EMBO/sd-character-level-ner huggingface dataset:
(C) Neutralizing activity (EC50) of sera from individual LV::S-vaccinated mice against pseudo-viruses harboring SCoV-2 from the ancestral strain or D614G, Alpha, Beta or Gamma variants. Red asterisk indicates significance versus ancestral, blue asterisk indicates significance versus D614G variant, while orange asterisk indicates significance versus Alpha variant. Statistical comparisons were made at the respective boosting timepoint. In homologous settings, sera from mice immunized with LV::SBeta or LV::SGamma, fully inhibited pseudoviruses bearing S from Beta or Gamma, validating the assay for all pseudo-viruses used. Data information: Statistical significance was evaluated by Mann-Whitney test (*= p < 0.05, **= p < 0.01, ****= p < 0.0001).
Q Confocal isosurface image of neurofilament (green) and bungarotoxin (red) immunofluorescence in the artificial muscle section shows a mature neuromuscular plaque. Scale bar: 10 μm.
Anchorage independent cell growth assays of the HNRNPC-deficient MCF7 (top) and T47D (bottom) cells.
A Activities of gene expression signatures, as indicated, in single cell transcriptomes from control (DMSO) condition CRC organoids, ordered along latent time. Correlation between cell state distributions and latent time was calculated using Pearson´s r. For correlations and significances, see Table EV6. Color code red: high activity; blue: low activity.
C Illustration of the non-canonical p52/RelB NFκB2 pathway and inhibitors used in the study.
C. Plot of eRab7- or Arl8b-GFP / Myc-Arl8b-positive pixel distribution in response to the indicated effector perturbations, expressed as fractional distance along a straight line from center of nucleus (0) to the plasma membrane (1.0), number of (pixels) plotted given above each scatter, n≥6 cells per condition analysed from 2 independent experiments.
(I) Mcp3 behaves like an outer membrane protein in density gradient centrifugation. Mitochondrial vesicles isolated from cells over-expressing HA-Mcp3 were subjected to sucrose density gradient centrifugation. Fractions of the gradient were collected and analysed by SDS-PAGE and immunodecoration with antibodies against the indicated proteins. The processed form of HA-Mcp3 is shown. Right panel: The intensities of the various bands were quantified and depicted. The sum of all intensities for each protein was set to 100%.
C AUC of the body weight of nondiabetic and diabetic mice transplanted with FI or PI+MVF from day 0 to day 28 (n = 7 each). Mean ± SD.
(E) Example of Western blot analysis of protein extracts of DIV4 cortical neurons electroporated on DIV0 with pSUPER (control) or pSUPER encoding one of three DCLK1 shRNAs. Levels of actin were used as an equal loading control.
(c) Cells were treated with 200 nM epoxomicin for 4 h and then immunoblotted and probed with anti-pTyr-416-Src, anti-Src, anti-p53 and anti-actin antibodies. Uncropped images of blots are shown in Supplementary Fig. S9.
E The number of paraspeckles per nuclei in each cell line. The mean numbers are shown (mean PS (paraspeckle) #/nuc) (WT: n = 83, ∆3′: n = 99, ∆5′: n = 103, ∆5′/∆3′: n = 115). Statistical analysis showed a significant reduction in the paraspeckle numbers in the ∆3′ (P < 0.0001), ∆5′ (P < 0.0001), and ∆5′/∆3′ (P < 0.0001) mutants compared with the WT. The number of paraspeckles in the ∆5′/∆3′ was significantly fewer than that in the ∆3′ and ∆5′ (P < 0.0001 compared with ∆3′, P = 0.0023 compared with ∆5′).
(E) Western blot examination of caspase-11 and processed caspase-1 (p20) and gasdermin-D (p30) in supernatants and pro-caspase-1 (p45), pro-gasdermin-D (p55), pro-caspase-11, Gate16 and GAPDH in cell lysates of Gate16-silenced WT, Irgm2-/- and GBPChr3-/- BMDMs exposed to 2,5.105µg/2.105 cells of OMVs for 16 hours. Si Scramble (siScr.) refers to RNAi pools with non-targeting sequences.
Western blot showing the protein level of ELKS in negative control and ELKS siRNA transfected hRPEs. α-tubulin was used as loading control. Bar chart shows quantification of protein levels normalized to α-tubulin in each condition.
ApoE-/- (-/-) and ApoEYF (YF) mice were subjected to partial ligation of the left carotid artery (LCA) and given a cholesterol-rich diet. Percentage of neutrophils and monocytes infiltrated into the LCA 7 days after ligation and high cholesterol diet feeding; n=9-10 mice per group (Unpaired Student's t test).
B. Quantitative proteomics of lysine (K) succinylation was performed in HepG2 and HAT1 knockout HepG2 cells. Graphs show the overlap of the total number of succinylated sites (left) and proteins (right) identified with those targeted by HAT1 (>1.2-fold decrease and P < 0.05, Student's t-test).
C, D Down-regulation of PKAc1-Ty-iKD upon ATc treatment leads to increased parasite dispersion after 40 hours and premature egress (data is from three independent biological replicates).Data information: In D, data are presented as mean ± SD.
(A) Immunofluorescence staining against Iba-1 in Cb of ASMko and wt mice treated or not with PLX for 2 months. DAPI staining shows cell nuclei. Scale bar, 100 μm. (B) Magnified images (from A) showing ramified (left) versus amoeboid (right) morphology in wt and ASMko microglia treated or not with PLX. Scale bars, 30 μm. (C) Mean ± SEM number of Iba-1 positive cells in the Cb of the different mouse groups (n = 7 mice per group, Two-way Anova, Bonferroni post hoc).
H Linear correlation of membrane association index of α-Tubulin and β-Tubulin with the conversion rate to mature ookinete among WT, dhhc2kd and ∆isp1/3 parasites. Horizontal and vertical values are means ± SD.
E Averages of quantified strand exchange assays with ssDNA, RAD51 (270 nM) and varying concentrations of MMS22L-TONSL or MMS22L. n = 2; error bars, SEM.
(B) Percentage of GAPDH levels quantified by qPCR in reactions containing increasing doses of protamine (n=3). Data represent mean values ± SEM.
B Anti‐Ub Western blot of an identical reaction run for 3 h.C Comparison of the number of Ub chain linkages in the reaction in (B).D Ub chain linkage profile for the reaction in (B).
B Representative images of colons of DSS-treated Ccdc50+/+ and Ccdc50-/- mice (Ccdc50+/+ mice, n = 8 mice; Ccdc50-/- mice, n = 7 mice)
Three TZ markers (NPHP-4, CEP-290 and MKS-6) are shown at both the permissive (15ºC) and restrictive (25ºC) temperatures in the ts-che-3 mutant. At the permissive temperature, all three markers localise to the TZ, while at the restrictive temperature exhibit ectopic localisation (leakage) distally into the ciliary axoneme. While NPHP-4 and MKS-6 show significant accumulations, CEP-290 is grossly normal. At the permissive temperature, both IFT co-markers (CHE-13 and XBX-1) display strong localisation to the basal body (bb) and along the axoneme. At the restrictive temperature, the IFT markers show accumulation in the axoneme. Accumulations emphasized using asterisks
Experiments were performed using human primary monocyte-derived macrophages. (K) Cell extracts from LPS-stimulated, inhibitor-treated primary human macrophages were immunoblotted for p-ERK1/2, ERK1/2, p-p38, p38 and HSP90.
(D) IC50 (up, in nM) and normalized IC50 folds (bottom, normalized against the wild-type) of FD20 and control antibodies measured using different SARS-CoV-2 pp harboring S mutants or variants. E406W is an escape mutant from REG10933 and REG10987 cocktail generated in vitro (Starr et al, 2021). K417N is an escape mutant for CB6 (LyCoV.016) and is present in the B.1.351 lineage first identified in South Africa (Li et al, 2020; Starr et al, 2021). Y453F increases the ACE2 binding affinity, and with A475V and F490L, is found in independent mink-related SARS-CoV-2 variants (Larsen et al, 2021; Oude Munnink et al, 2021) identified in Denmark and the Netherlands (B1.1 and B.1.1.298) that may escape human antisera and REG10933 (Starr et al, 2021). D614G appeared early during the pandemic and is now the dominant form worldwide, and is associated with other mutations in new variants of concern (Korber et al, 2020). A222V and S477N are described in 20A.EU1 (B.1.177) and 20A.EU2 (B.1.160) that emerged in early summer 2020 and subsequently spread to multiple locations in Europe at the end of 2020 (Lemey et al, 2021). N439K is in B.1.141, B.1.258, and in mink strains; it increases affinity to ACE2 and reduces neutralization of sera from convalescent patients (Thomson et al, 2021). Finally, ∆69/70-N501Y-D614G are characteristic mutations in RBD for the UK/B.1.1.7 lineage (501Y.V1) (Leung et al, 2021), one of the three fast-spreading new variants of SARS-CoV-2 that have emerged in recent months. The B1.351 (501Y.V2) identified in South Africa has raised concerns that the efficacy of current vaccines and therapeutic monoclonal antibodies could be threatened (Tegally et al, 2021). The P.1 (Gamma or Brazilian variant) has contributed to a surge in cases in the northern city of Manaus and it has been reported in January 2021 in Japan. The highly contagious B.1.617.2, commonly known as the Delta, is currently responsible for over 90% of the cases in the UK and over 80% of the cases in the USA and has caused concerns about vaccine efficacy (Lopez Bernal et al, 2021). The background is color-colored based on the neutralizing activity (up) or change in neutralizing activity (bottom). IC50 values are the mean from at least two independent experiments.
D Heat map showing log2 fold change differences of interferon-related genes expression between ENU treatment and control (saline) in WT and G1 Tert-/- mice by RNA-seq. n = 3 mice per group. E Heat map showing log2 fold change differences of cytokine/chemokine between ENU treatment and control (saline) in WT and G1 Tert-/- mice by cytokine/chemokine array. n = 5 mice per group. F
C Enriched biological processes (BP) for WT versus G1 Tert-/- mice. GO was analysed for upregulated genes in WT mice compared to G1 Tert-/- mice under control or ENU treatment.
(B) Trypan blue staining indicates the extent of cell death for each genotype/strain combination, including an agar plug control. All images were recorded 48 hours post inoculation.
(A) Schematic representation of the experimental setup to address the effect of ChP specific miR-204 inhibition on the number of LRCs and neurogenic priming.
Reactivation from latency is quantified by Us11-GFP expressing neurons following addition of the PI3K inhibitor LY294002 (20μM) in the presence of WAY-150168, which prevents cell-to-cell spread. The arrow indicates the time of LY294002 treatment at 5 days post-establishment of latency. n=9 biological replicates.
Treatment with the Myosin II inhibitor Blebbistatin statistically significantly reduced number of kugeln per embryo (25 µM 1h; ****p <0.0001; control n=22 embryos 3.77 ± 0.56 (mean ± s.e.m.), Blebbistatin n=24 embryos 1.08 ± 0.22 (mean ± s.e.m.); 3dpf; 3 experimental repeats; Mann-Whitney U test).
(E) Deleting the putative VxrB binding site from the murJ promoter abrogates induction of murJ by PenG exposure. Transcript levels were measured by S1 nuclease mapping. Numbers represent induction as measured by band intensity, normalized to pre-exposure WT. n.d., not determined.
(D) Strong interaction of a perivascular IL-17hi2d2Th17 with a perivascular CD11c-GFP+ cell (insert upper left contact).(E) Time lapse of the insert in (D): Stopping motility of the round-shaped IL-17hi2d2Th17 cell is followed by entry into the CNSparenchyma.(F) Magnified image of interaction of the upper left and (G) lower right perivascular T cell-DC contacts as shown in (D) and (E).
(F) FAIRE assay was performed in cells treated as in (D) and qRT-PCRs were performed for the same gene promoters and plotted as in (E).
(D) significant cases of significant enrichment (FDR<0.1) of top 10% MTA-predicted targets from each dataset for the host proteins involved in host-SARS-CoV-2 protein-protein interactions (combined from Stukalov et al. 2020 and Gordon et al. 2020). Axes and the meanings of dot color and size are similar to (C).
Increased ER stress-induced apoptosis in the MITOL-KO spinal cord. 3 month-old WT or MITOLnestin mice were treated with Tu for 24 hours and each spinal cord was stained using cresyl violet (G). Arrowheads indicate the representative neurons.
A. Q25-GFP and Q97-GFP were expressed in wild type cells for 4.5 h. Cell extracts were subjected to mass spectrometry-based proteomics. The levels of Mia40 and other mitochondrial proteins (mito., yellow) and carrier proteins (orange) are visualized in a volcano plot (p-values were derived using a moderated t-test). The position of Rnq1 is indicated in blue.
E. Quantitative real-time PCR analysis of RUP2, CHS, HY5 and ELIP2 expression in wild-type (Ws), uvr8-7 and uvr8-7/Pro35S:UVR8HY5C44, uvr8-7/Pro35S:UVR8HY5VP and uvr8-7/Pro35S:UVR8TRIB1 4-day old seedlings grown under white light in response to 2h of UV-B (+UV-B vs. -UV-B). Error bars represent SEM of 3 biological replicates. Note: the primers used to detect the HY5 transcript abundance also bind to an identical region present in UVR8HY5C44 chimera.
C) Aggregation of washed platelets induced by ADP (5 or 10 μM) or collagen (0.6, 0.8 or 2 μg/mL) was evaluated in at least one member of each family. Patients from families 1 and 2 had increased platelet aggregation in response to low doses of agonist versus controls, suggesting that TUBB1 affected by homozygous p.P160L and heterozygous p.Y106X mutations affected platelet function. Platelet aggregation to both agonists was normal in both patients from family 3 (heterozygous c.35delG). Family F1, n=3 independent experiments; Family F2, n=1 experiment; Family F3, n=2 independent experiments. Statistical significance was determined by one-way ANOVA, followed by Dunnett"s multiple comparisons test (*p<0.05, **p<0.01, ***p<0.001, nd: statistical significance not determined because
B BN-PAGE analysis of OXPHOS complex assembly in enriched mitochondria from subject and control fibroblasts solubilised using DDM. Immunoblotting was performed using antibodies to structural subunits from each OXPHOS complex (CI [NDUFB8], CII [SDHA], CIII [UQCRC2], CIV [MT-CO1], and CV [ATP5A]).
(A) Schematic representation of the experimental design. By DOX addition, male TXY mouse ESC lines allow for expression of full length XistFL or XistΔBC. Cells induced for 48h in the absence of LIF were used for combined IF and RNA FISH.
D. Simulated population proportions of CD34+α6+ HFSCs and CD34¯α6+ non-HFSCs derived from the mathematical model describing steady state cultures. Experimental data from (A) are shown as reference (in grey). See also Appendix figure S4 and Dataset EV4.
f, Enrichment of pathways associated with human orthologues mapped from genes differentially expressed in ATG16L1-deficient Paneth cells relative to WT cells, using the canonical pathway collection from MSigDB. The bar chart displays the negative log of the enrichment P values for each pathway using the hypergeometric distribution (see Methods). Pathways with only one gene assigned were excluded from the chart. † refers to the Wnt/Frizzled receptor-mediated cyclic GMP pathway obtained from the Signal Transduction Knowledge database (STKE, http://stke.sciencemag.org/cgi/cm/stkecm;CMP_12420). ‡ and ‡‡ denote similar pathways associated with γ-hexachlorocyclohexane degradation as curated by KEGG and GenMAPP, respectively.
(B) PER2::LUC binding to BMAL1 in WT and CKO cells. Cells were harvested at the peak of PER2 expression, BMAL1 was immunoprecipitated, and PER2::LUC binding was measured by bioluminescence measurements (n=3, mean ±SD).
D. Western blot analysis of CTRL#3 or BRD9-KO#3 cells stably transduced with lentiviruses expressing empty vector (EV), or HA-tagged wt and chimeric mutant constructs described in (C).
(d) RHQ reduced the levels of aggregated and soluble forms of tNHTT-150Q-EGFP by 81.8% and 33.6%, respectively. WB, western blot. (e) Quantification of tNHTT-16Q-EGFP protein levels.
(C) Soft agar colony formation assay following ZEB1 expression. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student's t-test).
B. Simple western analysis (Peggy Sue) of EZH2 immunoprecipitates shows abolition of TGFβ1-induced profibrotic transcriptional complex of EZH2/POL2/actin upon the convergent treatment of TGFβ1 and Y27632. Unspecific IgG binding was used as a negative control. Representative from 3 biological replicates is shown.
Outline of RNA-seq based screening for the introns regulated by HSATIII-dependent sequestration of YTHDC1.
(B-C) Confocal scans of immunolabelled retinal cross sections (14 μm) stained for GFP and DAPI at 6 WPI time point. : DAPI was used a nuclear marker. GFP=eGFP; RPE, retinal pigmented epithelium; OS, outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer.
(a) Western blot analysis of myosin-VI-depleted HeLa cells untreated or treated with 100 nM bafilomycin A1. (b) Quantification of western blot LC3-II intensity (±s.d.; n = 3). **P0.01, ***P0.001
Stroma IMC quantification per lung in Npc2+/+ (+/+) or Npc2+/hypo (+/hypo) BVE mice at different ages (39-109 days p.p.).
(S) Survival curve of L1 larvae under food depletion conditions in wild type, epg-1 mutants, and epg-7 mutants. This experiment was completed once (wild type: n = 2,964; epg-7: n = 602; epg-1: n = 215). Statistical analysis of L1 survival shows that epg-7 mutants exhibit significant difference to wild type and also to epg-1 mutants (log-rank test, P = 0.000).
C. Co-immunoprecipitation (Co-IP) of LORE with PBLs. 35S promoter-driven LORE-T7 and PBLs-FLAG were transiently co-expressed in N. benthamiana by agroinfiltration. Plant leaves were immunoprecipated with anti-FLAG beads and the proteins were immunoblotted by anti-FLAG antibody. Co-IP proteins were immunoblotted by anti-T7 antibody. The experiment was repeated three times with similar results.
A-E) Expression of 3xFLAG::GFP::ZNFX-1 and PGL-1::mTagRFP-T in a wild type (A), pid-2 (B), pid-4;pid-5 (C), pid-4 (D), and pid-5 (E) mutant backgrounds. The indicated dashed boxes reflect zoom-ins on specific nuclei to better visualize the granules, and their overlaps. One L4 gonad is shown. Arrow heads indicate individual condensates. Scale bar: 25 µm. F) Quantification of the ratio Z / P granules in wild type, pid-2, pid-4/-5, pid-4 and pid-5 mutant backgrounds. The number of granules is indicated in brackets, next to the genotype.
Western Blot of phospho-serine-296-Chk1 (p-Chk1) in U2OS cells. Cells were treated 1.5 h with the Chk1 inhibitor Gö6976 (Chk1i) or DMSO, irradiated with 100J/m2 UV to induce high levels of p-Chk1, and collected 1.5 h afterwards. Actin was used as a loading control.
G Co-immunofluorescence of tissue stained for the epithelial marker (cytokeratin 19; yellow) and the tumor-associated macrophage marker CX3CR1 (magenta). DAPI is shown in white (n=2 preneoplastic samples; n=2 tumors). Scale bar, 100 μm.
(E) Genome-wide association of CG34015 expression. Manhattan plot shows a strong association of CG34015 RNA with X chromosome in both sexes. P-values are plotted against ordered SNPs along the genome. eQTLs associated with CG34015 are designated as red dots.
MITOL ubiquitylated IRE1α in the spinal cord of mice. Lysates of the spinal cord in mice were immunoprecipitated with anti-IRE1α antibody, followed by immunoblotting with indicated antibodies. WT: MITOLF/F mice, MITOLnestin: MITOLF/F, Nestin-Cre mice.
IE were isolated and binding to HBMEC and HDMEC was determined under flow conditions. Number of IE bound per mm2 EC surface was calculated and shown is the mean ± 95% CI for 26 CM and 33 UM cases on HBMEC and 21 CM and 35 UM cases on HDMEC on a log scale. P-value was calculated by two-tailed unpaired t-test. The dotted line is 20 IE/mm2, the cut-off value for inclusion of the inhibition data.
Fluorescence immunohistochemistry for CD59 in the ependymal layer and choroid plexus of the lateral ventricle from CWH43WT/WT, CWH43M533/M533 and CWH43M533/A530 mice. Arrowheads point to apical surfaces of ependymal and choroid plexus cells. Nuclei are counterstained using DAPI (blue). Scale bar is approximately 5 µm.
A. Scramble and Rab22a KD JAWS-II DCs were infected with OVA-YFP-expressing T. gondii (TgRHYFPSAG1-OVA) for 8 h and confocal images detecting the parasite (green), endogenous Rab22a (red) and GRA6 (magenta) were taken. Top panels: Scramble cells; bottom panels: Rab22a KD cells. White boxes are shown at higher magnification in the insets. The nuclear marker DAPI (blue) and DIC images are shown in the left panels. Overlays are shown in the right panels. Scale bars: 5 µm. Images are representative of at least 30 analyzed from three independent experiments.
A Ex vivo flow cytometry on LN cells of mice 7 days after two s.c. immunizations (14 days apart) with PBS + DMSO (Veh), KLH + DMSO (KLH), KLH + IL-2, KLH + RA, KLH + RA + IL-2. Results are representative FACS plots of LAG3+CD4+ or CD25+Foxp3+ cells after gating on live single CD3+CD4+CD49b+Foxp3- and live single CD3+CD4+ lymphocytes respectively.
D-G Confocal images of ddaC neurons expressing control RNAi (D), msps RNAi (E), tacc RNAi (F) and αTub84B RNAi (G) that were immunostained for TACC at wL3 stage. ddaC somas are labeled by dashed lines. ddaC neurons are identified by ppk-Gal4 driven mCD8::GFP (green channel) expression, as shown at the top right corner.
D and E. Quantification of the TIM23:Actin and TOM20:Actin ratios from (B and C). All data are from 3 independent experiments.
A Plants expressing LUC fused with full-length DOG1 (pDOG1LUC::DOG1) were sprayed with mock solution or ABA 10, 20 and 40 days after germination and analysed 24 h after treatment. The graphs show mean emitted light intensity per plant.
(B) Calcium responses in individual tumors cells were recorded in (upper table) control tumors (developing without CAR T cells) or (lower table) after CAR T cell transfer in tumor cells contacted by at least one CAR T cell during the imaging period. Representative of 3 independent experiments. Data is representative of three independent experiment.
(E) BI‐1 KO cells were stably transduced with retroviruses expressing BI‐1-GFP or empty vector, and then exposed to EBSS for indicated time points. Cell viability was monitored after PI staining by FACS. Mean and standard deviation are presented of triplicates representative of two independent experiments.
B: left: Biocytin-filled pyramidal cells in the CA1 region. DAPI staining of CA1 bundle allows differentiation between deep (bottom) and superficial (top) CA1 neurons (scale bar: 100 µm). right: Schematic representation of Sholl spheres around the soma.
(D) Immunostaining of BMDMs treated with 2.5 μg/ml rRv2626c for 30 min. and then immunolabeled with antibody to His-rRv2626c (Alexa Fluor 488) or TRAF6 (Alexa Fluor 568). DAPI (blue) stained nuclei.
(G) Plasma LH levels at P45 in control and mutant mice. Mann-Whitney U test, n=5 to 6 mice.
C) Magnified view of the structure around phosphorylated T651CENP-C. Key residues in this region are shown as stick models. The side chains of R656CENP-C and R71H2A are situated in the vicinity of the phosphoryl group of T651CENP-C in the distance ranges of 3.5-4 Å and 3.5-4.5 Å, respectively.
(C) Representative images of double-immunofluorescent stained for GFAP and GSDMD, for Iba-1 and GSDMD, and for NeuN and GSDMD in post-ischemic brains after tMCAO.
(A) WT and FAK−/− PEMs were incubated with S. typhimurium strain ΔinvG for 0-24 hours before immunoblotting with the indicated antibodies.
Exogenous application of SA mimics DA-induced IPS1 gene induction (E) patterns in Pi-deficient plants. Data information: qPCR results show values of means ± SE (n=3), two biological replicates were analyzed with similar results. Different letters denote significantly different means at p < 0.05, Tukey's multiple comparison test.
C. Representative Ca2+ current (top) and Cm changes (bottom; finite impulse response filtered) in Wrbfl/fl:CreA and Wrb+/+:CreA IHCs in response to a 100 ms step depolarizations to -14 mV.
(A) Volcano plot of all detected proteins from proteomics of TGFβ-treated naïve (WT) and COUP-TFII overexpressing (COUP-TFII-OE) cells. PDK4 expression is significantly decreased in OE cells (n=2).