EMBO/sd-character-level-ner huggingface dataset:
Both mouse Nup50 orthologues can replace the Xenopus protein (A) Western blot analysis of mock and Nup50 depleted Xenopus egg extracts (∆Nup50), with or without addition of recombinant mouse Nup50 orthologues.Figure 7(A) Western blot analysis of mock and Nup50 depleted Xenopus egg extracts (∆Nup50), with or without addition of recombinant mouse Nup50 orthologues. Samples were analyzed with Xenopus Nup50 antibodies, which does not recognize the mouse proteins, which in turn were detected with an His6-antibody. (B) Confocal microscopy images of fixed nuclei assembled for 120 min in mock depleted (mock) and Nup50 depleted (∆Nup50) Xenopus egg extracts supplemented with recombinant mouse Nup50 orthologues. Nuclei were stained for Nup50 (Nup50 antibody for Xenopus protein, His6 for mouse protein) and NPCs (mAB414, red) on the chromatin (DAPI). Scale bar: 10 µm. (C) The average percentage of mAB414 positive nuclei for 100 randomly chosen chromatin substrates in each of three independent experiments (performed as in B) is shown. Data points from individual experiments are indicated. (D) Sequence comparison of the conserved 46 aa fragment of the human, mouse, rat and Xenopus laevis sequences, with the residue 178 (Xenopus numbering), crucial for NPC binding in the Xenopus protein is highlighted (black box). The color scheme indicates the type of amino acids according to the alignment software default setting. (E) GST-fusion constructs of the Xenopus Nup53 RRM domain (aa 162-267, control) full-length Xenopus Nup50 and the two mouse Nup50 orthologues were incubated with Xenopus egg extracts. Starting material as well as bound proteins were analyzed by Western blotting with indicated antibodies The right panel shows the average MEL28/ELYS, Nup153, importin β and ran bead bound signal from two independent experiments normalized to their respective Xenopus signal. Data points from individual experiments are indicated. (F) HeLa cells were transfected with EGFP-tagged constructs of both mouse Nup50 orthologues and the Nup50B Q177D (orthologue to the position 178 in Xenopus) mutant. After 24h, the cells were analyzed by live cell imaging. Panel shows cells exiting mitosis (time normalized to metaphase-anaphase transition). The merge shows histone 2B in pink and Nup50 in green, the black and white panel shows EGFP-Nup50 signal. Scale bar: 10 µm.
Figure 3(a) A schematic of the breeding scheme resulting in highly efficient conditional deletion of Trim28 during cortical development and analysing the adult tissue 3 months later by IHC and RNA-seq. (b) IHC for Trim28 in the adult cortex revealed that the protein was lost in cells exposed to Cre-activity during brain development (GFP+ cells). Scale bars: low magnification 75 μm, high magnification 20μm. (c) RNA-seq analysis of the expression of TE-families using TEtranscripts (d) Significantly upregulated TE families upon the Trim28-KO, in which the families with the highest fold change are listed. (e) RNA-seq analysis of full length MMERVK10Cs in the adult tissue. The location of the full length MMERVK10Cs are indicated as a thick black line under each histogram.
Distant HIF-binding sites make physical contact with the promoters of HIF target genes.Figure 2A) Capture-C from hypoxicMCF-7 cells (top) and ChIP-seq tracks for subunits of HIF, H3K4me1, H3K27ac, CTCF and RNAseq in normoxic and hypoxicMCF-7 cells as indicated at the ARRDC3 (arrestin domain containing 3) and LUCAT1 (lung cancer associated transcript 1 - non-protein coding) gene loci. RNA-seq tracks are shown in both low-scale and high-scale to represent regulation of transcripts with differing transcript levels. Capture-C was performed using oligonucleotides to a 'viewpoint' region at the HIF-binding site (highlighted in red). Interaction with the TSS of both LUCAT1 and ARRDC3 is highlighted in blue. Association with regions including additional enhancers, are highlighted in green.B) Regions associated with HIF-binding sites were classified according to the presence of a UCSC annotated TSS, or coincidence with H3K4me1 or H3K4me3 ChIP-seq signal. The bar chart shows the average number of each type of site that interacted per HIF-binding site.C) Histogram showing the frequency distribution of elements interacting with HIF-binding sites according to absolute distance from the 'viewpoint' site on the horizontal axis. D) Genes at which the TSS interacted with a HIF-binding site and E) genes adjacent to HIF-binding sites, which did not interact with the site were subjected to GSEA using a ranking metric combining fold-change in hypoxia and significance[25]. The ranking metric on the horizontal axis is shown as a color scale at the bottom. All the genes whose promoters were associated with HIF-binding sites appeared amongst the most strongly hypoxia-induced genes, whilst non-interacting genes showed no enrichment.
Aspergillus fumigatus induces sustained NFAT responses in murine macrophages.Figure 5A J774A.1macrophages were stimulated with live AF SC (MOI=5), and macrophage cytoplasmic and nuclear extracts were probed by Western blot for NFATc2. NFATc2 shuttling to the nucleus was observed and was maximal at 2 h p.i. B J774A.1 macrophages were stimulated with live or fixed swollen conidia (MOI = 5) or zymosan (50 μg/ml), and NFAT translocation was assessed by confocal microscopy. NFAT is indicated in green, the nuclei are indicated in red, and AF conidia can be seen in pink. Live conidia were observed to stimulate sustained nuclear translocation compared to dead conidia or zymosan. Data represent mean ± SEM. Scale bar: 50 μm. Arrows indicate A. fumigatus or zymosan-positive cells. C J774A.1 macrophages were stimulated with zymosan after FK506 (10 ng/ml) or control treatment, and macrophage nuclear extracts were probed by Western blot for NFATc2 and NF-κB translocation. NFATc2 and NF-κB nuclear translocation was observed, which was maximal at 1 h p.i., in stimulated macrophages. FK506 specifically inhibited NFATc2 translocation, but had no effect on NF-κB. D J774A.1 macrophages were pre-treated with FK506 (10 ng/ml) or vehicle and stimulated with live swollen conidia or zymosan. NFATc2 translocation was evaluated 30 min after stimulation. Box and whisker plot shows median ± maximum/minimum. Scale bar: 50 μm. FK506 completely inhibited nuclear translocation of NFATc2 in response to AF or zymosan. Statistical analysis was carried out by Student's t-test. NS, non-stimulated. Arrows indicate A. fumigatus or zymosan-positive cells.
Figure 2A 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). B L3MBTL3-Δ(1-64) does not interact with RBPJ. IP of HA-FLAG-tagged RBPJ in the presence of FLAG-tagged L3MBTL3 (WT or deletion mutants) in HEK293T cells followed by Western blotting using FLAG antibody. The experiment was independently replicated twice. C Schematic representation of the RBPJ protein and the deletion mutants used in panels D and E. The RBPJ protein (XP_005248218.1) consists of the N-terminal domain (NTD), the β-trefoil domain (BTD) and the C-terminal domain (CTD). D Deletion of the BTD domain impairs the RBPJ/L3MBTL3 interaction. IP of HA-tagged L3MBTL3 in the presence of FLAG-tagged RBPJ (WT and deletion mutants) in HEK293T cells followed by Western blotting using HA or FLAG antibody. The experiment was independently replicated twice.  E RBPJF261R point mutant does not interact with L3MBTL3. IP of HA-tagged L3MBTL3 in the presence of FLAG-tagged RBPJ (WT and point mutants) in HEK293T cells followed by Western blotting using HA or FLAG antibody. RBPJV263R and RBPJA284R also show a reduced ability to interact with L3MBTL3. The experiment was independently replicated twice. WB: Western blot; IP: immuno-precipitation.
Figure 5(A, B Images of Plin2-GFP in 3rd instar larval fat body cells of different genotypes. Scale bar represents 25 µm. (A) CSN2 RNAi or RDH/CG2064 overexpression reduces the peripheral localization of Plin2-GFP and increases the localization of Plin2-GFP on small peri-nuclear lipid droplets (boxed). DAPI (blue) stains nuclei. White arrows indicate peripheral lipid droplet. Red arrows indicate medial lipid droplets. (B) The peripheral localization of Plin2-GFP is greatly reduced in fat body cells from larvae with CSN2 RNAi or RDH/CG2064 overexpression. Images were taken by focusing on the periphery of fat cells. C, Images of Plin2-GFP in 3rd instar larval fat body cells of different genotypes. Scale bar represents 25 µm. (C) In fat body cells from ppl>DGAT1 larvae with CSN2 RNAi or RDH/CG2064 overexpression, the localization of Plin2-GFP is greatly reduced at the periphery and is dramatically increased on large medial lipid droplets. White arrows indicate peripheral lipid droplet. Red arrows indicate medial lipid droplets. (D) Fluorescence intensity line plots of the images in (C). GFP intensity along the line across a lipid droplet was measured by ImageJ. In ppl>DGAT1 larvae with CSN2 RNAi or RDH/CG2064 overexpression, Plin2-GFP localization on large medial lipid droplets is represented by two peaks. More than 30 lipid droplets were measured for each genotype. The plot shown is a typical image curve for the indicated genotype. , E Images of Plin2-GFP in 3rd instar larval fat body cells of different genotypes. Scale bar represents 25 µm. (E) The peripheral localization of Plin2-GFP is greatly reduced in fat body cells from ppl>DGAT1 larvae with CSN2 RNAi or RDH/CG2064 overexpression. Images were taken by focusing on the periphery of fat cells. F) Images of Plin2-GFP in 3rd instar larval fat body cells of different genotypes. Scale bar represents 25 µm. (F) The localization of Plin2-GFP is greatly reduced in peripheral lipid droplets and increased in medial lipid droplets in CSN2 RNAi larvae fed on a 30% high-fat diet. DAPI (blue) stains nuclei. White arrows indicate peripheral lipid droplet. Red arrows indicate medial lipid droplets. (G) The peripheral lipid droplets in larval fat body cells from different genetic backgrounds were stained by BODIPY (green). CSN3 RNAi or RDH/CG2064 overexpression reduces the number of peripheral lipid droplets in both wild-type and ppl>DGAT1 larvae.
Figure 9(A) Euc1 is recruited to ub-HSs upon mild heat stress (37°C, 90 min). ChIP-qPCR experiments with strains and conditions as indicated. Data represent means ± SD (n = 4), see Appendix Fig. S11B for statistical analysis. The ability to form ub-hotspots is crucial for endogenous EUC1 function. The genetic interaction of EUC1 with SDS3 (Rpd3L complex) was rescued with plasmid-borne EUC1-alleles and serial dilutions were spotted on selective media. (-) denotes empty vector. SLX5 also shows negative genetic interactions with SDS3 upon heat stress. Serial dilutions of the indicated strains were spotted on YPD and incubated as indicated. See also Appendix Fig. S12C-D. Note that all strains used in (A-C) contained an extra copy of MED11,
EGFR controls c-Fos via MAPK-dependent CREB activation in primary OS cells.Figure 4Western Blot analysis of primary OS cells isolated from H2‑c‑fosLTR/Egfrwt and H2-c-fosLTR/Egfr∆Ob mice c-fos and transgenic c-fos (c fostg) mRNA expression levels in primary H2-c-fosLTR OS cells after 4x in vitro passages, cultured under standard conditions (n=3 independent cell lines) Western Blot analysis of H2-c-fosLTR/Egfrwt OS cells treated for 24h with Erlotinib c-fos and c-fostg mRNA expression levels in H2-c-fosLTR/Egfrwt OS cells treated for 24h with Erlotinib (10µM) or DMSO as control (n=4 independent cell lines) Western Blot analysis of starved H2-c-fosLTR/Egfrwt OS cells, pre-treated with DMSO (1:1000), Afatinib (5µM), GSK2233470 (10µM), Rapamycin (10nM) or U0126 (10µM) for 30 minutes and stimulated with EGF (50ng/ml) as indicated Western Blot analysis of primary OS cells isolated from a p53f/f Rb1f/f Osx-Cre mouse after 24h Erlotinib treatment c-fos mRNA expression levels in p53f/f Rb1f/f Osx-Cre OS cells treated for 24h with Erlotinib (10µM) (n=3) Western Blot analysis of starved p53f/f Rb1f/f Osx-Cre OS cells, pre-treated with DMSO (1:1000) or Afatinib (5µM) for 30 minutes and stimulated with EGF (50ng/ml) as indicated
EGFR is essential for proliferation, survival and c-Fos protein and mRNA expression via RSK2/CREB phosphorylation.Figure 3PCNA and cleaved Caspase 3 IHC staining and quantification shown as % positive cells (for PCNA) and as positive cells per mm² (for cleaved Caspase 3) in OS from H2-c-fosLTR/Egfrwt (n=6) and H2-c-fosLTR/Egfr∆Ob (n=5) mice. Scale bars: 100µm Egfr, Ccnd1, c-fos and transgenic c-fos (c-fostg) mRNA expression levels in tumors of H2-c-fosLTR/Egfrwt and H2-c-fosLTR/Egfr∆Ob mice normalized to Tbp. n=17 wt, 14 ∆Ob (Egfr, Ccnd1), n=16 wt, 13 ∆Ob (c-fos), n=16 wt, 14 ∆Ob (c-fostg IHC staining and quantification showing pRSK2 (n=4), pCREB (n=7 wt, 6∆Ob) and c-Fos (n=5) positive cells (%) in OS from H2-c-fosLTR/Egfrwt and H2-c-fosLTR/Egfr∆Ob littermates. Scale bars: 100µm
Figure 7Interactions of the linker helix (pink) with the cNMP sensor domain (dark/light blue in cAMP-bound form, yellow/orange in apo state, residues from the opposing monomer labeled by a '). (A) Sidechains along the full span of the linker helix contact those from both chains of the sensor dimer, forming both polar (S139, K145, E147, N148) and hydrophobic (A140, L141, I144) interfaces. The linker helix conformation in the bound state would be sterically incompatible with the position of the cNMP body in the apo state (transparent, overlaid). (B) The hydrophobic A140/L141/I144 triplet forms a "wedge" that inserts between two faces formed by the cNMP body (I28, I55, A80) and C-helix (V97', L100'). In the apo state this linker feature is absent, allowing direct contact of these faces (closure of cleft). (C) Analogous role of N3A motif (green) from the cNMP sensor of M. loti MloK (PDB 1vp6, main fold in white). The hydrophobic patch in Bd1971 linker helix formed by A140/L141/I144 is spatially equivalent to one from MloK (V233/F236/I247) despite a difference in secondary structure between the two proteins. Similarly to Bd1971, the MloK N3A hydrophobic patch contacts the fold at a region between the hinge and cNMP body (right).
Figure 5A. Colocalization of MCH and the receptor for CCL2 (CCR2) in the LHA of mice expressing CFP under the promoter of MCH. The overlap of MCH and CCR2 immunoreactivity indicates that CCR2 is expressed on MCHneurons in the LHA. B, D. CCL2 effects on MCH neurons of MCH-CFP knock-in mice recorded in current-clamp mode. Representative trace of the effects of CCL2 on MCH neurons (B). The CCR2 antagonist INCB3344 prevents the small hyperpolarization of MCH neurons elicited by CCL2. Effects of CCL2 at various concentrations, alone or in the presence of the INCB3344 (1µM) or barium (200µM) on the membrane potential of MCH neurons (n= 5 to 16) (C). B, D. CCL2 effects on MCH neurons of MCH-CFP knock-in mice recorded in current-clamp mode. Representative trace of the effects of CCL2 on MCH neurons Discharge pattern of two representative MCH neurons in response to a depolarizing current pulse injection (current pulses applied every 10s) in control condition and in the presence of CCL2 (D). The control trace is recorded just before the application of CCL2 while the CCL2 trace is recorded 1 min after the beginning of CCL2 application. CCL2 delayed the third action potential (left panel) and induced failures in the action potential evoked in the right panel. E. Effect of CCL2 on KCl-induced MCH release. The perifusion of hypothalamic tissues with 60mM KCl for 30 min induces an up to 3.1-fold increase in MCH release. CCL2 (100 nM) dramatically blunts KCl-induced MCH release, an effect partially by the addition of INCB3344 (10µM) (3 to 5 independent experiments, 3 chambers per condition in each experiment). * or $ p<0.05, ** p<0.01, *** p<0.001. * KCl vs KCl+CCL2 conditions. $ KCl+CCL2 vs KCl+CCL2+INCB3344 conditions. Data are expressed as mean fold-increase in MCH release per chamber vs basal secretion, ± SEM. F. Effect on MCH-R1 antagonist on LPS- and CCL2-induced weight loss. Data are expressed in mean % of weight variation compared to initial body weight at different times (from 2 to 48h) after acute icv injection of saline (black bar), H6408 (dark blue bar), LPS (red bar), or LPS+H6408 (light red bar), CCL2 (orange bar), CCL2+H6408 (yellow bar) in WT mice (n=3 to 12). Data are expressed as means ± SEM. *p<0.05, **p<0.01, ***p<0.001, color-coded asterisks indicate a significant difference from the experimental condition assigned to the respective color-coded bar.
a, Immunohistochemistry of brain sections from control (Atg5flox/+; nestin-Cre) and Atg5flox/flox; nestin-Cre (Atg5flox/flox) mice at six weeks of age, stained with an anti-ubiquitin antibody (1B3).figf3a, Immunohistochemistry of brain sections from control (Atg5flox/+; nestin-Cre) and Atg5flox/flox; nestin-Cre (Atg5flox/flox) mice at six weeks of age, stained with an anti-ubiquitin antibody (1B3). Scale bar, 10 µm. b, Ubiquitin-positive inclusions in neurons. Sections of medulla from Atg5flox/flox; nestin-Cre mice at six weeks of age were stained with an antibody against NeuN (a neuron-specific nuclear protein) and ubiquitin. Nuclei were stained with Hoechst 33258. Scale bar, 10 µm. c, Immunoelectron microscopy of ubiquitin-positive inclusion bodies. DRG neurons isolated from Atg5-/- neonates were analysed by immunoelectron microscopy using an anti-ubiquitin antibody. Scale bars, 500 nm.
Figure 2A. Uniform manifold approximation and projection (UMAP) embedding of single-cell RNA-Seq data from human ileum biopsies colored by the cell type (n=8,800 cells). B. Dot plot of the top three marker genes for each cell type. The dot size represents the percentage of cells expressing the gene; the color represents the average expression across the cell type. C. Predicted pseudo-time trajectories for the goblet (top) and enterocyte lineages (bottom) projected onto the UMAP embedding. D. Normalized gene expression for genes associated with differentiation of the goblet (top) and the enterocyte lineage (bottom) eatmap showing changes in gene expression levels along pseudotime for the enterocytes and goblet lineages. Dendrograms on the left of the heatmap indicate the results of hierarchical clustering of the genes. Colored bars above the heatmap indicate the types of cells ordered along the pseudotime, colored according to A.
Figure 9A Immortalized primary myoblasts from a healthy control showed a progressive pattern of α-dystroglycan glycosylation during five days of differentiation (D0-D5), as has been previously described by Goddeeris et al. Immortalized primary myoblasts from patients displayed an irregular pattern of glycosylation, with a final level of glycosylated α-dystroglycan that was lower than control. B α-dystroglycan glycosylation of infected immortalized myoblasts from patient-LV-NICD-GFP at differentiation day 5 (D5) showed a striking reduction, in line with the strong inhibition of myotubes formation and differentiation induced by NICD overexpression. α-dystroglycan in myoblasts from patient-LV-GFP showed a reduction of glycosylation compared to control-LV-GFP at D5, similar to the results obtained in the adult muscle from patients (Fig. 2). C-D C2C12 myogenic cells showed a reduced level of glycosylated α-dystroglycan when the Notch signaling inhibitor DAPT or LY3039478 was added to the differentiation medium. This indicates that reducing Notch signaling can affect α-dystroglycan glycosylation in wild-type C2C12 myoblasts cells, which do not harbor any known mutations in α-dystroglycan glycosyltransferases or Poglut1. E-F qRT-PCR experiments show that upon DAPT or LY3039478 treatment, a remarkable decrease in Hes1 mRNA is induced in C2C12 cells during differentiation.
Figure 7In the absence of POT1 the telomeric C-strand is resected and RPA and recombination proteins associate with the overhang. RAD51-coated overhangs invade telomeric DNA of adjacent chromosome ends and the invading 3'end is extended by DNA polymerases. Accumulation of R-loops at telomeres facilitates strand invasion. In case of proper dissolution of the HR intermediates, telomeres are elongated and fragility is due to abnormal chromatin condensation after HDR. Defective dissolution of the HR intermediates leads to accumulation of branched DNA structures. Incomplete fill-in synthesis leads to accumulation of G-rich single stranded DNA.
Figure 7SQR (A) and TST (B) protein levels in human skin fibroblasts supplemented with the H2S donor GYY4137. TST protein level in kidneys (C) and cerebrum (D) of Coq9+/+ mice supplemented with the H2S donor GYY4137. Levels of neurotransmitters in cerebrum of Coq9+/+ mice supplemented with the H2S donor GYY4137 (E).
Figure 3A. Schematic illustration of the establishment of the murine syngeneic tumor models and drug treatment schedule. Established tumor models were orally treated daily with vehicle or TP-16 when tumor volumes reached 100-200 mm3. B. The antitumor activities of E7046 (150 mg/kg) and TP-16 (37.5, 75, and150 mg/kg) in CT26 tumor-bearing BALB/c mice (n = 11 per group). Tumor growth curves in the CT26 model (left panel). Bar graphs show the individual changes in tumor growth relative to after and before drug administration (right panel). Tumor volumes reached 100-200 mm3 on day 7. C. Representative graph showing that the antitumor activity of TP-16 is lost in CT26 tumors engrafted into BALB/c nude mice (left panel) (n = 8). Bar graphs show the individual changes in tumor growth relative to after and before drug administration (right panel). Tumor volumes reached 100-200 mm3 on day 7. D. Single-cell suspensions of tumor tissues from CT26 tumor-bearing BALB/c mice treated with vehicle or TP-16 for 2 weeks were analyzed for immune cell infiltration by flow cytometry analysis. Representative flow cytometry and dot plots of intratumoral frequencies of CD8+ T cells (n = 5). E. Growth curves (left panel) and relative change after 18 days treatment (right panel) in colon cancer (MC38) xenograft tumors in C57BL/6 mice (n = 7). Tumor volumes reached 100-200 mm3 on day 7. F. Single-cell suspensions of tumor tissues from MC38 tumor-bearing C57BL/6 mice treated with vehicle or TP-16 for 2 weeks were analyzed for immune cell infiltration by flow cytometry analysis. Representative flow cytometry and dot plots of intratumoral frequencies of CD8+ T cells (n = 5). G. The representative bioluminescence images (left panel) and quantitative growth curves (right panel) of an orthotopic colorectal cancer mouse model, CT26-Luc model (n = 4).
Figure 5A Western blot of muscle homogenates shows reduced expression of Notch1 intracellular domain (NICD) in patients. B-C qRT-PCR on RNA extracted from skeletal-muscle shows that expression of HES1 (B) and PAX7 (C) was significantly lower in D233E patients compared to healthy controls. Mean ± SEM, Student´s t-test (B) and Mann-Whitney U test (C). D PAX7+ cells in skeletal muscle sections, demonstrating that satellite cells are less abundant in D233E patients than in controls (n = 3 muscles with 10-15 fields analyzed per muscle). Mean ± SEM; Mann-Whitney U test; Scale bar, 50 μm.