EMBO/sd-character-level-ner huggingface dataset:
D-E. Effect of PI3K inhibitor PI103 on cellular glycogen content and ATP production. Ovarian cancer cells were pretreated with PI103 for at least 2 h in complete media. Cells were then subjected to 2 hglucose and FBS withdrawal to deplete endogenous glycogen followed by culturing cells in RPMI-glucose media in the presence of PI103 for 2 h (2 hSF). After 2 h of nutrient stress, complete media containing PI103 was added to the cells for 30 min (5% FBS) for recovery. A second glucose and FBS withdrawal (15 min SF) followed immediately to examine the effect on glycogen and ATP levels. a, p < 0.001 5% FBS versus 2 hSF, b, p < 0.01 15 min SF versus 5% FBS.E. Utilization of glycogen to produce ATP.
(F, G) Current was measured with pipette solution contacting the fast and strong Ca2+ buffer 10 mM BAPTA in HEK cells transfected with STIM1, Orai1, and with (red) or without ANO8 (black). Panel (G) shows the increase in current density at peak current. Note the prominent current inactivation in the presence of ANO8. Data information: The first number in parenthesis indicates the number of similar experiments performed and the second number is the number of cells analyzed. All results are given as mean±s.e.m of the indicated number of experiments or cells analyzed and difference were analyzed by unpaired t test.
(I) 293T cells cultured with cystine-deficient medium or complete medium for 8 h were harvested and subjected to immunoprecipitation with anti-AMPKα, followed by WB analysis with anti-AMPKα and anti-CaMKK2.
D. Heat map depicting top 100 hypervariable genes in each cluster (cf. Dataset EV5). Color scale represents scaled gene expression (z-score values).
G. Quantification of lysosomal delivery of endocytosed cargo in fibroblasts, based on EM data. VPS41WT/WT, VPS41WT/S285P, VPS41WT/R662* and VPS41S285P/R662* fibroblasts were incubated with BSA-Au5 for 2 hours and labeled for LAMP-1 (10 nm gold particles) immuno-EM (Fig 2D). LAMP-1-positive lysosomes were scored for presence of BSA-Au5 and the ratio between BSA+ and BSA- lysosomes was calculated. >46 Lysosomes per condition were quantified. Both VPS41WT/R662* and VPS41S285P/R662* show a strong decrease in BSA-positive lysosomes indicating a fusion defect between late endosomes and lysosomes.
H Promoter-capture Hi-C plot depicting interactions of the 6q23 super-enhancer in stimulated CD4 T cells.
(d) TSC2 functional assay was performed using TSC2−/− MEFs co-transfected with Flag-TSC1, HA-S6K and Flag-TSC2 wild type or Flag-TSC2 mutants (RQ or RQ-9NT), with mock transfected cells as controls. Arrows denote the positions of Flag-TSC1 and Flag-TSC2. (e) Quantification of the ratio of phospho-S6K to total HA-S6K from Fig. 7d. (±s.e.m., n = 3 independent experiments). *P0.05;**P0.01.
A Cartoon illustrating the domain structure of human VN and the VN(1-64)-Fc chimera. The N-terminal part of VN contains the SMB domain (residues 1-44) responsible for uPAR and PAI-1 binding as well as the flanking 45RGD-motif responsible for integrin binding. The remaining C-terminal part contains hemopexin-like repeats intersected by a heparin-binding site and mediates binding to the ECM. The VN(1-64)-Fc chimera contains residues 1-64 of human VN fused to the Fc region of a human IgG heavy chain. The locations of tc-uPA and plasmin cleavage sites experimentally determined in this study are indicated in red while previously reported sites are reported in black.
(B) Western blot detection of p62 and LC3 in H1299 cells transfected with the indicated shRNA in normal medium or after H2O2 (500μM) treatment.
B Axin2 mRNA expression in LGR5+ cells of 12‐ to 16‐month‐old G3 mTerc−/−mice and mTerc+/+mice (n = 3 mice per group).
(A) Comparison of Yki isoforms activity in luciferase assays using UAS-luciferase or 2xSd-Luciferase reporters in S2R+ cells. Error bars represent SD, n=3. *** p-value<0.001; **** p-value<0.0001 (unpaired two-tailed t-tests).
Model of T6SS dynamics. After membrane complex has formed, TsaC assists in recruitment of baseplate components and sheath-tube copolymerization. Once extending sheath-tube has reached opposing cell membrane, TsmA replaces TsaC at the distal end and holds it in place. Shortly after TsmA disappearance, sheath contracts and releases spike-tube to the environment. Tube components are then recycled by the ClpV ATPase. TsaB localizes at the baseplate and assists in the initiation of T6SS biogenesis.
D. LincGET overexpression in mouse ESCs decreases the protein level of hnRNP U, FUBP1, and ILF2 by western blot. Three experimental replicates were performed and about 1 106 cells were used for each time.
Total RNA was isolated from ALPK1‑KO cells and analyzed using quantitative RT‑PCR for the ALPK1 transcript. Data shown depict the average of triplicate determinations normalized to the RPL13A housekeeping gene. Error bars denote RQ ± RQmin/RQmax.
(B,C) Accelerated thermal stability of PD-1 proteins obtained from 293T cells (green line), insect cells (pink line) or E. coli (blue line) is characterized in all-in-one UNcle platform. Protein unfolding is observed as an increase in barycentric mean (B) while small particle formation of the samples is observed as an increase in SLS intensity at 266 nm (C).
Purified GST-SH3 domains of ITSN were incubated with lysates of HEK-293T cells expressing Flag-DENND2B. Total proteins and bound proteins were detected by Ponceau S staining and Western blot, respectively.
(e) Western blot against PINK1, GLUT1, GLUT3 and HIF1α in WT and Pink1 KO mice skeletal muscle samples; α-Tubulin was used as loading control. Only representative western blots are shown per condition; the replicates and the semi-quantitative estimation of the band intensities are shown in the Supplementary Information. The mean±s.e.m. values of the mRNA data were calculated from the fold change of each ß-Actin-normalized transcript abundance in the Pink1 KO samples versus that in the WT. Thus, in all cases, the WT values were considered=1.00. *P0.05 versus the corresponding WT (Student's t-test; n=3-4 independent experiments).
A: Schematic representation of STARD3. Transmembrane helices in the MENTAL domain are in dark blue. The Phospho-FFAT motif of STARD3 and the conventional FFAT motif sequences are aligned and highlighted in pink. Upper numbers correspond to the position of residues in STARD3. Lower numbers correspond to the position of residues in the FFAT sequence as described in (Loewen et al, 2003). Acidic (D and E), alcoholic (S and T) and aromatic (F and Y) residues are in red, green and blue, respectively; the other residues are in black. Phosphorylated serines identified by LC/MS/MS are boxed, and the phosphosite probability determined with PhosphoRS is indicated.
A-D Comparison of chymotrypsin-like activity from female (n=9) and male (n=10) mice in young (3-5 months old) or older (10-15 months old, female (n=6) and male (n=7)) groups. Each point indicates a single mouse. A) Tissues that did not show significant decline, B) Tissues that show significant decline in females only, C) Tissues that show significant decline in males only or D) in both males and females. Each central line and error bar indicate mean +/- SEM of a biological replicates (n=9 young females, n=6 older females, n=10 young males, n=7 older males). P values obtained by unpaired two-tailed students t-test comparing young and older samples are indicated.
(d) RPE cells stably expressing GFP-LC3 were depleted of myosin VI and Tom1 by siRNA. Cells were pulse-labelled with Texas-red (TR)-dextran for 16 h followed by a chase period of 4 h. Cells were processed for immunoelectron microscopy and labelled with 15 nm gold particles against GFP-LC3 and 5 nm gold particles against Texas-red-dextran. Scale bars, 20 μm (a,b); 200 nm (d).
(A) HeLa cells were transfected with the indicated siRNAs. After 72 h, the cells were subjected to immunofluorescence assay using antibody against mTOR (red). DAPI (blue) was used for nuclear staining. The stained cells were visualized using confocal microscopy. Scale bar, 5 µm.
A) Scheme of binding sites of Okp1 and Ame1 in budding yeasts' kinetochores that we identified; we also show the binding site for MIND (PDB code: 5T58) in Ame1.
(E,F) ChIP assay to analyze the interaction of NRF1 (E) or PGC-1α (F) proteins with the Fundc1 promoter.
(E) LN229 cells stably transduced with 6x-Histidine-tagged Ubiquitin (His-Ubi) were then stably transduced with indicated shRNAs targeting NEDD4L or a scrambled shRNA. These cells were detached as in (D), lysed and subjected to nickel-charged affinity purification followed by western blotting for endogenous Merlin. The ratio of mono-ubiquitinated to native Merlin in each lane of the lysate blot was quantified by Image J and is shown under the blot.
D Immunofluorescence of PC3-LN4-EDC3 S161A (SA) cells under normal culture condition with anti-DCP1a and anti-EDC3 Abs as well as DAPI. Images captured under 40x magnification; scale bar: 10µm.
(C) Inner membrane damage (% Sytox positive) of convertase-labeled perimCherry/cytoGFP E. coli exposed to a concentration range of preassembled C5b6 or a mixture of C5 and C6, in the presence of 100 nM C7. After washing, bacteria were exposed to 20 nM C8 and 100 nM C9. Data information: (B-D) Data represent mean ± SD of 3 independent experiments. (B) Statistical analysis was done using a ratio paired two-tailed t-test and displayed only when significant as ** p≤0.01.
(A-F) Munc18-1 protein levels were measured in glia free cultures of munc18-1 null mutant neurons expressing M18WT, M18S241A or M18S241D.(F) Mean synaptic Munc18-1 intensity in cultures treated with GABAA receptor antagonist Bicuculline (40 μM, 48 h). (M18WT: 761 ± 121 a.u., n = 26; M18S241A: 1482 ± 150 a.u., n = 31, ** p < 0.01).
e, TIS cells in primary human acute myeloid leukaemia (AML) samples by SA-b-gal staining of treated (0.1 µg ml−1 ADR for 5 days) versus untreated cells in vitro. Data represent means ± s.d. (n = 5 each).
Histograms presented the luc activity obtained from HEK 293T cells co-transfected with puORFchop-luc, phRG-TK, and each one of the plasmids as indicated and treated with either DMSO (control group) or Thapsigargin (TH; stress group) followed by analysis of luc activity. The luc activity of cells transfected with pCS2 vector and kept at normal condition served as a control group. The relative luc activity of transfected cells shown on the right was normalized by the amount of RNA in the transfected cells shown on the left. The relative luc activity is represented by the fold increase of Fluc/Rluc ratio over that obtained from pCS2-transfected control group normalized as 1. The luc activity mediated by the huORFchop transcript was measured by the dual-luciferase assay, and its corresponding huORFchop-luc transcript was measured by RT-qPCR.
BALB/c mice fed with a gluten-free diet for at least 3 generations, orally challenged with vehicle or gliadin for 4 weeks (5 mg/daily for one week and then 5 mg/daily thrice a week for 3 weeks) in the presence or absence of intraperitoneal VX-770 administered 15 minutes prior gliadin challenge (n=10 mice per group of treatment). protein levels (by specific ELISA) of IL-10 and TGF-β (H) from small intestine homogenates. Mean ± SD of triplicates of independent pooled samples. ***p<0.001 or ****p<0.0001 gliadin vs VX-770+gliadin (ANOVA, Bonferroni post hoc test).
Transient expression of SipB in BMDPM from caspase-1−/−mice results in cell death. Plasmids expressing either SipB, SipC, or SipD fused to YFP were introduced into BMDPM from caspase-1−/− mice as indicated in the Materials and methods section. Macrophages were then fixed, stained with DAPI (to visualize chromatin), and observed under a fluorescence microscope. Cells expressing SipC or SipD do not show any signs of cytotoxicity. In contrast, cells expressing SipB show clear signs of cytotoxicity and chromatin condensation. Arrows indicate the nucleus of transfected cells.
Effect of cl-HK2pep on human B-CLL cells freshly isolated from patients. cell death, measured by cytofluorimetric analysis of Annexin V-FITC and 7-AAD staining Cells are treated with 5 µM cl-HK2pep; PD150606 (50 μM) is pre-incubated for 1 h. Experiments are carried out on samples from at least 10 patients and on CD19+, primary B lymphocytes from 5 healthy controls. data are presented as mean±SEM; all data were obtained from 3 technical replicates in all analyzed patient samples. Bonferroni post-test in graph ***p<0.001(cl-HK2pep vs cl-SCRpep and cl-HK2pep vs PD150606+cl-HK2pep) Student's t test; ***p<0.01, *p<0.05.
(G) Female C57BL/6J mice were injected with 14.5 mg/kg LPS (normoxia) or 5 mg/kg LPS (hypoxia) after 24h normoxia or hypoxia, with or without pre-treatment with 10 mg/kg DEX 1h before LPS injection. During the follow-up of lethality, mice remained under normoxic or hypoxic conditions. Mice in normoxia: black circles (LPS), black squares (DEX-LPS); mice in hypoxia: white circles (LPS), white squares (DEX-LPS).
(A) The three top enriched DNA-binding motifs identified by HOMER known motif analysis on 200 bp regions centred on the ZEB1 peak summits.
(A) Representative confocal images of muscle-6/7 NMJ synapses of abdominal hemisegments A2-A3 for the indicated genotypes labelled with anti-Synaptotagmin (green) and HRP (red) to reveal the synaptic vesicles and the neuronal membrane. Scale bar: 20 μm.
Analyses of recombination in 40 clusters. Bars representing single clusters are grouped based on the number of Kit+ cells. Recombination induction follows the schema in the black square. (n=12 embryo).
(a) Colocalization of lysosomes (Lysotracker Green) with phagophores (mCherry-ULK1 and mCherry-glutamine puncta) in glutamine-deprived U2OS cells. Scale bar, 25 μm.
EC-miR-483-Tg rats and WT littermates were injected with SU5416 and then exposed to hypoxia for 3 weeks and had reoxygenation for 2 weeks or injected with DMSO and exposed to normoxia for 5 weeks. Analysis of RV hypertrophy [RV/(LV+S)] (F) for the indicated groups. Data information: Values are expressed as mean ± SEM. Statistical test: t-test (*P < 0.05 vs. respective controls or between the indicated groups).
A A somatic insertion may arise in a normal tissue and be present in a fraction of cells of the tissue (red star). If a second somatic event (yellow) inactivates the Notch pathway, the mutant cell (indicated in green) will initiate the clonal expansion amplifying somatic variants already present in its genome. Finally, any insertion that occurs after the clonal expansion (blue triangle) will be present in a subset of neoplastic cells. The graph represents theoretical allele frequencies of somatic variants obtained from the sequencing of clonal tissue samples. The allele frequency of a Notch inactivating event, marking the onset of neoplasia is represented with a green horizontal line. A somatic insertion with allele frequency higher than the Notch inactivating event was likely present in the tissue before the clonal expansion. In contrast, an insertion with allele frequency lower than the Notch inactivating event, likely occurred after the initiation of neoplasia and is thus subclonal.
A Commasie blue stained SDS-PAGE showing results of F-actin co-sedimentation assay. In vitro polymerized actin filaments sediment irrespectively of the presence and absence of calcium ions. BSA was used as a control to estimate the amount of "passively" co-sedimented non-actin-binding protein and/or residual non-actin-binding protein in the pellet. There was no difference between the amount of BSA in the pellet with or without F-actin.
Significant Pearson correlations between calcium levels (Fluo4AM) ; or pHDAC3, r2: 0.6366 (H) in cultured DRG neurons after KCl. The Pearson correlations were disrupted by administration of Fostriecin calcium and pHDAC3, r2: 0.3025). Data is expressed as single cell fluorescence levels. N=50 cells per condition from 4 biological replicates.
G. Purified recombinant FLAG-FAM111A proteins were incubated at indicated temperatures for 4 h, and FAM111A auto-proteolytic activity was analyzed by immunoblotting with FLAG antibody. H. As in (G), using recombinant human FLAG-FAM111B proteins.
D) Radial bar plot with percentages of proteins following each pattern (patient-wise pattern) in 35 patients
(E) Time-course analysis of PIN2 mRNA levels in response to nitrate treatments in Arabidopsis roots. Bars represent the mean plus standard deviation of 3 biological replicates.
G-I Sagittal sections showing the corticospinal axons in injured spinal cords following injection of LV-nc-GFP (G) and LV-NB-3 shRNA-GFP (H) into the lesion sites. High-magnification image (I) of the area in (H) (asterisk). The arrows in (C-E and G-H) indicate the lesion sites; the asterisks in (D and H) indicate the lesion epicenters; the white dashed lines in (D and H) indicate the regenerative corticospinal axons extending into the distal spinal cord.F, J Quantification of the intensity index of BDA-labeled axons at certain distances from the lesion border in (C, D, G, and H). *p < 0.01; two-way ANOVA followed by Fisher's LSD. n= 19 mice per group in (F), and n= 17 mice per group in (J).
Glucose and mitochondrial metabolism in npTh17 cells from WT (grey or black) and Stim1fl/flCd4Cre (blue)mice differentiated for 3 days in vitro. (B) Glucose uptake by npTh17 cells were loaded with 2-NBDG (+) or not (-) and analyzed by flow cytometry 90 min later. Bar graphs show the delta MFI of 2-NBDG fluorescence normalized to unlabeled cells. Data represent the mean ± SEM from 3 independent experiments.
Mcm2‐7 is loaded at ORC binding sites immediately after entry into G1. As G1 progresses, increasing cyclin E/Cdk2 activity promotes the loading of additional Mcm2‐7 complexes resulting in the full complement of Mcm2‐7 being loaded by the end of G1. All Mcm2‐7 loading is dependent on Cdc6 and Cdt1. Prior to or coinciding with the entry into S‐phase, the full complement of Mcm2‐7 redistributes along the chromosomes and is displaced from transcribed genes.
(E) The majority of S-GFP-p62 cytoplasmic bodies are stained with antibodies recognizing transiently expressed LC3. S-GFP-p62 cells were transiently transfected with myc-LC3. Myc-LC3 was stained red using an anti-myc tag mAb. The boxed area indicates the part of the cell that is shown to the left at a higher magnification. Bars, 5 μm.
E Venn diagram showing the rescue of the transcriptome in learning mice, by comparing differentially regulated genes before (TAU VEH vs. WT VEH) and after (TAU MOL vs. TAU VEH) the treatment for all genes with an adjusted p-value <0.05
(F) WIPI2 was immunoprecipitated from lysates from WT or FIP200−/− MEFS after treatment with 0.5 mM DSP. Bound Atg16 and Atg12-5 were detected by immunoblotting.
Western blotting on fractionated materials of OSCs before (siEGFP) and after (siWde) Wde depletion. Anti-Egg, anti-Wde, anti-Tub, and anti-H3 antibodies were used. H3 and Tub were detected as markers for nuclear (Nuc) and cytoplasmic (Cyto) fractions, respectively. Whole: whole OSC lysates.
(C) 3D MINFLUX nanoscopy. Mic10-KO cells were immunolabeled for Mic60 using a directly labeled antibody. Colors encode depth information.
B. Meta-analysis of 3′ end counts in dmDis3l2CM-IP mapping to the indicated region around the annotated 3′ end of 68 tRNA loci in the Drosophila melanogaster genome. Cumulative relative distribution of 3′ end signal, relative to the annotated 3′ end, is reported (bottom). The average genome thymine (T)-content for the same regions is displayed (top).
C Reconstitution of a complex of ELDR components on ubiquitin. Experiments as in (A) with combinations of p97-wt or p97-EQ, YOD1, PLAA and UBXD1 as indicated. Note that PLAA associates with p97 and YOD1 on ubiquitin only in the case of p97-EQ.
(G) Representative images of organoid formation from indicated ISCs were shown (upper panel). Scale bar, 200 μm. n=6 for each group. Organoid number per well was counted as means ± S.D. (lower panel). Lentivirus-carried sgPrdm16 and sgPpard were prepared in 293T cells and infected into ISCs derived from TAM-treated LRCas9 mice to obtain Prdm16-/- and Ppard-/- ISCs. 1×104 ISCs from indicated mice were collected for organoid formation. Scale bar, 200 μm. n=5 for each group.
(C) STAM mice were fed a high-fat diet and orally administered 0.0375 mg/g body weight of DFP, 0.075 mg/g body weight of DFP or distilled water from 4 weeks of age to 16 weeks of age (n=6). Arrows indicate liver tumors. Scale bar: 1.0 cm. The number and maximum size of liver tumors were compared among the three groups. 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.
Inhibition of Prmt6 decreases mitochondria mas of control cells, but not Sirt7-knockdown MEF cells Control cells and stable Sirt7-knockdown MEF cells were treated with or without 5 µM PRMT6i for 24 hrs Mitochondria mass was determined by Mito Tracker Red staining (H) ( Data shown are mean±SD, n=3 experimental replicates, *p<0.05; **p<0.01; ***p < 0.001; n.s.=not significant, unpaired two-tailed t test
(b) The ratio of ER-associated autophagic structures (ER-IM complexes) to total autophagic structures. Data are expressed as the mean ± s.d. of triplicates from representative experiments.
(b) Mean ± s.e.m. of relative mRNA level (normalized to Ctrl mice as 1) of Cdkn1a, Bbc3, Fas, Pax6 and Stat3 in neurospheres of Ctrl, FIP200GFAP cKO, 2cKO and Trp53GFAP cKO mice are shown (n = 3 mice for each).
a) Venn diagram showing the intersection between putative miR-29a target genes (grey) and age-upregulated (green, bottom) or age-downregulated (red, top) genes. Ellipse area is proportional to the size of the sets. The numbers indicate the numerosity of the sets. 1051 miR-29a predicted targets by Targetscan, 5429 genes downregulated with age; 554 genes in the intersection, odds ratio 4.40; Fisher exact test, p< 0.0001; 4339 upregulated genes with age; 164 genes in the intersection, odds ratio 0.93; Fisher exact test p=0.427.
C) BNGE in gel activity for cIV. Sc: supercomplexes. Note that the COX reaction is slightly increased in rapamycin-treated vs. untreated Cox15sm/sm samples
(P) Representative flow cytometry analysis of control and IRGM siRNA transfected THP-1 cells stained with MitoSox red dye (1µM, 20 min). The percentage of control and IRGM knockdown cells with increased red fluorescence (mitochondrial ROS generation) is depicted.
Platelet apoptosis (Annexin V) were measured by flow cytometry analysis in HC (n=9) and PD (n=13) platelets. (**p<0.01 vs. HC). The nonparametric t test was performed for comparisons of 2 groups. Analysis was performed with Prism software (GraphPad Software, Inc, La Jolla, CA). A difference of P<0.05 was considered significant.
(A) Detection of VgpA in supernatants from indicated strains by immunoblotting (IB) with anti-VgpA antisera.
(C) Still images of a fluorescence recovery after photobleaching experiment. Size bar, 5 μm. Bleach area radius, 2 µm.(D) Graph depicting the normalized intensity after photobleaching to quantify turnover of sororin (n = 15).(E) Quantification of the relative abundance of sororin-LAP-AID on chromatin. Error bars denote s.e.m.(F) Quantification of the chromatin residence time of sor-LAP-AID at different times. Error bars denote s.e.m.
A Mean senescence profiles of the est2∆ (n=10) and est2∆ shs1∆ (n=16) clones. The error bars are SDs. B Mean senescence profiles of the est1∆ (n=6) and est1∆ bud6∆ (n=7) clones. Est1, similarly to Est2, is essential for telomere maintenance. est1∆ has been used in this experiment instead of est2∆ because EST2 and BUD6 genes are linked on chromosome XII. The error bars are SDs.
(A) Serum levels of miR-483-3p/-5p in IPAH patients (n = 139) and HC (n = 95) measured by qPCR. The data are fold change normalized to the averaged level of HC. Data information: Values are expressed as median ± interquartile range. Statistical test: Mann Whitney U test (A)