EMBO/sd-character-level-ner huggingface dataset:
Figure 7Representative images of H&E-stained lung sections from KrasG12D mice treated with either vehicle (control) or the ADAM17 prodomain inhibitor, A17pro (1mg/kg, 3 times a week), for 6 weeks starting on the day after Cre inhalation. Scale bars, 3mm. Quantification of lung parenchyma area occupied by tumor lesions in the indicated groups (n = 6 per group) Representative images of lung sections from the indicated mice from (A) stained with antibodies against TTF-1 (C), PCNA (E) and pERK1/2 (G). Scale bars, 100μm. Quantification of positive cells/high power field (HPF) in the lungs of mice from (C), (E) and (G) stained for TTF-1 (D), PCNA (F) and pERK1/2 (H). n = 6 per group. ELISA of serum sIL-6R protein levels in the indicated mice (n = 6 per group) Tumor volume (mm3) of a KRAS mutant PDX treated with vehicle control (Ctl) or A17pro (1mg/kg) every second day. Treatment started when tumors reached a volume of 100-150mm3 after injection of 2 × 106 cells in NSG mice. n = 5 per group. Weight (grams) of tumor PDXs representative images (L) of tumor PDXs ELISA of human sIL-6R protein levels in serum of the indicated mice (n = 5 per group). * Immunoblots with the indicated antibodies of representative lysates from individual PDX tumors treated with vehicle control or A17pro. Representative image of pADAM17 immunohistochemical staining on an untreated KRAS mutant PDX tumor. Scale bar, 100μm.
Figure 5Cycling cells normally contain a single mature parent centriole that is decorated with distal appendages. PIDD1 is recruited by ANKRD26 to the centriole distal appendage. In the presence of extra mature parent centrioles, PIDD1 is activated at the distal appendage and released into the cytoplasm to promote PIDDosome assembly and Caspase-2 activation. Active Caspase-2 cleaves MDM2 leading to stabilization of P53 and subsequent cell cycle arrest or cell death.
Correlation between DNA methylation values of differentially methylated CpGs (DMCpGs) and expression levels of the associated genes in PD iPSC‐derived DAn.Figure 4Graphical representation of the percentage of DMCpGs associated with gene expression. Examples of genes showing significant correlation including a brief functional description: OTX2, transcription factor for midbrain DAn development which blocks LMX1A; DCT, dopachrome tautomerase, induced by OTX2, is a detoxifying enzyme of DA metabolites involved in the synthesis of neuromelanin; DRD4, DA receptor type 4; CASP8, apoptosis extrinsic pathway member inducing CASP3; ERC2, cytoskeleton organizer at nerve terminals for neurotransmission; NELL2, neural epidermal growth factor‐like 2 involved in neural differentiation. Counts of DMCpGs associated with gene expression across gene‐related regions. Relative distribution of DMCpGs across chromatin states. Poised P, poised promoter; Txn, transcription; Heterochr, heterochromatin. Counts of DMCpGs associated with gene expression across chromatin states.
Figure 5A, B Unmethylated (WT-C) and hydroxymethylated (WT-hmC) I3-I7 clones were transfected with siRNA against Tet1 and Tet2 (siTet1/2) or non-target siRNA (siNT). qRT-PCR (A) and Western Blot (B) confirmed knockdown efficiency relative to CHO GAPDH and the p84 loading control, respectively. C 5hmC MedIP and qPCR for human CD45 exon 5 in siTet1/2 and siNT WT-C and WT-hmC clones, relative to a minigene region lacking CpGs. D CTCF-ChIP and qPCR for human CD45 exon 5 in siTet1/2 and siNT WT-C and WT-hmC CHO clones. Rabbit IgG ChIP served as control. E qRT-PCR with human CD45 primers in siTet1/2 and siNT WT-C and WT-hmC CHO clones. Per each condition, exon level values are normalized to exon 6 and summarized data are presented relative to siNT to distinguish splicing changes from transcriptional variability.
Functional interaction between DAPK and beclin 1.Figure 1(A) HEK293 cells were transfected with DAPK ΔCaM or with a control vector (pcDNA3-luciferase, LUC), together with shRNAs targeting beclin 1 or HcRed, and with GFP-LC3 plasmid. After 72 h, cells were counted and lysates were prepared. (A) The percentage of cells with punctate GFP-LC3 fluorescence per total GFP-LC3-positive cells was quantified. Data presented are the mean±s.d. from a triplicate of 100 transfected cells. The asterisks denote a significance level of P=0.001. (B) Western blot analysis was performed using the indicated antibodies. (C) Representative GFP-LC3 staining of cells transfected with the control shRNA (HcRed) together with pcDNA3‐luciferase or DAPKΔCaM. CaM, calmodulin; DAPK, death‐associated protein kinase; GFP, green fluorescent protein; HEK, human embryonic kidney; shRNA, short hairpin RNA.
Figure 4(A-D) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were re-transfected with FLAG tagged wild type or mutant TDP-43 for 24 h.(A, C) Cell lysates were subjected to immunoblot analysis using anti-raptor, FLAG, TDP-43 and GAPDH antibodies. (A-D) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were re-transfected with FLAG tagged wild type or mutant TDP-43 for 24 h.(B, D) Cells were processed for qRT-PCR analysis. The level of raptor mRNA was quantified and normalized relative to GAPDH. The data from three independent experiments are presented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (A-D) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were re-transfected with FLAG tagged wild type or mutant TDP-43 for 24 h.(A, C) Cell lysates were subjected to immunoblot analysis using anti-raptor, FLAG, TDP-43 and GAPDH antibodies. (A-D) HeLa cells were transfected with the indicated siRNAs. After 48 h, the cells were re-transfected with FLAG tagged wild type or mutant TDP-43 for 24 h.(B, D) Cells were processed for qRT-PCR analysis. The level of raptor mRNA was quantified and normalized relative to GAPDH. The data from three independent experiments are presented as means ± S.E.M., ns, not significantly different; **, p<0.01, one-way ANOVA. (E) Similar transfection as in (C) was performed, and transfected cells were processed for RIP analysis. The inputs and RIP products were subjected to RT-PCR amplifying raptor and GAPDH, and immunoblot analysis using anti-FLAG and GAPDH antibodies. (F) HEK 293 and HeLa cells were transfected with the indicated siRNAs. After 72 h, the newly transcribed RNA in cells were metabolically labeled and isolated by Click-iT, and then subjected to qRT-PCR analysis. The level of newly transcribed raptor RNA was quantified. The data from three independent experiments are presented as means ± S.E.M., ns, not significantly different, one-way ANOVA. (G) Similar transfection as in (F) was performed. The cells were treated with ActD for indicated times, and then were processed for qRT-PCR analysis. The level of raptor mRNA was quantified and normalized relative to GAPDH mRNA. Data from three independent experiments represented as means ± S.E.M., *, p<0.05; **, p<0.01, one-way ANOVA.
Figure 2(A) Autoradiograph of a cyclin specificity analysis of the indicated substrates with wild-type or docking site mutant cyclin-Cdk1 complexes. Far1(1-150 mut) is L131A L135A L136A mutant, Sic1ΔC is the non-inhibitory mutant of Sic1 (deletion of 216-284). The experiment was repeated twice, a representative example is shown. (B) Mean±SEM fluorescence intensities of wild-type and NLxxxL motif mutant Far1(1-150)-GFP in either wild-type or clb5(hpm) clb6(hpm) strain over the cell cycle.
Fig.Figure 7WT INVS- transduced MDCK cells in 3D cultures form uniform round tubules. However, expression of 3A or NPHP2-related truncated INVS mutants, which lack Akt phosphorylation site (s), disrupts this uniformity. Results presented are representative of three independent experiments and show mean ± SE of percent normal acini in vector- or WT INVS-transduced MDCK cells (n=422 for Vector, n=398 for HA-WT, n=401 for -3D, n=365 for -3A, n= 344 for -R899X, n=331 for -Q671X, and n=325 for -R603X INVS stably transfected MDCK cells, respectively). Three independent experiments showed similar results. Statistical significance was determined by student's t test. WT transduced MDCK cells form a relatively smaller lumen; however, expression of 3A INVS or the indicated NPHP2-related truncation mutants result in relatively larger acini. Both truncation mutants (Q671X or R603X) lack the Akt phosphorylation site and exhibit a larger lumen size. Three independent experiments showed similar results. C. Quantification of normal lumen in cells transduced with WT or mutant INVS. Results presented are mean ±SE of percent normal acini in vector- or WT INVS-transduced MDCK cells (n=166 for Vector, n=204 for HA-WT, n=233 for -3D, n=150 for -3A, n=164 for -R899X, n=128 for -Q671X, and n=137 for -R603X INVS stably transfected MDCK cells, respectively). Three independent experiments showed similar results. Statistical significance was determined by student's t test. D. Size of lumen in cells transduced with WT or mutant INVS is shown. Results presented are scatter plots of acini size (n=205 for Vector, n=143 for HA-WT, n=131 for -3D, n=167 for -3A, n=144 for -R899X, n=128 for -Q671X, and n=144 for -R603X INVS stably transfected MDCK cells, respectively). Two independent experiments showed similar results. Statistical significance was determined by Mann-Whitney's non-parametric median test.
deletion partially inhibits LPS induced gene expression in BM-derived macrophages (A) Experimental scheme for generating BM macrophages.Figure 3(A) Experimental scheme for generating BM macrophages. BM cells from Brd4fl/fl ERT2Cre mice were cultured in the presence of M-CSF for 7 days and treated with LPS. Brd4 was deleted by Tamoxifen treatment (see Figure 1B for verification of Brd4 deletion). (B) Flow cytometry profiles of CD11b+, F4/80+ macrophage population harvested on Day 7 from untreated (WT) or tamoxifen treated (KO) cultures (left). Histogram depicting F4/80 expression levels in WT and KO macrophages (middle). Total number of macrophage yields calculated from > 15 independent experiments. Values represent the average of 21 WT and 24 KO experiments +/- S.D. (C) MA plots of RNA-seq data from untreated (UT) or LPS treated (4h) WT and KO macrophages. Differentially expressed genes were identified by a cut off line of log2FC>1 (FDR < 0.1). (D) Venn diagram depicting the number of LPS induced genes in WT and KO macrophages. (E) qRT-PCR analysis of genes representative of the BRD4 independent group (unaffected by KO), dependent group (downregulated by KO) or upregulated by KO. Data were obtained from three independent macrophage samples. Values are the average of 3+/- S.D. (F) GO terms of BRD4 dependent and independent genes, analyzed by the Enrichr program. Values in the overlap columns indicate the number of genes found in this study vs total number of genes in the GO terms.
Figure 1(A) RPE1 cells were transfected with either scramble or TMEM135 siRNAs and immunostained for LAMP1 as a lysosome marker (red) and PMP70 as a peroxisome marker (green). Scale bar, 10 μm. (B) Quantification of overlap signal between lysosomes and peroxisomes shown in (A). Data represent mean ± SD (n=3 experiments), 50 cells were scored per condition per experiment. *P < 0.05, Student's t-test. (C) Subcellular fractions of a discontinuous sucrose gradient collected from top to bottom, separated by SDS-PAGE, and immunoblotted for LAMP1, EEA1, Rab11, Rab8, PMP70, GM130, and Na+/K+ ATPase. (D) Quantification of total cholesterol in the subcellular fractions Data represent mean ± SD (n=3 experiments), *P < 0.05, Student's t-test. (E) Cells transfected with TMEM135 siRNA were subjected to a SREBP2 cleavage assay for the precursor of SREBP2 and nuclear SREBP2. (F) Cells transfected with TMEM135 siRNA were subjected to qPCR. Data represent mean ± SD (n=3 experiments), *P < 0.05, Student's t-test.
BMP4 caudalizes in an FGF-dependent manner.Figure 5One-cell stage embryos were injected animally with increasing concentrations of bmp4 encoding mRNA (5-50 pg). AC explants were removed from control and injected embryos at blastula stage 9, and explants were cultured to neurula stage 16. Total RNA was isolated from five control embryos (lane 2), and from eighteen ACs from each group (lanes 3-6). FGF3-4-8 expression was determined by sqRT-PCR. ODC is the control for quantitating RNA levels. -RT-PCR was performed on total RNA isolated from control embryos (lane 1). One-cell stage embryos were injected animally with mRNAs encoding the bmp4 (50 pg) and/or FGF dominant-negative receptor (FGF-DNR, 1.5 ng) proteins. AC explants were removed from control and injected embryos at blastula stage 9, and explants were cultured to neurula stage 16. Total RNA was isolated from five control embryos (lane 2), and from eighteen ACs from each group (lanes 3-6). In addition to fgf3, neural, epidermal and mesodermal markers were examined by sqRT-PCR: hindbrain (krox20, hoxb3), spinal cord (hoxb9, hoxc10, cdx4), lateral mesoderm (osr1), dorsal-lateral mesoderm muscle actin (MA), and epidermal cytokeratin (E13). ODC is the control for quantitating RNA levels. -RT-PCR was performed on total RNA isolated from control embryos (lane 1).
Figure 53 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice with n mice per group (n=7 for DACT + anti-PD-1, n=8 for DACT, n=9 for Ctr, anti-PD-1, anti-CD4/anti-CD8 and DACT + anti-CD4/anti-CD8). When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. Anti-CD4 and anti-CD8 were administered i.p. at days -1, 0 and 7 days before/after chemotherapy and anti-PD-1 at days 8, 12 and 16 3 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. Tumor size was assessed regularly and individual tumor growth curves of DACT versus Ctr 3 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. DACT + anti-CD4/CD8 versus anti-CD-4/anti-CD-8 Mean tumor area for each group was calculated and significances were tested using a type II ANOVA test Overall survival is depicted and p-values were calculated with a Log-Rank test Stars indicate the p-values of each treatment versus Ctr and hashes indicate the p-values of the DACT + anti-CD-4/anti-CD-8 versus DACT alone 3 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. DACT + anti-PD-1 versus anti-PD-1 are depicted. Overall survival is depicted and p-values were calculated with a Log-Rank test Stars indicate the p-values of each treatment versus Ctr and of DACT + anti-PD-1 versus anti-PD-1 alone 3 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. Five naïve mice or the eleven mice that were cured by treatment with DACT alone or in combination with PD-1 blockade were (re) challenged with WEHI 164 cells, and individual tumor growths (I, J), as well as overall survival (*** p<0.001, Log-Rank test) (K), were monitored.
Figure 1RNA-Seq analysis of: different time points of primary CD4+ T-cells infected in vitro with HIV-1 or mock infected Expression levels were normalized as Log2 fold change in infected vs matched mock-infected controls For (A) data were analyzed by Fisher test (number of donors =3 biological replicates). Boxplots in (A) depict median and 25-75 percentiles while whiskers extend from the hinge to the highest or lowest value that is within 1.5 * IQR (inter-quartile range) of the hinge. Data beyond the end of the whiskers are outliers and plotted as points. For each time point, dots illustrate the pathway enrichment analysis of genes up-regulated in infected vs matched mock-infected controls. Dots are color-coded based on the enrichment q-values and their size indicates the fraction of differentially expressed genes (DEGs) in the pathway; grey dots are not statistically significant RNA-Seq analysis of PBMCs of macaques infected with SIVmac239 before and after suppression of viremia with ART Expression levels were normalized as Log2 fold change or as enrichment score in ART-treated vs ART-naïve animals (B). (B) data were analyzed by Gene Set Enrichment Analysis (GSEA, number of animals =8). Symbols in the GSEA enrichment plots represent the position of the gene set members in the transcriptome ranked by differential expression between ART-naïve and ART-treated time points. Red color indicates leading edge genes. All analyses were conducted on the genes of the pathway GO cellular response to oxidative stress (184 genes; GO:0034599).
Figure 5(A) BLM-induced mice were treated every other day beginning on day 10 with 10 nmol/dose FA-TLR7-54 or TLR7-54. (B) Survival analysis of the treatment groups (Healthy, n=5; others, n=10). BALF was collected on day 21 and centrifuged to isolate cell pellets. Cells (primarily macrophages) were analyzed by qPCR for Arg1 (C), MMP9 (D), TIMP3 (E) BALF was collected on day 21 and centrifuged to isolate cell pellets. Cells (primarily macrophages) were analyzed by qPCR for CD86 (F) and IRAK4 (G) (n=5). BALF supernatant was analyzed by ELISA for IFNγ (H) (n=5). (I) Lungs were resected and subjected to hematoxylin-eosin (H&E), trichome (collagen) and α-SMA IHC staining (scale bars, 200 μm), Lungs were (J) hydrolyzed and analyzed for hydroxyproline content as a measure of collagen content (Healthy, n=5; others, n=10), (K) Ashcroft score quantitation of fibrosis (n=5).
Figure 5A Overview of the COP1 WD40-AtHFR1 complex (PDB ID 6QTV). The COP1 WD40 domain and the AtHFR1 VP peptide are shown in surface representation and colored in blue and orange, respectively. The N-terminus of HFR1 VP peptide, the amino acid of which differs between AtHFR1 and ChHFR1, is highlighted in magenta. B Table summaries of the microscale thermophoresis binding assay The sequence of the respective synthetic peptides is indicated. C Cartoon of constructs containing ChHFR1, AtHFR1, ChHFR1* and AtHFR1* derivatives under the 35S promoter used for transient expression of transgenes in N. benthamiana leaves. D Relative HFR1 protein levels, normalized to the GFP levels, are the means ± SE of four independent biological replicates. Asterisks mark significant differences (Student t-test: * p-value <0.05, ** p-value <0.01) between the indicated pairs.
Figure 3(A) Immunostaining of cells with antibody against IFT dynein subunit D1bLIC. D1bLIC is absent in the cilia bulges at the ciliary tip in IFT54Δ261-275 mutant while enriched at the cilia bulges at proximal end of cilia in IFT54Δ342-356 mutant. WT, wild type cells. Arrows indicate ciliary bulges. Scale bar, 5 μm. (B) Immunostaining of cells with antibody against kinesin-II subunit FLA10. FLA10 is enriched in cilia bulges at the ciliary tip in IFT54Δ261-275 mutant or at proximal end of cilia in IFT54Δ342-356 mutant. WT, wild type cells. The insets show enhanced and/or enlarged images. Arrows indicate ciliary bulges. Scale bar, 5 μm. (C, D) Immunoblot analysis of whole cells (C) and isolated cilia (D) of wild type and the three IFT54 deletion mutants. The membranes were probed with antibodies against IFT complex and motor proteins as indicated. Wild-type levels of the various IFT components were detected in the whole cell samples of the deletion strains (C). IFT121, IFT38 and FLA8 accumulated in cilia of both IFT54Δ261-275 and IFT54Δ342-356 mutants. D1bLIC was relatively reduced in IFT54Δ261-275 mutant cilia but was substantially increased in IFT54Δ342-356 mutant cilia (D). Ratios of protein amounts from one representative experiment are in parentheses.
Figure 4 Immunofluorescence microscopy analysis reveals highly similar and mostly nuclear localization of the SMARCB1 wild type and the R377C mutant, visualized by anti-HA staining (green). Phalloidin and DAPI staining was used to visualize the actin cytoskeleton and the nucleus, respectively. A novel MS-microscopy approach was used to further define the molecular context of the proteins. This analysis identified possible chromosomal, endosomal and membrane localization of the proteins. The possible endosomal localization is in agreement with the anti-HA immunofluorescence microscopy results. (key: the scale bar for immunofluorescence images is 10 µm, and the color gradient on the MS-microscopy indicates the localization scores calculated by the MS-microscopy tool.  The physical (AP-MS, green) and functional (BioID, red) interactions of SMARCB1 wild type and the R377C mutant (key: lower right corner). The majority of the physical interactions remained highly similar with the R377C mutant, whereas, several functional interactions decreased. The interactions that decreased (<0.6 fold) with the R377C mutant are shown with green node color, and the interactions that increased (>2 fold) are shown in blue. The interaction map of the proteins is grouped based on participation in known protein complexes (CORUM) or on Gene Ontology Biological Processes of the proteins  The cell proliferation assay in HCT116 CRC cells shows growth advantage conferred by the SMARCB1 R377C mutation compared with the wild type SMARCB1 or the vector control. The error bars designate the standard deviation (SD)
Figure 1A. Model for uridylation-triggered RNA decay. 3′ terminal uridylation by the TUTase Tailor may trigger the degradation of RNA species by unknown reader enzyme(s). B. Protein interaction analysis by Nano LC-MS. Unique peptide counts and protein sequence coverage, as well as signal intensities (PSI) for Tailor (bait) and CG16940/dmDis3l2 in control IP (FLAG-GFP) and FLAG-TailorIP are indicated. A.u., arbitrary units. C. Protein domain architecture of Tailor/CG1091 and dmDis3l2/CG16940. DUF1439, domain of unknown function; NTase, nucleotidyltransferase; PAP assoc, polyA polymerase associated; CC, predicted coiled-coil motif; CSD, cold-shock domain; S1, RNA binding domain; D. Co-immunoprecipitation of FLAG-dmDis3l2 (bait) and GFP-Tailor full-length and truncations expressed in Drosophila S2cells. GFP-Nibbler (Nbr) served as negative control. Domain architecture of GFP-Tailor truncations are indicated. E- G. Recombinant protein interaction analysis using the indicated epitope tags and purification methods. Domain architecture of bait and prey are indicated. E- G. Recombinant protein interaction analysis using the indicated epitope tags and purification methods. Domain architecture of bait and prey are indicated. E- G. Recombinant protein interaction analysis using the indicated epitope tags and purification methods. Domain architecture of bait and prey are indicated. H and I. Immunostaining and imaging of Myc-Tailor and GFP-dmDis3l2 (H) or endogenous dmDis3l2 (I) in S2 cells. Single color channel images show total inversions. Scale bar = 5 µm.