EMBO/sd-character-level-ner huggingface dataset:
(D) Quantification of histone H3 and H4 acetylation in +/atpcl mutants at 4 weeks old (midlife). Age-associated hyper-acetylated histone states are reduced in +/atpcl mutant flies (H4K12, H3K14, H3K9/14 and H3K23). N=5-6 per group.
siRNAs against Bclaf1 and control siRNAs (siCtrl) mixed with in vivo-jetPEI (Polyplus) were injected into C57BL/6 mice. The mice were then treated with mTNF for two hours before sacrifice. The small intestines were excised and processed for western blotting analysis (G).
mEPSC (E) mean amplitude of cortical neurons of S or SD mice. Control neurons (Ctrl/S n=8 cells/4 mice, Ctrl/SD n=8 cells/4 mice), Fxr1 overexpressing (Fxr1/S n=7 cells/5 mice, Fxr1 over/SD n=9 cells/5 mice), and Gsk3 sKO (Gsk3sKO/S n=6 cells/3 mice, Gsk3sKO/SD n=7 cells/4 mice). Student's T-test *p<0.05.
(H) Assessment of cardiac fibrosis by Masson's trichrome staining (n = 4). White scale bars, 100μm; black scale bars, 1 mm.
A Actin expression levels shown by western blotting for strains expressing S. cerevisiae's actin or other actins, with tubulin (Tub1p) as a loading control.
A. Quantification of in vitro matrigel invasion assay (bottom) of P-CAF and L-CAF (P-CAF # 36, 138 and L-CAF #189, 484) transfected with control siRNA (CNT) or hMENA siRNA (hMENA(t)) indicating that the siRNA‐mediated knock‐down of hMENA/hMENA∆v6 reduces the invasive ability of CAFs with respect to siCNT CAFs. Number of invading cells was measured by counting 6 random fields. Data are presented as the mean ± SD of two biological replicates, performed in triplicates each. Immunoblot showing hMENA/hMENAΔv6 expression (detected by Pan-hMENA mAb and by the specific anti-hMENAΔv6 antibody) of the CAFs employed is reported (top). TUBULIN was used as loading control. P values were calculated by two‐sided Student's t‐test. *P<0.05, ***P<0.001.
(B) Boxplots of allelic ratio of X linked genes (n = 294). Upper dashed line indicates biallelic expression with a ratio of 0.5, the lower dashed line indicates the X-inactivation threshold of 0.135. Box plots depict the first and third quartiles as the lower and upper bounds of the box, with a band inside the box showing the median value and whiskers representing 1.5x the interquartile range. Number of X-inactive genes are shown at the bottom.
D. Immunoblot of PARP1 cleavage of PeTa cells after 6 days of indicated treatment. Etoposide serves as positive control for apoptosis, H3 serves as loading control. c.PARP1, cleaved PARP1.
Serum anti-Insulin-immunoglobulin titers of mice immunized with InsA-peptide (red: 0:1, n=10 and green: 100:1, n=5) and control-immunization (CI: CpG only, grey, n=3) measured by ELISA at indicated days (coating: Insulin). Dots represent individual mice. Mean ± SD, statistical significance was calculated by using Kruskal-Wallis test, *P < 0.05, ***P < 0.001.
E. Two O6SKM iPSC lines immunostained for pluripotency markers Sox2 and Nanog. Oct4 expression was confirmed by the Oct4-GFP transgene. DNA stained by DAPI. Scale bars: 100 μm.
I. HEK293 cells were transfected with YFP-EML4-ALK V1 WT or V3 WT for 48 hours and treated for 4 hours with ALK inhibitors, ceritinib (500 nM), alectinib (100 nM) and lorlatinib (100 nM) or an equivalent volume of DMSO. Western blots of pALKY1604 and α-tubulin were used to assess relative abundance in transfected HEK293 cells.
(E, F) Samples mean value of Eigengene analysis of TNFα signaling via NF-κB pathway (E) and inflammatory response pathway (F) of HeLa NOD1 or NOD2 cells upon indicated stimulations.
(H) Protein levels of Tead1, Tead3, Tead4, and Pou5f1 upon KD of Tead 1/3/4. N.S. depicts non-specific.
(F, G) Percentage of CD4+ and CD8+ cells within OFP- BM cells (F) and maturation state (G) of CD8+ lymphocytes (CD62L-CD44- double negative, CD62L-CD44+ effector memory, CD62L+CD44- naive and CD62L+CD44+ central memory) in the BM immune infiltrate at 12- and 17-days after B-ALL (mean ± SD, each dot represents an individual mouse; ** p = 0.005, **** p ≤ 0.001, Two-Way ANOVA).
F. A representative control HC expressing Wrbcc-EGFP (white arrow), immunolabelled for otoferlin (magenta). The Wrbcc-EGFP-expressing HC shows significantly less otoferlin (F'), suggesting a dominant negative effect of Wrbcc in otoferlin biogenesis. The transfected HC is encircled with a dashed line.
C, 3D reconstruction of confocal microscopy images of whole-mounted retinas from C57BL6/J (C) recipients 21 days after transplantation with Nrl::GFP donor photoreceptors (top layer) shows that donor and GFP+ acceptor photoreceptors appear to be attached via protrusions. Higher magnification 3D reconstruction (C) showing protrusions (pink arrows) and GFP labelling in acceptor cells.
C Recombinant TFG in the presence of varying potassium acetate concentrations was imaged by negative stain‐EM. Large arrowheads highlight TFG polymers (only found in the presence of elevated potassium acetate). Small arrowheads highlight individual 11 nm cup‐like TFG octamers. Scale bar, 30 nm.
D. Images of 10 μm-thick sections from lateral ventricle CP villi of Mpdz+/+ and Mpdz-/- mice, immunolabeled for Nkcc1. The areas in the marked squares are magnified below. Scale bars, top, 50 μm, bottom 20 μm.
(i) Western blot analysis of cortical neurons from wild-type and SV mice treated with 1 μM MG132 in the absence or presence of 100 nM bafilomycin A1. (j) Quantification of western blot LC3-II intensity was performed (n = 2). (k) To evaluate the effects on autophagosome biogenesis, the results are shown as the fold increase in normalized LC3-II intensity with bafilomycin A1 compared with the untreated control (n = 2).
Human FXS-patient derived fibroblasts (FXS-1, FXS-2) and control human fibroblasts were synchronized in early G1 by Monastrol release and analysed by immunofluorescence microscopy examples of nuclear architecture defects are shown in (D).
Responsiveness to gemcitabine (GEM), either alone or combined with Nab-paclitaxel (NAB-P), was evaluated in mice bearing orthotopic HuPa8 in the pancreas. Nab-paclitaxel (25mg/kg) and gemcitabine (150mg/kg) were given i.v. on days 1 and 8 of each 21-day cycle (for a total of 8 treatments) B) Magnetic resonance imaging of HuPa8. Representative images are shown, the white dotted lines indicate tumor masses
(C) Representative distribution of Tubulin and CDC42 in Ctrl, 4-months old Npm1 cKO and 2-years old WT HSCs determined by IF. Scale bars, 5 μm.
(D) Knockdown of IP3R1 prevents ER stress-induced apoptosis. Cells were treated with 4 μM TM for the indicated times. Protein expressions were analyzed by immunoblotting.
MCF-10AT1k.cl2 cells were transfected with control or ELYS siRNA. Representative images of cells stained for Ran and lamin B1 are shown. (H) Representative images of cells stained for NTF2 and lamin A/C are shown. (I) Nuclear Ran and NTF2 staining intensities were quantified and normalized to the negative control. To measure the N/C staining intensity ratio of a given cell, the average fluorescence intensity of a nuclear region was divided by the average fluorescence intensity of a cytoplasmic region. For each experiment, 54-216 nuclei were quantified per condition (112 nuclei on average). Two biological replicates, data from one representative experiment shown.
(f) Knockdown of Atg5 expression abolishes α-synucleinA53T mutant-induced neuronal death, whereas it reduces neuronal survival in vector-transfected cells. Data are means ± s.e.m.; n=3.
B Bar graphs demonstrating the number of up‐, non‐, and downregulated ubiquitination sites in USP22 KO HT-29 cells versus control under TBZ-treatment.
E RNA velocity analysis of organoids under DMSO and preferred treatment conditions. Latent time is given as color code in the control (DMSO) condition UMAP, dynamical velocities are displayed as arrows.
C The relative changes in the PS and polyspike areas in the presence of picrotoxin (50 µM) and a subsequent treatment with DMSO or VPS34IN1 (10 µM). VPS34IN1 significantly reduced the PS and polyspike area compared to DMSO. N = 6 slices per condition from 6 mice. D Mean area of PS and polyspikes in picrotoxin-treated slices 40 min post-application of DMSO or VPS34IN1. N ≥ 6 slices per condition from ≥ 6 mice; Student's t-test. Data information: Data presented as mean ± SEM ; *p < 0.05; ***p < 0.001.
A. Relative levels of mtDNA in tissues of 1-year-old Fbxl4 knockout mice determined by quantitative real-time PCR (normalized to controls). Data are presented as mean ± SEM, n=6 for controls and n=8 for knockout animals. Student's t-test; **, p<0.01; ***, p<0.001.
(A) Overlay of right and left wings of a yki2-only-A female showing fluctuating asymmetry.
(B) Example of interaction screening using an α-H3 antibody against tethered EGFP (EGFP-OMP25), tethered H3.1 (H3.1-EGFP-OMP25) and tethered H4 (H4-EGFP-OMP25). Background corrected, single Z-slices of representative cells are shown with 2D histograms displayed on the right. Nucleus and cytoplasm are portioned with a white line. Pearson's coefficients (R) for the cytosolic region of the depicted cells are shown in the histogram inset. Scale bar represents 10 μm
B. Quantification of β-gal+ cells in FACS-purified AT2 and Club cell fractions isolated from 3 months old BASC v-race mice (mean±SD, n=3) and example of β-galactosidase label distribution in lung sections. Scale bar: 100 µm.
E Bulk-RNAseq analysis (n=3 biological replicates; individual data points are shown with bar graphs representing mean value).
Vessel stability. IsolectinB4 (IsoB4, green) and collagen IV (red) in P4 wildtype (WT) and Vegfr2Y1212F /Y1212F retinas. Arrows; collagen IV-positive empty sleeves. A; artery. Scale bar, 50 µm.
C. Cell length profile as a function of the cell number position from the QC for three wild-type seedlings (symbols, top) at day 8 post germination and three simulated root files for the Sizer model (symbols, bottom). Notice the use of a logarithmic scale in cell lengths, which visualizes the cell lengthlog10 rEZ
D Quantification of total number of alveoli by design-based stereology in wild-type mouse pups at post-natal day (P) 14, treated with either scrambled antimiR (S), or antimiR-34a (A34a), during normal and aberrant lung alveolarization (n = 5 animals for each group).
E. Heatmap depicting the expression of various neurotransmitter genes for all cells across the 7 clusters analyzed. Clusters are color-coded and labeled according to depiction in 2B. Clusters are labeled to reflect clusters with progenitors, migrating interneurons and mature interneurons.
E. Co-immunoprecipitation between TRAPPII and HA-Rab18 in control (siFFL) and γ-COP (si-γ-COP) siRNA depleted cells. TRAPPII was precipitated with transfected Myc-TRAPPC10 and the presence of HA-Rab18 was determined by immunoblotting.
At necropsy, the percentage of the area of the lungs affected by gross lesions was estimated by a board-certified veterinary pathologist (c)
Percentage of origin firing (mean+SD) from DNA fibers in C (n=2). >490 fibers per condition were scored.
B. Representative image showing the phenotype of wild-type (Ws), uvr8-7 and uvr8-7/Pro35S:UVR8HY5C44, uvr8-7/Pro35S:UVR8HY5VP and uvr8-7/Pro35S:UVR8TRIB1 seedlings grown for 4 days under white light (- UV-B) or white light supplemented with UV-B (+ UV-B). The scale bar represents 5 mm.
A Yeast two-hybrid assay of the interaction between ATX1 and SEC. The full-length coding sequence (CDS) of ATX1 was cloned into the bait vector pGBKT7. A full-length SEC CDS and a truncated fragment were cloned into the prey vector pGADT7 to express complete or truncated SEC-N (including only TPR domains at the N-terminus), respectively. AD vectors expressing SEC or SEC-N were each cotransformed with BD-ATX1. SD/2, SD/-Leu/-Trp medium; SD/4, SD/-Ade/-His/-Leu/-Trp medium. Cotransformed pGBKT7-53/pGADT7-T was used as a positive control.
(G) Diagram of the post-translational Smad4 modifications by modifying enzymes and their downstream functions. P, phosphorylation; Ub, monoubiquitination; Me, methylation.
Cartoon visualizing the proposed mechanism by which both GPR56+ LSC enriched compartments are maintained: GPR56 enhances pathways, which reciprocally inhibit each other and are differentially active in the two fractions. This should result in a constant transition between the compartments and thus prevent exhaustion of the two populations.
RT plus anti-PD-L1 (B) reverses T-cell exhaustion . Bar graphs show quantitation of T cell activation markers in tumor samples based on flow cytometry analysis, as indicated (n=5 per group; means ± SD, n=1, One-way ANOVA, Bonferroni test).
C Quantification of the ratio of cleaved/uncleaved HybA in strains with (+) or without (-) HybB. mean ± S.D. of three experiments. *, p<0.05; ****, p<0.0001 (One-way ANOVA).
E Cells were transfected with each plasmid encoding PB1-F2. 18 h after transfection, cells were treated with MG132 for 6 h and the level of IFNβ mRNA was determined by semi-quantitative RT-PCR (left) and qPCR (right). PB1-F2 protein expression was assessed by Western blotting. All data are shown as mean (±SEM) from at least three independent experiments (*p < 0.05, **p <0.01, ***p <0.001).
(C and D) Cytosol containing autophagosome‐like vesicles accumulating in the cytosol of aut2Δ cells (D) can be isolated with an additional 100 000 g centrifugation step yielding a P100 pellet fraction. In wild‐type cells (C), no P100 is detectable. Fatty acid synthase (Fas) was used as a cytosolic protein. Further details are given in the text.
Top view of the ribbon diagram of TssAVC CTD model. Two interfaces are highlighted with green circles. Enlarged side view of interface between helices α9-α11 of two neighboring subunits (top right), enlarged side view of interface between α11-α12 linker of one subunit and helix α10 from the neighboring subunit based on conserved WEP-motif (bottom right). Part of Nt2-CTD linkers are highlighted with red circles.
c, Autophagic flux in WT and Ift88−/−KECs by mCherry-GFP-LC3 puncta quantification. Puncta: yellow, autophagosomes; red only, autophagolysosomes; total, both together (**P = 0.008, *P = 0.025).
(g-h) DT treatment effectively ablates Atoh1+ cells shown by reduced number of tdTomato+ cells per organoid. Data information scale bars =100μm. Data are represented as mean ± SEM analyzed using Student's t-test. *P≤0.05.
A. Representative flow cytometry plots showing gating strategy to identify splenic GC B cells 14 days after LCMV Armstrong infection in WT and Dot1L-KO mice (left panel) and statistical analysis of their relative number. Results represent the data from two experiments and numbers represent biological replicates for each group (WT; n = 7, KO; n = 8).
A. Linear representation of the structure of EML4-ALK V3 and EML4-GyrB fusion proteins including residue numbering indicating domain boundaries.
C. Interaction of endogenous hTrmt13 with FOSL1, E2F1, and USF1.Whole-cell lysates from MDA-MB-231 cells were immunoprecipitated with antibodies against hTrmt13 or IgG followed by immunoblotting with the antibodies against the indicated proteins. * and ** are nonspecific bands.
B) HAP1 cells were fixed and stained with antibodies examining Golgi morphology markers (B). (C) Western blot of GBF1, PI4KB and B-Actin levels in both wild-type and c10orf76 KO HAP1 cells. Data information: Nuclei were stained with DAPI (blue). Scale bars represent 10 μm.
(B) Western blotting for Yap1 in nuclear or cytoplasmic proteins from primary intestinal epithelial cells cultured in the supernatant with or without mIslr. Histone H3, a positive control for nuclear proteins. α-Tubulin, a positive control for cytoplasmic proteins.
C. Fluorescence anisotropy measurements using 40 bp dsDNA or 40mer ssDNA substrates. Representative binding curves (top graph) and the resulting Kd values (bottom graph) indicate that both hexameric and octameric Smc5/6 complexes interact with both substrates, whereas the Nse5/6 complex alone does not. The bar graph shows mean values with standard deviations from technical triplicates. Individual data points are also displayed.
Images of a single RAW 247.6 cell displaying yellow puncta indicative of successful re-positioning of CB (in green) to the lysosome (in red) in the presence of rapalog but not EtOH.
A Rosette phenotype of 3-weeks-old Col-0, fer-4, lrx3/4/5 and fer-4/lrx3/4/5 (upper panel). Vacuolar morphology (MDY-64-stained) of late meristematic atrichoblast cells of Col-0, fer-4, lrx3/4/5 and fer-4/lrx3/4/5 (lower panel). Scale bars: 1 cm (upper row) and 5 µm (lower row).
(F) Abundance comparison of MTS-GFP-degron fusion proteins in cells treated with shRNAs against various BC-box proteins. The MTS and C-degrons used are labeled at top and left, respectively. The MTS and C-degron sequences are provided in the Materials & Methods.
(D) Shown are tumor volumes corresponding to individual animals of each group. The numbers of mice with undetectable tumors are indicated. The grey areas represent treatment phases and they are followed by drug holidays (blank).
c, Effects of oligomycin and DMSO on spherogenic potential of cells treated (AB) or not with AZD8330 plus BEZ235 in p53−/− and Ink4a/Arf−/− backgrounds (n = 3).
A) Schematic drawing of the EGFP-BIR-5085 reporter and the BIR repair product by SDSA (BIR-SDSA) or end joining (BIR-EJ) which result in EGFP expression after splicing.
C. Oligo(dT) FISH and IF analysis of Cajal body protein coilin and nuclear speckle protein SRRM2.
A. The wildtype and CDKA;1-DE mutants were grown on control plates for 10 days. Root lengths were measured 10 days after germination.B. The wildtype and CDKA;1-DE mutants were grown on plates containing 1 mM hydroxy urea for 10 days. The mutant wee1 was used as a positive control for hydroxy urea sensitivity. Root lengths were measured 10 days after germination.C. The wildtype and CDKA;1-DE mutants were grown on plates containing 0,6 μg/mL bleomycin for 10 days. The mutant ku70 was used as a positive control for bleomycin sensitivity. Root lengths were measured 10 days after germination.D. The wildtype, cdkb1;1, cdkb1;2 and the double mutant cdkb1;1 cdkb1;2 were grown on control plates for 10 days. Root lengths were measured 10 days after germination.E. The wildtype, cdkb1;1, cdkb1;2 and the double mutant cdkb1;1 cdkb1;2 were grown on plates containing 1 mM hydroxy urea for 10 days The mutant wee1 was used as a positive control for hydroxy urea sensitivity. Root lengths were measured 10 days after germination.F. The wildtype, cdkb1;1, cdkb1;2 and the double mutant cdkb1;1 cdkb1;2 were grown on plates containing 0,6 μg/mL bleomycin for 10 days. The mutant ku70 was used as a positive control for bleomycin sensitivity. Root lengths were measured 10 days after germination.
A-F. Schematic representation of capped (m7G-capped) and A-capped (non-functional capped) monocistronic mRNAs with poly(A)-tail-encoded firefly luciferase (Fluc) and fused upstream with (A) c-myc IRES, (B) no insertion, (C) non-specific 105-nt luc RNA (Non105), (D) huORFchop-1-105-nt, (E) huORFchop-69-105-nt, and (F) huORFchop-81-105-nt as shown above each bar graph. The RNA transfection assay of each transcript equipped with m7G-capped or A-capped monocistronic mRNA in HEK 293T cells was compared. To normalize the luc activities of capped and A-capped Fluc transcripts, the m7G-capped Renilla luc (Rluc) mRNA was used as an internal control. The luc activity of cells transfected with Cap-monocistronic mRNA in each graph was set as 100%.
A. An A549-derived BRD9-KO cell-clone (KO#1) was generated using a crRNA targeting exon 8 of BRD9. The target sequence of the crRNA (termed crRNA1), and the resulting genomic alterations determined by NGS for the two BRD9 alleles, are shown in comparison to an unedited control clone (CTRL#1). Generated indels lead to a premature termination codon (PMT) in the following exon. Encoded amino-acids are shown below the CTRL nucleotide sequence.
D HepG2 cells were treated without or with 5 μM Tg for 1 h. Endogenous IRE1α-immunoprecipitates were analyzed by PDI and BiP immunoblotting.
A, B ChIP-qPCR analysis of Scc1 association with early replication origin ARS305 or ARS607. PK-tagged Scc1 interaction with chromatin was monitored in wild type (JC1513) and irc5Δ-1 (TB064) cells. Error bars represent mean value ± standard deviations of mean (n=3). ARS305 + 7 kb locus was used as a control for cohesin-free chromosomal region. POA1 was used as a control locus for the chromosomal region that is bound by cohesin but is located ~ 30.000 bp from the nearest replication origin
(A) Schematic representation of the arrangement and number of PPxPxY motifs present in the indicated host proteins (left panel). Multiple sequences aligned using ClustalW, of peptides containing PPxPxY motif derived from cellular proteins and from the EBOV NP protein (right panel).
YUMM1.7 Ctrl or STING KO cells were injected into mice. 5-FU and DTIC responses were followed according to the schematics in (A). (E) Representative images of tumors and spleens. Image panels were cropped from the same picture.
F. Mice tracking images of elevated plus maze test from WT and KO+AAV-mWwox mice (age 8-10 weeks). O. A. (open arm) C.A. (closed arm) are shown with dotted white boxes on the left mice tracking image.
RT-PCR assays amplifying the ORF1ab region in pseudoviral RNA extracted by automated protocol, and (B) RT-PCR assays amplifying the N gene in pseudoviral RNA extracted by an automated protocol.
F, G, H Absolute numbers of B lymphocytes in Bone Marrow (F, G) and spleen (F, H) from MaxKO-mb1 (n=6), MycKO-mb-1 (n=3), DKO-mb1 (n=5) and control HET-mb1 (n=4) mice. Columns represent mean values and error bars standard deviations. *p<0.05, **p<0.01, ***p<0.001. The different B cell populations were identified by flow cytometry Experiment representative of at least three independent experiments.
E, Venn diagram showing the comparison between TSN2_NS and TSN2_HS protein pools. TSN2-interacting proteins are divided into three classes: HS-sensitive, HS-independent and HS-dependent. Within each class, the proteins are further classified into two groups. Group 1 contains known human or yeast SG proteins (Jain et al., 2016), including SG remodelers (marked in grey color), whereas group 2 represents components of recently isolated Arabidopsis RBP47-SG proteome (Kosmacz et al., 2019). The full lists of TSN2-interacting proteins, including previously uncharacterized and potentially novel SG components not belonging to either group 1 or group 2, are provided in Dataset EV1.
(D) Interactome analysis shows network of proteins identified from quantitative iTRAQ proteomics. Red box highlights the KLHL9-KLHL13-CUL3-NEDD8 complex interaction within the CLEC12A interactome.
c, Abnormal limb-clasping reflexes in Atg7flox/flox; nestin-Cre mice at P28. When lifted by the tail, Atg7flox/+; nestin-Cre mice behave normally, extending their hind limbs and bodies. In contrast, Atg7flox/flox; nestin-Cre mice bend their legs towards their trunk or tighten their back limbs to their bodies and anterior limbs.
Western blotting of samples after ectopic overexpression of ZMYND19 (C) alone, or together with WDR26 or GID4 in HEK-293T cells. ZMYND19 levels were monitored after treatment of MG132 or DMSO for 10-12 h (n=3).
(C-D) mRNA levels of hmgcr and fdft1 in liver and lung of WT (n=7), R6/2-untreated (n=8) and R6/2-Chol (n=4) mice. As no differences were found between R6/2 mice treated with saline or treated with empty g7-NPs, data were pooled.
C. Proposed model for regulation of RAB13 activity through local RNA translation. See text for details.
G Same cells as in E were left untreated or treated with Baf A1 for 6 hours, and then immunostained for endogenous p62 and LC3B. Scale bars are 5 μm for the confocal microscopy images and 2 μm for the airyscans.
Quantification of lignin content in wild-type and caspl mutant leaves after Pst DC3000 (AvrRpm1) inoculation. ata are shown as means ± SD (n = 4; 3-9 leaves each). ata information: Different letters indicate significant differences (Tukey's HSD test; P < 0.05). Experiments were repeated 3 times with similar results. AvrRpm1, Pst DC3000 (AvrRpm1); dpi, days post-inoculation.