EMBO/sd-character-level-ner huggingface dataset:
Figure 1A Proteins captured by BGL3 and RMRP antisense purifications. Proteins with an absolute log2 (fold change) > 1 and -log10 (p-value) > 1.3 (compared with control purification) were considered as proteins enriched by BGL3 specifically. B Protein-protein interaction network of the DDR-related proteins captured by lncRNA-BGL3. C&D RNA pull-down assay for BGL3-BARD1/PARP1 interactions before and after irradiation. Biotinylated in vitro-transcribed LncRNA-BGL3 sense or antisense transcripts were incubated with HEK-293T cell lysates with or without ionizing radiation (10 Gy) with 1 hr recovery for in vitro streptavidin RNA pull-down assays, followed by Western blots using the indicated antibodies. Schematic representation of BARD1 (E) HA-tagged full-length or deletion mutants of BARD1 were transfected into 293T cells. 48 hr later, BGL3 RNA pull-down assay were performed, and arrowheads indicate the bands for HA-tagged full-length or deletion mutants of BARD1 Schematic representation of PARP1(G)-truncated mutants used in this study. HA-tagged full-length or deletion mutants of PARP1(H) were transfected into 293T cells. 48 hr later, BGL3 RNA pull-down assay were performed,
Figure 2A Identification of parental origin of the chromosomes was distinguishable based on H2B-mCherry fluorescent intensities (paternal chromosomes exhibit lower intensities; n = 20 oocytes). Bars and error bars denote means ± SD. The z-projection image shows major satellite-mClover (centromeres, green) and H2B-mCherry (chromosomes, red). Time from anaphase onset is shown in h:min. Scale bar = 4 μm. The 3D-reconstructed image shows maternal (magenta) and paternal (cyan) chromosomes. Spots indicate centromeres. B Chromosome tracking in 3D. The reconstructed images are viewed from the side of the metaphase plate. Signals are interpolated in the Z axis for visualization. White and red arrowheads, as well as red surfaces, indicate univalent-like chromosomes that underwent unbalanced predivision (premature segregation of sister chromatids). Scale bar = 4 μm. C Halving the recipient ooplasmic mass rescued chromosome alignment. The numbers of misaligned chromosomes and their parental origin were determined in 3D (n = 39 and 17 oocytes). Error bars show the standard deviation. Student's t-test was used to compare means. *P < 0.05. N.S., not significant.
Figure 2Low-pass filtered monomer map features of Ca2+/acidic pH (grey) and water structure (green) with differences at lower radius (left). Zoomed inset (right) with maps displayed at a false discovery rate (FDR) threshold of 1% showing significant differences. Detailed map comparison at lower-radius region of Ca2+/acidic pH (grey, left column) with the water condition (green, right column). A total of 3 atomic models (model 1: cyan, model 2: pink, model 3: green) describe the map of TMV in water whereas the Ca2+/acidic pH map could be modelled with a single atomic model (center). Located Ca2+ ion in the Ca2+/acidic pH map with different conformations in the water structure (bottom).
T.Figure 4A, HBMEC cells were challenged with RH T. gondii and cell lysates were obtained to probe for total EGFR, phospho-tyrosine 1068 EGFR and phospho- tyrosine 1148 EGFR by immunoblot. B, HBMEC were challenged with live vs killed tachyzoites. Total EGFR and phospho-tyrosine 1068 EGFR expression was examined by immunoblot. C, D, Human RPE cells (C) and mouse microglia (D) were challenged with RH T. gondii and total EGFR and phospho-tyrosine 1068 EGFR expression was examined by immunoblot. Results shown are representative of 3 independent experiments.
High-content trafficking assay coupled with systematic siRNA library screening.Figure 4A-B Interactors identified in MaMTH-HTS that, when knocked-down in CFBE cells, affect CFTR membrane trafficking. Interactors affecting A) F508del-CFTR and B) wt CFTR are indicated. Green bars (all with a Z-score greater than or equal to 1) indicate a significant enhancement of CFTR trafficking to the PM. Red bars (all with a Z-score of less than or equal to -1) indicate a significant reduction in CFTR PM trafficking. The 'rescued' trafficking effects of the corrector compounds lumacaftor (VX-809) and tezacaftor (VX-661) are shown, as dotted red lines, for comparison. All conditions were measured across n=4 biological replicates and the number of valid replicates is indicated between parenthesis for each condition.
single cell analysis of the in-house cohort of healthy livers.Figure 2.Cell type annotations of all four patients by the tSNE plot. Hepatocyte-cholangiocytes cluster includes potential stem-like cells capable of differentiating into both cell types. B) tSNE plot colored by patients Heatmap of marker genes of 16 cell types identified. The red box highlights the cell type specific expression of ACE2. The violin plot of ACE2 gene expression across all cell types.
In vitro Vasculotide vs.Figure 7A-F Primary human umbilical vein endothelial cells (HUVECs) or primary human dermal microvascular endothelial cells (HMVEC-DBls) were stimulated at 80% confluency with Vasculotide (treatment), Ang1 (positive control; ligand of Tie2), PBS (vehicle control), or VEGF (negative control; non-ligand of Tie2). Tie2 was immunoprecipitated from cell lysates and immunoblotted for total Tie2 or phosphotyrosine. Vasculotide treatment did not lead to increases in the pTie2/Tie2 ratio in HUVECs after 45-min (A-D) or 15-min (E) treatments, with (E) or without (A-D) serum/supplement starvation. Vasculotide also did not activate Tie2 receptors in HMVEC-DBls, whether in the presence or absence of serum, growth factor, and cytokine supplements (F).
a–d) dRagAQ61L suppresses autophagy.figf7(a-d) dRagAQ61L suppresses autophagy. (a) Drosophila fat body cells clonally expressing dRagAQ61L (marked in green by GFP expression) failed to accumulate autolysosomes (shown in surrounding control cells by punctate Lysotracker Red staining) in response to starvation for 4 h. Nuclei are marked in blue by DAPI. (b-d) Induction of autophagosomes in response to 4-h starvation is shown by the punctate pattern of GFP-Atg8a expression in control fat body cells (b), but not in cells expressing dRagAQ61L (c). The average number of GFP-Atg8a-marked autophagosomes per cell in control and dRagAQ61L-expressing clones is shown (d). Data are mean ± s.d., *P = 2.91 × 10−6, Students two-tailed t-test (n = 33 fat body samples imaged per genotype). Scale bars represent 25 μm in each panel. (e) RagA regulates LC3 conversion in mammalian cells. Myc-LC3 was co-transfected with RagAQL and RagCSN or RagATN and RagCQL into HEK293 cells as indicated. One day after transfection, cells were cultured in amino-acid-sufficienct medium (+AA) or amino-acid-depleted medium (−AA) for 4 h before collection. Western blotting for Myc-LC3 and HA-Rag were performed. Autophagic conversion of LC3I into the lipidated LC3II form was blocked by active RagA and stimulated by dominant-negative RagA. Full scans of blots are provided in Supplementary Information, Fig. S6.
Figure 3 Figure 3. DNA damage with nuclear accumulation of p53 in MGC A, B BMMΦ were infected with BCG (MOI15) or supplemented with NO-donor sodium nitroprusside (SNP) (300µM) for 6 days and cells were lysed with RIPA-buffer for western blot analysis of γH2Ax and p53. Densitometry of western blots relative to untreated MΦ (-). Depicted are individual experiments with mean ± SEM.  Figure 3. DNA damage with nuclear accumulation of p53 in MGC A, B BMMΦ were infected with BCG (MOI15) or supplemented with NO-donor sodium nitroprusside (SNP) (300µM) for 6 days and cells were lysed with RIPA-buffer for western blot analysis of γH2Ax and p53. Densitometry of western blots relative to untreated MΦ (-). Depicted are individual experiments with mean ± SEM. C BMMΦ were stimulated with LP for 6 days, fixed and stained for immunofluorescence by p53 (red) and DAPI (blue) for microscopy with Olympus ScanR; scale bar, 50µm. D, E BMMΦ were stimulated with LP for indicated times, stained and imaged as described in (C) and quantified by Olympus ScanR analysis software for colocalization of p53 and DAPI staining at indicated timepoints (D) Depicted are means ± SEM of 3 independent experiments >1000cells per condition. D, E BMMΦ were stimulated with LP for indicated times, stained and imaged as described in (C) and quantified by Olympus ScanR analysis software for colocalization of p53 and DAPI staining day 8 of LP stimulation compared to unstimulated cells (E). Depicted are means ± SEM of 3 independent experiments >1000cells per condition. F Samples of a patient with M. xenopi osteomyelitis from repeated biopsies at onset of disease (1st) and 2 months after (2nd) were quantified by immunohistochemistry for p53 and hematoxylin counterstaining. G Representative images of human NTM granuloma from lymphnodes, immunohistochemistry for p53 (brown) and hematoxylin counterstaining. H Human NTM granuloma from lymphnodes of 51 patients were stained as in (G) and quantified by microscopy. Depicted are means ± SEM. I Representative images of human NTM granuloma from lymphnodes, immunohistochemistry for p53 (brown), nitrotyrosine (red) and hematoxylin counterstaining.  J Human NTM granuloma from lymphnodes of 7 patients were stained as in (I) and quantified by microscopy and QuPath analysis software [54]. Depicted are means ± SEM. *p < 0.05, **p < 0.01 (two-tailed unpaired t-test).
Cancer-secreted EVs alter the spectrum of de novo protein synthesis in fibroblasts.Figure 6A. Schematic of 13C6-Arg labeling strategy to profile de novo protein synthesis in EV-treated NIH3T3 cells. B. A Venn diagram showing the numbers of 13C6-labeled proteins identified in NIH3T3 cells pretreated with MCF10A or MDA-MB-231 EVs. C. Detected 13C6-labeled proteins were analyzed by IPA for prediction of functions associated with proteins decreased or increased by >2-fold in MDA-MB-231-EV-treated cells. Pie charts show the numbers of proteins categorized by subcellular localization. D. A heatmap showing the comparison of log2 fold change (FC) of the abundance of each identified 13C6-labeled protein and its corresponding mRNA level determined by RNA-seq.
Figure 2(A) Assay of Tcf7l1 mRNA by RT-PCR for the first 4 days of differentiation in the presence or absence of 3 μM CH. Average and SD of three independent experiments. Day2 *p= 0.048, Day3 *p=0.036. B) Immunoblot for Tcf7l1 at day 3 of differentiation in the presence (+) or absence (-) of 3 μM CH. (C) Assay of FoxA2 mRNA by RT-PCR for the first 3 days of differentiation in the presence or absence of 3 µM CH. Average and SD of three independent experiments. **p=5x10-7. (D) ChiP-seq data from a compendium of transcription factor ChIP-seq analyses (Sánchez-Castillo et al, 2015). Gene tracks represent binding of Tcf7l1 at the FoxA2, Nodal and Eomesodermin (Eomes) gene locus. Red lines indicate the regions analyzed by ChIP PCR for Tcf7l1. (E) ChIP for Tcf7l1 followed by qPCR for the regions indicated in Fig. 2D. Analysis was performed in wild-type ES cells in 2i culture conditions. Average and SD of three independent experiments. Klf2 *p=0.025, FoxA2 *p=0.050, Eomes *p=0.023. (F) ChIP for Tcf7l1 followed by qPCR. Analysis was performed in wild-type ES cells on day 3 of differentiation in the presence or absence of 3 µM CH. Average and SD of three independent experiments. FoxA2 *p = 0.049.
Figure 9Representative electron micrographs of Wt and 1/2-DKO specimen indicate accumulations of ELVs and high numbers of coated pits forming from the ELVs in ribbon proximity (radius r = 1 µm from the center of the ribbon) in the DKO after 15 min stimulation with extracellular solution supplemented with 50 mM K+. Scale bars: 200 nm. Significantly reduced numbers of RA-SVs in IHCs of 1/2-DKO compared to Wt after stimulation, as quantified using random ultrathin sections of ribbon-occupied AZs from several IHCs per genotype. Mann-Whitney test; ***p < 0.001. Numbers of MP-SVs were slightly reduced in stimulated Wt compared to stimulated 1/2-DKOs, where SV numbers closely matched the ones of unstimulated 1/2-DKO. Mann-Whitney test; *p < 0.05. Reduced numbers of small vesicles are present in a 1 µm radius around the ribbon of 1/2-DKOs compared to Wt after stimulation. RA-SVs were excluded from this quantification. Student's t-test; ***p < 0.001. Stimulated 1/2-DKOs exhibited accumulations of ELVs in comparison to stimulated Wt. Mann-Whitney test; ***p < 0.001. Increased overall number of coated structures in stimulated endophilin 1/2-DKOs. (F') Both, coated vesicles and coated pits forming at ELVs were significantly increased in 1/2-DKO after stimulation. Mann-Whitney test; **p < 0.01; ***p < 0.001.
Fig.Figure 3a 231 genes were regulated in wild-type (WT) parental HEK 293T cells upon CHIR treatment (a minimum of 2-fold change). 166/231 of these transcriptional changes do not occur in dBcat cells and are therefore considered as β-catenin-dependent (red box). 27/166 β-catenin targets are also regulated in d4TCF cells indicating that they are TCF-independent b, c RT-qPCR-based validation of selected TCF-independent β-catenin-dependent target genes (B) upregulated or (C) downregulated in d4TCF cells (TCF-independent) treated with 10μM CHIR or DMSO for 24hr. Data represent the mean ± s.e.m. of averages of three independent experiments (N = 3). Samples were compared using Student"s t-test. Asterisks (*) indicate a p-value<
a) Fluorescence microscopy of wild-type yeast cells expressing an EGFP–Atg8p fusion protein with or without (control) treatment of 4 mM spermidine for 48 h.figf6(a) Fluorescence microscopy of wild-type yeast cells expressing an EGFP-Atg8p fusion protein with or without (control) treatment of 4 mM spermidine for 48 h. White arrows indicate vacuolar localization of EGFP-Atg8p indicative of autophagy. Scale bars, 5 μm. (b) Relative alkaline phosphatase activity (ALP activity) indicative of autophagy during chronological ageing of pho8ΔC60 yeast with (open bars) or without (closed bars) application of spermidine (4 mM). Data represent means ± s.e.m. (n = 3 *; P 0.01 and **P 0.001). (c) Relative alkaline phosphatase activity (ALP activity) indicative of autophagy during chronological ageing of wild-type (closed bars) and Δiki3Δsas3 (open bars) cells. Data represent means ± s.e.m. (n = 3; *P 0.01 and **P 0.001). (d) Chronological ageing of wild-type (▪, o) and Δatg7 (▴, ▿) with (open symbols) or without (closed symbols) addition of spermidine (4 mM) at day 1. Data represent means ± s.e.m. (n = 4). (e) Chronological ageing on water of wild-type (▪, o) and Δatg7 (▴, ▿) with (open symbols) or without (closed symbols) addition of spermidine (8 mM) at day 0. Data represent means ± s.e.m. (n = 4). (f) Quantification (fluorescence reader) of ROS production (DHE→Eth conversion) by wild-type and Δatg7 cells with and without supplementation of spermidine (8 mM), obtained from the ageing experiment shown in panel e. Data represent means ± s.e.m. (n = 4; *P 0.07 and **P 0.01).
Figure 1Proliferation curves of parental and AGO2KO HeLaS3 cells are plotted (n=6 experimental replicates). Colony-forming activity of HeLaS3 and AGO2KO cells was determined by colony-formation assay (n=3 experimental replicates). Tumour growth curves of xenografts derived from HeLaS3 or AGO2KO cells are shown as tumour diameter at different time points (n=5 mice for each group). Xenograft tumour weights were measured 30 days post- injection (n=5 mice for each group).
Figure 3A. Condensin binding assessed by ChIP against Cnd2-GFP. Mitotic indexes are indicated in parentheses. %IP are averages and s.d. calculated from 12 ChIPs on 6 biological replicates. For repeated 5S and gly05 genes, qPCR primers were designed within adjacent, unique 5' intergenic sequences. Note the use of different scales in the arm: high-occupancy and arm: low-occupancy panels. *** P<0.001, ** P<0.01, ° P>0.05. B. The level of Cnd2-GFP by western blotting. C. Condensin binding assessed by chromosome spreading. Cut3-HAimmunofluorescence microscopy signals were quantified on n> 100 chromosome spreads exhibiting Dam1-GFP at kinetochores (mitotic, M) or lacking Dam1-GFP (interphase, I). For each strain, four representative nuclei extracted from a same image acquired with same settings are shown. Asterisks indicate nuclei corresponding to Cut3-HA surface plots. Bar: 5 µm. Boxes indicate the 25th, median and 75th percentile and whiskers the min and max values from 3 independent experiments. *** P<0.001. D. Cut3-HA level by western blotting.
a) Ba/F3 cells expressing FOXO3(A3)-ER were stimulated with 4-OHT in the presence of mIL-3.figf3(a) Ba/F3 cells expressing FOXO3(A3)-ER were stimulated with 4-OHT in the presence of mIL-3. Cell lysates were analysed for glutamine synthetase (GS) activity in an enzyme assay (left). In addition, the expression of glutamine synthetase, p27 and actin was determined using western blot (right). Shown are the mean ± s.e.m. (n=3) and representative blots of these experiments. **P0.01. (b) Ba/F3 cells expressing FOXO3(A3)-ER were stimulated with 4-OHT for 16 h in the presence of mIL-3 together with MSO, as indicated. Cell lysates were analysed for glutamine synthetase activity in an enzyme assay (left). Furthermore the expression levels of glutamine synthetase, p27 and actin were determined using western blot (right). Shown are the mean ±  s.e.m. (n=3) and representative blots of these experiments. *P0.05, **P0.01. (c) Ba/F3 cells expressing myrPI(3) K-ER were cytokine-starved overnight. The next day, cells were washed in PBS and put in a medium without serum, with or without 4-OHT. At the times indicated, medium samples were taken and analysed for amino acid levels by high-performance liquid chromatography. Cells were lysed and equal amounts of protein were analysed by western blotting for levels of phospho-PKB (S473), phospho-FOXO3 (T32) and actin (inset). Shown are the mean of relative amino acid levels, compared with t=0 (n=2), and representative blots of these experiments. (d) Ba/F3 cells expressing FOXO3(A3)-ER were stimulated with 4-OHT in serum-free medium containing mIL-3. The medium was analysed for amino acid levels by high-performance liquid chromatography. Cells were lysed and analysed for protein levels of glutamine synthetase, p27 and actin (inset). Shown are the mean ±  s.e.m. of relative amino acid levels, compared with t=0 (n=4), and representative blots of these experiments. **P0.01. Uncropped images of blots are shown in Supplementary Fig. S7.
Figure 9(A) Immunofluorescence analysis of the old APPPS1 slice (14 DIV) treated with GM-CSF and vehicle Ctr and immunostained with CD68 (red), cell proliferation marker Ki67 (green) and M3.2 (blue). Scale bar: 50 µm.(B) Quantitative analysis of Ki67 and CD68 double positive microglial cells in the old APPPS1 tissue (14 DIV) treated with GM-CSF and Ctr reveals increased microglial proliferation upon treatment with GM-CSF. The values are expressed as percentages of CD68 and Ki67 double positive microglial cells from the total number of CD68 positive cells and represent mean ± SEM from 2 independent experiments, each experiment including 4 independent slice culture dishes (***P < 0.001). (C) Immunofluorescence analysis of the old APPPS1 tissue cultured alone or in co-culture with young WT brain slices (14 DIV) and immunostained with CD68 (red), Ki67 (green) and M3.2 (blue) Scale bar: 50 µm.(D) Quantitative analysis of Ki67 and CD68 double positive microglial cells in the old APPPS1 tissue cultured alone or in co-culture with young brain slices (14 DIV) reveals increased microglial proliferation upon co-culturing of old and young brain slices. The values are expressed as percentages of CD68 and Ki67 double positive microglial cells from the total number of CD68 positive cells and represent mean ± SEM from 3 independent experiments, each experiment including 2 independent slice culture dishes (**P < 0.01). (E) Old APPPS1 tissue was incubated with conditioned media collected from young WT slices and in addition treated with proliferation inhibitor AraC (young CM + AraC) or vehicle Ctr (young CM + Ctr). Immunofluorescence analysis was performed at 14 DIV using CD68 (red) and M3.2 (green). Scale bar: 50 µm.(F) Quantitative analysis of core-only plaques in the old APPPS1 tissue (14 DIV) incubated with conditioned media from young WT slices and in addition treated with AraC or Ctr reveals a decreased number of core-only plaques upon AraC treatment. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, each including 2 independent slice culture dishes (***P < 0.001).
Figure 2Approach to achieve targeted drug delivery and selective killing of metastatic stem cells: CXCR4-nanoconjugate interaction triggers CXCR4-mediated internalization in MetSCs, in primary tumors and metastatic foci, followed by FdU release to the cytosol and diffusion to the nucleus to induce double stand breaks leading to selective killing of CXCR4+ cells. Selective T22-GFP-H6-FdU nanoconjugate biodistribution in subcutaneous CXCR4+ SW1417 CRC tumor tissue 5h after a 100µg single intravenous dose, as measured by fluorescence emission using IVIS Spectrum 200 (N=5/group). Biodistribution is similar to that achieved by the T22-GFP-H6 targeting vector and undetectable after Buffer or free oligo-FdU treatment. (N=5 mice/group) Co-localization (yellow merged) of the T22-GFP-H6-FdU (green) and the CXCR4 receptor (red) and release of T22-GFP-H6-FdU into the cytosol in CXCR4+ tumor cells 5h after a 100ug dose of nanoconjugate, as measured by dual anti-GFP/anti-CXCR4 immunofluorescence (IF). DAPI (blue nuclear staining). Fluorescence emission was measured in the green and red channels using the Image J software and expressed as mean Area (A)±s.e.m (µm2) (N=10, 2 tumor fields x 5 mice; 200X). Note the significant (P=0.003) increase in the area occupied by the green dots (nanoconjugate realeased to the cell cytosol) in T22-GFP-H6-FdU-treated tumors, compared to free oligo-FdU-treated control tissues. Scale bar, 50 µm. Administration of the CXCR4 antagonist AMD3100 completely blocks T22-GFP-H6-FdU tumor biodistribution, as measured by fluorescence emission. Fluorescence is not detected in Buffer or free oligo-FdU controls (N=5 tumor fields/group). The uptake of T22-GFP-H6-FdU observed in CXCR4+ SW1417 tumor tissues is almost completely blocked by prior AMD3100 administration, as quantified using the anti-GFP IHC H-score. (N=5 tumor fields/group). Representative images of T22-GFP-H6-FdU uptake and AMD3100 competition by anti-GFP inmunostaining, which quantitation is reported in panel E. Scale bar, 50 µm
Figure 5(A) Immunoblotting of SH-SY5Y cells stably expressing AR-24Q (SH24Q) or AR-97Q (SH97Q) for Dnmt1, Dnmt3a and Dnmt3b. (B) Densitometry quantification showing that Dnmt1 level was up-regulated in SH97Q cells compared with SH24Q cells (n = 3). (C, D) Immunoblots for Dnmts of SH97Q with or without DHT treatment (C) and quantification data (D) (n = 3). (E) Seven genes with DNA hyper-methylation in their CpG islands were identified by DNA methylation array analysis. (F) The relative mRNA levels of CDC25B, GFRA3, NPY, HES5, SCTR, LEF1-AS1 and CABS1, normalized to beta-2 microglobulin, in DHT-treated SH24Q and SH97Q cells were measured using RT-qPCR (n = 3). (G) RT-qPCR analysis indicated the decrease of Hes5 mRNA level in DHT-treated SH97Q cells compared with DHT-untreated SH97Q cells (n = 3). (H) Methylation-specific PCR of SH24Q and SH97Q cells that were treated with DHT. (I) Hes5 immunoreactivity of spinal motor neurons in wild-type, AR-24Q, and AR-97Q mice (n = 3). (J) Hes5 mRNA levels in the spinal cords of wild-type, AR-24Q, and AR-97Q mice (n = 3).