EMBO/sd-character-level-ner huggingface dataset:
Figure 5(A) Experimental paradigm performed in all the trials. (B) Fall latency from an accelerating rotarod for 5-11-week-old WT and R6/2 mice during cholesterol supplementation (WT=17; R6/2-untreated=21; R6/2-Chol=13). (C) Rearing activity in open field at 10 weeks of age (WT=14; R6/2-untreated=21; R6/2-Chol=15). (D) global activity in the open field test at 10 weeks of age (WT=14; R6/2-untreated=21; R6/2-Chol=15). (E) Index of discrimination (%) in WT, R6/2-untreated and R6/2-Chol mice during disease progression, at 8 weeks of age (WT=24; R6/2-untreated=36; R6/2-Chol=21), at 10 weeks of age (WT=25; R6/2-untreated=35; R6/2-Chol=20) and at 12 weeks of age (WT=24; R6/2-untreated=30; R6/2-Chol=19); the index above zero indicates a preference for the novel object; the index below zero indicates a preference for the familiar object. As no differences were found between R6/2 mice treated with saline (R6/2) or treated with empty g7-NPs (R6/2-emp), data were pooled.
Figure 5(A) Immunoblot analysis of fibronectin in indicated tissues isolated from Wt, Hpn+/- and Hpn-/- mouse (representative of at least three repeats). GAPDH blot is used here as the loading control. (B) Immunoblot analysis of fibronectin and β-tubulin (loading control) in lysates from Wt and Hpn-/- mouse mammary tissue (N = 5 animals each) from another hepsin knock out mouse model (C) Immunoblot analysis of fibronectin, hepsin, and β-tubulin (loading control) in prostate lysates of control mice or mice with prostate-specific hepsin overexpression N=2 mice each, the two prostate lobes were run separately (a and b).
Figure 7A. Simple western analysis (Peggy Sue) and quantifications (right panels) of mouse lung epithelial cells shows increased ph-EZH2 (T311), ph-TAK1, myosin activity (ph-MLC2) and POL2-K7m levels in AAV-mediated TGFβ1 over-expression. Note, increased ph-EZH2 and POL2-K7m levels are attenuated by the EZH2 inhibitor GSK126, whereas ph-TAK1 and ph-MLC2 levels cannot be rescued by GSK126. Quantifications (right panels) show violin plots, *p < 0.05, **p < 0.01, ***p < 0.001, ns = non-significant, Kruskal-Wallis/Dunn's. Data information: All violin plots display minimum, first quartile, median, third quartile and maximum; n = 5 control, 12 AAV-TGFβ1 and 13 GSK126-treated AAV-TGFβ1 mice. B. Representative of 3D computed tomography (CT) reconstruction of the lung from control, AAV-TGFβ1 and GSK126-treated AAV-TGFβ1 mice (green: lung tissue, red: airways, and region-of-interest (ROI): blue). Insets show µCT slices in the middle of the lung from respective mice. Note, GSK126 attenuates TGFβ1-induced lung injury. Quantification (right panel) shows mean intensity of ROIs from the whole lung (violin plots, *p = 0.0385, **p = 0.0012, ANOVA/Holm-Sidak's). Data information: All violin plots display minimum, first quartile, median, third quartile and maximum; n = 5 control, 12 AAV-TGFβ1 and 13 GSK126-treated AAV-TGFβ1 mice. C. qPCR analysis of differentiation genes in epithelial cells reveals that EZH2 is required for the effect of TGFβ1 on metaplastic differentiation gene expression. Data show mRNA levels of profibrotic genes normalised to S26 (violin plots, *p < 0.05, **p < 0.01, ***p < 0.001, ANOVA/Holm-Sidak's). Data information: All violin plots display minimum, first quartile, median, third quartile and maximum; n = 5 control, 12 AAV-TGFβ1 and 13 GSK126-treated AAV-TGFβ1 mice. D. Immunofluorescence analysis of KRT5 as a marker for alveolar metaplastic basal cells and ph-EZH2 (scale bars 100 µm), pro-SFTPC as a marker for alveolar type 2 epithelial cells (scale bars 50 µm) and quantifications (right panels) show percentage of KRT5+ pods area per 10X field and percentage of pro-SFTPC+ cells per 20X field (*p < 0.05, unpaired t-test). Data information: All violin plots display minimum, first quartile, median, third quartile and maximum; n = 5 control, 12 AAV-TGFβ1 and 13 GSK126-treated AAV-TGFβ1 mice.
/6 conformations by cysteine cross-linking.Figure 5A. Cross-linking of a purified preparation of wild-type Smc5/6 hexamer in the absence and presence of Nse5/6. ATP and plasmidDNA were added as substrates as denoted. Products were analysed by SDS-Page and Coomassie staining. A cross-linked species derived from natural cysteines is indicated by an arrowhead ('XL'). Note that a fraction of Nse4 is converted into a more slowly migrating species, presumably by intra-molecular cross-linking. B. Cross-linking of engineered variants of the Smc5/6 hexamer. As in (a) using Smc5 and Smc6 cysteine mutants. Schemes indicate the location of engineered cysteines and their expected ability to cross-link in a rod-like and a ring-like conformation. High-molecular weight species were analysed by SDS-Page and Coomassie staining. Wild-type hexamer ('wt') is included as cross-linking control. Species occurring only in the presence of engineered cysteines are labelled by coloured arrowheads. Cross-linking efficiencies were calculated from the intensity of Coomassie-stained bands by comparing the band of the corresponding cross-linked species to the bands of unmodified Smc5 and Smc6. Numbers below the gel quantify the percentage of cross-linked protein species in the displayed gel. Comparable numbers were obtained in at least one additional independent experiment. C. DNA effects on Smc5/6 arm co-alignment as judged by CC-Cys cross-linking. As in (B) but also including 40bpDNA. Additon of plasmidDNA but not 40bpDNA reduces CC-Cys cross-linking in the Smc5/6 hexamer. D. DNA effects on head engagement as judged by E-Cys cross-linking. As in (B) also including 40bpDNA. plasmidDNA binding, but not 40bpDNA binding, overcomes inhibition of E-Cys cross-linking by Nse5/6. E. Effects of 40bpDNA and plasmidDNA on head engagement (as judged by E-Cys cross-linking) of the Smc5/6 complex with wildtype (wt) or hydrolysis-deficient (EQ) heads, in both the presence or absence of the Nse5/6 complex. Cross-linking efficiencies were calculated from the intensity of Coomassie-stained bands by comparing the band of the corresponding cross-linked species to the bands of unmodified Smc5 and Smc6. Numbers below the gel quantify the percentage of cross-linked protein species in the displayed gel. F. Effects of plasmidDNA on head engagement of the Smc5/6 complex (as judged by E-Cys cross-linking) in the presence of ATP or the non-hydrolyzable analogue ATPγS. Calculations and quantifications as in (E).
Figure 2(a) Growth assay using the ACT1-CUP1 reporter system. Yeast cells carrying the ACT1-CUP1 reporter were deleted of pseudouridylase genes (indicated on the left), and were then assayed for growth at 30°C on media containing various concentrations of [Cu2+] (indicated at the bottom). (b) Growth rescue by restoration of pseudouridylation. The wild-type strain [from (a)] or the snr81Δ pusΔ strain [also from (a)], which exhibited the most severe growth-deficiency phenotype, was transformed with an empty vector or a plasmid carrying a pseudouridylation guide RNA gene targeting either position 42, position 44, or both (indicated). The resulting cells were assayed for growth at 30°C on media containing various concentrations of [Cu2+] (indicated at the bottom). (c) Schematic representation of U2-pre-mRNA interaction. The U2 BSRR sequence and the pre-mRNA branch site sequence are shown. The arrows indicate several point mutations at the pre-mRNA branch site. Stem-loops I, IIa and IIb are also indicated. (d) Splicing assay using the wild-type and mutant ACT1-CUP1 reporters. RNAs isolated from the wild-type and the snr81Δ pusΔ strains (indicated on the top), which carry the wild-type ACT1-CUP1 reporter pre-mRNA or any of the mutant ACT1-CUP1 reporter pre-mRNAs [indicated, also see (c)], were used for splicing assay (primer-extension analysis). The un-spliced pre-mRNA, lariat intermediate, and spliced mRNA are indicated. A primer complementary to U6 was also used (as an internal control) in the assay, and the U6 band is indicated as well. In addition, the growth phenotype of each strain (in various concentrations of [Cu2+]) is also shown. Lanes 1-12, lanes 13 and 14, and lanes 15 and 16 are from separate gels. (e) Quantification of ACT1-CUP1 mRNA levels. Spliced ACT1-CUP1 mRNA levels were calculated relative to U6 in each lane. The quantification was based on three independent experiments. (f) Relative improvement/reduction for the mutant reporters. Relative improvement or reduction in splicing was calculated by normalizing the splicing efficiency (mRNA/U6) of each mutant reporter to that of WT reporter (set at 1).
Figure 2(A) Determining the number and density of CD22, CD19, IgM and IgD on the surface of wild-type primary B cells. Cells were stained with PE-conjugated antibody against CD22 (blue profile), CD19 (red profile), IgM (red profile) or IgD (red profile) and their fluorescence profiles compared to those of standard beads (grey profiles), which each possess a well-defined number of binding sites (st0=blank, st1-st4=increasing number of binding sites) against the primary antibody. For IgM, where the range of expression is large, the low and high 25 percentiles were calculated as in Mattila et al. 2013 and shown in brackets.Data are representative of three independent experiments. (B-E) Dual-colour SIM analysis of CD22, IgM, IgD and CD19. Wild-type primary B cells were fixed, stained with Atto633 or 488-conjugated antibody against CD22, IgM or IgD and Alexa647-conjugated antibody against CD19 and settled onto nonstimulatory coverslips. Cells were then embedded in agarose, imaged with SIM and analysed.(B) SIM images of CD22, IgM, IgD and CD19.(C) Cross-correlation function.(D) Pearson correlation coefficient.(E) Cluster size calculated from autocorrelation analysis.
Figure 7Schematic representation of VE- cadherin tension sensor (VE-cad FL) and VE-cadherin tailless sensor (VE-cad FL-TS). VE- cadherin tension sensor has a ferredoxin-like (FL) linker-based FRET module inserted within VE-cadherin between the p120 and the β-catenin-binding site, whereas VE-cadherin tailless sensor lacks the catenin binding region of VE-cadherin. The FRET module (depicted in box) consists of two fluorophores, YPet and mCherry separated by an elastic domain. When the module is under tension, FRET from YPet to mCherry decreases. HUVEC were transfected with control or VE-cadherin-specific siRNA and transduced with VE-cad FL or VE-cad FL-TS. Cell lysates were immunoblotted for VE-cadherin and actin. C Immunofluorescence staining for VE-cadherin of HUVEC transfected with control or VE‑cadherin specific siRNA (VE-cad kd) and transduced with VE-cad FL or VE-cad FL-TS. D HUVEC were either transfected with control or VE-cadherin targeting siRNA and transduced with VE‑cad FL or VE-cad FL‑TS. The tension sensor was immunoprecipitated from cell lysates using an anti-GFP antibody. Precipitates as well as total cell lysates were analyzed by immunoblotting for indicated antigens. Molecular weight markers are indicated in kDa. E, Quantification of FRET efficiency (percentage) in junctions of HUVEC expressing VE-cad FL or VE-cad FL-TS, after thrombin stimulation (1 U/ml) or under control conditions.
Fig.Figure 4A-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. C Comparison of growth kinetics between WT WNV and WNV-poly(A) viruses in MEF cells. MEF cells were infected with either WT WNV or WNV-poly(A) virus at an MOI of 0.01. Values indicate mean ± sd from two replicates of one representative experiment. 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. D Survival rate of IFNAR-/- mice infected with different dosages of WNV-poly(A) (n=5). 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. E Cell morphology changes of MEF cells infected with WT WNV and WNV-poly(A). 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.
Anchor of PPM1H is a folding motif.Figure 6(A) Interactions between the anchor of PPM1H against the electrostatic surface of the core catalytic domain. The region is placed in context with the dotted box on a ribbon model of PPM1H (right). (B) Incremental deletions of the N-terminus from residues 1-37 to 1-44, one residue at a time. Upon deletion of R43 (44-end), a reduced level of soluble PPM1H expression has no significant catalytic activity. (C) Sequence alignment of the N-terminal regions of the evolutionarily related PPM1H/J/M enzymes. The degree of conservation is above the alignment, and residue numbers correspond to PPM1H. A conserved anchor motif (RPxFL) is annotated below the sequences.
Figure 3A Diagram of the dissected miniature pig mandible slice illustrating the deciduous (DC) and permanent (PC) canine and application of compression in vitro using Flexcell FX-5000 Compression System. B-D H&E staining of canine frontal sections from embryonic day 60 (E60) (B), after culturing for two days without stress (0 kPa) (C), or with stress (3 kPa) (D). (B'-D') are magnifications of boxed regions in their corresponding figure panels. Scale bars = 50 µm. n = 6/6 in E60 group; n = 12/12 in 0-kPa group; n = 4/8 in 3-kPa group. E Diagram illustrating the required time during PC initiation; regular process from resting to initiation stage (left) and when the mandible is cultured without stress (0 kPa; middle) or with stress (3 kPa; right). F RT-qPCR of several mechanosensitive proteins (TGFB1, NFKB1, EGR1, and RUNX2) and of four mechanoreceptors (ITGB1, ITGB3, ITGAV and ITGA2) in PC and surrounding soft tissue at E60 and after culturing for two days with (3 kPa) or without extra mechanical stress (0 kPa). n = 3 for each group. Data represent the means ± SEM. One-way ANOVA (Newman-Keuls test for post-hoc comparisons between two groups), *P < .05, **P < .01, ***P < .001; NS, not significant. =
Human CEACAM1 binds to group B Streptococcus (GBS) via the surface-expressed β protein.Figure 1Binding of recombinant (r)CEACAM1 (CC1)-HIS (10 μg/mL) to (A) a panel of Gram-positive bacteria, namely Enterococcus faecalis, Enterococcus faecium, Group A Streptococcus (GAS), Group B Streptococcus (GBS), Group C Streptococcus (GCS), Group G Streptococcus (GGS), Streptococcus pneumoniae, Staphylococcus aureus, (B) an expanded collection of GBS isolates, with serotype and carriage of bac gene shown. rCC1 binding to live bacteria was quantified by a secondary anti-His-FITC monoclonal antibody (mAb). Mean and standard deviation (SD) values are reported for n = 3 independent experiments. In (B), GBS strains from left to right are A909, BS39, 515, BS22, H36B, BS29, 18RS21, BM110, COH1, SBL3066, NCTC10/84, SB35, SB10, SB20, BS26. Correlation between rCC1-binding capacity and β protein expression in GBS strains, respectively. β protein expression was quantified using rabbit anti-β protein serum and a secondary PE-conjugated goat anti-rabbit-IgG. rCC1 binding to live bacteria was quantified by a secondary anti-His-FITC mAb. Mean binding values from n = 3 independent experiments. Concentration-dependent binding of rCC1-HIS to wild type (WT), ∆bac and ∆bac + pLZ.bac complemented A909 strains. Mean and SD values are reported for n = 3 independent flow cytometry experiments. Pull-down of human rCC1-HIS (30 μg/mL) by GBS strain A909 strain, detected using Western blot analysis. Human rCC1-HIS (30 μg/mL) binding to GBS A909 and A909∆bac strains analyzed by pull-down experiments followed by Western blot analysis. Western blot analysis of rCC1-HIS (30 μg/mL) binding to purified β protein, but not to control GBS surface proteins α and Rib. Panel on the left show staining of proteins after separation by SDS-PAGE. Binding of purified β protein to dynabeads (DB) coated with rCC1 (DB.CC1) or control. Binding of β protein was detected using mouse anti-β serum or normal mouse serum (NMS), and PE-conjugated goat anti-mouse-IgG. (H) shows mean and SD values compiled from n = 3 independent replicates, and (I) shows representative flow cytometry plots using 10 μg/ml rCC1.
Figure 6Iba-1 (green), CD169 (red) and MXO4 staining in plaque-associated areas (cortex and hippocampus) of 5 and 15 months old of APP and APP/Nlrp3-/-. Note the colocalization between Iba-1 and CD169 (white arrows) in APP 15-month-old mice 2 days post LPS injection. Scale bar: 20µm
Figure 2(a) Illustration of experimental protocol outlining DSS induced colitis in Krt19BAC-CreERT2;ROSA26tdTomato mice. (b-c) Krt19+ cells lineage trace entire colonic crypts during both normal homeostasis and injury (N=3-4 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines outline the basement membrane. Scale bars (b) =45µm Data are represented as mean ± SEM *P≤0.05, **P≤0.01. (d) DSS and DT treatment of Krt19CreERT2;ROSA26tdTomato/DTR mice. DT ablation of Krt19+ cells (N≥3 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines outline the basement membrane. scale bar (e) =30µm DT ablation of Krt19+ cells significantly reduced the number of lineage labeled crypts (N≥3 per condition). Data are represented as mean ± SEM using Student's t-test *P≤0.05, **P≤0.01. (g) Mice body weight and survival remain unchanged between DSS and DSS+DT treated groups (N=6 control; N=7 DT). Data are represented as mean ± SEM using Student's t-test P≤0.05, **P≤0.01. Hematoxylin and Eosin staining of the colonic epithelium after DSS versus DSS+DT showing more damage is seen in mice treated with both DSS+DT treatment (N=6 control; N=7 DT). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines outline the basement membrane. scale bar (h) =1mm. quantification of damaged epithelial area (i), showing more damage is seen in mice treated with both DSS+DT treatment (N=6 control; N=7 DT). Data are represented as mean ± SEM using Student's t-test *P≤0.05, **P≤0.01.
ATP-induced NLRP3 inflammasome activation leads to secretion of distinct EVs from BMDMs.Figure 6Schematic illustration of workflow for EV isolation and characterization (panels B-G) from BMDMs that were left untreated or LPS-primed in the presence or absence of either ATP, Nigericin, poly(dA:dT) or Flagellin. BCA analysis of EV protein concentration in EVs isolates. Each bar represents a mean of n=3 technical replicates, vertical lines indicate SD. *, p < 0.05; **, p < 0.01; ***, p < 0.001; n.s. not significant (two-tailed t-test). Exocet quantification assay of EVs particle numbers. Each bar represents a mean of n=3 technical replicates, vertical lines indicate SD. *, p < 0.05; ***, p < 0.001; n.s. not significant (two-tailed t-test). Transmission electron microscopy (TEM) of EV isolates. Three representative pictures are displayed. Scale bar indicates 200 nm. Analysis of size distribution of EVs. Each dot indicates the diameter in nm of an individual vesicle. SD. ***, p < 0.001; n.s. not significant (one-way ANOVA, followed by a Tukey multiple comparison test). Prdx4 concentration in EV lysates. Each bar represents a mean of n= 2 technical replicates, vertical lines indicate SD. **, p < 0.01; ***, p < 0.001; n.s. not significant (two-tailed t-test). Caspase-1 and IL-1β concentration in EV lysates. Each bar represents a mean of n= 2 technical replicates, vertical lines indicate SD. **, p < 0.01; ***, p < 0.001; n.s. not significant (two-tailed t-test).
DRP-1 K42A protects from autophagy induced by steroid withdrawal and amino acid starvation.Figure 7.(A and B). Quantification of autophagy in MCF-7 cells. MCF-7 cells were transfected with luciferase or FLAG-DRP-1 K42A followed by steroid withdrawal (serum starvation plus 10−6 M tamoxifen treatment) (A) or by serum and amino acid starvation (B) (mean ± SD calculated from triplicates of 100 cells each). These experiments were repeated three times with reproducible results. Proteins extracted from the transfected cells were subjected to Western blot analysis with anti-FLAG and anti-β-tubulin antibodies. (C) Photographs of the MDC-stained steroid withdrawn MCF-7 cells taken from the same experiment shown in A. Transfections: luciferase (1a and 1b) and DRP-1 K42A (2a and 2b) at low (a) and high (b) magnifications.
Genetic background influences position within a pluripotency spectrum through differences in chromatin accessibility.Figure 1A. Phase contrast images of representative cultures for B6 and D2 strains maintained in conditions supporting naive pluripotency and after transitioning to formative EpiLCs. B6 ESC colonies adopt a classical ground state morphology, whereas D2 ESCs grew with a flat morphology and fewer cells per colony. Morphological differences persisted in EpiLCs (Scale bar = 50 µm). B. First two principal-components shows major source of variation in transcript abundance is cell state (PC1, 65.4%) and strain (PC2, 20.6%) for 3 biological replicates of B6 and D2. C. MA plot highlighting genes differentially expressed between state independent of strain (glm state term, false discovery rate-adjusted P value (FDR) < 0.05 and log2FC >1). Core pluripotent TFs highlighted for each state (maroon = naive ESCs, teal = formative EpiLCs). D. Scatterplot of expression for core naive TFs in 3 biological replicate ESCs per strain. Equal high expression of naive TFs observed in both B6 and D2 ESCs. E. MA plot showing differentially regulated genes between strains within ESCs as determined by pairwise comparison (FDR < 0.05 and logFC >1). Core naive TFs are highlighted as not significantly differentially expressed between strains. Genes significantly different between strains within cell state with known roles in promoting naive pluripotency (B6 = Obox6, Cdh1, Smarca1, Ube2s; D2 = Med12l, Sfi1) as well as self-renewal in progenitor cell populations are highlighted (B6 = Olig2, Sox11; D2 = Epha4). F. PCA of full transcript abundance comparing average expression from B6 and D2 ESCs (3 biological replicates) collected here to previously collected RNA-seq from Hackett et al. (2017). PC1 separated experimental origin, indicating batch effects between labs, and was not explored further. B6 expression was similar to that of ground state conditions which exclude serum; whereas D2 expression more closely resembled conditions that include serum. Arrow indicate developmental progression towards primed pluripotency. G. Volcano plot showing the mean difference in bias-corrected accessibility at TF motifs from ATAC-seq (3 biological replicates) versus P value for that difference. Select TFs critical to pluripotency and differentiation are highlighted. H. Heatmap of motif deviations from 3 biological replicates of B6 and D2 ESCs for TFs highlighted in G.