EMBO/sd-character-level-ner huggingface dataset:
A. The total observed and predicted metabolome of uRBC and iRBC. The total number of metabolites and those with a unique KEGG identification number are reported. Numbers in parenthesis refer to unmatched metabolites that were predicted from the genomic reconstruction but not observed, or observed metabolites that were not predicted. The total number of metabolites common to both predicted and observed lists (percentage in parenthesis) are referred to as 'matched'. An UpSet plot summarising the overlap of metabolites present in the predicted and observable metabolomes across uRBCs and iRBCs, with the inset depicting the metabolite size of each cell type.
G: Pericentrin immunofluorescence showing MTOCs in cultured WT, Cnot6l-/- and Btg4-/- oocytes at MI and MII stages. Spindle and DNA were labeled by microtubule nucleation factor (TPX2) and DAPI, respectively. Scale bar, 20 μm
(F) Interaction between in vitro translated TMEM33 and RNF5. FLAG-tagged vector or TMEM33 and HA-tagged RNF5 were expressed using an in vitro transcriptional and translational kit, followed by FLAG antibody pull down.
Principle component analysis (PCA) of TB IL-2, TB IL-2nil, TB+ IL-2 and TB+ IL-2nil from 3 replicates.
Gene set enrichment analysis (GSEA) plot of Il6/Jak/Stat3 signalling, day 8 Ronin ko ESC.
(E) sgRNAs counts in tumors versus sgRNA detected in BRAFi-resistant cell library (in vitro) (respectively, black and orange points) for selected candidates. Each black point corresponds to one tumor. EGFR was the most potent BRAFi-resistant gene Two replicates have been shown for CRISPR-SAM cell library (orange points). SMAD3, BIRC3 and SLC9A5 were identified as hits in the three screens
(C-D) ssDNA repair efficiency of the rad5∆ and rev1∆ mutants as determined from the maximal and final percentages of cells with Rad54 foci during the time course (right panels). Cells were synchronized in G1 and released into S phase in the presence of 0.033% MMS for 1 hour, treated with 2.5% sodium thiosulfate to inactivate the MMS, washed and released into fresh medium for different times. The percentage of cells with foci at each point was normalized to the highest value of the wild type, taken as 100 (left panels). Data information: The mean and SEM of independent experiments are shown. Statistically significant differences according to an unpaired two-tailed Student's t-test are shown, where one, two and three asterisks represent p-values <0.05, <0.01 and <0.001, respectively.
A Diagrammatic sketch of in-situ binding kinetic assay and functionalization of RBC.
SOL muscles from Ctrl or YY1dKO mice were subjected to measurement of maximal isometric tetanic force. Left: Representative trace images of normalized tetanic force. (Right): quantification of the force by normalizing with cross-sectional area (CSA). (n = 3 mice, each). Error bars represent s.d.'s of the mean. Student's t-test (two-sided): *P<0.05, **P<0.01, ***P<0.001.
(A) Representative confocal image of a stage 17 embryonic head with Dfd expressing cells (purple), Myosin expressing muscles (blue) and FasII expressing axonal projections (green) highlighted. The MN2a is identified as a Dfd expressing neuron projecting a FasII expressing axon to the Dfd positive MHE muscle. This stereotypic innervation is the basis for identifying wiring defects after RNAi interference shown in (D).
A. Most significantly altered transcriptomic pathways in PEO muscle (n=4) and in control subjects muscle after mAD (n=8). Blue color represents down-regulated and red up-regulated pathways.
(F) Dot-plots of the localized type-I interferon (IFN-α and IFN-β) concentrations at 15 hpi. Data are expressed as the means ± SD.
Real-time PCR determines the action of TGF-α and YAP levels on the mRNA expression of AREG. Each bar represents the mean ± SEM (n = 5). Bars with different letters are significantly different from each other (Ctrl vs. TGF-α, P < 0.0001; MXIV vs. YAP, P < 0.0001; MXIV vs. YAPS127A, P < 0.0001).
Quantitative data of the wound-healing assay showing the migration of ME180 cells that were treated with control (siCTRL) or YAP siRNA (siYAP) prior to treatment with or without TGF-α for 12 h. Each bar in bar graphs represents the mean ± SEM (n = 4). Bars with different letters are significantly different from each other (siCtrl vs. siCTRL+TGF-α, P < 0.0001; siYAP+CTRL vs. siYAP+TGF-α, P < 0.0001; siCTRL+TGF-α vs. siYAP+TGF-α, P = 0.0041).
(D) RT-qPCR analysis of expression of CaSR in hind paw tissue. n=3, Student's t-test.
C) After transfection of siCon, siEWS, PARP1, and double siRNA, the effect of co-depletion of PARP1 and EWS on the γH2AX and phosphorylated CHK1 upon MMS treatment was analyzed by western blot.
(B) H1299 cells were fixed and double stained with anti‐NAF‐1 and anti‐Calnexin or anti‐Cytochrome c antibodies. Scale bar represents 10 μm.
(C) Analysis of LD mobility in WT and SKO cells. Cells were incubated with OA for 45-75 min, LDs were visualized with LD540 and cells imaged by widefield microscopy. Bars: 1 - [Pearson's colocalization coefficient between subsequent frames/cell], ± SEM, n= 149-151 cells, 2 experiments, **p<0.005 (Mann Whitney test). (D) Examples of LD trajectories from cells treated and imaged , arrowhead indicates the tracked LD. (E) Analysis of the LD mobility from (C) and (D), individual LDs plotted for volume and mean velocity.
(B) Chart of Δψm over time for typical fission events; (i) fission results in temporary depolarization of one unit, (ii) fission results in permanent depolarization of one unit, (iii) fission results in the generation of a hyperpolarized daughter mitochondrion and a mitochondrion of the pre‐fission potential.
(f) Western blots of protein extracts from MCF-7 cultured with (+) or without (−) glucose for 24 h following RNAi. Fr, fragment; percentage PARP cleavage = 100 × PARPFr / (PARP + PARPFr).
E. Same as B-D. except that BrdU-sensitized cells stably expressing GFP-NLS-CDKL5 were also pre-incubated with olaparib as control. Cells were subjected to line micro-irradiation, fixed and then subjected to indirect immunofluorescence using antibodies against GFP, PAR and γH2AX. Scale bar is 10 μm
Left image: SOCE mediated by STIM1 and ORAI1 leads to Ca2+ influx, recruitment of the AKAP79/NFAT signaling complex and the phosophodiesterase PDE8. Locally recruited PDE8 reduces cAMP at ER-PM junctions. The AKAP79 signalosome recruitment is instable due to limited membrane PIP2 levels. CAN: Calcineurin. Right image: SOCE mediated by STIM1A and ORAI1 leads to reduced Ca2+ influx due to destabilized gating and hampers recruitment of PDE8. Reduced recruitment leads to reduced local cAMP degradation, which enhances PIP2 levels by activating PIPkinases. Increased levels of PIP2 stabilize the AKAP79 signalosome, enabling more efficient NFAT translocation.
(C) RT-qPCR analysis of osteogenesis markers in hBMSC cells. n=3, one‐way ANOVA, Bonferroni post hoc.
(d) Representative immunoblots showing high autophagy levels in normal cells and low levels in stem cells and cancer cells. Autophagic flux (autophagic activity) was measured by changes in the levels of LC3-II, in the presence or absence of lysosomal inhibitors E64d-PepA. U, uninhibited. I, inhibited. Below, the average of the percentage change in LC3-II levels after lysosomal inhibition from three experiments. α-tubulin, loading control.
G. Quantification of Boyden chamber invasion after 24 hours in 3D matrigel of MDA-MB-231 cells, transfected with ZsGreen (control) or ZsRASSF1C (RASSF1C) and treated with inhibitors against ROCK (Y27632, 10 μmol/L) or Rho (C3, 2 μg/ml). Data information: All data are from n=3 independent experiments. Data are analyzed by Student T-test and represented as mean ± SEM.* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001.
F. Docked pose of TP-16 with critical residues in the putative binding pocket of human EP4 protein. EP4 is shown as a color cartoon, the residues important for the interaction are depicted in magenta sticks, and TP-16 is shown as a cyan stick figure. G. The LIGPLOT diagram summarizes key interactions between TP-16 (purple lines) and residues that originate from EP4. T69, T76, T168 and R316 establishes hydrogen bonds with TP-16. Semicircles with radiating lines indicate non-polar interactions.
(B) Bovine LIF ELISA of BCE cells and bovine pericyte. Cells were cultured for 48 hrs before harvesting the medium. Data information: Bars and error bars represent mean ± SEM. All experiments were carried out in three independent studies. Two-way ANOV was used as statistical test.
(F) WT and SKO cells were transfected with ER marker plasmid (sfGFP-ER-3, green), delipidated overnight and incubated with OA and LipidTox Deep Red (magenta) for 15-75 min. Airyscan video snapshots exemplifying different modes of LDER-associated movement, note the different time scales. Panel I and II: WT cell, panel III: SKO cell. (G) Analysis of LDER-associated movement from live airyscan microscopy as in (F). Bars: % of LDs/ROI displaying indicated mode of movement, ± SEM, n= 43-55 ROIs (201-467 LDs) from 4 experiments, **p<0.005 (Mann Whitney test). (H) Analysis of LD velocity. Bars: mean velocity of tracked LDs, ± SEM, n=29-42 LDs/group, 2 experiments, **p<0.005 (Kruskal-Wallis test, followed by Dunn test).
D) GSEA indicating that tumors with deletion of the miR-424/503 locus present higher canonical Wnt-signaling activity. Independent analysis for TCGA and METABRIC data sets are shown. . P-values were obtained from the GSEA pipeline based on permutation tests.
HCT-116 or HT-29 cells were treated with 10 μg/mL cycloheximide for 30 min followed by sodium butyrate (NaB) for 24 h. Representative Western blots showed the expression of IRE-1a, BIP, PDI, and GADPH (loading control) in HCT-116 (A) or HT-29 (C) cells. Protein expression was quantified by densitometry and normalized to GAPDH (ratio of protein:GAPDH). The fold change from control for each protein is expressed as mean ± SD of three independent experiments for HCT-116 (B) and HT-29 (D) cells. are shown. One-way ANOVA was used for statistical analysis. * P<0.05, ** p<0.01, compared to the respective control group.
B. Kaplan-Meier plots of overall survival of 496 stage I and II breast cancer patients with different levels of promoter/CpG island methylation of RASSF1A, previously reported to be associated with outcome in breast cancer patients. P values were obtained from a log-rank test.
(d) FoxO3 mRNA levels in neonatal rat cardiomyocytes transfected with Scr Ctrl, anti-miR-212 and anti-miR-132 after phenylephrine (PE, 10 μM) treatment (n=6-9; P-values against Scr+PE).
B: Confirmation of the purity of sorted populations by qRT-PCR: c-Kit is highly expressed only in the c-Kit+ (D20LSK and D20LK) populations, and Sca1 is highly expressed only in the in Sca1+ (D20LSK and D20LS) populations. Error bars represent standard deviation (SD), n=3. Student's t-test. *p<0.05.
(G) Quantifications of the extent of fibrous cap and necrotic areas in brachiocephalic artery of Apoe-/- and Frs2SMCKO/Apoe-/- mice. (*p<0.05, **p<0.01 compared to Apoe-/-; unpaired two-tailed Student's t test).
(A) WT and atg1Δ cells were transferred to non-buffered SD-N medium for the indicated time. Cell viability was determined by phloxine B staining. Nitrogen-starved cells were plated onto YEPD agar and overlaid with TTC agar to examine the respiratory competency of formed colonies. The black and gray areas indicate the percentage of viable cells that are respiratory competent or respiratory deficient, respectively.
A. AFM topograph of GSDMDNterm bound to lipid membranes of E. coli extract polar lipids. Overview topograph showing arc-, slit- and ring-like GSDMD oligomers.
a, Seckel cells contain normal centrosome numbers and mitotic spindle poles. Interphase centrosomes of Seckel cells have no CPAP immunoreactivity but recruit similar levels of centrosomal proteins (ii and iii).
B. Growth comparisons of selected kinases with the kinase‑dead mutant match. 24h growth curves (OD595) from liquid culture of yeast strains (W303) expressing human kinase in the presence or absence of 3.2% (v/v) DMSO. Upper panel: BUB1: BUB1 wild type, BUB1-KD: BUB1(K821M); upper middle panel: NEK6: NEK6 wild type, NEK6-KD: NEK6(K74M&K75M); lower middle panel: PKCα-ac: PKCα(A25E), PKCα-KD: PKCα(K368R); lower panel: Control with empty plasmid. Error bars represent SD from three biological replicates.
Co-IP analysis of nucleolar proteins with NF90 in HEK293 cells transfected with EV, and the following plasmids: GFP-S5, GFP-L9, GFP-B23, GFP-UBF, GFP-C23. * represents the target protein.
WT and Mfn2 KO cells were transfected with plasmids encoding: GFP and the indicated combination of non-targeting siRNA (siCT), siRNA targeting MCU (siMCU), ChiMERA or control (indicated as WT or Mfn2 alone) plasmids. (R) MMP was analyzed (n= 90 cells analyzed in 3 independent experiments).
E. Microtubule stimulated ATPase activity of wild-type (grey), mutant 2 (red), mutant 5 (orange), and mutant 13 (purple). F. Bar plot of basal ATPase activity of wild-type (grey), mutant 2 (red), mutant 5 (orange), and mutant 13 (purple). Data information: Error bars show standard deviation of three repetitions of different dynein preparations.
(D) In vivo cleavage of endogenous MgtE in the presence of ectopically expressed full-length YqgP.S288A (strain BS73), YqgPΔNTD.S288A (BS185, Table EV2) or YqgPΔCTD.S288A (BS186, Table EV2), in rich LB medium shows that YqgPNTD is necessary for the FtsH-dependent processing of MgtE.
(A) The lysates of MCF10A cells treated with 500 ng/ml TRAIL for the indicated times were analysed by immunoblotting. The control lane (0 min TRAIL) originates from the same blot and has been treated and exposed identically. Similar results were obtained in three independent experiments.
Fluorescence intensity of the FRET donor (GFP) is shown before and after photobleaching of the FRET acceptor (mCherry) in ImageJ Smart pseudocolor scheme (for intensity values see bars on the right). FRET is observed as an increase of donor fluorescence after acceptor photobleaching. The indicated GFP- and mCherry-tagged endocytic proteins localize at the endocytic patches on the plasma membrane of live yeast cells. The enrichment of individual endocytic patches (diameter of 50-80 nm) on the plasma membrane, caused by the latA-induced block of their subsequent invagination and/or their higher abundance at incipient buds, resulted in their apparent clustering on the diffraction-limited fluorescence images (pixel size, 178 nm). All raw acquisitions of GFP fluorescence intensities before and after photobleaching are shown
C. Fractionation and immunoblot analysis for GSDMD, Na+K+ ATPase, VDAC (Voltage-dependent anion channel), HDAC1 (Histone deacetylase 1) and GAPDH (Glycerinaldehyd-3-phosphat-Dehydrogenase) of WT macrophages infected for 10 and 20 minutes with log phase S. typhimurium (MOI=50). Fractionation was carried out as described in the Material and Methods section and equivalent amount of protein was loaded per lane.
Model showing the role of Rad9 in activating the Rad53-dependent checkpoint and preventing DNA end resection. For simplicity, the ssDNA-binding heterotrimer RPA and the obligatory Mec1 cofactor Ddc2 have been omitted from the diagram.
H Representative images of LysoTracker staining (red) and DAPI (blue) in Drosophila larval fat body in which dGcn5 is overexpressed (OE) or silenced (KD). Drosophila (cg-GAL4/+) was used as the control (Graph represents data from three independent experiments with ≥ 30 cells per condition; mean ± SEM; *p < 0.05, **p < 0.01, Student's t-test; Scale bars, 10 µm).
A and B, ChIP-qPCR assay of HDA15's (A) and NF-YC9's (B) residence at target promoters in presence or absence of TOC1 and PRR5. GFP-HDA15 and GFP-NF-YC9 driven by 35S promoter were transiently expressed in protoplasts isolated from Col-0, toc1 single and prr5 toc1 double mutant grown in SD condition. Results were normalized by % input of PIL1 coding region (PIL1 CDS). Data from at least 3 independent experiments were averaged, error bars indicate SEM. Asterisks indicate significant differences (* p<0.05, ** p<0.001, *** p<0.0001, Student's t test).
(m) Summary of the characteristics of Sμ-Sα recombination junctions. Statistical significance as evaluated by Fisher's exact test is shown. ns = not significant.
A. (Top) BrdU-sensitized U-2-OS (Flp-In T-Rex) cells stably expressing GFP-NLS-CDKL5 were treated with indicated transcription inhibitors before subjecting to spot micro-irradiation (405 nm). (Bottom) Quantitation of spot intensities. Data represent the mean ± SEM of two independent experiments; > 50 micro-irradiated cells per point. Scale bar is 10 μm
c) Lung viral RNA yields (measured using an RT-qPCR assay) expressed in virus genome copy/g of lung.
(A) Heatmap showing the altered metabolic pathways in PKM2 KO MCF7 and MDA-MB-231 cells relative to the parental cells (n=4). Fatty acid metabolism (Acyl Carnitine) and long chain fatty acid pathways were significantly changed in both cell lines.
C. Volcano plot of RNA-seq data obtained from human oocytes in control and U0126 group. 'Up' and 'Down' are the upregulated and downregulated transcripts in oocytes treated with U0126. The genes with upregulation and downregulation (abs[log2FC] ≥ 1; FDR ≤ 0.05) were labeled in red and blue, respectively.
Immunofluorescence images illustrating how palbociclib blocks the paclitaxel-induced accumulation of cleaved caspase 3+ (G) cells in the K15+ bulge and proximal bulb ORS (pbORS) compartments. CTS - connective tissue sheath; HS - hair shaft; pbORS - proximal bulb outer root sheath; wo - washout. 20 µm scale.
Left image: Fo-Fc difference density omit map (2.5σ; blue) for the region Lys389−Thr408 of Mac2 (orange) in this complex. Right image: Conformational change of this region between free Mac2 (blue; PDB entry: 2W2G, Tan et al, 2009) and Mac2 in this complex.
Inhibitory activity of EK1 on live HCoV replication for SARS-CoV-2 (a), MERS-CoV (b), HCoV-OC43 (c), HCoV-229E (d), and HCoV-NL63 (e).
(E) Proliferation curves using time-lapse analysis of cells with the IncuCyte system. Graph shows quantification of cell confluence. Two-way ANOVA analysis was used for statistical analysis. ****P≤0.0001.
F Detection range comparison in affinity measurement of NKG2D and indicated ligands between in-situ and in-solution assay. Bars in different colors are the ratios of the affinities of indicated ligands divided by that of ULBP1. Data information: In-solution affinities of proteins purified from E. coli In-solution affinities of proteins purified from mammalian cells were measured by BLI
G. Dot blot of different FLAG-DnaJ overexpression effect on extracellular tau release in HEK293T cells. Intracellular protein levels are shown with representative Western blot. DnaJ levels were detected by FLAG antibody. Data are mean ± SEM, n=3; *** p<0.001 one-way analysis of variance with Tukey's multiple comparison post-hoc analysis.
E Quantification of hair follicles (HF) with BrdU+, proliferating cells in bulge of control (Ctr), Bcl-2EOE, K15ΔNLef1 and K15ΔNLef1;Bcl-2EOE mice (n=6 biological replicates; mean ± standard deviation (SD); **** p<0.0001, multiple t-test comparisons). nd: not detected.
(A-C) Reduced immuno-reactivity of S270 phosphorylated gephyrin but not total gephyrin levels after 4-AP treatment, revealed by conventional fluorescence microscopy (KS test, p < 0.001 in B1 and p < 0.0001 in B2, p < 0.0001 in C). Total gephyrin was probed with polyclonal rabbit primary antibody (rbGPHN), and pS270 phosphorylated gephyrin with monoclonal mouse primary antibody (m7a). Number of synapses: n = 4040 in TTX and n = 3818 in 4-AP conditions from two independent experiments. Scale bar: 2 µm.
C. Knockdown of SNAP23 by siRNA inhibits DnaJC5-mediated α-synuclein release in M17 cells as shown by dot blot. Quantification of extracellular levels are mean ± SEM, n=3, **p<0.01 by one-way ANOVA with a Tukey's post-hoc analysis. DnaJC5 is detected by FLAG antibody.
Principal component analysis (PCA) of brain samples based on proteome profiles obtained by Data Independent Acquisition (DIA) quantification treated with Bortezomib or vehicle control (DMSO). n=10 per sample group. The smaller dots represent individual samples and the larger dots the centroids of each age-matched group. Ellipses represent 95% confidence intervals. The percentage of variance explained by the first two PC axes is reported in the axis titles.
F. Number of RAB13 mRNA smFISH spots plotted against the respective Polarisation Index (PI) (n=29 cells; ns: not significant; linear regression).
(c) Schematic depicting MCM-binding by Sld3 fragments. Two essential CDK phosphorylation sites are shown by vertical bars. The Sld3-Treslin Domain (S.T.D.) is shown as a black box. Also see Fig. EV1
A. Hematoxylin and eosine staining of longitudinal sections of P9 pups at the central part of the left celiac ganglion. B. Quantification of the area of celiac ganglia cross-section. Largest sections from the central part of left celiac ganglions of different individuals were chosen for the analysis. **p<0.01, one-way ANOVA followed by Tukey multiple comparison test. Data shown represents mean ± SD. C. Hyperplasia quantification in central sections of P9 left celiac ganglions shown as a percent of hyperplastic regions areas per ganglion cross-section. **p<0.01, ****p<0.0001, one-way ANOVA followed by Tukey multiple comparison test. Data shown represents mean ± SD.
isolates.BALB/c mice and Wistar rats were immunized with various doses of PiCoVacc or control (adjuvant only as the sham group) (n=10). Serums from recovered COVID19 patients (RECOV) and non-infected people (NI) act as positive and negative controls, respectively. The antibody responses were analyzed in mice (A), humans (B) and rats (C). Top: SARS-CoV-2-specific IgG response measured by ELISA
D Size-exclusion chromatography (SEC) analysis of wild-type and mutant FICD proteins (each at 20 µM). The elution times of protein standards are indicated as a reference. Note that the Leu258Asp mutation monomerises FICD, while Gly299Ser causes partial monomerisation.
F) Barplots showing mean solubility as determined through quantification of western blot bands in (E), whiskers indicate standard deviation (n=7, except for the AA construct, where n=4). Statistical significance was determined through two-way ANOVA followed by Tukey's multiple comparisons test. P-values are indicated.
Sections of K14CreER:H2B-mCherry mice at P4. Scale bar: 100 μm. (Bottom) Quantification of mCherry-positive cells (n=3).. The data from individual mice are connected by lines. Student's t-test. NS, no significance. Whole-mount imaging of K14CreER:R26R-confetti samples at P4. Scale bar: 200 μm. Sections of Lrig1CreER:H2B-mCherry mouse skin at P4. Scale bar: 100 μm. (Bottom) Quantification of mCherry-positive cells (n=3). The data from individual mice are connected by lines. *0.01 test. Whole-mount imaging of Lrig1CreER:R26R-confetti mouse samples at P4. Scale bar: 200 μm.
G Representative Masson's trichrome and wheat germ agglutinin (WGA)-FITC staining in cross-sectional LV, scale bars = 100 μm and 10 μm, respectively.
The characteristics of 5C-Oct4GFP+ cells were summarized and compared to naïve and primed PSCs in (E).
F. Evolutional conservation of domain A. Identical amino acids within black boxes.
(A-D) Effect of rad52∆, rad51∆ (A), rad57∆ (B) and rad54∆ (C) on PCNA ubiquitylation in cells synchronized in G1 and released into fresh medium in the presence of 0.025% MMS. Cell cycle progression was followed by cell sorting analysis and western blot against Clb2. Pgk1 was used as loading control. The amounts of mono- and polyubiquitylated PCNA were normalized to the total amount of PCNA. For each time point, rad mutant values were relativized to those of the wild type, taken as 1. The mean and SEM of 3 independent experiments are shown (D). An asterisk indicates a mean significantly different than 1, according to a One-sample t-test.
(C) Quantitative analysis of the number of CaSR+ and Runx2+ cells per area (mm2). n=5, Student's t-test.
Western Blot analysis of starved H2-c-fosLTR/Egfrwt OS cells, pre-treated with DMSO (1:1000), Afatinib (5µM), GSK2233470 (10µM), Rapamycin (10nM) or U0126 (10µM) for 30 minutes and stimulated with EGF (50ng/ml) as indicated