EMBO/sd-character-level-ner huggingface dataset:
A, Treatment of PRL2 with a synthetic substrate leads to complete phosphorylation of the catalytic residue, cysteine 101. Recombinant PRL2 was treated with 3-O-methylfluorescein phosphate (OMFP) and analyzed by SDS-PAGE with the Phos-tag reagent. Phosphocysteine is hydrolyzed by boiling.
B. Srs2 requirement in de novo telomere addition in cells with and without functional HR. All strains are pif1-m2. Strains used: NK1264; NK2375, NK2376; NK2014, NK2015; NK2451, NK2452; NK2012, NK2013; NK2457, NK2458; NK2363, NK2364; NK2469; 2369, NK2370; NK2473-2475.
E Two dimensional cell-cycle analysis (BrdU/PI) of cells described in (C) and (D). Apoptotic indices represent ratios of sub G1 to G1/S cells and are shown for analyses at the indicated timepoints. **, P = 0.0020; ***, P = 0.0004; Student's t test.
C) Quantitative representation of percentage of DIV14 neurons transfected as in (A) with constructs showed in Figure 1A, in which peroxisomes after addition of rapalog redistributed to either axons ("a", blue bars) or to axons and at least 2 dendrites ("a+d", red bars). Kinesins were considered "dendrite targeting" if dendrites were targeted in ≥ 50% of cells and are highlighted in red. Kinesin constructs are transfected as indicated; the number of analyzed cells is summarized in Appendix Table S1. Error bars indicate SEM
D. NLK induces YAP phosphorylation. HA-YAP was co-transfected with NLK-WT or NLK-KN in HEK293A cells. The phos-tag gel showed NLK-WT but not NLK-KN caused a significant mobility shift of YAP.
(H) Schematic representation of an organoid electroporation. PX458 plasmids were injected in ventricular-like cavities, organoids electroporated and processed after 7 days of in vitro culture.
D. Top 5 genes with ≥10-fold shRNA depletion in BM, spleen and thymus in comparison to the reference.
(E) Expression of the genes nearest to target enhancers with constitutively bound ("stable") CTCF vs. enhancers that lost CTCF in CLL. Loss of CTCF binding correlated with reduced gene expression.
δWDphag mice lack non-canonical autophagy in myeloid (LysMcre) cells Offspring negative for LysMcre were used as littermate controls. Mice (n = 6 per group) were challenged intranasally with IAV X31 (103 pfu). (D) Precision-cut lung slices from control and δWD mice were infected with IAV. Virus titres were determined at indicated time points.
Figure 7. CHCHD10 mutant fibroblasts are less sensitive to apoptotic cell death compared to control fibroblasts. A. Control (C1, C2) and patient (P1, P2) fibroblasts were treated with 1 μM of staurosporine (STS) for 16 h. Cell death was determined by flow cytometry using Annexin V/DAPI staining. Three independent experiments were performed per condition with two points analyzed per experiment. Differences between the control and patient fibroblasts were analyzed by Student's t-test (two-sided): significant (*: p=0.0116) or extremely significant (***: p=0.0001).
K. Kinetics of the impact of rIFN-β on S622 and S643 phosphorylation. Quantified in J.
(A) Inhibition of cell-cell fusion by mAbs. Cell fusion was quantified by measuring the luciferase expression induced by full cell membrane fusion and mixing of cytoplasm, and the rate of inhibition by indicated antibodies compared to the condition without antibody is reported. Data depict mean ± s.d. (n = 4 biological replicates).
D. Scatter plot of the mean cell area versus the mean nucleoid area for cells with 1, 2, 3 or ≥4 nucleoids for each strain. The histogram in the inset illustrates the average proportions of cells with 1, 2, 3 or ≥4 nucleoids per strain. Although there were typically few cells in each strain with 3 or ≥4 nucleoids, at least one cell with ≥3 nucleoids was detected for 61% of the strains.
(j) NRK cell lines stably expressing LAMP1-Cherry;clathrin-GFP were transfected with nonspecific- or PIP5K1B-RNAi and starved for 12 h, and then observed by confocal microscopy. Scale bars, 5 μm. The insets in a, h-j represent enlarged regions of interest.
A. and B. Overlay of F-actin:ADP bound LifeAct (actin in blue and lifeAct in red cartoon) and jasplakinolide (in gray).
A Measurement of the ventilatory mechanic by barometric plethysmography: dot plots showing inspiratory (A1) and expiratory times (A2), the relaxation time (A3) and the respiratory frequency (A4) in WT (n=8), mdx (n=11) and mdx/CD38-/- (n=9) mice. Data information: Each dot of the graphs represents a mouse. one value/mouse After normality and variance comparison tests, significance was assessed using: A1,A3 ANOVA followed by Fisher's LSD test; A2, A4 : Kruskal-Wallis followed by Dunn's test Values are expressed as means ± SEM. Significance: *p<0.05, **p<0.01, ***p<0.001.
B, C. ISG induction in humanPBMCs was assessed at 4 and 24hrs post IFNα (21 U/ml) or IFNλ (1.2 ng/ml) stimulation (B) (data shown is pooled from 6 independent donors).
B) Quantification of telomere length data from two STELA experiments using the same genomic DNA, shown in (A) and (Appendix Figure 2C). Indicated in red is the mean telomere length and the error bars indicate the standard deviation.
(d) Knockdown of eIF4A in Kc167 cells does not prevent a drop in intracellular amino acids levels when amino acids are removed from the medium for 30 min. Quantification of total intracellular amino acids, analyzed in a blinded fashion. Levels of individual amino acids shown in Figure S2D. For CHX samples, cycloheximide (50µg/mL) was added 5 minutes prior to, and during treatment with medium containing or lacking amino acids. Statistical significance tested by ANOVA2 using Scheffé's multiple comparisons method (p<0.05). Error bars: std. dev. n=5.
The proliferation curves of human WI38 fibroblasts treated with control shRNA or shRNA against GADD45A.
c) UbcH7~Ub conjugates were preformed with either with WT-Ub or I44A-Ub. After the addition of apyrase to quench the charging reaction, UbcH7~UbWT (left) or UbcH7~UbI44A (right) was incubated with ParkinRBR. The disappearance of each UbcH7~Ub species and appearance of auto-ubiquitinated E3 was visualized under non-reducing conditions by western blotting for HA-Ub. Time was recorded post addition of ParkinRBR. E2~Ub conjugated with I44A-Ub does not disappear over the time course of the reaction.
(O) Representative images of hippocampal neurons (DIV4) cotransfected with an empty pSUPER (control) or pSUPER encoding an indicated shRNA together with a GFP fill fixed at DIV8 and immunostained for MAP2 and sodium channels (AIS). Scale bar = 50 µm.
F. Schematic representation of RIG-I and PKR pathways. Indicated is PKR inhibition of translation and induction of NF-κB and IRF3 by RIG-I and PKR. NF-κB response to TNFα and activation of EGOT is also indicated.
Bumetanide interferes with the interaction of CRTH2 with LARP6 in MRC-5 human lung fibroblasts MRC-5. MRC-5 cells were co-transfected with myc-LARP6 and flag-CRTH2 expressing plasmids for 24 h, and then treated with Bumetanide (0.1, 2 μM) for an additional 24 h. Whole cell lysates from MRC-5 cells were immunoprecipitated and immunoblotted with the indicated antibodies.
A-B Total amount of progenitors as a percentage of ckit and Il7rα enriched bone marrow (BM) cells. Shown are hematopoietic stem cells (HSCs), Flk2- and Flk2+ multipotent progenitors (MPP), common lymphoid progenitors (CLP), common myeloid progenitors (CMP), megakaryocyte-erythroid progenitors (MEP), and granulocyte-monocyte progenitors (GMP) Data information: Data were collected at month 7 post transplantation for the uMT-/- group and month 8 post-transplantation for the NSG group, and presented as mean ± SEM. n=7 mice for the uMT-/- group and n=6 for the NSG group. *p<0.05 and **p< 0.01 (two-tailed and two-sample equal variance Student"s t-test)
C Detection of pS357-PDI and UPR signaling in HepG2 cells after Tg treatment and washout for indicated times.
Schematic illustrates the use of different technologies for measuring the absolute or relative abundance of centrosomal proteins in total cell lysates or purified centrosomes. The flow chart refers to the main Figures and also indicates the cell lines and cell cycle stages analyzed in each experiment. Arrows on the right emphasize the use of data from different experiments for comparison and calibration.
E The fraction of cells in asynchronously proliferating cultures of the indicated strains with a DNA content of > 2C was determined by FACS analysis (n = 3). Error bars represent SD.
METTL14 is arginine methylated in cells. Endogenous METTL14 was immunoprecipitated from HEK293 cells under denaturing conditions and detected using the ADMA antibody ASYM26. the black triangles indicate arginine methylated-METTL14; open triangles indicate the immunoprecipitated METTL14 proteins.
(E, F) (E) Overview of the POST-2 eEF3-80S molecular model highlighting the L1 protein (yellow) and ES30L (orange) and its (F) zoom depicting the magnitude of the L1-stalk movement from the POST‑2 state (L1-stalk ´int´) to the POST-3 state (L1-stalk ´out´). L1-POST3 (light gray), ES30L-POST3 (dark gray).
(e) Overexpression of EndoB1T145A attenuates MPP+-induced autophagy in neurons. Data are means ± s.e.m.; n=7.
(D,E) PH3 (green; dividing cells) IF on cross-sections of day 4 neurospheres. White arrowheads point at mitotic figures, which are quantified in (E) as percentage of dividing cells over DAPI-stained nuclei (blue). n ≥ 3 neurospheres from n = 2 batches. Data information: data are represented as means ± SEM. Student t-test (E) (**P<0.01, ***P<0.001). Scale bars: 50µm.
A. Seven LncRNAs targeted for BMP4 were identified by RNA-seq, and the relative positions of these 7 LncRNAs and BMP4 are shown.
Second harmonic generation (SHG) representative Images and Quantification (bars) showing deposition and organization of collagen fibres produced by H1299control and H1299RASSF1A spheroids embedded in collagen I matrix (2mg/ml), treated with siNT, siRNA against P4HA2 or 4μM DPCA to restrict P4HA2 activity. Red arrowheads show highly organized, long collagen fibres. Scale bars 20µm. Data information: All statistical analyses were performed using Student's t-test (2-tailed) of n=3 for in vitro experiments and error bars represent the mean ± S.E.M.
Knockdown of cyclin F caused a delay in DNA lesion recovery that is dependent on E2F7/8. The cumulative curves represent the add-up number of cells that overcome the DNA damage lesions, for a time frame of 24 hours. For each condition, 50 cells were quantified. Log-rank tests were performed to analyze the statistical significance.
B) Relative frequency distribution of the number of genes per TU. The average as well as the maximal number of genes per TU are indicated.
F Relative mRNA expression of ITGA6, ITGB1, and KLF4 in PC3-LN4 WT and EDC3 S161A mutant cell lines. Data information: Real-time PCR data (F are presented as mean ± SEM, (n = 3/group). Unpaired student's t-test was used for statistical analysis. *P < 0.05, **P < 0.01 and NS, not significant.
H Effect of cyclosporin A (CsA, 1 μmol/L) on the percentage of cells with depolarized mitochondria. n=6-8/group.
C. Real-time RT-PCR analysis of CDK inhibitor expression in CMs with FoxM1 or Id1 overexpression, Jnk3-shRNA or combined treatment.
DSCR1 interferes with binding of U1 and U2 snRNPs to regulate splicing of TET1 and level of TET1. TET1 then affects demethylation of miR-124 promoter, thereby modulating miR-124 expression. Optimum level of miR-124 controls expression of genes necessary for adult neurogenesis. In the absence of DSCR1, there is increased TET1 expression due to reduced interference in splicing by DSCR1, leading to decreased methylation of the miR-124 promoter, and altered gene expression affecting adult neurogenesis. Too much DSCR1, on the other hand, competes with the U1 and U2 snRNPs to inhibit normal splicing of TET1, leading to reduced TET1 level. This then leads to increased methylation of miR-124 promoter, reduced miR-124 expression, and altered gene expression affecting adult neurogenesis.
qPCR analysis of ERdj3 mRNA in HEK293T cells treated with or without thapsigargin (Tg; 6 h, 100 nM). Error bars represent the mean ± 95% confidence interval as calculated in DataAssist 2.0 (n = 3).
C. Representative images of the small intestines 24h after TNF-α injection in Casp8WT and Casp8ECko mice (blue arrowheads point to Peyer's Patches).
C. SPATA2 is involved in TNF-α-induced necroptosis. SPATA2 was knocked down in L929 cells using RNAi, and cells were pretreated with DMSO, Z-VAD, or Z-VAD+NEC1 for 1 hour followed by treatment with TNF-α for 2.5 hours. Cell viability was assessed with propidium iodide staining and flow cytometry. Knockdown of SPATA2 mRNA was verified using real time PCR. p** < 0.05 (two-tailed, unpaired Student´s t-test).
Heat map showing the probability (or p-value) that the simulation produces mean cluster size and fraction of colored cells that match those observed experimentally for the IgG treatment. This probability is calculated for different values of cluster lifetimes and mean recruitment times (values in x and y). 4000 simulations were performed for each set of parameters (each point in the heat map). The most likely parameter values (yellow) correspond to a cluster lifetime of 21 hours and mean recruitment time of 11 hours. Red dashed line indicates the cross-section with the most likely cluster lifetime (21 hours). (C) A graph showing the probability that the simulation produces mean cluster size and fraction of colored cells that match those observed experimentally for the αDll4 treated clusters (blue line). Here, the cluster life time is taken to be 21 hours (taken from b) and the probability to match the experimental data is calculated for different recruitment times in the final 5 hours of the simulation (x-axis). The most likely mean recruitment time for the αDll4 treatment is 5 hours (peak of blue line). For comparison, the most likely mean recruitment time for the IgG treatment is 11 hours (Red dashed line, corresponding to the red dashed in (B)). Hotelling's T-Squared test.
Secreted ANG level in conditioned medium from THP1, HCT116WT or HCT116KO (n = 3).
Time from NEBD to mitotic exit in control depleted, Rod depleted, Bub1 depleted and Rod and Bub1 co-depleted HeLa, U2OS and RPE1 cells. Cells were treated with nocodazole.
(B) Barrier permeability (log Papp) measured under control conditions within the human Airway Chip (-Virus) or 48 h post-infection with WSN (+ Virus) with (+) or without (-) OSV.
(f) Atg7+/+ and Atg7+/− primary MEFs were loaded with a mixture of the indicated concentrations of PA and OA for 48 h, and TG content was estimated by ORO staining. **P0.01, ***P0.001; two-way ANOVA, n=4.
Fluorescence microscopy of T6SS dynamics in ∆retS TssB1-mCherry2 strain harboring pPSV35 plasmid with TssA1PA-mNeonGreen fusion. Scale bar: 2 µm.
A 5-fold dilution series of cells from exponential SC cultures of the indicated strains were spotted on SC +/- the indicated dose of HU.
B. MST signal (normalized fluorescence) of P1 (red curve), P2 (green curve) and P3 (cyan curve) plotted against TBC1D31, at increasing concentrations of peptides. The threading modelled structure of the overlapping binding segment of praja2 (praja2550-570) is shown.
D Scatter plot showing the correlation between CDK12 expression and its copy number alteration (CNA) in METABRIC (left). The r value was calculated as the Pearson's correlation coefficient. Box plots showing the mRNA levels of CDK12 in the indicated subtypes from METABRIC (right). P-values were calculated using one-way ANOVA, followed by post-hoc LSD test.
Kinetic study of the reaction catalyzed by recombinant hGS. Lineweaver-Burk plot reporting the hGS activity at the indicated concentrations of glutamate in the absence (), or in the presence of MSO Symbols- (): 2 mM MSO ; () 3 mM of MSO ; () 4 mM of MSO ; () 5 mM of MSO
A HeLa cells were transfected with the import/export reporter plasmid XRGG-GFP, treated with the indicated siRNAs and synchronized in early G1 phase by Monastrol release. Dexamethasone was added for 3 hours to induce XRGG-GFP nuclear import. Following wash-out the nuclear export of XRGG-GFP was analysed by live video spinning disk confocal microscopy. The selected frames of the movies are depicted in Figure EV5C. The percentage of cytoplasmic XRGG-GFP over time was quantified in Figure EV5D and quantifications of individual cells from the 20 and 30 minutes time points are depicted in (A), 199 cells were analysed (mean ±SD, *P < 0.05; **P < 0.01; N = 3).
A-E Chemokine-galectin interactions were detected by using a solid-phase immunoassay. For this, 46 human CC and CXC chemokines were adsorbed on nitrocellulose membranes and the stripes incubated in parallel with (A) TBS or (B) TBS containing biotinylated galectins (the representative image shows a processed membrane tested with labeled Gal-3). Signals had been generated by using SA-HRP and chemiluminescence reagents. (C-D) The blots were subjected to densitometric analysis, and (E) all independent experiments were combined (binding chemokines in light blue, Gal-3: n = 5, Gal-3 CRD: n = 5, Gal-1 n = 4).
All panels show immunofluorescent staining. Blue shows nuclear DAPI staining and green shows cones marked with PNA. (a-f) Staining for HIF-1α (red signal). (a) Wild type (PW10) stained for HIF-1α (inset shows higher magnification). (b, c) Cross sections in wild type stained for HIF-1α (PW10). DAPI overlap is shown in c. (d-f) During cone degeneration in Pde6b−/− (PW10) mice, we found increased levels of HIF-1α in cones (inset in d shows higher magnification with DAPI overlap). Cross sections indicated that the increase of Hif-1α occurred mainly in cones (arrows point to cones that are located in the top layer of the inner nuclear layer at this stage; e). DAPI overlap is shown in f.
Percentage of tumors that have deleted Trf1 quantified by TRF1 immunofluorescence after mice had been sacrificed. Post-mortem analysis of Trf1 deletion in each tumor revealed that none of the Trf1lox/lox K-Ras+/G12V p53+/+ ones had excised Trf1.
C Summary of T1 and T2 relaxation time analysis for (15N) Ub(G76C) in various E2 conjugates. The table shows the mean T1/T2 ratios ± standard deviation over all Ub peaks in a given conjugate (or for the free protein) as well as their molecular weights. Bottom: Cartoons depict open/closed conformation equilibria for different conjugates.
Immunoblot detection of NCOA4, FTL and ACTIN levels from normoxic lysates of B16-F10 cells cultured in the presence or absence of BafA 5nM for 24h (n=3).
(D) WT and EGFR-/- HeLa cells were transfected with cGAMP; after 5h IFNβ mRNA was measured (n=3).
Representative Western Blot of Collagen I in wild-type MEFs and Fam134 knockout MEFs reconstituted for the respective wild-type (WT) or ∆LIR mutant Fam134 protein. Vinculin has been used as reference for ratio calculation. The statistical significance was estimated by unpaired Student's t test. All data are represented as mean ± s.e.m. of n=3 biological experiments and the statistical significance is defined as * p<0.05, ** p<0.01, *** p<0.001.
C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.  The percentage of infected cells was quantified by the automated cell‐imaging system Hermes WiScan and ImageJ 48h post-infection. Cells from a representative donor were used for immunoblotting. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).
(D) Plotting individual runs from the obstacle course (B) to a planar matrix facilitated parametrizing the positions of the left (red) and right front leg (red) as well as the time when animals touch the ground (in seconds) and comparison of the trajectory to the positions of the hurdles. Data were then introduced in TrajR for evaluating standard motion parameters. Coordinates in the parcour were indicated in cm and Y-axis of the respective parameters are given according the TrajR output. Error bars and numbers indicate mean values (MV) ± standard error (SE).
J, K Normalized mRNA expression of TCF4-regulated proteins (Axin-2, c-Myc, Cyclin D1) and DDX3 were measured by qRT-PCR in H1299 cells after knockdown of DDX3 (J) and treatment with RK-33 (K). All experiments were repeated three times.
TEM analysis of the NE in 5DO fat body cells expressing Ctdnep1 with DAGK or Sec61 (control). Red arrows indicate nuclear pores
Quantification of log2 fold change and -log10 p-value of MS spectral counts from UBR7-BirA*-HA (heavy) compared to parental (light) cells. Positive log2 fold changes are presented. Full dataset displayed as inset bordered by dotted line. The two proteins most abundantly labeled by UBR7-BirA*-HA are UBR7 and NASP. Experiment was performed twice.
U2OS cells were transfected, synchronized at the G1/S-border by thymidine for 24 hours and then either released into nocodazole for 16 hours (unperturbed mitotic entry) or released for 7 hours, treated with 0.5 μM Adriamycin for one hour and after 16 hour G2 arrest were induced to recover by addition of caffeine (checkpoint recovery). Mitotic index was scored based on the percentage of Histone H3-pS10 positive DAPI-nuclei and normalized to the untransfected controls. Black diamonds indicate individual siRNA-targeted genes from the library, light grey diamonds indicate positive (Wip1-depleted) and negative (untransfected and GAPDH-depleted) controls and dark grey diamonds indicate the hits based on the two screens. Dotted lines indicate selection criteria for recovery-specific genes.
In MM.1S cells treated with mycolactone and/or BZ at the indicated concentrations, or vehicle as control for 6 h: (C) ATF4 protein levels in cell lysates were assessed by Western blot (top panel) and quantified relatively to GADPH levels (lower panel) Data information: Thapsigargin (Tg, 2 µM, 6 h) were used as positive controls. shown data are representative of 2 independent experiments with similar results.
(D) HEK 293T cells transfected with control siRNA or ATG1α siRNA were deprived of nutrients for 90 min, and then replenished with DMEM for 30 min. The phosphorylation and protein levels of endogenous S6K were examined. For quantification, the levels of S6K Thr 389 phosphorylation were measured using Adobe Photoshop, and normalized to the S6K protein levels. Results are expressed as a fold change compared with the first indicated sample.
(E), (F) Upper panels: scatter plot associating the expression of the GCD (CFTR) vs. identified PMs in healthy colon GTEx tissue; the expression of CFTR (X-axis) vs. that of (E) CLCA1 and (F) SLC4A4, respectively, in healthy colon tissues. Bottom panels: Boxplots associating the expression of the identified DPMs in case-control studies; the expression of (E) CLCA1 and (F) SLC4A4 in colon tissues from CF and healthy controls. Empirical P-value significance is indicated qualitatively for two thresholds. There are sixteen CF (red) and thirteen control (blue) biological replicates. Data information: ** is P-value<0.01 and *** is P-value<0.001, using the permutation test The P-values in panels , E, F are for the hyper-geometric enrichment test.
Localization of FUS in R495X_N2A cells (R495X), and wild-type N2A cells (WT). Cells were fractionated to separate nucleus and cytoplasm. Equal proportion of cell extracts from nuclear and cytoplasmic fractions were immunoblotted with indicated antibodies.
(D) Ectopic expression of Gadd45b-Myc-Flag antagonizes LY294002-induced HSV-1 reactivation. Latently-infected SCG neurons were either transduced with vector control (Ctrl) or Gadd45b-Myc-Flag from lentivirus for 3 days prior to addition of LY294002. Reactivation was quantified by scoring the percentage of wells expressing GFP fluorescence at the indicated days. The percentage of wells expressing GFP-positive was scored as the mean ± SEM (n=3 biological replicates). Reactivation rates were quantified from 30 wells for each condition, 3 biological replicates.
Representative images of pADAM17-stained lung sections from KrasG12D mice injected with a single dose of vehicle (control), SB203580 p38 MAPK or U0126 ERK1/2 inhibitors. Scale bar, 100μm.