EMBO/sd-character-level-ner huggingface dataset:
Figure 1Cell surface H2-Kb levels of wild type and TAP1-/- BMDC transduced with control vector or a vector expressing hβ2m were analyzed. Cross-presentation of OVA by wild type and TAP1-/- BMDC expressing hβ2m were compared to control BMDC, by measuring IL-2 production by a Kb-SIINFEKL specific T-cell hybridoma (B3Z) cultured with paraformaldehyde fixed BMDC that were incubated with varying numbers of OVA-coated latex beads for 6hr, prior to fixation. The effect of hβ2m on the presentation of peptides derived from endogenous antigen was assessed by measuring IL-2 levels in the culture supernatant of the B3Z hybridoma incubated with fixed VV-OVA infected WT and TAP1-/- BMDC transduced with control vector or hβ2m.
Figure 9Measured log2(H/M) values at four time points as a function of their half-lives estimated here and elsewhere (Cohen et al, 2013). All log2(H/M) values shown here are averages of values obtained in 5 experiments (3 using lactacystin, 2 using epoxomicin). Proteins for which statistically significant differences at t=24 hours were observed (P<0.05, two-tailed Welch's t-test) are shown in red. Expected log2(H/M) values based on equation 4 are plotted as light blue lines. To minimize the masking of potential dependencies by the slight imperfections in the H/M normalization process (which introduces small offsets along the Y scale), average population log2(H/M) values of each time point (Fig. 6E) were subtracted from all measured Log2(H/M) values. Data for 1,416 proteins for which half-life estimates were available.
Functional interactions between uPAR-mediated cell adhesion to VN, plasminogen activation and PAI-1.Figure 8A Binding of sc-uPA to uPAR induces conformational changes in the receptor increasing its avidity and affinity for matrix-associated VN (I) leading to increased mechanical cell-matrix coupling and subsequent cellular signalling. When at the plasma membrane, sc-uPA and Plg activate each other (II) and cleave VN in the RGD-motif (IIIa). Cleavage of VN at this position inactivates the pro-adhesive properties of the molecule by destroying integrin binding and through release of the SMB domain from the extracellular matrix, thereby attenuating the mechanical coupling between cells and the extracellular matrix.B In conditions where PAI-1 is also present, the activity of sc-uPA in promoting cell adhesion is counterbalanced by PAI-1 binding to an overlapping epitope in VN. When proteolysis is triggered, tc-uPA reacts with VN-associated PAI-1 (IIIb) resulting in the formation of a transient quaternary uPAR:uPA•PAI-1:VN complex (IV). The complex formation between uPA and PAI-1 permanently inactivates the proteolytic activity of uPA and leads to major conformational changes in PAI-1 that release it from VN (V) thereby liberating the SMB-domain for interaction with uPAR (VI).
Figure 7 A Cortical mouse neurons from tau knockout (KO) mice were serum-starved in Hank's balanced salt solution for 2 hours. The cells were then imaged for NiMA, after which insulin or amino acids were immediately added, and the cells were then imaged again 30 minutes later Data information: Each colored lin refers to a single field of view containing 2-15 cells, and each pair of solid and dotted lines (same color) refers to the same field of view. Statistical analyses were performed using Student's two-tailed unpaired t-test  B Cortical mouse neurons from tau KO mice were treated with AβOs for 18 hours before being serum-starved in AβO-containing Hank's balanced salt solution for 2 hours. The cells were then imaged for NiMA, after which insulin was immediately added, and the cells were then imaged again 30 minutes later. Note that NiMA occurred in the absence or presence of AβOs, which inhibited NiMA in wild type human neuron Data information: Each colored lin refers to a single field of view containing 2-15 cells, and each pair of solid and dotted lines (same color) refers to the same field of view. Statistical analyses were performed using Student's two-tailed unpaired t-test
Figure 3A-C. ThT kinetics of 10μM rAβ1-42 alone or in presence (1:1) of 3 homologue peptides (full screen on Appendix Figure S3,S4, n= 2 independent experiments with 4 repeats). Reused images in Appendix figure S3 D. Lag time difference between rAβ1-42 alone (rAβ1-42 = 0) and in the presence of peptides (Statistics: Brown-Forsythe and Welch Anova tests with Dunnett T3 multiple comparison corrections, n=2 independent experiments with 4 repeats).Graph: Mean difference and 95%CI. * P ≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001. E. Fluorescence amplitude difference between rAβ1-42 alone (rAβ1-42 = 0) and in the presence of the peptides (Statistics: Brown-Forsythe and Welch Anova tests with Dunnett T3 multiple comparisons correction, n=2 independent experiments with 4 repeats). Graph: Mean difference and 95%CI. * P ≤0.05, *** P≤0.001, **** P≤0.0001. F. Representative TEM images of fibrils made in presence of 1:1 rAβ1-42:peptides. Scale bars: 500nm G. Fibril length difference between Aβ alone and in presence of peptides (Statistics: Brown-Forsythe and Welch Anova test with Games-Howell multiple comparison correction). Graph: Mean difference and 99%CI. ** P≤0.01, **** P≤0.0001. At least 9 different positions on grid and at least 100 fibrils were counted for each condition (except Aβ+P23, Aβ+P24). Fibril length distribution in Appendix Figure S7. H. Curcumin binding to Aβ fibrils alone or in presence of P5. (n=2, at least 4 repeats, statistics: Kolmogorov-Smirnov test). Graph: mean±SD. P= 0.049. Reused image in Appendix Figure S9. I. Representative AFM height images of Aβ fibrils alone or in a 1:1 mixture with P3, P5, P8 and P12 peptides are show in the top row. The boxes indicate the magnified regions shown in the second row. Arrows indicate the locations of representative individual fibrils shown in magnified detail, each shown as a 200 nm digitally straightened segment and a 100 nm segment of the corresponding 3D surface envelope model that was calculated from the image data. The scale bar for each row are shown to the left, with both the 3D model and the straightened image data representing 10 nm. The colour scale of the 3D models from blue to yellow indicate the distance (from low to high) between the fibril surface and fibril centre axis to demonstrate their twist patterns. The average fibril height distribution of around 80 manually selected filaments per sample that showed twist patterns characteristic of single, not fragmented, amyloid fibrils are shown in the bottom row.
Figure 5a, Schematic of prolonging G1 by DNA damage using NCS. Asynchronously proliferating U2OS mother cells were treated with 100 ng/mL NCS, and their daughter cells were analyzed for a full cell cycle. b, Shift in phase durations of U2OS cells treated with NCS. , boxplots representing the distributions of phase durations in untreated cells are underlaid for comparison. *, P < 1 × 10-5; ***, P < 1 × 10-20, 2-sided Kolmogorov-Smirnov test. Number of cells: NCS, n = 114 c, Pairwise correlation between phase durations for U2OS cells treated with NCS. Number of cells: NCS, n = 114 d, Schematic of prolonging S phase by replication stress using aphidicolin. Asynchronously proliferating U2OS cells were treated with 50 ng/mL aphidicolin for 8 hours, washed with PBS, and then replenished with fresh media. Only cells whose S phase overlaped with the 8-hour treatment window were analyzed. e, Shift in phase durations of U2OS cells treated with 50 ng/mL aphidicolin. boxplots representing the distributions of phase durations in untreated cells are underlaid for comparison. *, P < 1 × 10-5; ***, P < 1 × 10-20, 2-sided Kolmogorov-Smirnov test. Number of cells: aphidicolin, n = 153. f, Pairwise correlation between cell cycle phase durations under aphidicolin treatment. Number of cells: aphidicolin, n = 153.
Figure 2Immunoblot analysis of C99-PS1 NTF or full-length (FL) crosslinks (CL) of the indicated mutants. Samples that were not UV-irradiated were loaded to control for specificity. Changes in the ratio of crosslink efficiencies at positions T48 and L49 compared to corresponding controls (n = 4-5 biological replicates). Changes in the ratio of crosslink efficiencies at positions K54 and V44 compared to corresponding controls (n = 4-5 biological replicates).
Figure 4(A) MCF10A cells were either not treated or treated separately with Latrunculin B, Blebbistatin, EGTA, serum starvation, and Y27632, and were stained for TRIP6 and LATS1. Merged images show LATS1 (green), TRIP6 (red) and DNA (blue). Scale bar=20µm. (B) Cells were treated as in (A), then lysed and anti-TRIP6 antibodies were used to isolate immune complexes. Immune complexes and lysates were probed by western blotting for LATS1 and TRIP6. (C) Quantification of (B) is shown. (Mean ± SD; n=3; *P≤0.05, **P≤0.01, T-test).
Figure 4FACS analysis of cell cycle progression in rpb mutants. Cells were synchronized in G1 with α‐factor and monitored at different times after release in the presence of 40 mM HU. Scheme of the migration pattern of the bubble‐, single Y‐, double Y‐ and X‐shaped replication intermediates in 2D gel electrophoresis. Slowdown of RF progression through a chromosomal region. 2D gel electrophoresis of replication intermediates of 4.3‐kb PstI DNA fragments from WT and RNAPII mutants in the presence of 40 mM HU at different times after G1 release. A black arrow indicates accumulation of long Y molecules, and a white one indicates the specific accumulation of X molecules.
Figure 2(a-f) Microtubules in the DC of pig (a,b), horse (c,d), and mouse (e,f) sperm traced from Volta phase plate cryo-tomograms of intact sperm. Doublets are colored blue (A-tubule in light blue, B-tubule in dark blue), while singlets are pink. (g-i) Tomographic slices through cryo-FIB milled lamellae of the DC-to-axoneme transition in pig sperm show how the change in geometry (g, white arrows and white dashed lines) coincides with the appearance of axoneme accessory structures (h, white arrows) and with density in the A-tubule (i, compare insets in white and black boxes). In (i), the white and black arrows indicate where the cross-sections in white and black boxes were taken from. (j) In situ structure of the pig sperm DC microtubule doublet with the tubulin backbone in grey and microtubule inner protein densities colored individually. The gold and turquoise densities on the luminal side of the doublet are consistent with the positions of parts of the inner scaffold. This structure represents the DC doublets closest to the axoneme
Figure 3A. Schematic overview of SCRN1 and VAP constructs. Indicated is if expressed VAP/SCRN1 proteins co-localize in both hippocampal neurons and COS cells, and co-precipitate in pull-down assays. B. COS7 cells co-expressing GFP-SCRN1 with HA-VAPB-K87D/M89D. Scale bars: 10 µm (full size) and 5 µm (zoom). C. COS7 cells co-expressing HA-VAPB with GFP-SCRN1-Y40A, GFP-SCRN1-F144A, GFP-SCRN1-F153A or GFP-SCRN1-F402A. Scale bars: 10 µm (full size) and 5 µm (zoom). D. Hippocampal neurons (DIV16) co-expressing HA-VAPB with GFP-SCRN1-Y40A, GFP-SCRN1-F144A, GFP-SCRN1-F153A or GFP-SCRN1-F402A. Scale bars: 10 µm (full size) and 5 µm (zoom). E. Quantifications of SCRN1 recruitment to VAPB-positive structures in COS7 cells (%). Left graph: co-expression of GFP-SCRN1 with HA-VAPB or HA-VAPB-K87D/M89D ( N=2-3, n= 44-46). Right graph: co-expression of HA-VAPB with GFP or GFP-SCRN1, GFP-SCRN1-N, GFP-SCRN1-C, GFP-SCRN1-Y40A, GFP-SCRN1-F144A, GFP-SCRN1-F153A or GFP-SCRN1-F402A (N=2-3, n=41-64). Data information: Data represent Mean ± SEM; NS: not significant; *P < 0.05; **P < 0.01; ***P < 0.001, by Chi-square test with post-hoc analysis including Bonferroni correction. F. Pull down of HEK293T cells co-expressing Myc-VAPB with GFP, GFP-SCRN1, GFP-SCRN1-Y40A, GFP-SCRN1-F144A, GFP-SCRN1-F153A or GFP-SCRN1-F402A. G. Sequence alignment of the C-terminal human SCRN1, SCRN2 and SCRN3. Amino acid position three (asterix) in FFAT-like motif (orange) of SCRN1 is not shared in SCRN2 and SCRN3.
Figure 3A, B Lysates from NSC34 cells treated for 24 h and immunoblotted for SQSTM1/p62 and LC3 expression. (B) Quantification from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test, **P = 0.0047, *P = 0.0393. Concentration used: 1 μM GELD, 10 μM ERY, SPL, FSK. C Relative expression level of Sqstm1/p62, Lc3, Tfeb, Hspb8 and Bag3 mRNAs in NSC34 cells treated for 24 h. Data are mean ± SEM from three biological replicates. 2-way ANOVA followed by Dunnett's multiple comparisons test, ***P<0.001. Dotted lines represent RNA expression in the DMSO control. Concentration used: 1 μM GELD, 10 μM ERY, SPL, FSK. D Lysates from NSC34 cells transfected with a proteasome activity reporter (GFPu), treated for 24 h and immunoblotted for GFP expression. Quantification from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test, *P = 0.0398 GELD vs DMSO, *P = 0.0124 SPL vs DMSO, *P = 0.0253 FSK vs DMSO. Concentration used: 1 μM GELD, 10 μM ERY, SPL, FSK. E Co-immunoprecipitation (IP) analysis on 66R-derived poly-GP and ubiquitin interaction. Lysates from NSC34 cells transfected with 66R and treated with 10 µM MG132 for 16 h, immunoprecipitated for poly-GP and immunoblotted for ubiquitin and poly-GP. F Lysates from NSC34 cells transfected with scrambled-GPx100, treated for 24 h with GELD, SPL and/or 16 h with MG132 and immunoblotted for scrambled-GP expression. Quantification from three biological replicates. Data are mean ± SEM. 1-way ANOVA followed by Uncorrected Fisher's LSD, P* = 0.0186 for GELD vs DMSO, ***P = 0.0001 GELD + MG132 vs GELD and SPL vs DMSO. Concentration used: 1 μM GELD, 10 μM SPL G Lysates from NSC34 cells transfected with scrambled-GPx100, treated for 24 h with SPL and/or 10 mM 3MA and immunoblotted for scrambled-GP expression. Quantification from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test, ****P<0.0001 for SPL vs DMSO and 3MA vs DMSO, ***P = 0.0008 SPL + 3MA vs SPL. Concentration used: 1 μM GELD, 10 μM SPL
Nucleoli disruption in mouse cells by depletion of B1‐containing RNAsCLSM images of UBF immunofluorescence in mouse NIH 3T3 cells treated for 5 h with α‐amanitin to inhibit Pol II transcription show the dispersion of nucleoli, as previously also imaged via RNA staining (Caudron‐Herger et al, ).Figure 6CLSMimages of UBFimmunofluorescence in mouseNIH 3T3cells treated for 5 h with α‐amanitin to inhibit Pol II transcription show the dispersion of nucleoli, as previously also imaged via RNAstaining (Caudron‐Herger et al, ). CLSMimages showing the localization of NPM (immunofluorescence, red) in mouse NIH 3T3 cells treated with ASO as indicated and counterstained with DAPI (blue).
Figure 3A, B) Schematic depiction of ftsj1 and wdr6, and target sites of mutations introduced by the CRISPR-Cas9 system in HEK293T cells. Shaded and open boxes indicate coding regions and untranslated regions of exons, respectively. Lines indicate introns. For ftsj1, two sgRNA sequences for targeting exons 2 and 3 are noted. For wdr6, two sgRNA sequences for targeting exons 1 and 2 are noted. Sequences of both alleles of ftsj1 or wdr6 in KO1 and KO2 cell lines are aligned. Deleted nucleotides are indicated as dashed lines. (C) Secondary structures of human tRNAPhe(GAA) with modified nucleosides. Mass chromatograms of the nucleosides, Cm (Q1/Q3=258.1/112.1), Gm (Q1/Q3=298.1/152.1) and A (Q1/Q3=268.1/136.2) of tRNAPhe(GAA) isolated from WT, ftsj1 KO and wdr6 KO cells. Target peaks are indicated by black triangles. Cm, 2'-O-methylcytidine; Gm, 2'-O-methylguanosine; Q1/Q3: the mass of the precursor ion and the mass of the product ion. Mass chromatograms of the nucleosides m1G (Q1/Q3=298.1/166.1), m7G (Q1/Q3=298.1/166.1) and m2G (Q1/Q3=298.1/166.1), o2yW (Q1/Q3=541.2/409.0), m5C (Q1/Q3=258.1/126.1) and A (Q1/Q3=268.1/136.2) of tRNAPhe(GAA) isolated from WT, ftsj1 KO and wdr6 KO cells. Target peaks are indicated by black triangles. m2G, 2-methylguanosine; D, dihydrouridine; m22G, N2,N2-dimethylguanosine; m5C, 5-methylcytidine; m7G, 7-methylguanosine; m5U, 5-methyluridine; m1A: 1-methyladenosine; ψ: pseudouridine; o2yW, peroxywybutosine. Q1/Q3: the mass of the precursor ion and the mass of the product ion. Combined the retention time of standard product, we marked the o2yW in Figure 3G. Considering the change of this peak area was consistent with that of o2yW, we speculated the other peak was generated by the intermediate product of o2yW with nature isotope labelled.
Figure 6A. Western blot of LC3B in lymphoblasts of OFD type I patients and controls, either untreated (-) or exposed to Baf-A1 (10nM, 2h)(+). Cells were cultured in complete medium (FM, top) or under serum starvation for 4h (STV, bottom). ACTIN and GAPDH were used as loading controls. B. (Left) Graphs show LC3B-II levels normalized on ACTIN in patients lymphoblasts and controls cultured in complete medium (FM). (Right) Graphs show LC3B-II levels normalized on GAPDH in patients lymphoblasts and controls in serum starvation for 4h (STV). Normalized LC3B-II levels are expressed as fold change versus untreated conditions (-) of control cells, n=4 patients and 3 controls. C. Western blot of ATG13 and ATG101 proteins in serum starved lymphoblasts from controls and OFD type I patients. (Right) Protein levels relative to ACTIN (loading control) are expressed as fold change versus controls, represented by the dashed line, n=4 patients and 3 controls.
VEGF-A is strongly expressed in the RPE, the lens and the ciliary body in the eye, and its expression is maintained with progressive age.Figure 1A.-E. Staining for β-galactosidase in 3-months old VEGF-Ahyper(lacZ/wt)mouseeyes.A. Low magnification image shows β-gal+ cells (in blue) in the RPE (white arrow), retina (blue arrow), ciliary body (black arrow), and lens (orange arrow). Images of Figures 1B to 1E are higher magnification images of Figure 1A. Scale bar 200 μm.B. Strong expression of VEGF with β-gal+ cells are observed in the RPE (short white arrow) and the inner nuclear layer (INL) (long white arrow), while less staining is observed in the ganglion cell layer (black arrow) of the retina. Scale bar 100 μm.C. Ciliary body epithelial cells are β-gal+, similarly as RPE cells (white arrow). Scale bar 100 μm.D. VEGF-A is strongly expressed in secondary nuclearfiber cells in the adult lens (white arrow). Scale bar 50 μm.E. No β-gal+ cells are observed in the corneas of adult VEGF-Ahyper(lacZ/wt)mouseeyes. White arrow shows the stroma of the cornea and the black arrow shows the corneal epithelium. Scale bar 100 μm. G. RPE cells maintain strong expression of VEGF-A (β-gal+ cells [white arrow]) in the retina with progressive age. Immunofluorescence for β-gal in the retina of a 24-months old VEGF-Ahypermouse is shown. Ocular macrophages (F4/80+ cells [yellow arrow]) show no strong β-galactosidase expression, while some immunolabeling for β-galactosidase is detected in retinal cells of the inner nuclear layer (orange arrow) of the retina. RPE: retinal pigment epithelium; ONL: outer nuclear layer; INL: inner nuclear layer. Scale bar 50 μm. H. VEGF-A continues to be highly expressed in secondary nuclear fiber cells in the aged lens (shown is a lens of a 24-months old VEGF-Ahyper mouse; nuclear β-galactosidasestaining (arrow) reflects cellular VEGF-A expression). Cor: lenscortex; Cap: lens capsule. DAPI labels nuclei (blue). Scale bar 25 μm.
Figure 7Gene expression profiles of bulk PBMCs from P. falciparum-infected asymptomatic individuals and healthy immune controls were compared. A. Hierarchical clustering heat map of the 171 differentially expressed genes (DEGs) in P. falciparum asymptomatic and healthy immune control participants. C. Mean-difference plot displaying DEGs between asyptomatic P. falciparum malaria and healthy immune controls. Each gene is plotted as a single point determined by log-fold-change and average transcript abundance. Red genes are overrepresented, and blue genes are underrepresented in asymptomatic malaria. Gene expression profiles of bulk PBMCs from P. falciparum-infected asymptomatic individuals and healthy immune controls were compared. B. Bar plots showing significantly enriched gene ontology (GO) terms scaled by Log10(P-value). Red GO terms are upregulated and blue GO terms are downregulated in asymptomatic P. falciparum malaria compared to healthy immune controls. Gene expression profiles of bulk PBMCs from P. falciparum-infected asymptomatic individuals and healthy immune controls were compared. D. Spearman correlation matrix (Benjamini-Hochberg adjusted FDR <5%) between parasitemia levels and immunoregulatory genes differentially expressed between asymptomatic P. falciparum-infected individuals and healthy immune controls. Significant positive correlations are shown in blue and significant negative correlations are shown in red. Gene expression profiles of bulk PBMCs from P. falciparum-infected asymptomatic individuals and healthy immune controls were compared. E. Mean RPKMs + SEM of selected genes in P. falciparum malaria asymptomatic individuals (n=5) and healthy immune controls (n=6). Dotted red lines depict transcriptional levels of P. falciparum-infected symptomatic individuals, Mann-Whitney test of biological replicates, *p<0.05.
Frequent irregularities in the adenine‐specific methylase pglX in BREX type 1Irregular genotypes (duplication, inversion, and premature stop codon) associated with pglX.Figure 7A Irregular genotypes (duplication, inversion, and premature stop codon) associated with pglX. B Genomic organization of BREX system type 1 in Methanobrevibacter smithii ATCC 35061. C Genomic organization of BREX system type 1 in Lactobacillus rhamnosus GG. A cassette switch between the short and the long forms of pglX is observed when the sequences of two isolates of Lactobacillus rhamnosus GG (accessions FM179322 and AP011548, respectively) are compared. Repeat sequences between the short and long forms are shown in black.
Figure 3(A) Western blot analyses of the degradation of endogenous p65 protein in BMSCs from Sp7-Cre;Cdc20f/f and Cdc20f/f mice. (B) Western blot analyses of the degradation of endogenous p65 protein in NC and CDC20si hBMSCs. (C) Western blot analyses of the degradation of nuclear p65 protein after the knockdown of CDC20. The cytoplasmic and nuclear protein of NC and CDC20si HEK293T cells were extracted after TNF-α treatment for 30 minutes. (D) The graphically presented amount of p65 of NC and CDC20si HEK293T cells was normalized with α-tublin and H3 expression. The percent of p65 protein was calculated accordingly. (n=6) (E) Western blot analyses of the degradation of nuclear p65 protein after the overexpression of CDC20. The cytoplasmic and nuclear protein of overexpressed Myc-CDC20 and Vector HEK293T cells were extracted after TNF-α treatment for 30 minutes. (F) The graphically presented amount of p65 of overexpressed Myc-CDC20 and Vector HEK293T cells was normalized with α-tublin and H3 expression. The percent of p65 protein was calculated accordingly. (n=5) (G) Western blot analyses of the degradation of p65 protein after the overexpression of Myc-CDC20. hBMSCs were transfected with Vector and Myc-CDC20 plasmids for 36 h, cells were treated with or without 10 μM MG132 for 6 h before collected.