EMBO/sd-character-level-ner huggingface dataset:
E Effect of plant growth hormones (1 mM SA, 1 μM ABA, 10 μM JA and 10 μM 1-aminocyclopropane -1-carboxylic acid (ACC) on CDF4 expression. Three independent experiments were conducted. Values are given as mean ± SD, n=3.
(a) Cell-cycle distribution and cell number count of cells transfected with control or VHR siRNA and observed for 4-5 days. The cells were stained with propidium iodide for DNA content and analysed by FACS after the indicated number of days in culture.
Immunoblot analysis of the mature IL-1β p17 and the active Caspase-1 p20 in cell supernatants (Sup) and the indicated proteins in the cell extracts (Cell ext) of WT or Spata2-KO BMDMs stimulated as in (A).
(b) Survival of Map1lc3b+/+ mice (n = 11) and Map1lc3b−/− mice (n = 10) after LPS challenge (100 mg per kg body weight), assessed over a period of 2 weeks.
(P) Schematic illustration of BACE1 delivery to lysosomes monitored via BACE1-mKeima-Red.
Double immunolabeling of PDS5B (green) and SYCP3 (red) in spread spermatocytes at the indicated stages. Data information: Sex chromosomes (X, Y) and bivalents (XY) are indicated.
D, E COS‐1 cells were transiently transfected with GFP‐lact‐C2 and stained with recombinant 2xPH and anti‐GM130 antibody. The asterisk indicates a cell expressing GFP‐lact‐C2, and the arrowhead indicates a non‐expressing cell. The graph in (E) shows fluorescence intensity per pixel of recombinant 2xPH stain in RE area, which was delimited by GM130. Data are normalized to the 2xPH intensity in GFP‐lact‐C2 (−) cells (mean ± SD, n = 13 cells for each condition). Scale bar, 10 μm.
AAV-eGFP (eGFP) or AAV-hTau-eGFP (hTau) (1.13×1013 v.g./ml) or AAV-Y701F-STAT1 (5×1012 v.g./ml) or AAV-Y701F-STAT1 (5×1012 v.g./ml) plus hTau was stereotaxically injected into hippocampal CA3 of 3-month-old C57 mice. After one month, learning and memory were detected by MWM test. (F) Expression of Y701F-STAT1 did not change the swimming speed of the mice in water maze task (n=7-10 each group). Data information: Data were presented as mean ± s.e.m two-way analysis of variance (ANOVA) followed by Bonferroni' s post hoc test *, p<0.05, **, p<0.01, ***, p<0.001 vs eGFP or hTau; #, p<0.05, ##, p<0.01 vs hTau.
B Protein levels (left) and mRNA levels (right) of RBM15 in MEG-01 cells expressing two different shRNAs against AS-RBM15 respectively were measured using WBs and real-time PCR assays, respectively (n=3, mean ± SD).
E, PTPN3 (L232R) attenuates TGF-β-induced growth inhibition on colony formation in HepG2 cells. Cells were treated with or without TGF-β (1 ng/mL) treatment for 10 days. Clonogenic assay Quantification of the results in clonogenic assays was analyzed by Image J. Data are shown as mean ± SEM; n = 3.
Figure 7g. DNA replication and repair genes are longer than other protein coding genes. Box plots show the length for the indicated groups of genes (according to GO annotations). Median gene lengths for each GO category were compared against all other protein-coding genes using a one-sided Wilcoxon rank sum test (p-values provided in figure, n.s.: p>0.001).
Figure 1e, f. Inhibition of CDK12 in AS CDK12 HCT116 cells results in down-regulation of CDK12-dependent HR genes. Graph shows RT-qPCR analysis of relative levels of mRNAs of described genes in AS CDK12 HCT116 (e) and WT CDK12 HCT116 (f) cells treated for indicated times with 3-MB-PP1. mRNA levels were normalized to HPRT1 mRNA expression and the mRNA levels of untreated control (CTRL) cells were set to 1. n=3 replicates, error bars indicate standard error of the mean (SEM).
A. Sanger DNA sequencing data from two iNPH patients confirming the presence of heterozygous CWH43 deletions. Arrows identify location of the deletion.
(C) Liver cells of starved mice carrying a fluorescently tagged LC3 transgene, labeling cup-shaped and ring-shaped structures that correspond to IMs and autophagosomes, respectively. Images courtesy of Ryan Scott (B) and Dr. Noboru Mizushima (C).
(H) Cold-induced 2-Deoxyglucose-6-phosphate (2DG6P) accumulation in BAT of AdRiKO and control mice infected with either AAV8-Akt2S474D or AAV8-empty housed at 4°C for 4h (n=7 (control AAV8-null), n=6 (AdRiKO AAV8-null), n=6 (control AAV8-AktS474D), n=6 (AdRiKO AAV8-AktS474D)). Data represent mean ± SEM. Statistically significant differences between AdRiKO and control mice were determined with unpaired Student's t-test and are indicated with asterisks (*=p<0.05; **=p<0.01, ***=p<0.001). Statistically significant differences between viruses were determined with unpaired Student's t-test and are indicated with a number sign (#=p<0.05; ##=p<0.01; ###=p<0.001). The exact p-value for each significant difference can be found in Appendix Table S2.
(d) Western blot analysis of HeLa cells treated (48 h) with an inhibitor of mTORC1 (RAP, 20 nM) or control (DMSO).
C. Log-odd ratio of random sampling from mouse proteome for both replicates. Red dot indicated the true values of analysis. (statistics: Z-test) * P ≤0.05
H. MAP4K4/6/7 were necessary for the LRP6 knockdown mediated activation of LATS1/2. HEK293T cells were transfected with siRNA for GFP, LRP6, and MAP4K4/6/7. Cells were lysed and the cell lysates were analyzed by immunoblotting.
D CTCF binding sites (CBS) with overlapping 5hmC in CD4+ T cells were examined for activation-induced changes in 5hmC as determined by MedIP-seq. Results for exon proximal CTCF sites are shown, as are all intragenic CTCF sites and random intragenic bins. Input adjusted changes in methylation > 10% are indicated.
C. Analysis of HNF1A function in 121 high-purity cases of the ICGC-PACA-AU cohort identified tumors with most pronounced downregulation of direct HNF1A target genes. We performed GSEA with a gene set of 106 human orthologs of HNF1A direct targets showing downregulation in Hnf1aaKO pancreas. For each tumor sample, we performed differential expression against all other samples, and used GSEA to ascertain abnormal expression of the mouse HNF1A-dependent gene set in the tumor. Samples were ranked by the resulting normalized enrichment score (NES), and classified as either HNF1A LoF samples (purple, NES < 0; P < 0.05), or Control 1 (beige, NES < 0; P > 0.05) and Control 2 (grey, NES>0). HNF1A LoF samples were predominantly non-classical tumors (Collisson et al., 2011, Moffitt et al., 2015, Bailey et al., 2016). Putative loss of function KDM6A mutations (KDM6A LoF mutants) were found in 19% of HNF1A LoF tumors vs. 2% of all others (Fisher's P = 0.005). KDM6A mutations were considered functional if classified as ´high´ functional impact in ICGC (small ≤200bp deletions/insertions, single base substitutions), or as likely loss of function structural variants in (Bailey et al., 2016), all of which were frame-shift mutations. Other KDM6A mutations were classified as unknown. Heatmaps show Z-score normalized expression of deregulated genes in Hnf1aaKO pancreas. We confirmed that 85% of 106 downregulated and 60% of genes of 146 upregulated human orthologs showed differential expression across the 3 HNF1A profiles (q<0.05, SAM multiclass analysis).
(I) Analyses of percentage CD3ε+ positive CD45+ cells (T-cells) in paws, and percentage CD4 or CD8 single positive T cells, (n = 3-4 biological replicates) Data information: Individual data points, mean ± S.E.M are shown. The data were analyzed by one-way ANOVA with Tukey's correction P values < 0.05 are considered significant.
B. Size-exclusion chromatography (SEC) experiments of Mdm12, tMmm1, and the Mdm12-tMmm1 complex comparing the molecular size of these proteins in solution. The proteins indicated were injected into a Superdex 200 column (GE Healthcare) with a buffer containing 25 mM Tris-HCl (pH 7.5), 150 mM NaCl, and 5 mM DTT. The standard molecular masses for the SEC experiments (top) are shown for relative molecular weight comparison (blue dextran, void; ferritin, 440 kDa; aldolase, 158 kDa; cobalbumin, 75 kDa; ovalbumin, 44 kDa; and carbonic anhydrase, 29 kDa).
Graphs representing the average number of nucleolar bodies after microinjection of in vitro transcribed RNA into HeLa cells that were pre‐treated with α‐amanitin (50 μg/ml) for 5 h or left untreated (control) (± 95% CI. **P‐value 0.01, n = 90, 87, 86, 83 or 86 cells, respectively). Representative CLSM images of propidium iodide‐stained RNA are shown on the right side.
B. The sequence of the 5′ UTR region of Homo sapiens PTEN mRNA. The codons that differ from AUG by only one nucleotide are highlighted in red. The initiation codons of PTENα, PTENβ, and canonical PTEN are separately highlighted in blue, yellow, and green. The potential initiation codons of PTENε are highlighted in red boxes.
Rate of caspase-1 activity in the presence of non-reduced decameric rPrdx4, reduced dimeric and monomeric rPRDX4, YVAD or control.
A volcano plot of presynaptic proteins included in the SynGO list to show that they are significantly changed in pTyr levels (p < 0.05).
(C, D) Quantification of intracellular K+ (C) and measurement of caspase-1 activity in the SN (D) of LPS-primed BMDMs pre-treated with the indicated dose of LicoB for 1 h and then stimulated with nigericin for 45 min.
F. Difference in sfGFP-MinD intensity between the top half and bottom half of the cell plotted against time.
A. Transwell migration of MDA-MB-231 cells treated with control PMOs or RAB13 PMOs (191+230). Cells reaching the bottom surface after 4hrs were counted. n=25 fields of view in each of 6 independent experiments. Bars: mean ± s.e.m..
Validation of HSATIII target introns by qRT-PCR. The graphs show the relative amounts of the intron-retaining (IR) (upper) and spliced (lower) forms in control and HSATIII knockdown cells under three conditions: 37°C (normal), 42°C for 2 h (thermal stress), and thermal stress followed by recovery at 37°C for 1 h. Expression levels were calculated as the ratio of each RNA to GAPDH mRNA and were normalized to the levels in control cells under normal conditions (37°C). Data are shown as the mean±SD (n=3); *p<0.05 (Sidak's multiple comparison test).
(D) Immunoblot of p-SMAD2/3 and SMAD2/3 proteins in response to TGF-β and poly (I:C) treatment. Pam212 cells were treated with poly (I:C) or PBS followed by incubation with and without TGF-β (5nM). Data represent three independent experiments with similar results. (E) Immunoblot of p-SMAD2/3 and SMAD2/3 proteins in response to TGF-β + poly (I:C) after knocking down of IL-33. Pam212 cells were transfected with siIl33 knockdown construct or siRNA control (siCon) for 30 hours followed by incubation with poly (I:C) and TGF-β. Data represent three independent experiments with similar results. (F) Immunoblot of p-SMAD2/3 and SMAD2/3 proteins upon the expression of IL-33 full length or cytokine domain. Pam212 cells were transfected with IL-33 full length or cytokine domain for 24 hours followed by incubation with and without TGF-β. Data represent three independent experiments with similar results. Data information: GAPDH is used as the control housekeeping protein in D-F). Graphs show mean + SD, NS: not significant, unpaired t-test.
d) Representative maximum intensity projections (MIPs) from the life cell cultures depicted in b. Cells were grown for the indicated times at hypoxic (1% oxygen) conditions and subsequently switched for the indicated times to normoxia (21% oxygen)(red arrows in b) to illustrate the dynamics of the different UnaG-based hypoxia sensors. Increasing destabilization is associated with reduced brightness but, also reduced background and improved switching behavior. Scale bars = 50 µm.
A, Images by confocal microscopy of mCherry-GFP-LC3 signal in HeLa cells across biological conditions: untreated mock, bafilomycin treated mock, altFUS, FUS, FUS(Ø), FUS-R495x and FUS(Ø)-R495x (representative images of n=3). The altFUS signal (white) is shown as an inset in the top or bottom left of the left panels. The white scale bar corresponds to 10 μm and the zoomed in region (right panels) is delimited by a white box.
As in C, but the cross-links are mapped onto the structure. Cross-links involving residues present in the atomic model are colored black, while cross-links between unmodeled residues are colored pink.
Multivalent Asp/Glu- and Ser-rich protein NSP5 (pink) is a scaffold that recruits RNA chaperone NSP2 (cyan doughnut-shaped octamers), and other RNA-binding clients. NSP5 and NSP2 undergo coacervation at low micromolar concentrations, forming protein droplets, also known as 'viroplasm-like structures'. RV transcripts undergo enrichment in these condensates via a mechanism distinct from other better characterised RNP granules. Mechanistically, this could be achieved via a specific protein-RNA recognition, e.g., binding of the RNA-dependent RNA Polymerase (RdRP) VP1 that recognises a conserved sequence present in all RV transcripts. Such RNP complexes are then absorbed into the NSP5/NSP2 condensates consistent with low nM affinity of VP1 for both NSP5 and NSP2(Arnoldi et al, 2007; Viskovska et al, 2014). Other similarly sized, non-viral transcripts (red), devoid of these proteins do not partition into viroplasms. Other multivalent RNA-binding proteins (RBPs), i.e., viral capping enzyme (Pizarro et al, 1991), and NSP2 can also assist in partitioning of the RNP complexes into the NSP2/NSP5 condensates, which can be dissolved with aliphatic diols. Upon NSP5/NSP2 condensation, NSP5 undergoes excessive phosphorylation ('hyperphosphorylation'), which can be also reversed by dissolving these condensates. Such RNP condensates may promote RNA-RNA interactions by increasing cognate RNA concentration bound by the RNA chaperone NSP2, thus being conducive to the assembly of eleven distinct transcripts required for packaging of a multi-segmented viral genome.
As in B, the dotted and solid curves show the mean number of RAD51 bound to the dsDNA oligonucleotides, as measured by SPR and the ODE model fits
To investigate a reciprocal scenario in which astroglial hyperactivity reduces Stat3 activation, we implanted osmotic minipumps into APP/PS1 mice and treated them with the network-normalizing P2Y1R inhibitor MRS2179 or vehicle for 6 weeks.
A-C, flow cytometric analysis of ROS levels in Du145TXR or MCF-7ADR cells treated with indicated agents for 12 and 36 hours. (A) Representative images and quantification of ROS in (B) Du145TXR or (C) MCF-7ADR cells are shown. One-way ANOVA was used to analyze statistical differences. Mean with ± SD Data information: Results are representative of three independent experiments.
(F) High magnification images and their 3D rendered replicates from cerebellar Npc1nmf164 microglia stained against Iba-1 and MBP containing myelin debris (arrowheads). Scale bars, 10 μm (up), 2 μm (down). The orthogonal projection of the cells in the right panels confirms the presence of myelin debris inside the cell and underneath the plasma membrane. DAPI staining shows cell nuclei. Scale bars, 10 μm.
(D) Estimated protein copy numbers based on MS data of components associated with the R-M system.
AP staining of V6.5 ESCs after mimic transfection (Full data are shown in Supplementary Fig S4B).
(F) Wide-field fluorescence image of fixed HCT116 cells, stained with Rab11a (yellow) and Rab7 (magenta), expressing constitutively active GFP-tagged Rab5 (GFP-Rab5CA; cyan), which stalls endosomal maturation and produces enlarged Rab5-positive endosomes. One of these is boxed in the Merge and magnified in Merge Zoom, revealing internal puncta marked by Rab11a (arrows) and Rab7 (arrowheads) and limiting membrane subdomains of Rab11a (yellow arrowhead) and Rab7 (magenta arrowhead). DAPI (grey) marks nuclei.
(B) For the various gene categories in panel A, the temporal kinetics of expression during the diauxic shift is plotted. Time 0 indicates time when glucose runs out. The series of RNA-seq through the growth transition was performed once.
Substrate motif identified by analyzing the sequences of hypo-phosphorylated peptides in Perseus
(H) Correlations between lncPSCA levels and the mRNA levels of the P53 signaling PMAIP1, CDKN1A and SESN2 genes in gastric cancer tissues Discovery cohort (n = 96) and Validation cohort (n = 30). RNA levels were determined by qRT-PCR relative to GAPDH. The r values and P values are from Pearson's correlation analysis.
(D, left) Ref(2) P protein migration profile in ref(2) P loss-of-function alleles. Ref(2) P mutant protein for the PB1 domain has an apparent molecular mass of 85 kD (ref(2) Pod2/ref(2)Pod2) and the Ref(2) P mutant protein for the UBA domain has an apparent molecular mass of 69 kD (ref(2) Pod3/ref(2)Pod3). (D, right) Western blot analysis of insoluble protein fractions of adult heads of double mutants for atg8a and ref(2) P probed for ubiquitin. Genotypes: (1) atg8aKG07569/Y; ref(2) Pod2/Cyo, (2) atg8aKG07569/Y; ref(2) Pod2/ref(2) Pod2, (3) atg8aKG07569/Y; ref(2) Pod3/CyO, and (4) atg8aKG07569/Y; ref(2) Pod3/ref(2) Pod3. The insoluble ubiquitinated protein profile of the double mutants is diminished compared with the one of the respective control heterozygous for ref(2) P.
(C) MEFs were transfected and treated with CCCP as described in A, followed by an immunoblotting analysis with antibodies for cytochrome c, actin, and parkin. Note that levels of parkin R275W and R42P mutant were lower, as previously reported (Wang et al., 2005).
A) Representative zygotene-like Stag3 mutant and Smc1β−/− univalents. Nuclear spreads were immunostained for SYCP3, SYCE1 and REC8. Bellow: graph showing the percentages of Stag3 mutant axes with sites of LSAEs with and without flanking REC8 foci. 78 axes with LSAEs were analysed. Bars, 1 μm.
(B) Parental Raji cells and the different Raji-Env clones were cultured with 10-1074 or an isotype control (mGO53) and NHS for 24h. The % of CDC was calculated as the relative percentage of dead cells compared to the "no antibody" condition. n=3 donors of serum.
A For the NeutrobodyPlex on RBD, two concentrations of NM1267 (1 µM and 1 nM) were applied (n = 1). Light-colored squares (high MFI (%control)) are indicative for IgGs outcompeting NM1267 from the RBD:ACE2 interface, dark-colored squares (low MFI (%control) show a continuous displacement of IgGs from serum samples in the presence of NM1267.
Hierarchical clustering of 815 genes correlating with the first two PCs identified three groups of cell types and four major distinct clusters (a-d) of genes (p < 1 ×10-9, cell cycle-related genes are excluded). Each column is a single-cell, and each row represents one gene. Cluster-specific TFs are listed on the right. The genes in bold are known to have roles in pancreatic development. L, GFPlow; H, GFPhigh.
C. For each experimental mouse group means for a- and b-waves of ERGs were calculated and p-values are shown for left and right eyes using a two-tailed unpaired Student's t-test.P-values of the VEGF-Ahypermouse group are compared to those VEGF-Ahypermice lacking either CASP1/CASP11, IL1R1 or IL18, as well as to the KO mice (CASP1-/-/CASP11-/-mice, IL1R1-/-mice, or IL18-/-mice) without the VEGF-Ahyper allele. In addition, p-values are shown comparing values between to KO mouse groups and those that have the VEGF-Ahyper allele. Mouse numbers for each experimental mouse group is indicated as well.
M Cells were transfected with GFP-Parkin and hTau-V5, hP301L-V5 or an empty vector control, and treated with CCCP. PLAs were performed for tau and Parkin. Notably, at Parkin clusters (arrow), no interactions between tau and Parkin were evident. Data information: Scale bars = 10 μm. Data are given as mean and SEM, ** = p < 0.01, **** = p < 0.0001.
B Catalytic turnover activity as measured in a coupled kinase assay is shown. Plotted are mean values from at least three independent experiments.
, PTPN3 depletion impairs TGF-β signaling in tumors. Levels of PTPN3, GAPDH and TGF-β signaling associated proteins, such as TβRI, P-Smad2, P-Smad3, Smad2/3, Smad4, PAI-1, c-Myc and p15 in tumors were analyzed by Western blotting analysis.
K Medium Gln levels (left), intracellular Gln levels (right) of MeWo cells Data information: Statistical analysis was performed by ordinary one-way Anova for the comparison of more than two groups. Unpaired t-test was used for the comparison of two groups, N.D., not determined. Data are shown as the mean ± SD, n = 3. ns: not significant, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001.
A) Pan-glial (repo-GAL4) htlACT overexpression causes upregulation of hh, fasn1 and lsd2 transcripts (n = 3 biological replicates pooled from 20 brains for each genotype; for each biological replicate, we ran 3 technical replicates for each PCR reaction). The lipogenesis genes (acc, lipin), and lipolysis gene bmm transcripts are not significantly altered. We utilised rpl32 as a reference gene in these experiments, as it is not altered by htlACT overexpression. The data are represented by log2 fold change relative to the control (repo-GAL4> w1118).
f,g) Linear regression of calculated hazard ratio (± s.e.m.) as a function of total TDP43(WT)-EGFP (R2 = 0.9353) (f) or TDP43A315T-EGFP (R2 = 0.9574) (g) level. The total TDP43 level was determined by quantitative immunocytochemistry using TDP43-specific antibodies (Supplementary Fig. 3) and normalized to the amount of TDP43 in nontransfected neurons. Dashed lines, reference (HR = 1).
D A proposed working model. Under normal conditions, OST1 protein kinase interacts with PP2C, which inhibits the kinase activity of OST1. AtANN1 is localized in the cytosol and at the plasma membrane. Under cold stress, OST1 is activated and phosphorylates AtANN1, which, on the one hand, enhances the Ca2+ transport activity of AtANN1, and, on the other, promotes the Ca2+-binding activity of AtANN1. This dual role of phosphorylation results in increased cold stress-induced [Ca2+]cyt. Consequently, AtANN1 indirectly facilitates the expression of CBFs and CORs to positively regulate plant freezing tolerance.
(A) Immunoblots for FTMT, frataxin, mitoferrin, HSP60, FTH1 and TfR using the hepatic mitochondrial fraction lysate and whole liver lysate in control (C57BL/6J) mice and STAM mice treated with DFP (0, 0.0375, or 0.075 mg/g body weight) (n=6). The expression of FTMT, frataxin, mitoferrin, FTH1, and TfR were normalized to HSP60 or β-actin, respectively. The central horizontal bar and the error bards indicate mean ± SD. The Tukey's honestly significant test was used for statistical analysis. *: P<0.05, **: P<0.01. (B) The mean number of mitophagosome-like structures/100 μm2 from four randomly selected areas in the livers of DFP (0.075 mg/g body weight)-administered mice were compared between control and FTMT siRNA-treated groups for STAM mice (n=6) and DMBA + HFD mice (n=6). The central horizontal bar and the error bards indicate mean ± SD. Two sample t test was used for statistical analysis. NC: negative control siRNA, *: P<0.05.
(b) PFT-α or p53 siRNA-mediated GFP-LC3 puncta in MEFs transfected with siRNAs specific for mouse Atg5 or Beclin 1.
(A) WT or STX16KO HeLa cells were starved in EBSS for 2 h and subjected to HCM analysis of LAMP2 and LC3 puncta. Masks: white, cells identified based on nuclei; red, LC3 puncta; green, LAMP2 puncta; yellow, overlap of LC3 and LAMP2. Scale bar: 20 µm.
Courtship indices for one target (Canton-S) male and one tester male of the indicated genotypes. Changes were determined by comparing the data with relative control. n = 8, 13, 13 (D)
(G) Quantification of diphtheria toxin receptor positive neurons before and after injection of diphtheria toxin.
Shoot regeneration assay using Col and hag1-6 root explants on media with different cytokinin (2IP) to auxin (IAA) ratios. Col and hag1-6 root explants derived from 20 seedlings were first incubated on CIM for 2 weeks and then transferred onto 150 mg/ml IAA-containing media supplemented with 0, 500, or 5,000 mg/ml 2IP. Pictures were taken at 27 d after transfer onto each media using representative explants. Scale bar: 2 mm.
(B) Polyubiquitinated proteins in detergent-soluble (S) and -insoluble (I) fractions from brain and spinal cord homogenates of Epg5+/− and Epg5−/− mice.
K Model for the role of SIRT7 in NHEJ DNA repair: SIRT7 is recruited to DNA damage sites, where it regulates the extent of histone H3K18 acetylation, which in turn is required for efficient 53BP1 focus formation and overall NHEJ-mediated DNA repair.*P < 0.05; **P < 0.01; ***P < 0.001 by ANOVA Single Factor.