EMBO/sd-character-level-ner huggingface dataset:
A. Bar diagram shows the initial rate of GPX-like activity of Vs under different assay conditions.
(G) Confocal microscopy images of HeLa cells treated as indicated and immunolabelled for ER-KDEL (blue), NMHCIIA (green) and Gp96 (red).
D. The relative enrichment of the BZLF1 and BRLF1 mRNA in CNE2EBV cells with transfected with siYTHDF2, siYTHDF3 or siNC siRNA following EBV reactivation. After 24 h of siRNA transfection, CNE2EBV cells were treated with TPA (30 ng/ml) and NaB (2 mM) for 24 h. The RIP assays were performed using YTHDF1-specific antibody or IgG control in these cells. Fold enrichment was determined by calculating the 2-ΔCt of the RIP sample relative to the input sample.
The ART-like domain D4 of CNFY. Essential residues of canonical ARTs are not conserved in CNFY (RSE-ARTs exemplified by C. perfringens iota toxin, PDB entry 4H03 (Tsurumura et al, 2013); HYE-ARTs exemplified by P. aeruginosa ExoA, PDB entry 2ZIT (Jørgensen et al, 2008); carbon atoms of NAD+ shown in black).
F, G, C57BL/6J cells with mitochondria labelled with MitoTrackerTM-Green (MTG) or MitoTrackerTM-Red (MTR) exchange mitochondria after 3 DIV (0 DIV, n=6; 3 DIV, n=6). White dashed line delimitates both cell somas and the protrusion connecting them (F). No exchange is observed when the two photoreceptor populations are separated by a transwell (n=3), nor in co-cultures of live MTG-labelled and lysed MTR-labelled cells (n=3) (G).
G) Footprinting of AP-1 sites in TB+. DNase I upper and lower strand cleavage patterns were calculated as in (B) (left) plus the average DNase I profiles (right) for all AP-1 motifs within the subset of 2882 defined pDHSs in TB cells before and after stimulation, ranked in order of decreasing FP probability score. H) Distribution of the FP probability scores for the data shown in (G).
(F) Scheme showing the structure of TIP30-His deletion mutants that were used in GST-pulldown assays in (G). The C-terminal His-tag is highlighted in blue.
I ISRE reporter activity in Myc-SIRT5 (0, 100 ng or 200 ng)-transfected HEK293T cells with or without poly(I:C) transfection for 18~24 h. Data information: Graphs represent fold-induction relative to the luciferase activity in the control cells. UI, uninfected. All data are presented as the mean values based on three independent experiments, and error bars indicate S.E.M. (unpaired two-tailed Student's t test).
(I) Offspring of worms with overactive exopheresis develop faster. Y.A. - young adult stage, L4 - last larval stage. n = 317-372; N = 2.
C. Images of the heart of the patients as indicated. (a) M-mode echocardiography taken from the parasternal long axis view of the left ventricle (LV) illustrating poor LV function with severe involvement of the interventricular septum (IVS) and reduced motion of the left ventricular posterior wall (LVPW). (b) bi-dimensional apical four chamber view with swirling of SMOG heart chambers as a result of poor myocardial function. The SMOG is enhanced in the right atrium. (c) bi-dimensional apical four chamber view with free tricuspid valve regurgitation (TR) due to lack of cooptation of the tricuspid valve leaflets during systole (marked by a red bar) as a result of critical reduction of right ventricular function and right ventricular enlargement. (d) Right and left ventricular thrombi seen in the short axis apical parasternal view. T1-large right ventricular thrombus, T2&amp;amp;T3-left ventricular thrombi. (e) The color-flow Doppler picture: TR. Free regurgitation of the tricuspid valve shown in modified four chambers apical view. RA-right atrium, RV-right ventricle, LA-left atrium, LV-left ventricle, TR-tricuspid regurgitation color-flow Doppler.
(A, B) eEF3 binds to (A) non-rotated 80S in a pre-translocation (PRE) state bearing classical A/A- and P/P-tRNA (PRE-1) as well as to (B) non-rotated state occupied by A/A- and a hybrid P/E-tRNA (PRE-2). (C, D) (C) Rotation of the ribosomal subunits leads to unstable binding of eEF3 to a ribosome with A/A- and P/E-tRNA (PRE-3) as well as to (D) a fully rotated ribosomal species bearing hybrid A/P- and P/E-tRNAs (PRE-4). (E) Binding of eEF2-GTP facilitates 40S-head swiveling and translocation of the hybrid A/P- and P/E-tRNA into the chimeric ap/P and pe/E tRNA positions (POST-1). (F) After dissociation of eEF2-GDP and the resulting back-swivel and back-rotation of the ribosome, eEF3 binds stably to the non-rotated ribosome with a classical P/P- and E/E-tRNA (POST-2) with L1-stalk in the ´int´ position. (G) The eEF3-CD directly interacts with L1 stabilizing an ´out´ conformation that facilitates release of the E-site tRNA. eEF3 remains bound to the non-rotated ribosome bearing a P/P-tRNA (POST‑3). Transition from states E to F and F to G are accelerated by eEF3. Binding of eEF1a-ATP-tRNA ternary complex and subsequent peptide bond formation results in formation of PRE-1, as seen in (A). (H) In the absence of eEF3, we suggest that POST-2 ribosomes formed after eEF2 dissociation can bind an A-tRNA, but cannot translocate further because of the presence of three tRNAs on the ribosome. Data information: Volumes (A-G) are representing the cryo-EM reconstructions from the eEF3-TAP pull-out, whereas volume (H) shows a potential scenario based of the results of the eEF3-depletion studies. All maps are filtered to 6 Å. The outline shown in (C-E) assigns the disordered eEF3 ligand present in these volumes.
Atg5VC and p22 mut spheroids were treated with 300 μM H2O2 plus or minus 100 μM BAPTA‐AM (I) or PMA/ionomycin (J). (I, J) Quantification of average mucin area/goblet cell (n=5 sample/group; 150 cells were quantified/sample). Error bars indicate s.e.m. ****P0.0001 as determined by the Student's t‐test (I) or ANOVA with Tukey's multiple post‐test comparisons (J).
(E) Representative immunoblots for pPERK, cleaved-ATF6, and GAPDH, and relative protein levels of pPERK and cleaved-ATF6 in control (solid bars) and Yip1A-knockdown (open bars) cells. GAPDH was used for normalization. The intensity of the bands was quantified using the MultiGauge software, and the results are shown in the bar graphs. As a positive control for activation of PERK or ATF6, HeLa cells were treated with 5 μg/ml tunicamycin for 8 hr ('Tm'). The protein levels at time 0 hr were assigned the value 1. Data are means ± SD from three independent experiments.
(B) Fork asymmetry as measured by DNA combing assay in HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). From 40 to 200 total measurements were considered for each candidate. Median values are indicated. *p<0.05, **p<0.01, ***p<0.001 (Mann-Whitney U test). Black stars denote significant increases whereas red stars denote significant decreases.
E. Transverse sections from P0 GemC1WT/WT (left two images) or GemC1KO/KO (right two images) trachea, immunostained with antibodies against Muc5ac (marker for mucus-expressing cells, red) and E-cadherin (marker for cell boundaries, green). DNA was stained with Draq-5 (blue). Serial images have been merged to show the complete trachea section (left). Higher magnifications from the same section are shown on the right. Scale bars, 10 µm.
Quantification of EdU positive CMs (mono- or multi-nucleated) in vehicle and navitoclax treated animals. Data are mean±S.E.M of n=5-6 mice per group.
(H) Upper part: Western blot analyses of ZEB1 in shRNA-Control (1 to 4) or shRNA-ZEB1 (5 to 8) ESPxenografttumors, showing efficient ZEB1 knock-down directly in the tumors, after IPTG ±PLX4032 treatment in vivo. Lower part: Representative pictures of ZEB1 immunostaining in shRNA-Control or shRNA-ZEB1tumors, after IPTG treatment in vivo. Scale bar = 40µm.
F, G Expression pattern of pWOX5::GFP in the indicated genotypes at 5 DAG. Scale bars: 20 µm. H Quantification of GFP fluorescence in the indicated genotypes expressing pWOX5::GFP. GFP signal intensity in the WT was set to 1. n denotes the total number of scored samples. Data information: In (H) data represent mean ± SD of three independent replicates. **P < 0.01, *P < 0.05 (Student's t-test).
TRF2-overexpressing or -knockdown BJcl2 cells were co-cultured with MSC2 cells for 18h +/- mouse IL6 blocking antibody or Ruxolitinib. Alternatively, a 4h challenge with NIH3T3 cells was performed and the ability of NK cells to kill NIH3T3 cells were determined by colorimetric analysis (AlamarBlue) (H). Data information: Panels show all points with mean ± SEM corresponding to the percentage of specific target lysis (H) (n = 3 independent experiments; *p < 0.05, **p < 0.01, and ***p < 0.001; Student's t-test).
(G-J) Cbl is required for germline differentiation. Immunostaining of wild-type and CblEY11427/MB05683 germaria with anti-Hts to visualize spectrosomes and fusomes. White arrowheads indicate GSCs; the white arrow indicates increased number of spectrosomes. (I) Quantification of germaria with increased number of spectrosomes
Left: Western blotting comparing the abundances of Armi and Piwi in total OSC lysate (total) and the mitochondrial fraction (mito) before (control) and after (Gasz KD) Gasz depletion in Zuc-depleted OSCs (Zuc KD). Relative mito-localization intensity (*) shows the amount of proteins in "mito" normalized by the amount of proteins in "total" and HSP60. Right: Immunofluorescence shows that the Armi mitochondrial signal (green) found in Zuc-depleted cells (Zuc KD/control) mostly disappeared after additional Gasz depletion in the cells (Zuc KD/Gasz KD), but was found at Yb bodies. Mitochondrial signal is shown in red. The scale bar represents 5 μm. DAPI (blue) shows the nuclei.
(A) ROCKI is recruited to the MARCKS promoter in Pam3-stimulated THP1-derived macrophages. ChIRP analysis of THP1-derived macrophages treated with Pam3 for 8 h. ChIRP assays were performed using a non-specific lacZ probe or probes specific for lnc-MARCKS. Specificity of ROCKI probes (left), and enrichment at the MARCKS promoter (right).
D. The enrichment level of m6A, for LncBMP4 variants with the progressive accumulation of RRACH site mutations, was detected by RIP-qPCR (Data are shown as mean ± SEM, n =3 independent experiments, * p < 0.05, ** p < 0.01, one-way ANOVA).
(A) Growth measured by optical density (OD) at 600nm for 3 biological replicates each of the T- and A-strains over 6 hrs of exponential growth in YES media. The x-axis refers to the time since inoculation of the culture. (B) The same data as in (A) plotted on a log2 scale (solid lines) with lines fitted (dotted lines). The doubling time is the inverse of the slope.
(F) Lorenz curves generated with the reads of all clones in a sample to visualize deviation from perfect equality.
Confocal analysis of co-localization of VISP1-GFP and RFP-SGS3 with the CFP-NbATG8f-labelled autophagic bodies in N. benthamiana leaves. The infiltrated leaves were treated with 100 µM E64d or DMSO at 48 hpi and examined at 60 hpi. Arrow heads indicate autophagic bodies. Scale bar = 10 μm.
A. Alkaline phosphatase (AP)-shedding assays performed for Eiger in S2R+ cells expressing either GFP, Drosophila ADAM17, or activity dead mutants of Drosophila ADAM17, in the presence of either PMA, or PMA and TAPI-1 (DMSO is used as control; see methods); n=5. The box end points are the upper (75%) and lower (25%) quartiles, the whiskers define the maximum 95th percentile and minimum 5th percentile values respectively, the central band is the median and the square is the mean. Data were quantified for significance using Student's t test. ***p<0.001, **p<0.01.
H Glucose uptake, lactate production, and oxygen consumption rates were measured in Dgcr8−/−ESCs expressing exogenous Myc.
Mean CM area μm2. Data are mean ±S.E.M. of n=6 per age group, >150 CMs analysed per mouse.
H. HeLa cells expressing lncRNA-MIF or control RNA were transfected with miR-586 mimics or NC mimics. Twenty-four hours after transfection, cell lysates were analyzed by Western blotting.
Schematic representation of CENATAC annotated with zinc fingers (ZF1 and ZF2), predicted coiled coil, and conserved motifs 1-4 (M1-M4). Upper: sequence logos of both zinc fingers and the conserved residues defining motifs 1-4 (underlined). See Appendix Figure S2 for the full-length logo. Lower: C-terminal protein sequences of wild-type and MVA mutant CENATAC. The MVA truncation site is indicated by the red dotted line; the four conserved motifs are outlined in red.
A. Representative images showing morphological changes in spheroids from 3D cultures of HRPTEpi cells following Stx2a (10 ng/mL) treatment for 72 h in the presence or absence OSMI-1 (10 µM, final). B. Quantification of estimated spheroid diameter in (A) [n = 11 independent spheroids (biological replicates)]. The effects of Stx2a in vehicle controls were compared with those of spheroids maintained in the absence of Stx2a, and OSMI-1 treatment was compared with that of the vehicle (DMSO) controls in the presence of Stx2a. Data information: Error bars for bar graphs are presented as mean ± S.E.M. Statistical analysis was performed using two-tailed Student's t-test. *P < 0.05; **P < 0.01; and ***P < 0.001.
(A) Immunoprecipitation of endogenous Bcl‐2 and Beclin‐1. Untransfected HeLa or MV4.11 cells were treated by culture in nutrient‐free EBSS or with ABT737 (1 μM).
(C) Representative Western blot of SRSF10 protein levels from mouse liver nuclear extracts (NX) from different ZTs. The different SRSF10 variants are highlighted on the right. SRSF10-fl and SRSF10-2 are the result of differential last exon usage. hnRNP L was used as a loading control. The asterisks could represent hyperphosphorylated SRSF10-fl through higher CLK activity during the day.
U2OS mCherry-LacR-Fok1 cells were treated with the indicated siRNA and subsequently transfected with a GFP-SHLD2 construct. 24 h post-transfection DNA damage was induced using Shield-1 and 4-OHT. The cells were then fixed and analyzed for the intensity of the GFP-SHLD2 signal at mCherry-LacR-Fok1 focus. Shown is the quantification of the GFP-SHLD2 signal at the Fok1 focus. Data are represented as a box-and-whisker plot where the whiskers represent the 10-90 percentile. At least 75 cells were counted per condition.
B A neighbor-joining tree of bacterial defensins with the fungal defensin micasin as outgroup (Zhu et al, 2012). The evolutionary distances were computed by the p-distance method. Numbers on the nodes represent bootstrap values (from 500 replicates) and only >50% are shown. The scale bar represents the number of amino acid differences per site. Branches in green and red indicate peptides from actinobacteria and myxobacteria, respectively. Two clusters comprising members with structural variations are boxed in different colors (orange, dimer; cyan, vicinal disulfide).
(H) Presented are H&E-stained sections of the small intestine in a 'Swiss-Roll' form. Inset areas are enlarged in the right panel.
D, E Co-staining of PIKfyve and caspase-5 in WT and SNX10 KO Caco-2 cells treated with or without OMVs (100 μg/mL) for 24 h (D). Anti-PIKfyve and anti-caspase-5 antibodies were used to detect endogenous PIKfyve and caspase-5 respectively. Scale bar: 20 μm. Colocalized PIKfyve and caspase-5 were quantified by ImageJ software (E) (n = 3 independent experiments, n = 18 fields analysed). Data information: Data are means ± SD. One-way ANOVA followed by Bonferroni post hoc test was used for statistical analyzes. ***p < 0.001.
E. Dose-response curve of prazosin on GIC survival (24h treatment). EC50 was determined with curve fit using nonlinear regression.
H Violin plots showing plasma levels of 17-β-estradiol, progesterone, and testosterone in individual xenografted NSG females measured by LC-MS; n= 7-106 per treatment. Dotted line indicates lower limit of detection. Statistical significance was tested by non-parametric Kruskal-Wallis test, followed by Dunn's test. * P <0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001,.
(F) Cells were transfected with siRNAs as indicated, incubated with cholesterol-MβCD complex in serum-starvation media, and immunostained for ARL13B (red) and γ-tubulin (green). Scale bar, 10 μm. (G) Quantification of the percentage of ciliated cells shown in (F). Data represent mean ± SD (n=3experiments), 250 cells were scored per condition per experiment, *P < 0.05, Student's t-test.
Effect of BAX on DRP1 membrane density and DRP1-induced shape alterations of liposomes measured by flow cytometry. F) Representative flow cytometry plots outlining DRP1 (Alexa Fluor 488 signal) binding to LUVs (Rhodamine signal) in the absence or presence of BAX. % DRP1-positive LUVs indicated in green.
quantification (G) showing endogenous YAP nuclear translocation in DU145 control cells (siCTRL) or depleted for LATS1 and LATS2 (siLATS1+siLATS2) and/or UBTD1 (siUBTD1pool).
Co-immunoprecipitation of HA-PP1c β/δ and GFP-LUZP1. LUZP1 binds to PP1c β/δ. IB, immunoblotting.
(A-D) Immunostaining with dopamine antibody at late 3rd instar (96h AEL) in control background (domeMESO-GFP/+). The inset shows DomeGFP+ cells (B') and the corresponding dopamine levels (C') in them. (E-L) Similar expression analysis of dopamine at early 3rd (72h AEL, E-H) and early 2nd instar (48h AEL, I-L). (D, H and L) The spectral mode of iDopamine representation with blue pixels indicating low and red pixels indicating high intensity. (M) Quantifications of dopamine levels in DomeGFP+ progenitors (domeMESO-Gal4, UAS-GFP/+, n= 14 at 48h, n=13 at 72h and n=16 at 96h AEL). Data information: DNA is stained with Hoechst in blue, intracellular Dopamine (iDopamine) in red, domeMESO expression in green (representative of progenitors in the medullary zone, MZ). The iDopamine channel has been converted to spectral mode in panels D, H and L. All image panels show a 20µm scale bar. The inset represents a 2X zoom of region of interest (ROIs) marked in white dashed square. AEL indicates After Egg Laying. For better representation, the primary lobe of the lymph gland has been represented and outlined in white dashed lines while the MZ is outlined in yellow dashed line for segregation between Dome+ and Dome- cells. The quantification in M shows median with whiskers indicating the maximum and minimum values,. box indicates the lower and upper quartiles. The statistical analysis applied is One-way ANOVA with Tukey's multiple comparisons test. 'n' represents the number of lymph gland lobes analyzed, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001. For better representation, the primary lobe of the lymph gland has been represented and outlined in white dashed lines while the MZ is outlined in yellow dashed line.
Quantification using flow cytometry of measuring GFP and mCherry fluorescence. Cells were gated based on GFP and mCherry fluorescence and % mCherry positive cells gated used as an indication of autolysosome formation due to GFP quenching. Each symbol represents 1 independent experiment with 10,000 cells analysed per condition. A total of n=3 independent experiments were performed, and horizontal bar indicates mean ± SD.
(A) Venn diagram representing overlap of DVL3 ChIP-Seq peaks between MDA-MB-468 and MCF7 cells.
D) IHC labeling for MCM6 (D) of LRCs positive for BrdU only and neuroblasts marked by DCX.
SARS-CoV-2 is sensed by MDA5 and RIG-I. (A-D) Measurement of (A) viral genomic and subgenomic E RNA at 24 hpi, (B) fold induction of CXCL10 from (A), (C) IFIT2 and (D) IL-6 mRNA (qRT-PCR) from (A) after Remdesivir treatment (0.125-5 μM) of SARS-CoV-2 infected Calu-3 cells (MOI 0.04 TCID50/cell) with Remdesivir added 2h prior to infection. Mean +/- SEM, n=3.
(A) Heatmap of the altered Hippo related genes in colons from control and cKO mice one day after 5-day DSS treatment. The parameter of the color key indicated the fold changes converted to log2 of signal value normalized.
M. Quantification of BrdU and insulin dual positive cells (n=4 per group). Four mice for each group, and 5-10 islet images per mouse were analyzed. *P = 0.0220 (two-tailed unpaired student's t-test).
(A) Scheme for BrdU pulse chase experiment to track matrix cell differentiation into the upper inner lineages during anagen. The plus sign marks the starting point for TM or BrdU.
proliferation under hypoxic conditions of MeWo and A375 cells stably transduced with empty vector (EV) or LDHA-specific shRNAs. Data information: Statistical analysis was performed by two-way Anova for time-dependent proliferation changes and by one-way Anova for the comparison of more than two groups. Data are shown as the mean ± SD, n = 3. ns: not significant, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. statistical significance is denoted by blue (for si/sh-LDHA#1, hypoxia) and black (for sish-LDHA#2, hypoxia) stars respectively.
(e) qRT-PCR analysis of Irf7 and Irf9 expression in parental RM1 cells (n = 4) 48 h post-contact culture with naïve BM (n = 6).
Microautophagic degradation of peroxisomes is not observed in a vacuolar protease-negative strain (STK7) of P. pastoris. Kinetics of morphological changes in vacuoles and peroxisomal GFP-SKL during (a) glucose adaptation and (b) ethanol adaptation. (c) Fluorescence images taken after 2 h of glucose adaptation. Arrows show GFP-SKL in vacuolar matrix. Some cells showed diffusion of GFP-SKL into the vacuolar matrix.
f,g)Flow cytometric measurement of tomato expression in 14 weeks old Cx3cr1CreERT2:Rosa26-tdTomato mice eight weeks after TAM treatment (f) or with no treatment (g). Red lines represent the tomato signal and black lines the corresponding CreER-negative control. Data are presented as mean ± s.e.m. from four mice analyzed in one experiment.
Top: Examples of DAPI‐stained wt and cay1∆ cells grown in complete medium for 24 h at 30°C or 20°C. The white arrowhead indicates a chromosome bridge. Scale bar, 10 μm. Bottom: Quantification of chromosome bridges. Bars and error bars are averages and s.d. from three independent experiments and at least 200 cells were scored per sample in each experiment. Statistical significance was assayed using the unpaired, two‐tailed Student's t‐test. ***P 0.001 relative to 30°C.
A. Schematic representation of the experimental paradigm. Concentrations used: 5µM MB; 200-250ng/µL cy3-pre-miR-181a-1. Abbreviations: MB, molecular beacon.
(A) Schematic representation of S. cerevisiae Mdy2. Structural models of the N-terminal domain (NTD) (amino acids 1-59 of Mdy2, green, with Get4 in red, PDB ID: 2WPV), the central UbL domain (amino acids 74-148 of Mdy2, grey, PDB ID: 4GOC), the Cterminal dimerization domain (DD, amino acids 152-212 of Mdy2, blue, PDB ID: 2LNZ) of Mdy2.
B. Chemically synthesised f5C modified mt-tRNAMet and total RNA from wild-type (WT) cells or those transfected with siRNAs as in (A) were treated with TMI to specifically label f5C residues. Primer extension, using a radiolabelled antisense primer, was performed under limited dNTP conditions. Products were separated on a denaturing polyacrylamide gel alongside a sequencing ladder and RNAs were detected using a phosphorimager.
(C) Acetylated cohesinHalo488 was treated as in (A) but treated with Aurora B rather than Plk1. CohesinHalo488 particles were observed in the presence of ATP and 100 mM KCl. MSD versus time is shown. D indicates the diffusion coefficient (n = 45, mean ± s.e.m.).
(C) Cell cycle profile of individual RPE1-FUCCI cells (each bar represents one cell) after washout from 1 (top panel), 4 (middle panel) or 7 (bottom panel) days of treatment with CDK4/6 inhibitor, at the indicated doses (same concentration used in panel B). STLC (10 μM) was added to prevent progression past the first mitosis. 50 cells were analysed at random for each repeat and 3 experimental repeats are displ­­ayed (150 cells total). Underneath the single cell profiles are quantifications of the observed cell cycle defects and G1 durations. Note, G1 length is estimated by mKO-Cdt1 expression, and G1 lengths of less than 6h could not be quantified since movies were only stated after the 6h drug washout period. These are indicated on the graphs as ≤6h. Bar graphs show mean + SD. In the violin plots, horizontal lines display the median, and error bars show 95% confidence intervals.
G. Fork symmetry among DNA fibers in (F) (bars, mean; n=50 bidirectional forks, pooled from two independent experiments, per condition).