EMBO/sd-character-level-ner huggingface dataset:
I. Representative images showing mTFP (cyan) and Venus (yellow) fluorescence in HBVPs which have direct contact with control (upper panel) or MCT1 (lower panel) siRNA-treated BMECs. VECAD immunostaining was used for endothelial staining. J. Quantification of the mTFP/Venus fluorescence ratio of laconic in HBVPs which have direct contact with control (siCON) or MCT1 (siMCT1) siRNA-treated BMECs. (n=8 from independent experiments. Error bars indicate the standard error of the mean (SEM) from unpaired Student's t test.)
A Schematic representation of the L3MBTL3 protein and the deletion mutants used in panel B. The L3MBTL3 protein (XP_006715641.1) consists of a C2C2 zinc finger (ZnF #1; CDD: 128717), three MBT domains (CDD: 214723), a C2H2 zinc finger (ZnF #2; CDD: 201844) and a sterile α motif domain (SAM; CDD: 197735).
The left panel shows the timeline of drug exposure experiments. (A-D) Images show vRNA and vDNA in an infected ThP1 cell (MOI 20) for each of four experimental conditions. See Appendix Fig. S15-S17 for images of larger regions. (A,B) ThP1 cells were exposed to NVP for 48 h (A) or 72 h after infection (B), then NVP was washed out, and cells were fixed for click chemistry 24 h later. (C) Cells were exposed to PF74 for 72 h after infection, then fixed for click chemistry. (D) Cells were exposed to NVP for 24 h after infection, then NVP was washed out, and cells were exposed to PF74, before being fixed for click chemistry 24 h later. (E,F,H) Scatter plots show vDNA and vRNA intensities in colocalizing clusters with Spearman correlation r and associated p-values. Replicates of the four experiments yielded similar results. (G) qPCR measures DNA synthesis (left) and nuclear import (right) at 72 h p.i. in absence of drug treatment, or after exposure to NVP or PF74. Bars and error bars define mean and standard deviation, respectively. Samples were analyzed in triplicate and two biological replicates were performed.
(K-L) Immunoblotting of indicated proteins in the lysates of mouse peritoneal macrophages (K) and THP1 (L) cells stimulated with 2'3' cGAMP (0.1μg/mL) in the presence of DMSO or Palbociclib (10 μM) for indicated times. The data shown are representative of n=3 biological replicates.
light during hypoxia. 2 sample 2-tailed unpaired t-test, *p = 0.0276, n = 7 independent experiments, each averaged from 3 technical replicates with at least 15 animals per replicate. Data show mean ± SEM.
C. Co-staining of CLIMP63 (green) and TMEM192-HA (lysosomes, red) in control and TFEB;3KO RCS treated with FGF18 (50 ng/mL for 16 hours). BaFA1 was used at 100 nM for 3h. Scale bar 15 μm and 2 μm (higher magnification boxes).
F-I. Immunofluorescence images of dpERK staining of midgut sections of the R4 region of 40-day Drosophila (F), 40-day Drosophila with ALA administration (G), 14-day Drosophila carrying esgts-GAL4-driven UAS-lacZ (H), and Drosophila carrying esgts-GAL4-driven Las RNAi (I). dpERK (red). J. Quantification of the fluorescence intensity of dpERK in experiments (F-I). Each dot corresponds to one cell. n is indicated. The numbers of quantified guts from left to right are 11, 12, 12, and 13. K Data information: DAPI stained nuclei are shown in blue. Scale bars represent 10 μm Error bars represent SDs. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
f) AFOG staining of heart sections from 45 dpci ppargc1a+/+ and ppargc1a-/- animals; black dashed lines outline the scar area; scar area measured on the right (n = 3-5 ventricles of each genotype).
B. BrdU-sensitized U-2-OS (Flp-In T-Rex) cells stably expressing GFP-NLS, the GFP-NLS-CDKL5 deletion mutants shown in A, or full length (FL) GFP-NLS-CDKL5 were subjected to line micro-irradiation (355 nm) and time lapse imaging. Three independent experiments were performed, and one representative experiment is shown. Scale bar is 10 μm
Representative t-SNE- plots (n = 2-3) show the cutaneous immune cell phenotype at therapy end (Day 28). Numbers adjacent to gates give cell populations frequency among live, single, CD45+ cells. t-SNE Legend-Plot labels the populations defined by t-SNE- algorithm.
(F)-The sleep metrics of flies with silenced expression of the Atg7 gene in per-positive cells.
E TCLs from MEFi were analyzed by immunoblotting for CPT1A, CPT1B and β-tubulin. Results are representative of three independent experiments.
Model of the cellular effects of OTULIN deficiency in myeloid cells and fibroblasts in ORAS. Hyper-signalling and TNF secretion in myeloid cells as well as TNF-induced cell death of both haematopoietic cells and cell types with LUBAC downregulation, e.g. dermal fibroblasts, may contribute to the inflammation, pathogenesis, and clinical manifestation of ORAS.
(h-j) Analysis of the IgH/c-Myc translocation frequency in WT and Samhd1 KO CH12F3-2A cells. (h) Schematic illustration of the experimental design for the translocation assay. (i) Southern blot analysis of PCR-amplified fragments with a Myc-specific probe from two independent experiments. (j) Frequency of IgH/c-Myc chromosomal translocations derived from two independent experiments (mean ± sd; Fisher's exact test).
C BreastMark microarray platform; correlation of ESRP1 expression with overall survival in tamoxifen-treated patients. A log rank test was used to calculate P=1.218, e-06 (n= 210, number of events= 49).
Bar graph showing relative levels of trpml mRNA in Drosophila larval brain extracts from control animals and animals expressing dRasG12V in glia. All values represent mean±SEM. Data points represent values from biological replicates. Statistical test employed was Student's t-test.
D. Schematic representation of MS/MS analysis of TRAPPC2 interactors. In addition to the TRAPP components and known TRAPPC2 interactors, 53 RNA binding proteins known to associate with SGs were co-IP with TRAPPC2. Proteins that associate with TRAPPC2 only upon SA-treatment are highlighted in red.
C Schematic representation of the zebrafish Grk2 protein domains and the truncated peptide predicted to be encoded by the grk2i283 mutant allele.
Confocal images of Jurkat cells to show NF45 (left panel) or NF90 (right panel) (green fluorescence) colocalized with NFATc2 (red fluorescence) in nucleoli. Scale bar, 10 μm.
B Confocal immunofluorescence microscopy images of P1.HTR cells transfected with IDO1.WT incubated with class IA PI3K p110 isoform inhibitors (indicated) or medium alone (Ctrl) for 24 h and co-stained with antibodies recognizing IDO1 (green) and EEA1 (red). Nuclei were stained with DAPI (blue). The merge imagine is shown for all stainings or without DAPI (no DAPI). Scale bar, 10 µm.
(a) The UVRAG C-terminal 270-442 region interacts with RINT-1. Cells (HEK293T) were co-transfected with HA-RINT-1, together with Flag-UVRAG or its mutant derivatives, and whole-cell lysates (WCLs) were immunoprecipitated (IP) with anti-Flag, followed by immunoblotting (IB) with an anti-HA antibody.
G-K. Expressions of Rab7-GFP reporter in ISCs of 14-day WT Drosophila (G), 40-day WT Drosophila (H), 40-day Drosophila with ALA administration (I), 14-day Drosophila carrying esgts-GAL4>UAS-lacZ (J), and 14-day Drosophila carrying esgts-GAL4>Las RNAi (K). GFP (green). L. Quantification of fluorescence intensity of RAB7-GFP in experiments (G-K). Each dot corresponds to one cell. n is indicated. The numbers of quantified guts from left to right are 11, 10, 11, 13 and 12. M Data information: DAPI stained nuclei are shown in blue. Scale bars represent 2 μm Error bars represent SDs. Student's t-tests, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
Qualitative measurement of hydrogen sulfide in cerebrum and kidneys of Coq9+/+ and Coq9R239X mice (B).
I. Quantification of MT catastrophe frequency in the presence of different DCX constructs observed with MT stabilization TIRF assay. Total free tubulin concentration was 10 μM in all experiments. The basal (tubulin alone) catastrophe frequency level at this tubulin concentration is indicated with a grey bar.
F) Secretory profile of cytokines present in the medium of microglia, astrocytes or mixed astrocytes and microglial (2:1) culture as above (n=5-6 cultures type -microglia, astrocytes or mixed cultures- and genotype). The content of IFNγ, TNFα, IL4, IL6 was determined by Multiplex ELISA. Values are represented in absolute concentration. Error bars represent Standard Error. Statistical significance: ns P>0.05; *P<0.05; ***P<0.001; ****P<0.0001 by two-way ANOVA followed by Bonferroni's multiple comparisons test.
Representative microscope pictures (20x) of MIAPaCa-2, Suit-2, Capan-2 and Panc-1 cells. Scale bars, 200 μM.
The above harvested Dps were subjected to IF staining for Troponin T (TnT) together with Laminin. Scale bar = 50 µm. Quantifications of positively stained fibers per area are shown on the right (n=3 mice, each).
D283 cells were treated with DMSO (vehicle, black), with LY364947 (red) or with SB431542 (orange). Percentage of apoptotic cells measured by FACS analysis of cleaved caspase3 48 hours after TGFβ/Activin signaling inhibition. Bars represent the mean ± SD. Number of replicates is n≥3.
(G) Immunostaining of strain SEY6210 containing a 2μ APE1 plasmid grown in SD medium. N, Nucleus; V, vacuole.
The panel shows the estrogen-receptor (ESR1) pathway, which is significantly enriched for genes regulated by ATRA in Lum tumors. The green arrows indicate up-regulatory or stimulating interactions, while the red arrows indicate down-regulatory or inhibitory interactions. The gray arrows indicate unknown types of interactions. The red and blue dots above the protein symbols indicate the effect of ATRA in Lum tumors (red = up-regulation; blue = down-regulation).
(C) Image correlation analysis (ICA) of GlyR and GABAAR clusters at the same PSDs. The ICQ values between GlyR and GABAAR (blue trace, 0.36 ± 0.06, n = 395 synapses from three independent experiments) are significantly lower than between GlyR clusters labelled with two secondary antibodies conjugated with different fluorophores (yellow trace, 0.38 ± 0.04, n = 218 synapses; MW test, p < 0.0001).
A-D. Representative images of midgut sections from the R4 region of Drosophila carrying esgts-GAL4-driven expression of lacZ cDNA (A, control), Las RNAi (B), Las RNAi and RAB5-CA (C), or Las RNAi and RAB7-CA (D). GFP (green), Dl staining (red) was used to visualize ISCs. Data information: DAPI stained nuclei are shown in blue. Scale bars represent 10 μm
(A) Schematic of SILAC-mass spectrometry. Wild-type (WT) and Ews-/- mBA cells were labeled by heavy or light amino acid, respectively. Differently labelled proteins were analyzed by mass spectrometry.
(C) sgRNAs counts in BRAFi-resistant cells versus in DMSO-exposed cells for EGFR and BIRC3. (BRAFi for PBV,
(D) Inhibition of autophagy results in increased protein oxidative damage. Treatment of INS1 cells with bafilomycin (blocking autophagy by preventing fusion with lysosomes, 0.1 μM for 3 h) results in the accumulation of oxidized proteins in mitochondria, which is shown by increased level of carbonylated amino acids in isolated mitochondria.
B) Schematic representation of the synthetic peptide used as antigen to raise the β-monoE antibody. The modified glutamate residue is in red.
(C) Average number, normalized on cell size, of EEA-1+ endosomes as in a. Results are the average ± SEM of three independent experiments for a total 4483 early endosomes in 18 siCTL cells (299 ± 33 endosomes per cell) and 2454 early endosomes in 13 siSTIM1 cells (189 ± 17 endosomes per cell) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,01 **.
(G) Western Blot analysis of phenotype switch markers on lysates from M238P cells treated as in (A).
Immunoblotting of SPATC1L in testicular cells (TC), testicular sperm (TS), and epididymal sperm (S). An anti-ADAM2 antibody was used as a control.
Western blot analysis on liver extracts from the treated mice with antibody against type I collagen.
Kinetic schemes and equilibrium constants for WT (upper panel) or super-active GluN1-E698C/GluN2B-L795C (lower panels) receptors. Records were analyzed at equilibrium. Ligand-binding steps are shown in gray. Note that for simplicity, long-lived desensitized steps are not shown. *P<0.05 relative to WT GluN1/GluN2B (two-tailed Student"s t-test, unpa
B Comparison of the FRET-based protein proximity mapping with previously described interactions of studied proteins. Physical interactions of indicated proteins (observed in more than one study) were taken from Saccharomyces Genome Database as per February 2019. FRET proximities mirroring previously detected protein interactions are shown as violet lines and numbers. Proximities not found as interactions and vice versa are shown as blue and gray lines/numbers, respectively.
D. (left panel) iTreg were polarized from human naïve CD4+ T cells over 7 days (n=3 donors /experiment) receiving control (shCK), or shRNA knockdown constructs targeting USP44 (shUSP44-1, -2), or USP7 (shUSP7-1, -2), or both shRNA constructs. Freshly isolated nTregs were treated with either control or shRNA constructs. After transduction with lentivirus for 48 hours, cells were harvested and run SDS-PAGE gels. Protein levels were visualized by immunoblotting using antibodies specific for FOXP3, USP44, USP7 and GAPDH. Shown are representative findings from 3 independent experiments (biological replicates).
(b) Conservation of the apelin/angiotensin/bradykinin peptide receptor subfamily among all vertebrates except for the GPR15-C10ORF99 pair. * Indicated that these three fish species did not undergo a third round of whole-genome duplication during fish evolution.
A The family pedigree, where circles denote female members, squares male members, solid symbols affected members, and white symbols asymptomatic members with normal physical exam; the dots indicate heterozygous carriers and double line denotes a consanguineous marriage. The pictures show scapular winging which is a consistent clinical sign in affected individuals.
The between 20S and 26S+30S proteasome abundance assessed by immuno blot on native gels (Figure EV5A). ** p<0.001, Wilcoxon Rank Sum test. The bars indicate mean +/-SD.
At 2 days post-fertilization (dpf),Lyz:dsRed or mpx:GFPlarvae were transferred into DMSO ctrl or FK506 (1 μg/ml) containing 0.5 × E2. At 3 dpf, zebrafishlarvae were microinjected with AFeGFPconidia into the hindbrain and mortality, and fungal burden and neutrophil recruitment were assessed. D TNF-α mRNA levels were measured in whole non-infected or infected larvae 48 h p.i. Immunosuppression led to significant and almost complete inhibition of TNF-α expression during infection.
D) A yeast one-hybrid screening strategy to identify proteins binding to the ub-HS-motif. Three copies of the ub-HS4-motif (F7) were cloned upstream of a minimal promoter followed by a HIS3 reporter-gene and integrated at the URA3 locus. A yeast cDNA library with N-terminally fused Gal4-AD was used to screen for survival on media lacking histidine and multiple plasmids coding for 4 different genes were recovered (bottom).
B, Heat map of USP22, GCN5, and ATXN7L3 association at the TSS for 29 genes whose promoters undergo significant recruitment of USP22 following induction of ER stress.
b) mRNA expression of hCAT in bone marrow derived neutrophils from wild-type and MCAT mice; c) catalase activity in bone marrow derived neutrophils from wild-type and MCAT mice; d) Dihydrorhodamine 123 fluorescence was assessed by flow cytometry in neutrophils from wild-type and MCAT mice with or without stimulation with PMA
CSF extract was supplemented with Myc-XErp1 wt IVT at the indicated dilutions. An empty IVT reaction not expressing Myc-XErp1 served as control. All reactions were divided and treated with DMSO or CsA. Calcium was added to all reactions and samples were taken at the indicated time points, treated with λ-phosphatase and immunoblotted for XErp1, the Myc-tag, cyclin B2 and α-tubulin. Asterisks indicate unspecific bands.
(C) Heatmap illustrating gene expression changes in the inflammation and lysosome pathways in WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- spinal cord samples. Data information: Inflammation genes are highlighted in magenta and lysosomal genes are highlighted in blue.
I Detection range comparison in force-dependent affinity of NKG2D and indicated ligands under difference force. Bars in different colors are the ratios of the affinities of indicated ligands divided by that of ULBP1.
(C, D) Analysis of microglia/macrophage activation using Iba1 immunohistochemistry from complete spinal cord sections at 1 mm interval. One-way ANOVA, Tukey's post hoc test. ** p<0.01, * p<0.05, ns not significant. Scale bar indicates 100 μm. F(5,12)=0.6974, p=0.6357; TG-Ova-(GA)10 vs. TG-PBS p= 0.0131; TG-(GA)15 vs. TG-PBS p=0.7650. TG-PBS vs. WT-PBS p=0.0018.
(A) WT, and Irgm2-/- BMMs were stimulated overnight with IFNγ or left untreated and cell lysates were collected. Lysates were assessed for Casp11, Gbp2, and actin protein levels via immunoblotting.
a, Western blot analysis of flag-tagged beclin-1-transfected MCF7 clones. C, MCF7.control cells (clone 38); St, MCF7.beclin1stop cells (clone 70). Mr, relative molecular mass.
B Immunoblot analysis of in vitro kinase assay by the phosphorylation-gel. HA-AKT2 was immunoprecipitated from HEK293T cells by anti-HA/IgG antibody and Protein-G beads, and His-IRF3 was purified from E.coli cells by anti-His agarose beads. His-IRF3 alone and anti-IgG-beads added with His-IRF3 served as control. The arrow indicated the phosphorylated IRF3. Data information: * Data are representative of three independent experiments
(E) Quantitative comparison of MIC and MIC-SOX9 cells to migrate across 5 μm filter pore toward the laminin-coated trans-well for 4 hours. Quantification of cell migration were performed as described in (C) and presented as mean + standard error mean from 6 replicates.
b, Helical wheel projections of the red sequences from a. A schematic representation of the 7-bladed beta-propeller PROPPIN structure is also shown, illustrating the localisation of the putative amphipathic -helix (blue) of the CD loop between the two lipid binding sites for PI3P/PI(3,5) P2. Bold print marks phosphorylation sites in the loop of Pichia pastoris Atg18, which are relevant for its membrane insertion (Tamura et al, 2013).
(E, F) Mass spectrometry quantification of m5C (D) and hm5Cm (E) levels in total RNA from nsun mutants. RNA was extracted from populations of L1 animals synchronised by starvation, digested to nucleosides and analysed via LC-MS. n = 3 independent biological replicates. n.d. = not detected. Data information: In E, F data are presented as mean ± SEM.
Pancreatic chromatin from control or Tgif1KO mice was analyzed for binding of TGIF1 to the Twist1 promoter by ChIP and agarose gel.
(D) Representative images of the number of AP+ positive colonies. n = 5 biological replicates per condition.
(B) Quantification of the percentage of cells presenting LC3 puncta upon incubation under the different conditions. Data correspond to two independent experiments (n = 50 cells/condition).
F. Locomotor activity of control (black), heterozygous (blue) and mutants (red) showing significant hyperactivity of mutants in dark and light cycles (N=3, n=48).
(A) Volcano plots of common differentially expressed genes in shScr and Zfp207-depleted (sh1 and sh2) mouse ESCs. Up-regulated (Up) and down-regulated (Down) genes are indicated in red and blue, respectively (p < 0.05; > 1.5-fold). Zfp207 is depicted in black. Grey dots indicate non-significant (NS) and < 1.5-fold differential expressed genes.
B Vero E6 cells were inoculated with SARS-CoV-2, fixed with paraformaldehyde after two days, stained with 30 nM of the indicated Alexa Fluor 488 (AF488)-labeled anti-RBD VHH antibodies, and imaged by confocal laser scanning microscopy (CLSM). C Immunofluorescence (IF) staining as in B, but with the indicated AF568-labeled anti-S1ΔRBD VHH antibodies.
(G) The frequency of NKG2D+ IELs among CD3+CD4+ population (n = 8). Data information: Data were representative and were the median ± interquartile range from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.
C. Top, Binding of CDC and NDC at the vertex of 4 bent tubulin dimers of different MT nucleotide states with close-up cutaway views. Bottom, Superposition of CDC X-ray structure 5IP4 (darkened and transparent) with the GTP/GDP.Pi-MT-binding conformation (this study; bright yellow) and superposition of 5 NMR and X-ray NDC structures from Protein Data Bank (PDBs: 5IO9, 1MJD, 2BQQ, 5IKC, 5IN7) with the GDP-MT-binding conformation (this study).
D Representative force vs. time curve for measuring single NKG2D-ligand bond lifetime.
During reprogramming with mES medium, Bmi1, Ctcf, Ezh2, Kdm2b, and Wdr5 were overexpressed simultaneously with the four Yamanaka factors (OKMS+5F) or Oct4 (O+5F). All factors were delivered simultaneously via a retrovirus system on day 0 and 1. Reprogramming with only Yamanaka factors (OKMS) or Oct4 (O) served as control. The numbers of Oct4GFP+ colonies were determined on day 15 (F).
A. In left, normalized peak amplitudes of isolated AMPA EPSCs recorded at -60 mV, before and after pairing protocol, are illustrated. Representative traces of AMPA EPSCs before (1) or after (2) the pairing protocol are also illustrated (right panel) for each experimental condition: Vehicle-injected mice (white circles, n=3 from N=3), THC-injected mice (green circles, n=3 from N= 3) and THC-injected mice treated with SB258585 during adolescence (black circles, n=3 from N=3). Errors bars correspond to mean ± SEM.
Synaptic transmission in autaptic excitatory munc18-1 neurons expressing M18WT or a non-phosphorylatable Munc18-1 variant, M18Y473F, was tested with whole-cell patch clamp electrophysiology.(G) PDBu was bath applied during 0.05 Hz stimulation. Maximum potentiation of EPSC amplitude (M18WT: 2.56 ± 0.48 fold, n=7; M18Y473F: 2.82 ± 0.98 fold, n=8, t-test with Welch correction, p = 0.8168).
(A) Immunoblot analysis of phosphorylated Smad2 (P-Smad2) in Group 3 MB cell lines and PDXs. The level of total Smad2 (Smad2) was assessed and β-actin was used as a loading control. Quantification of P-Smad2 (P-S2) to β-actin are shown on right panel. Right (A) panels represent the relative quantification of P-Smad2 normalized to β-actin. Bars represent the mean ± SD. Number of replicates is n≥3.
(G H) Three-dimensional ribbon (PDB 3TH5) representations of the human Rac1 polypeptide which indicate the position of the T135 (S139 in MIG-2) located between the last two α-helixes (Krauthammer et al, 2012).
(D) Representative Western blot analysis of HeLa cells transfected for 24 h to produce HA-BspF, separated into saponin-, Triton X-100- and SDS-soluble fractions and probed for HA-BspF, Hsp27 (cytosol), Calnexin (membranes) and Lamin A/C (nucleus).
H. Lateral (top) and ventral (bottom) projections of medaka fish embryos with indicated genotypes. Scale bar 1mm. Bar graphs show quantification of total length and head size of medaka fish model of Fam134bmo expressed as % relative to the scramble. Mean +/- standard error of the mean (sem) of at least n=8 fish/genotype. Student un-paired T-Test *p<0.05.
c-fos mRNA expression levels in p53f/f Rb1f/f Osx-Cre OS cells treated for 24h with Erlotinib (10µM) (n=3)
C. Survival (percentage) of female Drosophila of indicated genotypes. The numbers of quantified Drosophila: 100 (UAS-lacZ), 100 (Las RNAi), 100 (Las RNAi + UAS-Rab5-CA) and 100 (Las RNAi + UAS-Rab7-CA). Three independent experiments were conducted Data information: Error bars represent SDs. p-values for lifespan curves (C) were calculated by the log-rank test. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
a, b, Fetal liver chimaeric mice were given 5% DSS in drinking water for 7 days. The survival (a) and weight loss (b) of each mouse genotype were plotted. The results shown are mean ± s.d. Statistical significance was determined by the Students t-test.