EMBO/sd-character-level-ner huggingface dataset:
Wild type and mps1-3 cells were synchronised in G1 with α-factor at 25°C and then released at 34°C in the presence (A) of nocodazole (t=0). Cells were collected at the indicated time points for western blot analysis of the indicated proteins. Equal amounts of protein extracts were loaded on two different gels, for western blot of Spc105-3PK and Clb2/Pgk1 respectively. Clb2 was used as mitotic marker and Pgk1 as loading control. Cyc: cycling cells.
(D-G) Cell death mechanisms of C3H BMDMs transfected with miR-342-3p mimic (D), or B6 BMDMs transfected with miR-342-3p inhibitor (F), followed by Mtb infection for 36 hours. Cell viabilities of C3H BMDMs transfected with miR-342-3p mimic (E), or B6 BMDMs transfected with miR-342-3p inhibitor (G), followed by stimulation with Mtb or z-VAD (20 μM) for 24 hours. Data are shown as the mean ± s.e.m. of n = 3 biological replicates.
B Schematic representation of control proteins and fusion proteins of interest for investigating the interaction between PA-mCit-BAD and NL-BCL2L1 in proof-of-principle LuTHy experiments.
(B) VAPB-PTPIP51 proximity ligation assays of NSC34 cells treated with either vehicle 1 M AR-A014418 or 100 nM CT99021 for 16 h. Cells were also stained for nuclei with DAPI. Bar chart shows relative number of proximity ligation assay signals/cell.
C. NanoBRET™ (Nano-bioluminescence resonance energy transfer) assay. Mdm2, p53 and Fbxw7 serve as controls. Mdm2 or MCAK were tagged with NanoLuc®-luciferase (Nluc), p53, Fbxw7 and Fbxw5 with HaloTag® (HT) and expressed in HeLa cells. After incubation with ligand overnight, substrate was added and plates were directly measured. Left: Quantification of 4 independent experiments. Error bars indicate standard deviation, asterisks the p-value of a two-tailed unpaired Student's t-test comparing each control with the MCAK/Fbxw5 pair (***P < 0.001). Right: Cartoon showing the NanoBRET™ principal.
Functional annotation of the 17817 peaks highly enriched in H2Bac performed with GREAT, GOTERM Cellular Component and Biological Process
C. As for B, but immunostaining wild type male meiocytes for MSH2 (red), MSH4 (green) and staining chromatin with DAPI (blue).
b) The corresponding HSP90 inhibitor, Tanespimycin, effectively suppressed SARS-CoV-2 proliferation (n=2). Calu-3 cells were pre-incubated with the compound, followed by the addition of SARS-CoV-2 and subsequent co-incubation in the presence of the compound for 20-24 hours. Viral load was quantified in parallel using antibody-based detection of double stranded RNA (orange). Compound toxicity in Calu-3 cells was assessed (purple) treated with the compound alone for 20-24 hours.
Activity-induced formation of nuclear infoldings is impaired in SATB2-deficient cortical neurons. DIV14 cortical cultures form Satb2flx/flx and Satb2NesCre mice were silenced with NBQX for 1 h followed by stimulation with Bic for 1 h. The percentage of infolded nuclei following AP bursting was increased in control Satb2flx/flx cultures but not in SATB2-deficient cultures (n = 3-4 independent primary cultures, two-way ANOVA, F1,10 = 39.124, significant interaction p = 0.000094, simple main effects analysis, Satb2flx/flx cultures: Bic-treated vs NBQX-treated p = 7.66E-07, Satb2NesCre cultures: Bic-treated vs NBQX-treated p > 0.05, adjustment for multiple comparisons: Bonferroni, number of analyzed nuclei: Satb2flx/flx cultures, NBQX - 606, Satb2flx/flx cultures, Bic - 910; Satb2NesCre cultures, NBQX -604, Satb2NesCre cultures, Bic - 835). Data are presented as mean ± SEM, ***p < 0.001.
Representative low (left) and high (right) power images of H&E-stained lung sections from KrasG12D, KrasG12D:Adam17ex/+ and KrasG12D:Adam17ex/ex mice at 6 weeks post Ad-Cre inhalation. Scale bars, 3mm (left) and 300μm (right). Quantification of lung parenchyma area occupied by tumor lesions (B), and tumor incidence (C), per whole mouse lung in the indicated genotypes (n = 6 per genotype).
(C-D) The genetic loci of lid-1 and atgl-1. The coding regions are in light blue boxes and the noncoding regions are shown as lines. The UTRs are in red boxes. xd288 is a point mutant of lid-1 and causes a missense S111L mutation in the α/β hydrolase domain. xd314 and xd310 are point mutants of atgl-1. xd314 harbors a missense G19R mutation and xd310 harbors a missense G210E mutation.
D Replication assay of PKAr-TyDD parasites grown for 24 hours +/- Shld-1 indicates that no more than four parasites are observed per vacuole upon PKAr destabilisation. (100 parasites were counted in three independent replicates).
Under normal conditions, ppMLC promotes the recruitment of LUZP1 to TJ-associated CRs, where LUZP1 inhibits myosin phosphatase in a MT-facilitated manner to up-regulate ppMLC levels. Without LUZP1, myosin phosphatase actively dephosphorylates ppMLC within CRs, leading to apical constriction defects. MT depolymerization causes attenuated LUZP1-mediated inhibition of myosin phosphatase, allowing myosin phosphatase to dephosphorylate ppMLC.
D. RT-PCR analysis of the serotonin 2C receptor minigene after oligonucleotide addition. Below is a quantification of three independent experiments. A statistical evaluation showed significant differences between oligo#5 (p=0.00008) and oligo#5-3 (p= 0.0019) and control.
A Domain overview of VCP and 10 UBX-domain containing proteins. The UBX proteins bind with their C-terminally located UBX-domains to the N domain in VCP, with the exception of UBXD1 that binds to the C-terminus of VCP via a PUB domain.
(b) Similar to (a), but only cells expressing GFP-VPS35 wild type were analysed, either mock treated or treated with siRNA to silence FKBP15 expression.
Kinetic representation of the ordinary differential equation (ODE) model describing WT RAD51 polymerisation on ssDNA, consisting of five parameters: kp (polymerisation forward rate), ku (unstable reverse rate), kq (quasi-stable reverse rate), ks (stable reverse rate) and KD (protomer-protomer interaction affinity). KD predicts the concentrations of RAD51 polymers of variable length in solution, while kp, ku, kq and ks predict the speed of formation of RAD51 polymers on ssDNA. B. Kinetic representation of the ODE model describing WT RAD51 polymerisation on dsDNA, consisting of four parameters: kp, ku, ks, KD. KD predicts the concentrations of RAD51 polymers of variable length in solution, and kp, ku and ks predict the speed of formation of RAD51 polymers on dsDNA. In panels A and B, purple arrows depict a simplified cartoon representation of RAD51 polymerisation in solution. The model allows for any RAD51 n-mer (1 ≤ n < 16) to associate with any other RAD51 m-mer (1 ≤ m < 16) to form an (m+n)-mer (1 < m + n ≤ 16), and any RAD51 k-mer to dissociate into any combination of n-mers and m-mers (k = n + m). The ssDNA and dsDNA models were calibrated by simultaneously fitting the SPR curves of ssDNA dN-X (dN-8, dN-14, dN-17, dN-50) and dsDNA dN-Xp (dN-5p, dN-8p, dN-11p, dN-50p) using the mode ABC-SMC particles. Mean values ± 1 SD of 3 mode ABC-SMC particles derived from model fits of 3 dN-X and dN-Xp repeats (n = 3). ssDNA kp, ku, kq and ks were fit to the ssDNA SPR curves, and dsDNA kp, ku ks were fit to the dsDNA SPR curves. A single KD was fit to all curves.
mRNA expression levels of the SLC2A transporter (GLUT) family members (1-14) in HUVECs. Data presented as mean ± StDev relative to RPL19 expression from 3 independent experiments.
J) Immunofluorescence staining for ACE2 (red) and KRT20 (green) of organoids grown in full medium (upper) or basic medium (lower) and additionally treated with IFN-γ (right), indicating expression of ACE2 in differentiated enterocytes. White arrows point to ACE2. Scale bar: 10 µm
(D) RIP assays show association of DDX5 with lncPSCA in MGC80-3 and HGC-27 cells. Relative enrichment (means ± SD) represents RNA levels associated with DDX5 relative to an input control from three independent experiments. IgG served as the control. HOTTIP was used as the negative control and SRA as the positive control during RIP. Data show one representative example of three biological replicates.
E: Relative expression of miR-7 in Cal27 and JHU029 cells compared to NOK cell line analyzed by qRT-PCR. U47 was used as an internal control. n = 3 biological replicates and 3 technical replicates. Data are represented as the mean ± SD,
Representative electron microscopy showing mitochondrial morphology in PC12 cells expressing Q23 (top panel, left) and Q74 (bottom panel, left) and in brain tissues from wild-type (WT) (top panel, right) and HD transgenic mice (bottom panel, right). An indicated portion of each image (in yellow) is expanded to illustrate the mitochondrial morphology. Scale bars: 1 μm.
(B) Sedimentation coefficient distributions for a selection of values from the dilution series are shown.
A, B RT-qPCR analysis of Ifnb1 mRNA level in the WT and lincRNA-EPS-/- iBMMs infected with VSV (MOI 0.1) for 6 h (A), ELISA analysis of supernatant IFN-β protein after infecting for 8 h (B).
D, E Recruitment of ubiquitin in GAS-infected cells. HeLa cells were infected with WT GAS, ΔgacI, and ΔgacI::gacI for 4 h, fixed, and immunostained for ubiquitin (FK2: magenta). Cellular and bacterial DNA were stained with DAPI (cyan). (D) Representative confocal images and (E) percentage of cells with ubiquitin-positive GAS. Scale bar, 10 μm.
FACS analysis of HLA‐class I and HLA‐DP expression on RCC1.24 (D) and EBV‐B1.11 cells (E) As compared to untreated cells (thick‐lined histogram), treatment of cells with 7.5 mM 3‐MA (shaded histogram) does not cause down‐regulation of HLA‐class I or HLA‐DP. Isotype control is shown as thin‐lined histogram.
C Quantitative mass spectrometry analysis for UBE2T, UBE2E1 and UBE2R1 with Ub and phosphoUb using UbAQUA peptides reveals impaired chain formation with phosphoUb (see also Supplementary Fig S10).
F: Upper panel: area (blue) and total traction force (red) as a function of time for the computational amoeboid cell in panel E. Lower panel: Corresponding correlation function (CF) between the area change rate and total force (dashed line), actin (red) and total myosin (green).
(F,G) Venn diagrams demonstrating cell type-specific DE genes in the SN of PD vs control tissues, up/down arrows indicate gene groups that were up/down regulated.
Representative western-blots of the cortical (Ctx) or hippocampal (Hip) extracts from mice at the indicated time after seizure activity in kindling (D,E) models. For D and E, samples obtained from mice evoked with a single kindling stimulation to induce seizure activity as evidenced in EEG. (C,F) Statistics of Gli1 or Shh expression levels shown in A,B or D,E respectively. n=8-14 mice in C and n=8-23 mice in F.
The violin plot represents distributions of statistically significant ∆PSI for different types of splicing events by comparison of PLB-treated cells vs DMSO control. The number of differential splicing events regulated by 2.5 nM PLB is denoted in brackets. we analyzed the differential splicing events with genes FPKM > 1 in at least one differentiation stage. Among them, the cutoffs of PSI > 0.2 and FDR < 0.05 were used to define differential splicing events. The dotted line indicates ∆PSI=0.
A) Immunofluorescence-based antibody feeding assay performed using HUAECs seeded on laminin 411, 511 or 111-coated coverslips, reveals more VE-cadherin at junctions and less in vesicles in cells plated on laminin 511 (arrow heads mark VE-cadherin positive vesicles). Scale bar is 10 µm. B) Quantification of VE-cadherin positive vesicles/ cell in HUAECs plated on laminin 411, 511 or 111. Values are means ± s.e.m from 300 cells from 3 independent experiments, unpaired t-test.
j. Tumor xenografts metastasis activity of constitutively expressing RFP A549 cells transfected with wild type or ISX AC3 mutant cDNA were imaged by IVIS imaging system at fifth weeks Data information: Each experiment was repeated at least three times.
(A) Micrographs of triple mutant hAPP after 15min internalization (red), BACE1 immunocytochemistry (green) and their superimposition in wild type hippocampal neurons infected with 5xFAD hAPP lentivirus. DAPI and MAP2 staining are shown in the left column. Insets show higher (3.5x) magnification of the areas indicated in the main images. Scale bar, 5μm. (B) Quantification of the proportion of BACE1 that co-localized with hAPP after 6 and 15 min of internalization at 37°C. Results are expressed as mean ± SEM of % BACE co-localized with hAPP. N=3 independent experiments, each performed in duplicate; **, P<0.01 vs. WT (one-way ANOVA followed by post hoc test). (C) Quantification of the proportion of internalized hAPP that co-localized with BACE1 after 6 and 15 min of internalization at 37°C. Results are expressed as mean ± SEM of % internalized hAPP co-localized with BACE1. N=3 independent experiments, each performed in duplicate; *, P<0.05; **, P<0.01 vs. WT (one-way ANOVA followed by post hoc test).
Transmission electron micrographs of developing sporozoites in WT and α1-tubulin(-) parasite lines. Note the slender sporozoites in the WT oocysts, which are absent in the mutant. Sb: sporoblast; scale bars: 5 µm.
Fluorescent in situ hybridization analysis of the same donor human peripheral retina at different time points post-mortem (7 and 13 hours, Retina 7), showing decreases in MALAT1-hi rod subpopulations in the outer nuclear layer (ONL) at later time point. INL: inner nuclear layer; OPL: outer plexiform layer. Scale bar = 20µm. White arrows indicated MALAT1-hi rod photoreceptors.
Figure 8a. Experimental outline for measurement of transcription elongation rates. AS CDK12 HCT116 cells were treated with DRB for 3.5 h to synchronize RNAPII at gene promoters. The cells were either pretreated (+) or not (-) with 3-MB-PP1 0.5 h prior DRB wash off. After DRB wash off (0 h) fresh medium either supplemented (+) or not (-) with 3-MB-PP1 was added and samples were taken at indicated time points for analyses of pre-mRNA expression by RT-qPCR.
(A) Kymograph (top left panels) showing fluorescently-tagged Tea2 (Kinesin) co-imaged with fluorescently-tagged Tip1 (Tip1-Tdtom). Dashed yellow line indicates the position of the cell end. Plots (bottom left panels) show both the relative fluorescence intensity and position for Tea2 (green) and Tip1 (magenta) corresponding to the numbered sections of the kymograph. Scale bar 2µm. Data quantitated from this kymograph by extracting the maximal intensity pixel value at the MT plus end for Tea2 (green) and Tip1 (magenta) over time (top right) and the distance of these pixels from the cell end (bottom right)
A potential unique drug target pocket in SARS-CoV-2 N-NTDFigure legend: A. Detailed view of ribonucleotide binding pocket in superimposition structures between SARS-CoV-2 N-NTD with HCoV-OC43 N-NTD AMP complex. AMP, interacting residues and equivalents are highlighted with stick representation; B. Electrostatic surface of the potential ribonucleotide binding pocket on SARS-CoV-2 N-NTD; C. Electrostatic surface of the ribonucleotide binding pocket on HCoV-OC43 N-NTD; D. Detailed view of phosphate group binding site in superimposition structures between SARS-CoV-2 N-NTD with HCoV-OC43 N-NTD AMP complex; E. Dot representation of SARS-CoV-2 residues Thr 55 and Ala 56, which indicates potential steric clashes with the ribonucleotide phosphate group; F. Dot representation of HCoV-OC43 N-NTD residues Ser 67 and Gly 68; G. Detailed view of nitrogenous base binding site in superimposition structures between SARS-CoV-2 N-NTD with HCoV-OC43 N-NTD AMP complex; H. Electrostatic surface of the potential ribonucleotide nitrogenous base binding pocket on SARS-CoV-2 N-NTD; I. Electrostatic surface of the ribonucleotide nitrogenous base binding pocket on HCoV-OC43 N-NTD. In electrostatic surface potential panels, blue denotes positive charge potential, while red indicates negative charge potential. The potential distribution was calculated by Pymol. The values range from −5 kT (red) to 0 (white) and to +5 kT, where k is the Boltzmann constant and T is the temperature.
(H) Downregulation of STAT1 ameliorated hTau-induced contextual memory deficits measured at 24 h during contextual fear conditioning test (n=8 each group). Data information: Data were presented as mean ± s.e.m. *, p<0.05, **, p<0.01, ***, p<0.001 vs eGFP; #, p<0.05, ###, p<0.001 vs hTau.
D Representative western blot of total protein extracts from livers of starved Li-CluhWT and Li-CluhKO mice probed with indicated antibodies. GAPDH was used as loading control. E, F Quantification of western blots as shown in (D). Antibody signal was normalized to GAPDH signal and signal of phospho-protein was normalized to signal of the total protein (n=8 mice per genotype). Data information: data are presented as histograms showing the mean ± SEM. Error bars show minimum and maximum values. ***, P≤0.001 (Student's t-test). (H, J) *, P≤0.05; ***, P≤0.001 (One-way ANOVA, Tukey's multiple comparisons test).
A Left panel: schematic representation of the luciferase constructs produced for Mlx. Mlx 5'- and 3'UTR-interacting regions were cloned respectively upstream and downstream the Renilla luciferase coding region (RLuc-Mlx 5'-3') and mutant derivatives devoid of the 5' interacting region (RLuc-Mlx-3') or the 3' UTR interacting region (RLuc-Mlx-5') were obtained. These constructs were co-transfected in C2C12 myoblasts in growth conditions together with plasmids expressing lnc-SMaRT (+) or with a control vector (-). Right panel: Luciferase activity data, presented as the mean ± s.e.m. of three biological replicates (dots), are shown with respect to each RLuc control vector (RLuc-Mlx 5'-3', RLuc-Mlx-3', RLuc-Mlx-5') set to a value of 1. Statistical analysis was performed with ordinary analysis of variance (ANOVA) followed by Dunnett's multiple comparison test. *P < 0.05.
(E) RPE were isolated at 10 AM (diurnal condition) from 2-month-old WT and miR-211-/- mice. Representative image at low exposure of Western blot analysis of the Ezrin protein from WT and miR-211-/- mice. The graph shows the quantification of Ezrin normalized to the Gapdh loading control. Bar graphs represent mean values ± s.e.m. of independent experiments (n=5 mice) Mann and Whitney test (miR-211-/- vs WT), **p ≤ 0.01.
(B) Serum-starved HaCaT cells were treated for 18 h with poly(I:C) (5 μg/ml) in the presence or absence of FGF7 (10 ng/ml). Protein lysates were analyzed by Western blot for total and pSTAT1 (Y701 and S727), total and pSTAT2 (Y690), IRF1, IRF3, pIRF3 (S396), IRF9, RIG-1, RSAD2 and GAPDH.
B, LDA (sphere forming) measuring the GSC frequency after IR (5 Gy) in METhigh and METneg subpopulations sorted from BT308NS. *: 2 test, P=0.001.
F. Fluorescence recovery after photobleaching of BiFC signals. Time-lapse images of agarose-embedded cells carrying the β'-COPVN•Dsl3pVC BiFC pair were recorded at RT with PM Glc+ura medium supply at 2 min intervals. Fluorescence of ROIs marked in dashed lines (where the full cell, full bud, or only the bud foci were bleached) were depleted by three repetitions of fluorescence excitation at 177 µs/pixel and 100 % laser intensity. Arrowheads: reappearing fluorescence signal; scale bar 2 µm.G. Densitometric measurements of fluorescence intensities in photobleached cells. Representative data sets from five independent experiments are displayed, featuring cells that had been bleached entirely (black lines), at the bud only (dark blue lines), or at the fluorescent foci at the bud tip only (light blue line). Values are displayed in percentage of initial fluorescence, and were corrected for photobleaching effects by normalization against fluorescence of unbleached cells. Fluorescence recovery was typically not continued to full recovery stage because of the photobleaching artefacts occurring during long-term imaging of the samples.
E-H Whole mount in situ hybridization (WISH) of notochord-specific marker col9a2 in uninjected, FLT3/WT mRNA and FLT3/ITD mRNA injected embryos on 2 dpf. Data information: ov: otic vesicles; cm: cephalic mesoderm; nc: notochord. Scale bar = 500 μm.
(H) Topology of the SLP2-PARL-YME1L (SPY) complex in the IM. IM, inner membrane; IMS, intermembrane space.
D Immunofluorescence microscopy analysis reveals that GFP‐KSHV‐TK expressed in the context of lytic infection (MuHV‐4 [g‐KSHV‐TK]) does not alter focal adhesion integrity (paxillin) in the presence of the ROCK inhibitor Y‐27632.
(C) Immunoprecipitation of Ago3 with Flag-tagged DDX43 WT and its D399A and E400Q mutants. Ago3 and DDX43 were detected by western blotting using anti-Ago3 and anti-Flag-antibodies, respectively. Flag-EGFP was used as a negative control. The E400Q mutation in DDX43 impairs the interaction between Ago3 and DDX43. IgG h.c.: IgG heavy chain.
A-B: Percentage of pDCs (A) and mDCs (B) from total PBMCs collected at D1 was quantified by flow cytometry and grouped to self-reported duration of symptoms prior to D1 (A-B; 0-4 n= 22; 5-8 n=39; 9-12 n= 39; ≥13 n=16). Data information: Each dot represents a patient, lines with error bars show the median values with interquartile ranges Statistical significance was determined using the Kruskal-Wallis test *<p0.05, **<p0.01 ***<p0.001, ns= not significant.
D and H. Quantification of at least five (D) or seven (H) independent replicates of experiment shown in B/C and F/G, respectively. Uridylation signal intensity for substrate S1 (indicated in B and F) was corrected for adenylation activity and normalized to wild-type 2 min time point. Data represent mean SEM. P-values were determined using Student's t-test. * p<0.05, ** p<10-2, *** p<10-3, **** p<10-4.
Immunostaining with (A-C) anti-Pvalb7 and (D-F) anti-zebrinII antibody show loss of cerebellarPurkinje cells in atg4da morphants. (A,D) Control embryos at 4.5 dpf. (B,E) Morphants with mild phenotype show partial loss of cerebellarPurkinje cells. (C,F) Morphants with strong phenotype show either total loss of Purkinje cells or presence of few differentiated neurons, which are laterally located in the cerebellum. (G-I) Labeling of cerebellar granule cells with anti-Vglut1 antibody in control and morphant embryos. (H) Mildly affected morphants show reduced expression of Vglut1 in the cerebellum. (I) Vglut1 expression is strongly reduced in embryos showing severe phenotype. White arrowheads indicate the region of cerebellum. Abbreviations: hb, hindbrain.
(F) Basal extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) in the early-passage cell lines determined using the Seahorse XF96 Extracellular Flux Analyzer; graphs represent mean ± SEM of 6-8 technical replicates for each biological replicate (n=3).
a Heatmap showing UniProt-Keywords (https://www.uniprot.org/) enriched in each cluster. Black dots indicate clusters with significantly enriched keyword terms (hypergeometric test P-value ≤ 0.01, fold-change ≥ 2, number of annotated sites ≥ 2; Grey squares: fold-change < 1).
(D) Ingenuity Pathway Analysis (IPA) identified TGFβ1 as one of the most significant upstream regulators (activation z-score=-4.753, P = 2.1E10E-29; predicted activation state: inhibited) of the specifically modulated genes after COMBO treatment, according to microarray analysis. Shades of red indicate the degree of up- regulation while shades of green indicate the degree of down-regulation of significant downstream genes.
(A-D) Control and si-IRGM transfected THP-1 IFN reporter cells were kept uninfected (Mock) or infected with (A) JEV (MOI 5) or (B) CHIKV (MOI 5) or (C) HSV-1 (MOI 2.5) or (D) VSV-eGFP (MOI 1) and the supernatant collected 8 hpi were subjected to luciferase assay. The graphs depict fold change in interferon response.