), and succinate (SUCC).
g and h, The Kaplan-Meier survival curve was used to analyze survival correlation between patients (n=157) with NSCLC and PCAF (h) levels. On the basis of the cut-off values of fold differences, the study population was dichotomized into the "high" and "low" expression group. p‐values were calculated by log‐rank (Mantel-Cox) test comparing the two Kaplan-Meier curves.
B, scRNA-seq data of adult zebrafish cardiac nonCM visualized on tSNE and colored by cell types. EC, endothelial cells; FB, fibroblasts; MC, macrophages; Mes, resident mesenchymal cells; T/NK/B, T/NK/B cells; Neutro, neutrophils; Eryth, erythrocytes; Throm, thrombocytes.
(A) qPCR analysis of mitochondrial DNA (mtDNA) on nuclear DNA (nDNA) in C2C12 myotubes treated for 48h with C26CM and ferric citrate. (n=6). Data information: For all data, n represents the number of biological replicates. Data are mean ± SEM. ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and ##p < 0.01, ###p < 0.001 compared to C26 CM-treated group.
G-J Representative transmission electron microscopy (TEM) images of spheroids or an in vivo WAE cell from a biopsy-injured mousecolon. Quantification of cytoplasmic:nuclear ratio (H) and microvillar length (I) from the TEM images (n = minimum of 5 images per group). *p<0.05, **p<0.01, ****p<0.0001 by 1-way ANOVA and Tukey's post-test.
Representative photographs of each group of retinal fundus of HEL-TCR transgenic mice at pn 35. Arrowheads indicate representative areas with retinal vasculitis.
E NE4C cells with and without MARS knockdown were treated with either Hcy (20 μM) or Met (75 μM), and cellular superoxide levels were detected 6 h after the start of the respective treatment and quantified relative to the untreated NE4C cells (n=4).
(E) T47D-MTVL/H1.2 and H1.3 knock-down cell lines (Sancho et al., 2008) treated or not for 6 days with DOX to induce specific H1 depletion, were incubated for 6h with 10nM R5020 as indicated; cDNA was generated and used as template for real time PCR with gene-specific primers. The extent of knockdown was analyzed by western blotting using specific antibodies (lower panel). (*) P-value < 0.05.
8-week-old male C57BL/6J mice were administered with AAV-GFP or AAV -Klf10 through tail vein injection, and then kept on HFD-feeding for 12 weeks. n=5 per group. (K) H&E staining of liver sections.
PGAM5 is an IMM protein that protects PINK1 from degradation by mitochondrial proteases including PARL. After CCCP treatment, full-length PINK1 protected by PGAM5 will move to the OMM, while PGAM5 remains on the IMM. In the absence of PGAM5, PINK1 loses the protection from PGAM5, and will be cleaved and degraded. CCCP can trigger PGAM5 stabilized PINK1 translocation from IMM to OMM where it associates with parkin leading to ubiquitination events associated with p62 recruitment and culminating in LC-3-mediated mitophagy.
16HBE cells were stably infected with pQCXIP, or pQCXIP expressing dominant negative myc-HRas N17. All data are representative of 3 independent experiments. (e) Cells were seeded sparsely on glass coverslips, incubated for 3 days and then fixed and stained for ZO-1 (tight junctions) and DNA. Scale bar, 20μm. (f) Quantification of tight junction phenotype (see c). ***, p = 0.0002.
A-B Sensitivity of WT WNV and WNV-poly(A) viruses to interferon α (IFN-α) treatment in Vero cells. Vero cells were infected with either WT WNV or WNV-poly(A) virus at an MOI of 10 and treated with different concentrations of IFN-α. The supernatants were harvested at 48 hpi and viral RNA copy numbers were measured by real-time RT-PCR. Data information: Three independent assays were performed for above experiments with similar results and data of one representative data was shown. Scale bars represent 50 μm.
Reimplantation assay (CRCM434). Two-week treated PDXs were reimplanted, in serial dilutions, into new recipient mice and tumor growth was monitored Each curve represents the growth kinetic from one individual injection.
C BMDMs derived from wild-type mice were stimulated by IMQ (10 µg/ml) for 30 min. Cell lysates were immunoprecipitated by anti-SHP2 and probed by indicated antibodies.
A Growth kinetic measurements of SM exposed to AMSIN or various antibiotics with known cellular targets. The peptide or the compounds used were 4×CL. VAN, vancomycin; RIF, rifampicin; KAN, kanamycin. OD600 were calculated as measured values subtracting the background value from broth medium (OD600 = 0.356).
C Lysates from 293T cells transiently expressing 3Myc-Atg14 or Atg5-3Myc, and GFP-CbpCT4 or GFP were immunoprecipitated with GFP-Trap, and the bound proteins were analyzed by immunoblotting.
F-H. Statistics of Cm jumps, Endo-5s, and Ca2+ current recorded from DRGneurons as in (B-E). Data were collected from 4 (Sc, Rescue), 8 (Ctrl), and 16 (KD) independent experiments.
(d) Autophagosomes were visualized through scanning electron microscopy. Scale bar, 50 nm. The arrows indicate autophagosomes. Immunoblots (IB) of cFLIP and actin expression are shown in Supplementary Information, Fig. S1c.
H, I Calcium transient frequency (number of peaks in 10 mins recording) normalized by CTR/KO untreated (H; one-way ANOVA, F9,239 = 6.18; Dunnett's multiple comparisons test vs CTR/KO untreated: Nefi 1 µM, *P < 0.05 and Z = 0.780; Nefi + PHA 10 µM, ***P < 0.001 and Z = 1.972; N = 15-61 neurospheres per condition) and calcium transient amplitude normalized by CTR/KO untreated (I; one-way ANOVA, F9,241 = 1.27, P = 0.255; N = 16-62 neurospheres per condition).
(A) Schematic representation of the m220 stromal feeders expansion culture to compare the meiotic capacity of XGFP- and XGFP+ PGCLCs. Meiosis is induced via addition of Retinoic Acid (RA) and Bone Morphogenetic Protein 2 (BMP2). c0 = starting day of culture, c9 = culture day 9 and last day of culture. (B) Representative images for the expression of XGFP (green) and SYCP3 (red) in germ cells at c5, c7 and c9 from XGFP+ and XGFP- PGCLCs. All cells with SYCP3 signal irrespective of localization pattern or intensity were scored as SYCP3+ cells. Cells were counterstained with DAPI (grey). Scale bars = 10 μm. (C) Number of SYCP3+ cells per m220 culture day originating from XGFP+ and XGFP- PGCLCs. Each white dot represents a biological replicate (n = 3). P-values shown are from a two-sided Mann-Whitney U test. n.s. = not significant. (D) Percentage of XGFP+ cells among SYCP3+ cells at the indicated m220 culture day, originating from XGFP+ or XGFP- PGCLCs. Green bars show constitutive GFP expression in XGFP+ PGCLC-derived cells, while striped bars signify XGFP reactivation in XGFP- cells. Each white dot represents a biological replicate (n = 3).
C The graph shows the percentage of EGL thickness reduction in GlaB‐treated mouse cerebella in comparison with vehicle mouse cerebella. Data show the mean ± SD of cerebella (n = 10) for each treatment. *P 0.05 versus Ctr.
(a) COS7 cells were transfected with Bif-1-HcRed together with GFP-Atg5 or GFP-LC3. Twenty hours after transfection, the cells were cultured in EBSS (middle and bottom panels) or complete medium (top panel) for 2 h and subjected to confocal microscopy analysis. Magnified images are shown as insets. Representative Bif-1-Atg5 or Bif-1-LC-3 double-positive foci are indicated by arrows.
Wild type, mps1-3 and mps1-1 mutant cells were synchronised in G1 with α-factor at permissive temperature (25°C) and then released at restrictive temperature (34°C, t=0). Cells were collected at the indicated time points for immunofluorescence using anti-tubulin antibodies in order to score metaphase and anaphase spindles (D). Budding and nuclear division were scored on the FACS samples.
B: Pull down assay for analysis of Dam1c-Bim1 binding to Ndc80c. Ndc80c immobilized on beads was incubated with either Dam1c or Bim1 alone or with pre-formed Dam1c-Bim1 complex with increasing amounts of Bim1. Input and elution samples were analyzed by SDS-PAGE. LC and HC denote the light and heavy chains of the M2 anti-Flag antibody used for immobilization of Ndc80c on beads. Protein names in blue, red and green refer to Dam1c, Ndc80c and Bim1, respectively.
(B) Lignin accumulation in WT and rbohD and rbohF single mutants and a double mutant with or without 2-hour 100 nM CIF2 peptide treatment. Arrowheads indicate excess lignification. Pictures are shown as overviews (maximum projection) or median sections. Lignin and cell walls are shown with magenta (stained with Basic Fuchsin) and gray (stained with Calcofluor White) respectively. Representative pictures are shown, 12 roots (overview) and 2 positions in 12 roots (median section) were inspected. Scale bars = 20 µm (lignin overviews), 5 µm (median sections). "inner" designates the stele-facing endodermal surface, "outer", the cortex-facing surface.
Significance of the identity of the canonical stop codon in AGO1 translational readthrough. AGO1-ISR-FLuc constructs containing TGA or TAA or TAG were transfected in HEK293 cells and translational readthrough was quantified as described above. FLuc mRNA levels determined by RT-PCR are shown below. ***, P = 0.0002; **, P = 0.0004.
Co-treatment with olaparib and Wnt inhibitor regulates expression of senescence associated genes. (C Expression of senescence-associated genes was analyzed in the tumors from all four treatment groups (treated for 56 hours) by qRT-PCR. Each data point represents an individual tumor and horizontal lines represent mean. p-values for the significant changes as calculated by Mann-Whitney U test are shown. Each lane represents an individual tumor.
Immunocytochemistry of untreated and Csf-1r siRNA treated BV2 microglia. BV2 microglia were stimulated with LPS and exposed to fluorescent opsonised latex beads for 1 hour before fixation and quantification of bead+ cells via microscopy. Cells were stained using MitoTracker (red) and DAPI (blue). Arrowheads (white) indicate bead+ cells.
C: Estimated ctDNA fractions for the plasma (10/12 detected), CSF (7/8 detected) and urine samples (10/16 detected) collected from 7 patients with primary glioblastoma and one patient (GB12) with anaplastic oligodendroglioma. The ctDNA fraction is expressed as IMAF (Integrated Mutant Allele Fraction). Detected cases are indicated by full circle and non-detected cases as an open circle. ND: non detected.
Expression of Blimp1 and Prdm14 measured by qPCR in PGCLCs derived from indicated ESC lines. The ∆Ct values from the average Ct values of Arbp and Ppia are shown (log2 scale, the mean value of two independent experiments with two technical replicates).
G FRAP analysis of dendritic lysosome movement. Quantitative analysis for F (N = 7, 7, and 9 neurons for shSc, shLAMTOR1, and shLAMTOR+rLAMTOR1, respectively, from 3 independent experiments). Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by Dunnett's post-test *P < 0.05, **P < 0.01, ***P < 0.001, as compared to shSc; #P < 0.05, ###P < 0.001, as compared to shLAMTOR1 ; n.s., not significant.
(c) DLD1 cells were cultured in the presence or absence of bafilomycin A1overnight, fixed and processed for confocal immunofluorescence microscopy to determine the cellular distribution of endogenous FTH1 or FTL with LC3, LAMP2 or EEA1. Regions outlined with white dashed lines are magnified to the right of each panel. Scale bars in full and zoomed panels correspond to 10 and 2 μm respectively.
B Tier of therapy and related molecular alterations. SNV with LOH refers to SNV in a tumor suppressor gene with LOH.
Oct4 immunohistochemical staining of teratomas derived from WT and H8-Bptf or H8-Tbx3 exon-KO ES cells. Representative Oct4-positive regions are shown (left). Scale bar, 100 µm. The percentage Oct4-positive region (%) is shown (right). The data represent the means± SD (n=3 biological repeats). **P＜0.01; ns, not significant. T-test was used to determine the significance.
(B) Representative images of tumor spheres. Spheres were cultured for 14 days before counting. Histogram shows the mean numbers of spheres cultured. Scale bar: 100 μm. Bars are the mean ± SD of three independent experiments.
(G) A20 mRNA expression via qRT-PCR in TNF-treated wt cells transfected with targeting (siA20) or non-targeting (siCon) siRNA (mean of three independent experiments ± standard deviation; two-tailed Student's t-test *P<0.05).
C. Immunohistochemistry images from the Human Protein Atlas (www.proteinatlas.org) for protein ANXA1 with nuclear staining (blue) for three selected tissues.
B Hemolysis by AMSIN. Meucin-18 was used as a positive control. Mean ± SD of three technical replicates is displayed.
D-F' Histological sections of LacZ‐stained CcnoTA/+ embryo at E16 reveal Ccno expression in the epithelium of (D) plexus choroideus and ependyme, (E) snout epithelium, and (F, F') trachea and bronchi. pc, plexus choroideus; se, snout epithelium; tr, trachea; and br, bronchus.
(B-G) Morris water maze test. Data represent the mean ± SEM. Colonic-injected mice (n = 7 per group) were trained in the water maze over five days. Shown are the percentage of time spent in the target quadrant in the probe trail, *P=0.0362 (*P < 0.05),**P=0.0072 (**P < 0.01), unpaired t tests (B), Latency to platform, *P=0.0434, *P=0.0166 (*P < 0.05), two-way ANOVA (C), the area under curve of Latency (AUC Latency) (D), Swim Speed (E), Swim Path Distance (F), the area under curve of Swim Path Distance (AUC distance) (G).
(A) Histogram shows genome-wide distribution of log10-transformed directionality scores at bidirectional promoters. Directionality score for promoters is defined as the ratio of mRNA and uaRNA reads counted within 1 kbp regions downstream sense and upstream antisense of the protein-coding TSS. Promoters with divergently transcribed protein-coding gene pairs were excluded The red dashed line marks the median.
(a) Speed of the EVL advancing front at different epiboly stages (φ angle) for two distinct simulated conditions: 1) a difference of elastic tension between the EVL and the yolk associated to a two-phase reduction of the contractile E-YSL width (from 20º to 5º) as epiboly advances (from 50º to 155º) (wild type - blue). The contractile E-YSL width decreases at a slower rate until 80º and shrinks afterwards at a rate 2.25 times faster, and 2) Same assumptions as in 1 but with no shrinkage of the E-YSL (constant 20º) (contractileless - red).
(G) Quantification of specific histone acetylation marks normalized to tubulin levels. Significant differences were calculated using a T-test and are indicated with ** (p<0.05) and *** (p<0.01). N=3, error bars represent SEM
Relative NP expression in PR8 IAV infected (HA+) or non-infected (HA-) epithelial cells isolated from BALO 48 h pi, FACS-sorted according to EpCAM and HA expression (n=3 biological replicates with pooled cells from 4 cultures per replicate)
Western blot analysis of , (C) p880GluA2 and GluA2 expression (S n=9, SD n=8) in the prefrontal cortex of sleeping and sleep deprived mice. Student's t-test *p < 0.05, **p < 0.01, ***p < 0.001.
(A) GFP antibodies immunolabel VenusClC-3 (green) in the somata of CA1 pyramidal neurons of Clcn3ven/ven, but not Clcn3+/+ brain sections. sp, stratum pyramidale (scale bar: 20 µm).
The average number of GFAP positive astrocyte cells over three fields of view per mouse of the hippocampus (C) and the cortex (D) were counted (n=4 mice per group, average of 3 fields of view per mouse). Data are expressed as mean ± STDEV and were tested by one-way ANOVA with Tukey's post-test; **P<0.01, ***P<0.001. Symbols above bars are versus WT
D Lysates from HEK293T cells, transfected with (G4C2) x2 hereafter 2R or (G4C2) x66, hereafter 66R vectors and treated for 24 h, immunoblotted using antibodies for poly-GA expression (HA tagged). GAPDH used as loading control. Quantification from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test; ****P<0.0001, **P = 0.0052 for SPL vs DMSO, **P = 0.0016 for FSK vs DMSO. Concentration used: 1 μM GELD, 10 μM ERY, SPL and FSK.
Rabin8+/+ and Rabin8−/− hTERT-RPE1 cells incubated for 24 h without serum were immunostained with anti-pericentrin (red) and anti-acetylated tubulin (blue) antibodies. Cholesterol was stained with Filipin III (green). Scale bar, 5 μm. Quantification of the Filipin III intensity at primary cilia from (A). Rabin8−/− hTERT-RPE1 cells exhibited a significant reduction of ciliary cholesterol (***p<0.001: one-way ANOVA with Tukey's HSD, n=3: 40-50 cells per experiment). In the boxplot, medians, 25th/75th percentile and min/max were represented by the central lines, the box limits, and the whiskers/error bars, representatively.
(D) EMSA using nuclear extracts of COS-7 cells transfected with AR WT or AR W752R and incubated with radiolabeled ARE, more specifically TAT-GRE (Denayer et al., 2010). Shift (S) occured through binding of the AR dimer on the ARE. Supershift (SS) occurred after addition of an AR-antibody. S = shift and U = unbound ARE. Western blot on AR, depicted on the right, shows similar expression levels for WT and mutated receptors.
U2OS cells stably expressing GFP-TFEB fusion protein were treated with indicated chalcones at 30 µM for 6 h. Representative images are shown in (B). Scale bar equals 10 µm.
(D) Quantification of Gadd45b mRNA signal intensity at 48 hrs post treatment with LY294002 or DMSO in uninfected neurons. Red line indicates the mean. 3 biological replicates, 25~30 cells were quantified for each replicate. Data information: P values equal to or less than 0.05 were considered significant, asterisks denote statistical significance (*, p<0.05; ****, p<0.0001). P values are calculated using two-tailed unpaired Student's t test. P values > 0.05 were not significant (ns).
(I) Corresponding images and isolated tumors are shown. The red dotted line represents cured tumors.
(E) Comparison of Aβ42/40 ratio at baseline and at day 91 for all participants in the placebo, 35 mg, and 85 mg dose group.
A BR enhances the stability of BIC1 proteins. The 5-d-old 35S:BIC1-YFP transgenic plants were treated with 100 μM cycloheximide (CHX) or co-treated with 100 μM CHX and 1 μM epibrassinolide (eBL). Samples were collected at indicated time points and BIC1-YFP protein levels were analyzed by western blots using anti-GFP antibody. Actin was used to verify equal protein loadings. Intensity of the bands was measured using Adobe Photoshop CS3 Extended program. Three independent experiments were performed with similar results.
I, J Spheroids were cultured in enterocyte media, WAE media or WAE media containing 100 pM C59. Quantification of the average expression ± s.e.m. of Cldn4 (I) and Fabp1 (J) mRNAs shown as fold change relative to EP4i group (n = 3 independent experiments). ***p<0.001, ****p<0.0001 as determined by one-way ANOVA and Tukey's post-test.
Fig. 3. Multilevel profiling approach of spironolactone treatment assessing target specificities and adapter recruitment.(E) Schematic representation of the most critical ERBB dimers tested in spironolactone dose-response assays using the split TEV protein-protein interaction detection technique. Note that not all possible combinations are depicted.
(A) The effects of RanT24N, T42A, and RanT24N on MI spindle assembly observed in maximum z-projection images from confocal time-lapse imaging of oocytes expressing CDK5RAP2-EGFP, histone H2B-mCherry and stained with SiR-tubulin. Time in hh:mm is relative to GVBD. Scale bar, 10 µm. (B, C) Live-cell imaging of oocytes as in (A) was used to quantify the effects of Ran mutant. Means ± SDs., Mann-Whitney test, oocyte numbers are indicated in brackets.
E. Maximum intensity projection of adult Tspan12-/- retinas after mice were injected with F4L5.13 or isotype control. Endothelial cells were stained with IB4-Alexa 647. Images are representative of 4 retinas per group. Scale bar: 100 µm.
Percentage of WT (black dots) and Arghap45−/− naive T cells (red dots) remaining adherent cells after application of a shear stress of 1 dyne/cm2 for 120 s. Same conditions as in (C). n -G mean and SD are shown. **** P ≤ 0.0001, unpaired T test.
(D) Northern blot showing the 5' NGD-IM derived from the R(CGN)12 reporter in ski2∆ cells expressing the indicated Hel2 mutant proteins. 5' NGD-IMs were detected with a DIG-labelled GFP probe.
(e) Analysis of EEA1 and VEGFR2 vesicles following PALD1 knockdown. Representative images of VEGFR2 (green)/EEA1 (red) double-positive (yellow) vesicles in negative control siRNA, and PALD1 KD#2 siRNA-silenced HDMEC at 0, 2 and 10 min of VEGF-A stimulation (50 ng/ml). DAPI in blue, scale bar: 10 µm. Inset shows only EEA1 channel, scale bar: 10 µm. (f) Quantification of (e), number of EEA1 positive (top) or VEGFR2-EEA1 double-positive vesicles (bottom) per field of view. Mean±SEM, Two-way ANOVA, n=3 biological replicates. Data information: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.
(A) Chromatin immunoprecipitation sequencing (ChIP-seq) identified a PBX1 binding core sequence motif composed of a 10-nucleotide motif (A) and a 5-nucleotide motif (B).
Clonal analysis demonstrated the presence of stem cells (holoclones) in a passage VII RDEB culture (95% of growing colonies).
F. Pull down assay of HEK293T cells co-expressing Myc-VAPA with BioGFP or BioGFP-SCRN1. G. Pull down assay of HEK293T cells co-expressing Myc-VAPB with BioGFP or BioGFP-SCRN1.Data information: Data represent Mean ± SEM; NS: not significant; *P < 0.05; **P < 0.01; ***P < 0.001, by Mann-Whitney U test.
(F) Loss of STXBP4 inhibits YAP phosphorylation and LATS activation. Western blotting was performed with the indicated antibodies.
(B) ICC images of FLAG-tagged SRSF1 after SRPIN340 treatment compared to vehicle (DMSO). Quantification shows the ratio of nuclear and cytoplasmic intensity of SRSF1 signal Error bars indicate mean +/- 95% CI (n= 85-126 cells/condition). Statistical analysis was performed using t test with Welch's correction, ∗∗∗∗p < 0.0001.
A-D Human ascites and urine samples were immunoprecipitated with HU3-conjugated beads and eluted material was analysed by MALDI-TOF mass spectrometry. Representative spectra are shown.