EMBO/sd-character-level-ner huggingface dataset:
Kinetics of ISG15, IRF7 expression at 0.75, 1.75, 3.75 and 8.75 days post-ΙFNα (600 IU/ml) treatment. Arrow indicates the time of HSV-1 infection at 18hr post-interferon treatment. n=9 biological replicates.
(B) Schematic representation of Gata6 protein displaying the different protein domains: PEST, GATA-type transcription activator, Zinc-finger (ZnF), Nuclear Localization Sequence (NLS) and the different Gata6 missense mutations and deletions found in human SebC. Heat-map displaying the predicted effect (deleterious or neutral) of W8C, S33C, G61R and S511F point mutations as assessed by PredictSNP, Polyphen-1, Polyphen-2, SIFT, SNAP and SNAP2 algorithms (right panel). Percentages indicate the level of confidence of the predictions.
(k, l) CftrF508del mice (n = 3 per group) were administered intranasally with a lentiviral vector encoding beclin 1 (LV-beclin 1) or GFP (LV-GFP). (k) LC3-positive dots per mm2 of lung tissues. Means ± s.d. for lung tissues from three mice per group. (l) Confocal microscopy micrographs of p62. L, lumen. Representative stainings from at least five airway epithelial areas per mouse. Scale bar, 10 μm.
(N) Quantification of the average number of recycling endosome entries into the primary dendrite in 50 s. N = 2. Error bars indicate SEM. ns - not significant (Mann-Whitney test).
A. 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).
Representative H&E and IF images of control, Lats1/2 dKO, and Raptor;Lats1/2 tKO airways at day 21 post tamoxifen treatment. Tomato (for Scgb1a1 lineage, red), CC10 (green, upper), AGER (green, lower), and DAPI (blue). Scale bar, 100μm.
Change in codon occupancy for cells harboring the PK-LacZ construct after induction by IPTG (1 mM) calculated from the Ribo-seq data. Each point corresponds to a codon, which are ordered by amino acid identity and then by abundance in the genome (left most abundant, right least abundant). Dashed horizontal line denotes no change. Outliers are labelled and highlighted in red (Tukey test: 1.5 times the interquartile range below the first quartile or above the third quartile).
(B) Number of cardiomyocytes (CM) in a defined low magnification (50x) microscopic field before the adenoviral infection and 48h later. The number in the bars indicates the number of cell culture plates analyzed. ****p<0.0001.
(C) Abnormal transcription of genes involved in various biological metabolic pathways derived from our RNAseq (RNAseq read counts/ person/ gene for n=6 RIRCD affected individuals, n=5 controls and n=1 (biological replicate analysed in 4 technical replicates) recovered) data showing that their expression returned close to normal levels in patient muscle after recovery. The central band represents the median, the lower and upper hinges correspond to the first and third quartiles (25% and 75%) while the whiskers extend to the highest and lowest points within the data (1.5x the inter-quartile range).
D) expression level (percentage and gMFI) of c-Maf in cKitlow and cKithigh ILC2s (D) (paired T tests, ****p<0.0001). Data information: Each dot represents the expression level in one donor (n=7). Bars represent mean ± SEM.
FACS analysis of EdU staining was performed on GSC#1 treated overnight with MPZ (10 μM). Data are presented as the mean + s.e.m. on 3 independent experiments.
I. Treatment with PRMT6 inhibitor reduces R388 methylation of endogenous SIRT7 in a dose-dependent manner. MEF and HEK293T cells were treated with increasing doses of PRMT6i for 24 hrs as indicated. R388 methylation of immunoprecipitated endogenous SIRT7 was determined by western blot
A qRT-PCR analysis of the efficacies of znrf3 AS normalized to odc. Data are shown as mean ± SEM. n = 3 biological replicates; ****p < 0.0001 by unpaired t test.
F. Immunohistochemical analysis of lipofuscin (green) in coronal brain sections. Representative images of thalamus are shown. Scalebars = 50 μm. G. Quantification of lipofuscin autofluorescence. Five images per mouse were taken, means were normalized to WT samples (n=3 per genotype, female). Data information: Data represent mean ± SEM. For statistical analysis one-way ANOVA with Tukey's post hoc test of Grn-/-, Trem2-/- and Double-/- was used. Statistical significance was set at *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001, and ns, not significant.
(F) qPCR analysis of levels of miR-29b, miR-30c and miR-27a in scr and circHIPK3 KD cells 0 and 24 hours post-induction. SNORD68 was used as a housekeeper (n=3). Data information: data are presented as mean ± SD. *P<0.05, **P<0.01, ***P<0.001 (Unpaired Student's t-test). All repeats are biological.
Thapsigargin (Tg) induced Fura-2 based cytosolic Ca2+ imaging in Ringer's buffer containing 0.25 mM Ca2+. (B) Quantification of basal cytosolic calcium levels and (C) SOCE quantification (plateau-basal) for WM3734 after stable silencing of TMX1 (two clones). : In (B-C), data are presented as mean ± SEM (n values: WM3734, control=939, TMX1 kds 1=988, TMX1 kds 2=508).
A RNA degradation is not essential for asymmetric HXT2 mRNA localization. FISH of wild-type and ∆xrn1 cells.
Quantification of tumor weights 21 days after transplantation of control or shVgll4 LLC cells into C57BL/6 mice from (C)
Effect of Bay U6571 on cellular glycogen (left panel) and ATP (right panel) levels in HEY cells. (a) p < 0.01 versus pcDNA control time 0 at 5% FBS and (b) p < 0.01 GPi versus control at each corresponding treatment.
B Percent eosinophils in blood of Dusp5+/+ Rag2-/- (open circles) and Dusp5-/- Rag2-/- (grey squares) mice prior to and at days 3, 6 and 13 following N. brasiliensis infection.
(A) GSH-Sepharose beads-immobilized full length or truncated GST-TAK1 proteins were incubated with K63-linked polyUb chains in 300 μl binding buffer, followed by washing and resolving in SDS-PAGE, and then immunoblotted with anti-ub. GST-fused NEMO serve as positive control and NEMO L329P mutant as negative control. The blotted membrane was stained with Ponceau S to demonstrate the amount of the input GST-fused proteins (lower panel).
NADPH/NADP+ and GSH/GSSG ratios in human endothelial cells expressing YF or YD eNOS; n=6-8 independent cell batches (Unpaired Student's t test).
Relative mRNA expression of ATGL and western blot analysis of FoxO1 and ATGL in C2C12 cells transfected with Ago-183/96 and FoxO1 as indicated (n=3).
A. Mechanism of D-amino acid oxidase (DAO) in the production of H2O2. Cell lines stably and inducibly expressing a mitochondrial matrix version of DAO (mtDAO) were generated and tested by immunoblot and immunofluorescence.
Western blot analysis of total proteins from early generation cay1+ and cay1Δ cells expressing Cay1‐YFP, Rap1‐YFP, and Taz1‐YFP using antibodies against Rap1, Taz1, and Act1 (loading control). Numbers at the bottom are ratios between Rap1 proteins (endogenous plus ectopic) and Act1 (Rap1/Act1). Values are expressed as fold increase over wt.
D. Plots of SNP density per 10 kb along the chromosomes for Arabidopsis Col×Ler and budding yeast S288c×SK1 crosses (Cooper et al, 2018). Telomere positions are shown by vertical lines, and centromeres by vertical dashed lines. Centromeres are also labeled above the plots in red, as 'CEN' or 'C'.
E Quantification of peak responses as shown in D. N = 11-19 cells from 5 independent experiments. Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by two-way ANOVA with Tukey's post hoc analysis *P < 0.05, **P < 0.01, ***P < 0.001, ###P < 0.001, n.s., not significant.
E. Blood glucose levels for insulin tolerance test of control (n=7) and NICDiOE-EC control (n=7) mice. Data represent mean ± SEM, unpaired t-test.
(b) Intracellular wild-type L. monocytogenes (WT Lm) or Δhly L. monocytogenes (Δhly Lm) counted manually in DAPI-stained infected hemocytes. LE112,hml>LE, hml-Gal4-driven expression of PGRP-LE in PGRP-LE112 hemocytes; imd1, imd; RelE20, RelishE20; hml>Atg5IR, inverted repeat sequence described in a; w, hml>Atg1, hml-Gal4-driven expression of Atg1 in w hemocytes; LE112,hml>Atg1, hml-Gal4-driven expression of Atg1 in PGRP-LE112 hemocytes; PGRP-LE112+rap, PGRP-LE112 hemocytes plus rapamycin. *, P 0.001, compared with wild type (t-test). Data are representative of four experiments (a) or at least three independent experiments (b; error bars, s.d. of triplicate measurements).
(E) UCSC genome browser view of normalized TT-seq coverage on the plus and minus strand at the PHLDA1 locus (hg38; chr12:75,612,350-76,042,552; in the colorectal cancer cell line HCT 116. TT-seq coverage is cut at 250 (purple lines) to allow for better visualization. eRNAs are shown between the plus and minus strand. Aggregated transcription factor ChIP-seq peak regions (TF ChIP-seq) comprise ChIP-seq binding profiles of 19 TFs in HCT 116 cells from CISTROME The height of the signal indicates the number of different TFs binding at a particular region. Binding regions for selected TFs (TCF7l2, YY1, SP1) are shown below together with p300 and RNA polymerase II (Pol II). TT-seq enhancer regions are shown at the bottom together with a H3K27ac-defined super-enhancer annotation, which was downloaded from SEdb 2019). At date of publication no Med1 ChIP-seq data was available for HCT 116.
(h) Representative images of immuno-histochemical staining of ATF4 and YAP proteins in HCC samples from patients. Scale bars, 50μm. (i) Quantification of the immunohistochemical staining in (j) showed a positive correlation of ATF4 and YAP expression (N=18). Statistical significance was calculated using Pearson correlation analysis.
G, H. Percentage of cell death in 2i-ESCs treated with 50 µM Eto in the presence or absence of 200 nM INK-128 or 100 µM of hexanoate (G) or octanoate (H) as indicated for 24 hours. n=4 biological repeats; error bars indicate SEM; p-values were calculated using two-sample t-test.
B Transcript levels of BIC1 and PIF4 in transgenic plants containing a chemical-inducible construct pERGW-BIC1. 8-d-old pERGW-BIC1 seedlings were treated with 10 μM estradiol for indicated time points before harvest for RNA extraction and RT-qPCR analysis. The PP2A gene served as internal control. Data are means ± SD (n=3).
(D) eWAT wt, (E) fat pads and (F) liver wt of 4‐mo‐old Con and KO mice on RD (n=6-8).
PCA of global gene expression in low T-inducible ZHBTc4 ESCs stimulated as indicated in Fig EV3G. Right: Heatmap of selected key pluripotency genes derived from mean-centered expression values (log2 scale).
(h-j) Log10 colony-forming units (CFU) at 2 days post infection with C. albicans SC5314 (wild-type) or different mutant strains in C57BL/6 (h), IL-17F-deficient (i) or IL-17A-deficient (j) mice. Data are mean±s.d. (n=3). The actual P-values are indicated (two-tailed t-test).
F Quantification of electrophoretic mobility shift assays with dsDNA or ssDNA, RAD51 and MMS22L-TONSL or MMS22L. Averages shown, n = 2; error bars, SEM.
250 µg of yeast protein extract was processed by R2-P2 using either Fe3+-IMAC, Ti4+-IMAC, Zr4+-IMAC or TiO2 magnetic beads and followed by peptide analysis with DDA-MS. Phosphopeptide enrichment was performed in triplicate. Venn diagram of identified phosphopeptides by the different phosphopeptide enrichment methods.
C Time-dependent incorporation of phosphate group into PDI WT or S357A catalyzed by recombinant Fam20C. Phosphorylated PDI was determined by anti-pS357-PDI immunoblotting on both regular and phostag gels.
(D) Quantification of relative tumor growth of the individual mice as area under the curve normalized to the survival time in weeks.
(D) Compared with wild type and epg-2 mutants, levels of SQST-1 are dramatically elevated in atg-3 and epg-7 mutant embryos in an immunoblotting assay.
(C) Distribution of GFP-Rab7 in parental (left panels) and two clones of PI4K2A K/O cells. Representative pictures show tubulation in the K/O cells reminiscent of those seen in wild-type cells expressing the GTP-locked Rab7Q67L mutant. Scale bars are 10 µm.
(B RNA-Seq analysis of different time points of primary CD4+ T-cells infected in vitro with HIV-1 or mock infected. The gene set used for the analyses is GO iron ion import (12 genes, GO:0097286). Data in (B) were analyzed by Fisher test. Boxplots 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. Dots below boxplots illustrate, for each time point, 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 DEGs in the pathway; grey dots are not statistically significant.
(B) NTERA-2 cells were transduced with either an empty vector (WT) or the same vector containing an shRNA against KAP1 (KD) prior to puromycin selection and transduction with increasing doses of GFP reporter vectors. GFP expression was analysed 72 hours post reporter transduction. A representative experiment of 2 experiments is shown. Two-tailed unpaired t test p-values: PBS-LTR-GFP: 0.0148; PBSChr15-LTR-GFP: 0.0377
BR1-mediated expression of NEMO or eGFP was driven by the CAG promoter.C Albumin in brain tissue as indicator for BBB leakage. In Nemo-/+ mice treated with AAV-BR1-NEMO, less albumin was found in brain tissue, indicating less BBB leakage. Representative Western blot with albumin from P8 Nemo-/+ mice treated with AAV-BR1-NEMO or AAV-BR1-eGFP control vector, respectively, as well as untreated wild type (WT) control mice. Right panel: quantitative analysis of the Western blots (n = 4 animals/ group, *p = 0.0283)
(B) Representative images of vessel lumen in A375 xenografts treated as indicated. Bar graphs indicate the quantitative analysis of lumen diameters in A375 and COLO205 xenografts (n=3 tumors), *P < 0.05, **P < 0.01, ***P < 0.001 versus vehicle (A375: PLX4720 P = 0.0078; COMBO P = 0.0012) (COLO205: PLX4720 P = 2.01E-06; COMBO P = 1.33E-07).
D, E. Gene Ontology (GO) terms (biological function) of Tfcp2l1-activated genes (D) and -repressed genes (E). GO terms related to metabolism are highlighted in purple, and those to transcription are orange.
D. Whole cell lysates from the indicated strains were analyzed by western blot with anti-Sre2 serum.
dHepaRG cells were infected with HBV at an MOI of 100 virions/cell and treated with 300 U/ml IFNα from day 7 to 9 p.i. or 200 U/ml IFNγ from day 7 to 10 p.i. Primary human hepatocytes were infected with HBV at an MOI of 100 virions/cell and treated with 500 U/ml IFNα or 200 U/ml IFNγ from day 4 to 6 p.i. Expression of ISG20 was detected by western blot.
Effect of hydrodynamic injection of plasmids expressing miR-511, miR-CTR or PBS on ConA-induced hepatitis in B mice (all groups n = 10). A total of 360 μg ConA was injected i.v. 24 h after plasmids and 8 h later mice were analysed: liver damage (serum ALT levels, left panel); body temperatures of mice 8 h after ConA injection (middle panel); TNF levels (right panel) 2 h after injection of ConA revealed similar concentrations of TNF in the three groups. miR-511-injected mice were significantly protected in the ConA model.
E. Model: MCAK is regulated by two distinct E3 ligases at different time points. While SCFFbxw5 targets MCAK for degradation during G2/M, the APC/C takes over after mitotic exit. Via the SCFFbxw5 pathway, cells ensure that levels of MCAK and its orthologs are kept low upon entry into G0 and thus permit ciliogenesis in the following cell cycle.
(A) WASH deficiency enhances the interaction of Vps34 with Beclin 1. WASH+/+ and WASH−/− MEFs were treated with EBSS at 37°C for 1 h and immunoprecipitated for Beclin 1. IP, immunoprecipitation. Ratio of Vps34/Beclin 1 was calculated by the Image J software and shown in the right panel.
A, Clustal alignment analysis of Trnp1 orthologs. Highly conserved and similar residues are shown in black and grey, respectively. Asterisks show 100% conserved residues among all orthologs. Predicted disordered and structured regions are depicted with a red line and a black line, respectively. Cylinders represent alpha-helices and arrows represent turns.
E: CRISPR/Cas9 control (CTR_1 and CTR_2) or PRMT1-deleted (KO_1 and KO_2) HeLa cell lines were irradiated at 150 J/cm2 UVC. After 4 hours, the apoptotic cell fraction was analyzed by flow cytometry using FITC-labeled AnnexinV and propidium iodide (PI). The increase in the apoptotic cell fraction upon UVC irradiation was quantified for three independent experiments (mean ± SD, **: p-value ≤ 0.005 and *: p-value ≤ 0.05 using Welch´s t-test).
Split-ubiquitin yeast two-hybrid assay revealing the UBP13 and BRI1 interactions. The indicated constructs were cotransformed into yeast cells. BRI1-Cub with Nub, Nub-CIPK8, and Nub-UBP13 with an empty vector were used as negative controls. Transformants were streaked onto solidified medium supplemented with X-gal. Blue patch indicates positive interaction. Cub, the C-terminal half of ubiquitin; Nub, the N-terminal half of ubiquitin.
B), C) Volcano plots showing the fold change in average expression of all proteins and phosphopeptides respectively, in CKO cells compared to WT (q = Benjamini-Hochberg corrected p-value, n= 24 time points over 3 days). Statistically significant changes (q ≤ 0.05) are shown in red. Some proteins are labelled as space allows.
(F) Schematic representation of the regulation of SPT activity via TORC2-Ypk1/2-dependent phosphorylation of Orm proteins and EGAD-dependent degradation of Orm2.
F Changes in ER calcium levels measured with an ER-targeted cameleon probe in serum-starved WT and Nox4KO MEFs after the addition of ATP (100 μmol/L, F). n=3/group (with >30 cells per individual experiment).
C Western blotting of the lysates from HepG2 cells infected with lentivirus encoding shATG5 or shCtrl and transfected with Myc-MOAP-1.
E) Representative western blots showing expression of phosphorylated p70S6K (T389) and AKT (S473), the mitochondrial protein NDUFB8 and the DDR downstream target p21 in MRC5 fibroblasts treated with or without 10µM of the ATM inhibitor KU55933 and in fibroblasts from a patient with Ataxia Telangiectasis (AT) at different time points after 20Gy X-ray. Data are representative of 3 independent experiments (ATM inhibitor) and 1 experiment (AT patient);
(c) Similar conditions as in a except that further CaCl2 additions (8 μM each time) were added to −Tet trypanosomes to show the high mitochondrial capacity to take up Ca2+. EGTA (8 μM) and CaCl2 (Ca2+) were added where indicated to show the presence of medium Ca2+. (d) Relative initial rate of Ca2+ uptake by +Tet as compared with −Tet trypanosomes (means±s.d., n=3, **P0.001, Student's t-test).
D A recombinant protein containing the H+CYC domain of GC‐G acquires coolness‐evoked activity. Diagram of recombinant GST.GC‐G‐CYC protein containing the H+CYC domain of GC‐G (amino acids 849-1,078) compared to the domain structure of full‐length GC‐G (upper panel). The purified GST.GC‐G‐CYC protein was exposed to the indicated temperatures for 20 min, and GST.GC‐G‐CYC cyclase activity was measured (lower panel; asterisks denote values significantly elevated compared to 37°C).
(A) Schematic diagram of the kinase-dead (KD) Pax5-Jak2 fusion protein, which is encoded by the Pax5Jak2-KD allele and contains the K272E mutation known to abolish the Jak2 kinase function.
H,I Western blot analysis of ubiquitination of cellular proteins (Pan-Ubi) in HT1080 and RAW264.7 cells treated with additional NaCl (+17, 34 and 51 mM) for 12 hrs (H), or in RAW264.7 treated with additional NaCl (+34 mM) for different times (I). Data information: Data are representative of at least two biological replicates.
(B) ARPE-19 cells were nucleofected with the indicated Rag- and TFEB-GFP-expressing plasmids. 18 h later, cells were lysed and subjected to immunoprecipitation with the anti-HA antibody (used to immunoprecipitate Rag proteins). The immunoprecipitates were analyzed by immunoblotting with antibodies against GST and GFP (used to detect Rag proteins and TFEB-WT, respectively).
J. Representative images of wt and Baz2a-KO ESC+serum before and after transition in 2i conditions.
F. Percentage of myelinated axons after 2.5 weeks of cuprizone withdrawal in the middle corpus callosum of vehicle (blue) or D-Asp- treated mice (red). Abbreviations: DEM, demyelination; REM, remyelination Data information: The values represent the means ± S.E.M. Level of significance was determined by usin F, for each axon diameter group, Student's t test, *P<0.05 versus vehicle (n=4 mice for each group)
(d) Viability of mouse fibroblasts transfected with the indicated concentrations of a plasmid encoding α-synuclein and left untreated (None) or treated with 1 mM paraquat alone or in the presence of 20 μM AR7; n = 3. In b-d, all values are mean ± s.e.m. Differences with cells that are untreated (marked with asterisk) or those treated only with paraquat (§) were significant for P 0.001. Full-length blots are shown in Supplementary Figure 21.
F Representative confocal z-stack images of LV-infected dendritic segments in the DG granule neurons from control and susceptible mice with different treatment. White arrows indicate stubby spines, yellow arrows indicate mushroom spines, and blue arrows indicate thin spines.
(A) Schematic representation of the phosphosite (Ser439) identified in PIN2 in our study. PIN2 protein possesses three specific regions: a region with five transmembrane segments (residues 1-163), a central hydrophilic loop extending from residue 164 to 482 and a region with five additional transmembrane segments (residues 483-647). Protein alignment with PIN2 or PIN-like proteins from different species indicates conservation of the serine residue in eudicot, monocot, and gymnosperm species. The red arrow highlights the S439 in the central loop of PIN2 proteins in different plants. The size of each protein in amino acids and the percentage of identity against the Arabidopsis PIN2 are indicated.
Chromosome parameters obtained for a representative oocyte with normal segregation pattern are shown in A-D on the vertical axis, and time in min on the horizontal axis relative to the anaphase II onset. Thin grey lines in A-D represent individual chromosomes; thick black line in C-D shows the mean value for each timepoint. On the schemes near the charts chromosomes are red with green centromeres; spindle equator in A and spindle axis in B-C are indicated by dashed lines. Changes in distance to the equator plane for all chromosomes in the representative oocyte with normal segregation pattern, shown in Fig 3. The analysed distance is indicated by a black arrowed line on the scheme above the chart. Changes in distance to the spindle axis (shown on the scheme by a black arrowed line) for all chromosomes in oocyte from Fig 3. Changes in chromosome orientation for all chromosomes in oocyte from Fig 3. The orientation is characterized by the angle (highlighted black) between the spindle axis and the line connecting the sister centromeres (black solid line on the scheme).
(F) 786-0 cells were transfected with siNC or siRNF213 for 24 hours and then were transfected with or without His-ubiquitin for 36 hours. The indicated cells were treated with or without MG132 (10 μM) under aa starvation. Beads against His were used to enrich His-ubiquitin-associated proteins, which were eluted by PBS containing 250 mM imidazole. WB was performed using the indicated antibodies.
B. Anti-KV10.1 antibodies recognize ciliary structures in hTERT-RPE1 cells. After serum starvation for 48h, serum was reintroduced for 4h to induce KV10.1 expression and ciliary resorption. Cells were then fixed and stained with a mixture of anti-KV10.1 mouse monoclonals and a rabbit monoclonal anti acetylated α-tubulin. Scale bar: 2 µm.
(E) Immunoprecipitates were submitted to kinase reactions but samples were treated with Volasertib (40 nM) (+) or treated with solvent only (-).