EMBO/sd-character-level-ner huggingface dataset:
miR‐290‐mediated suppression of Mbd2 induces Myc expression and glycolysisExpression of the candidates of MBD2 target genes in miR‐294‐ or siMbd2‐transfected Dgcr8−/− ESCs, compared to control group.Figure 5Expression of the candidates of MBD2 target genes in miR‐294‐ or siMbd2‐transfected Dgcr8−/− ESCs, compared to control group. Only 33 MBD2 targets upregulated greater than twofold in both miR‐294‐ and siMbd2‐transfected Dgcr8−/− ESCs were shown. Transcription factors were highlighted in red. GSEA of a gene set comprising Myc targets [from ChIP‐seq of Myc (Subramanian et al, )] in siMbd2‐ versus CTR‐transfected Dgcr8−/− ESCs. Mbd2 binding sites on Myc promoter in ESCs. Arrow denotes the position of ChIP-qPCR primers. ChIP-qPCR analysis of Myc promoter. E Promoter activity assay for Myc promoter upon Mbd2 depletion by siRNAs in Dgcr8−/−ESCs. Empty pGL3‐enhancer plasmid was used as a control. F qRT-PCR and Western blotting showing Myc expression in Dgcr8−/−ESCs infected with Mbd2 shRNAs. G Western blotting showing Myc protein expression in Dgcr8−/−ESCs stably expressing Mbd2 and further infected with miR‐290 cluster. A representative result is shown. H Glucose uptake, lactate production, and oxygen consumption rates were measured in Dgcr8−/−ESCs expressing exogenous Myc. I qRT-PCR and Western blotting showing Pkm2 and Ldha levels in Dgcr8−/−ESCs expressing exogenous Myc. J Glucose uptake and lactate production were measured in Dgcr8−/−ESCs stably expressing Myc shRNAs and further infected with miR‐290 cluster. K Western blotting showing protein levels of MYC, PKM2, and LDHA in Dgcr8−/−ESCs stably expressing Myc shRNAs and further infected with miR‐290 cluster. A representative result is shown. L Glucose uptake and lactate production were measured in Dgcr8−/−ESCs stably expressing Myc shRNAs and further infected with Mbd2 siRNAs. M Western blotting showing protein levels of MYC, PKM2, and LDHA in Dgcr8−/−ESCs stably expressing Myc shRNAs and further infected with Mbd2 siRNAs. A representative result is shown.
Phosphorylation acts as a switch for inter-organelle contacts formation Schematic representation of the two types of FFATs: (left) conventional FFATs (illustrated here with STARD11/CERT) which allow the formation of a stable complex between VAPs/MOSPD2 and thus the formation of MCSs; (right) a novel type of FFATs, that we named Phospho-FFATs (illustrated here with STARD3), which strictly depend on phosphorylation to be active.Figure 9Schematic representation of the two types of FFATs: (left) conventional FFATs (illustrated here with STARD11/CERT) which allow the formation of a stable complex between VAPs/MOSPD2 and thus the formation of MCSs; (right) a novel type of FFATs, that we named Phospho-FFATs (illustrated here with STARD3), which strictly depend on phosphorylation to be active. Thus, phosphorylation acts as a switch mechanism to turn on the interaction between VAPs/MOSPD2 and their partners possessing a Phospho-FFAT, and thus membrane contact site formation.
cac mutants show ERG defects.Fig 1A. In response to a 1 s light pulse, cac alleles lack on transients at day 3 and day 33. B. Quantification of depolarization amplitudes (top) and on amplitudes (bottom). Data are presented as means ± standard error of the mean (SEM). C. The cac alleles identified failed to complement deficiencies Df(1) ED7417 and Df(1) BSC543. The lethality was rescued by 80 kb BAC clone CH321-60D21, narrowing the candidate region down to the area in the red box. We then crossed the cac alleles to existing alleles of cac and show that they fail to complement each other. D. Schematic representation of the molecular lesions of cac alleles. E. Lethal staging of cac alleles.
Synthetic lethality between NSMCE2 and BLM in B cellsRepresentative pictures of the spleens from 2‐month‐old CD19+/Cre animals of the indicated genotypes.Figure 8Representative pictures of the spleens from 2‐month‐old CD19+/Cre animals of the indicated genotypes. Numbers of B and T cells from 2‐month‐old CD19+/Cre animals of the indicated genotypes evaluated by flow cytometry (B220: B‐cell marker; CD3: T‐cell marker). SCE events per metaphase on B cells obtained from CD19+/Cre animals of the indicated genotypes, 72 h after being stimulated in vitro with LPS. **P 0.01, ***P 0.001. Analysis of forward (FSC) and side (SSC) scatter parameters of B cells obtained from CD19+/Cre animals of the indicated genotypes, 48 h after being stimulated in vitro with LPS. The emergence of bigger cells is noticeable on cells lacking both BLM and NSMCE2. Representative images of B‐cell cultures of the indicated genotypes 48 h after being stimulated in vitro with LPS. Insets provide a magnified view of an individual cell (arrowhead) for better comparison of the observed differences in cell size. Scale bar, 100 μm. Examples of the types of nuclei found on Blm and Nsmce2 double‐mutant B cells (compared with wild‐type B cells), in cells obtained from (E). DAPI was used to stain DNA. Whereas wt nuclei are regular in size, double‐mutant cells invariably presented enlarged, multilobulated, and irregular nuclei. Scale bar, 2.5 μm.
FYCO1 redistributes Rab7- and ORP1L-decorated vesicles to the MT plus end.Figure 8.(A) Overexpressed FYCO1 is enriched in the cell periphery, close to the MT plus end. HeLa cells were imaged 48 h after transfection with mCherry-FYCO1 and GFP-tubulin. (B) Peripheral enrichment of FYCO1 is dependent on intact MTs. HeLa cells were transfected with GFP-FYCO1 and cultured in normal medium (left) or treated with 5 µM colcemid (middle) or 5 µM latrunculin A (right) for 2 h. (C) FYCO1-decorated vesicles move along the MT tracks. HeLa cells transfected with mCherry-FYCO1 and GFP-tubulin were live imaged by confocal microscopy 48 h after transfection. Movements of FYCO1-decorated structures were tracked with ImageJ MTrackJ plug-in (National Institutes of Health) and presented as 8-min-long tracks in the overlay image. (D) Full-length FYCO1 but not the FYCO1 lacking aa 555-1,136 can redistribute Rab7 and ORP1L to the cell periphery. HeLa cells were transfected with the indicated constructs and stained with DRAQ5. (E) The region of FYCO1 between aa 675 and 771 is essential for the MT plus end translocation of FYCO1-decorated structures. HeLa cells were imaged 24 h after transfection with the indicated constructs.
Figure 6A: upper panel: import of Aβ1-42 into mitochondria; lower panel: relative quantification from two independent experiments. Values of Aβ1-42 signal were normalized to HSP60 signal and the resulting value at 5 min without trypsin was arbitrarily chosen as 1. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p<0.05. B: upper panel: pulse and chase experiment to assess clearance of Aβ1-42; lower panel: quantification from three independent experiments. Values of Aβ1-42 signal were normalized to HSP60 signal and the pulse value was arbitrarily chosen as 1. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p<0.05, **p<0.01.
Figure 8The decoy antibody (ACE2-Fc) not only reduces SARS-CoV-2 infection but also decreases TNF-α secretion and ADAM-17 phosphorylation mediated by angiotensin II. Ang II: angiotensin II; ARDS: acute respiratory distress syndrome; CatB/L: cathepsin B and L; PPRs: pattern recognition receptors; AMP: amplifier; STAT3: Signal transducer and activator of transcription 3; ATIR: angiotensin II type I receptor; ADAM17: a disintegrin and metalloprotease 17; TMPRSS2: transmembrane Serine Protease 2.
Figure 4(A-B) Overexpression of Bch2 in absence of other ChAPs results in more efficient Chs5 recruitment and stabilization at the TGN. Fluorescence images of cells expressing Chs5-GFP (A) and binding kinetics of Chs5-GFP at the TGN (B) in WT, BCH2 and GPD-BCH2 strains. Bar, 5 µm. The mean of 20-30 FRAP measurements from different cells is shown. Calculated parameters are shown in Table 2. The schematic cartoons depict the predicted majority of the analyzed complexes; Chs5 dimer:violet ovals, Bch2:dark blue circles. (C-D) Overexpression of Chs6 in absence of other ChAPs results in more efficient Chs5 recruitment and stabilization at the TGN. (C) Fluorescence images of cells expressing Chs5-GFP in WT, CHS6 and GPD-CHS6 strains. Bar, 5 µm. (D) Binding kinetics of Chs5-GFP at the TGN in WT, , CHS6 and GPD-CHS6 strains. Data processing was carried out as in (A-B). The schematic cartoons depict the predicted majority of the analyzed complexes; Chs5 dimer: violet ovals, Chs6: light blue circles. (E-G) Overexpression of Chs6 rescues Chs3 export in absence of other ChAPs. (E) Fluorescence images of cells expressing Chs3-GFP in WT, CHS6 and GPD-CHS6 strains. Arrows point to Chs3-GFP signals at the bud neck. Bar, 5 µm. The inset represents a twofold magnification.(F) Quantification of phenotypes in (E); 100 small budded and 100 large budded cells were quantified per experiment. Average and SD of three independent biological experiments is shown. (G) Chs3 GFP GPD-CHS6 strain was sensitive to calcofluor to a similar extent as the WT strain. Plates were incubated at 30°C for 2-3 days. A representative drop test of three independent biological experiments is shown.
Figure 5Sagittal section of E12.5 Pdx1-Cre; Rosa26-LacZ mouse embryo counterstained for ALB (brown). X-gal staining (blue) showing cells derived from Pdx1-expressing cells. The arrowheads indicate cells co-stained with X-gal and ALB (See Fig EV5D for more images of different sections). Scale bar: 50 µm (left) or 20 µm (right).
Sir3 and Sae2 physically interact A.Figure 2A. Representative images of Sir3-mCherry and Sae2-GFP signal in WT and SIR3 overexpressing cells. Scale bars are 2 μm. B. Sir3-binding at TEL6R in untagged, WT, sir3Δ cells or in cells overexpressing Sir3 (oeSir3). Binding is probed by ChIP-qPCR 0.2 (red arrows) and 1kb (blue arrows) from telomeres and at the OGG1 control locus using antibodies against Sae2-GFP. The mean of three independent biological replicates is shown and error bars correspond to the variation between replicates (SEM). C. Co-immunoprecipitation between Sir3 and Sae2-GFP from cells overexpressing Sir3, analysed by Western blot with anti-GFP and anti-Sir3 antibodies. D. Co-immunoprecipitation between Sir3 and Sae2-GFP from WT cells using antibodies against Sae2-GFP, analysed by Western blot.
Timeline of key NCC-associated genes during differentiation.Figure 3Gene expression analysis across NCC differentiation of unaffected control ALX1165L/165L (green), heterozygous ALX1165L/165F (magenta) and homozygous ALX1165F/165F iPSC: ALX1, neural plate border specifier genes ZIC1, PAX7, PAX3, MSX1, MSX2, DLX5; neural crest specifier genes FOXD3, P75, TFAP2A, SNAI2, TWIST1; and lineage specifier gene HAND2. The RT-qPCR relative expression values were normalized to RPLP0 and GAPDH expression. Data is represented as pooled mean ± SEM of three experiments on three clones from each genotype. Exact p-values are provided in Table EV1. Data from each clone were pooled and the mathematical mean was calculated. SEM was used to determine the standard error. To test statistical significance, an ANOVA test was performed. A p-value <0.05 was considered to be statistically significant.
Figure 4A. DU145 PCa cells infected with virus expressing EV or SPOP Q165P were harvested for western blot analysis. B. MTS was performed to compare the growth between EV and Q165P DU145 cells after the treatment with indicated inhibitors (2 µM of JQ1, 2 µM of CPI-637, 2 µM NEO2734) for 72 h. All data shown are means ± SEM. The P value was calculated by the unpaired two-tailed Student's t-test; * P < 0.05, *** P < 0.001. Clonogenic survival assay was performed to determine the sensitivity of NEO2734 in SPOP Q165P DU145 cells. The survival curve showed IC50 for SPOP Q165P (0.69 µM) and EV cells (1.08 µM) (C). DU145 cells expressing lenti-EV or lenti-HA-SPOP-Q165 constructs were treated with 1 µM of NEO2734 for 4 days and cultured for another 8 days before harvest. The number of colonies with more than 50 cells was counted. Representative images of colonies are shown in (D) with quantitative data shown in (E). All data shown are means ± SEM. The P value was calculated by the unpaired two-tailed Student's t-test; * P < 0.05, ** P < 0.01. F. DU145 cells were treated with the indicated inhibitors and harvested for ChIP with BRD4 antibody. The enrichment of BRD4 at c-MYC enhancer and RAC1 promoter was analyzed using qPCR. All data shown are means ± SEM. The P value was calculated by the unpaired two-tailed Student's t-test; n.s., not significant, * P < 0.05, ** P < 0.01. G. DU145 cells were treated with the indicated inhibitors and harvested for ChIP with Ac-H3 antibody. The level of Ac-H3 at c-MYC enhancer and RAC1 promoter is analyzed using qPCR. All data shown are means ± SEM. The P value was calculated by the unpaired two-tailed Student's t-test; ** P < 0.01.
Loss of PIDDosome function reduces tumor formation in DEN-induced HCC.Figure 1(A) Male wt and PIDDosome-deficient mice were injected with 25 mg/kg DEN at the age of 15 days and their livers were analyzed 10 months later. (B) Numbers of surface tumors per liver were counted. (C) The cumulative diameter of all surface tumors per liver per mouse reflects the overall tumor load. (D) Weight of the livers including tumor mass relative to the body weight (LW/BW ratio) was recorded. (E) Representative pictures of total livers with tumors of the indicated genotypes.
Figure 7Upon ligand binding (androgen, A), the androgen receptor (AR) interacts with an androgen-response-element (ARE) in the promoter region of the RNA editing gene ADAR2, promoting its repression. This in turn increases circFNTA levels, which leads to elevated sponging of the microRNA miR-370-3p and increased expression of FNTA. High levels of FNTA activate KRAS to promote cell invasion and chemo-resistance (chemo-R).
Figure 5A) Snapshots of the velocity field generated by PIV from a representative movie. Measured velocity vectors in each point of the grid are represented in red. Data information: Scale bar = 40 µm. B) Snapshots of the computed Divergence field (expansion - red, contraction - blue) at different time points. Data information: Scale bar = 40 µm. C) HR modeled Pressure field (positive pressure - red, negative pressure - blue). D) HR modeled Power density (positive power / active contribution - red, negative power / resisting tissue - blue). Data information: Scale bar = 40 µm. E) Relative surface stress over time (positive tension / high contraction - red, negative tension / high expansion - blue). Data information: Scale bar = 40 µm.
Figure 4(a) Yolk microrheology. Mean squared displacement (MSD) of thermal fluctuations of fluorescent nanoparticles embedded in the yolk of zebrafishembryos. Solid and dashed black lines are Mean ± Standard Error computed from 99 particles. Red line is the fit of the Stokes-Einstein equation. MSD of nanoparticles embedded in the yolk exhibits a proportional dependence on time lag, Δt, consistent with a Newtonian liquid behavior with a viscosity of 129 mPa·s. A linear time dependence of MSD with similar values of yolk viscosity has been recently reported in Drosophila (He et al., 2014). Interestingly, the viscosity of the zebrafish yolk is two orders of magnitude lower than that of C. elegansembryos (Daniels et al., 2006) and of the cytoplasm of several cell types (Wirtz, 2009). (b) Viscoelasticity of the yolk cortex. Effective complex modulus (g*) measured by indenting the surface of zebrafishembryos with AFM. Red symbols are the elastic modulus (g') and yellow symbols are the viscous modulus (g''), respectively. Standard Errors are displayed. In all the measured frequencies cortex rheology is dominated by a solid-like behavior with the viscous modulus 5 times lower that the elastic modulus. No significant frequency dependence was found in the elastic (ANOVA, p = 0.123) and viscous modulus (ANOVA, p = 0.719). (c) Flow lines from snapshots of the PIV measurements (at 40, 60 and 80 % epiboly) of a two-photon video time-lapse (from Movie EV4) of a Tg (β-actin:m-GFP) embryo (top). Fitted flow lines using HR ar shown at the bottom. The relative mean square errors (RMSE) of the fitting are displayed as a percentage at the bottom left of each panel. Scale bar 100 μm. (d) Mechanical power maps over time obtained by HR of the same embryos as in (c) (from Movie EV5). The RMSE of the power is shown as a percentage at the bottom left of each panel. The mechanical work to produce doming (40 % epiboly) arises mainly at the blastoderm (left); at 60 % epiboly (middle) DCs undergo ingression (red) while the E-YSL resists constriction (blue). At 80 % epiboly (right), the active work leading to the active movement of the EVL / yolk margin mainly maps at the E-YSL (red) while the blastoderm undergoes elastic resistance (blue). White arrows point to the main observed events. Scale bar 100 μm. (e) AV (red) and CC (green) stresses and their differences (blue) normalized values in arbitrary units from the regression analysis (Movie EV6) were plotted as a function of the φ angle (0-1) along the cortex from animal to vegetal. The equator - dotted yellow line -, yolk surface - purple shadow - and the RMSE of the mechanical pressure as a percentage for each time point are displayed (40 %; 60 %; 80 % epiboly). The CC stress steeps up from animal to vegetal and the AV shows a more complex profile. Their difference changes senses around the EVL / yolk margin.
Figure 7A) log2(H/M) values for 5 synaptic proteins for which degradation rates were significantly slowed down in the presence of lactacystin. Each point represents average log2(H/M) from 3 experiments. B) log2(H/M) values for the same 5 synaptic proteins in experiments in which epoxomicin was used. Each point represents average log2(H/M) from 2 experiments. C) Average (± SEM) log2(H/M) ratios for the same 5 synaptic proteins, based on all five experiments (3 lactacystin, 2 epoxomicin). P values - two-tailed Welch's t-test, comparing the five log2(H/M) measurements at t=24 to those measured for the same proteins at t=0. D,E,F) Average (± SEM) Log2(H/M) values for three groups of synaptic proteins (synaptic vesicle, presynaptic, postsynaptic), based on all five experiments. None of the changes observed for these proteins were statistically significant. The temporal changes common to all proteins and all groups most likely represent slight imperfections in the H/M normalization process (Compare with Fig. 6E; see Results for further details). G) log2(H/M) values at t=24 hours for a group of well-studied synaptic proteins, sorted from highest to lowest. P values (two-tailed Welch's t-test) of comparisons with log2(H/M) values for the same proteins at t=0 are shown in parentheses. Proteins that exhibited statistically significant changes (P≤0.05) at t=24h are shown in red. Proteins for which (0.05 < P ≤ 0.10) at t=24h are shown in blue/red. The gray region depicts three standard deviations of log2(H/M) values at t=0 (Fig. 6F), to provide a measure of the method's sensitivity.
Single-marker association results for the combined non-Jewish and Jewish samples using the Cochran-Mantel-Haenszel (CMH) test.figf1Single-marker association results for the combined non-Jewish and Jewish samples using the Cochran-Mantel-Haenszel (CMH) test. Each chromosome is depicted as a different color. The red line indicates the threshold (P 5 × 10−5) selected to define regions for evaluation in the replication studies. The P value thresholds for suggestive and significant associations are 3.28 × 10−6 and 1.64 × 10−7, respectively, based on a Bonferroni correction for multiple testing. A modest correction factor (λ = 1.056) is necessary to correct for stratification between cases and controls, but it does not modify the current results.
Figure 4A Representative immunoblots of the expression of PGC1-1α in DC cells treated with vehicle or 3 mM NR. Quantification of the indicated proteins is from three immunoblots. B-D Cellular and mitochondrial ROS in DC and age-matched healthy control cells supplemented with vehicle and NR were measured by flow cytometry from three replicates. Cellular and mitochondrial ROS in DC and age-matched healthy control cells in the scramble and CD38 knockdown DC cells (D) were measured by flow cytometry from three replicates. E Representative images captured by transmission electron microscopy of DC1 cells treated with vehicle or NR. White arrows: mitochondria. Yellow arrow: autophagosome-like structures with engulfed mitochondria. Enlarged image within white frame is shown. F-H Quantifications of percentage of damaged mitochondria per cell (F), mitochondrial length (G), and mitochondrial diameter (H). A minimum of 200 mitochondria counted per group.
Fig.Figure 6(A) Molecular docking of S1P with rabbit NOD2. (B) SDS-PAGE analysis of purified NOD1-GFP and NOD2-GFP. (C) Microscale thermophoresis (MST) analysis of direct binding of S1P to NOD1, NOD2, NLRP3 or GFP. (D) MST analysis of direct binding of NOD1 to S1P and iE-DAP. (E) MST analysis of direct binding of NOD2 with S1P and MDP. (F) ELISA analysis of IL8 in supernatants of HEK293T NOD1/2 KO cells transfected with indicated NOD1 or NOD2 mutants. After 24 h transfection, cells were stimulated with S1P (20 µM), iE-DAP (20 µM) or MDP (20 µM) together with digitonin for 20 h. (G) with iE-DAP or MDP in the presence of S1P (2 µM). NOD2 (H) with iE-DAP or MDP in the presence of S1P (2 µM).
Figure 2A: cell growth in glucose (GLU) and galactose (GAL). C29V, C47V, TpLV: immortalized fibroblast cell lines from control individuals; PITRM1V: immortalized fibroblasts from subject II-2, carrying the PITRM1R183Q mutation. pLKO.1: empty vector; sh38: shRNA38; sh41: shRNA41. Each cell line was measured six times. Error bars indicate ±SD. Statistic analysis was by two-way ANOVA post-hoc Bonferroni test ***p<0.001. B: Western-blot analysis of PITRM1 in C29V cells transduced with the empty vector plKO.1 and the two shRNA, sh38 and sh41. SDHB and b-Actin are used as loading controls. C: co-localization of PITRM1 (red) with TOM20 (T20, green) in human fibroblast cells from a control (CTR) and subject II-2. Note that the intensity of PITRM1 immunofluorescence is much lower in II-2 cells than in CTR cells (see main text for further details). Nuclei are stained in blue by DAPI. A white bar corresponds to 10 µM. D: mitochondrial membrane potential (ΔP). In healthy cells with high mitochondrial ΔP, JC-1 forms complexes known as J-aggregates that show an intense red fluorescence. On the contrary in unhealthy cells with low ΔP, JC-1 remains in the monomeric form, showing only green fluorescence. Values are referred to as % of those of the control means, taken as 100%. The results are the mean of 3 independent experiments. Error bars indicate ±SD. Statistic analysis was by two-way ANOVA **p <0.01; ****p<0.0001.
Figure 2A-B. Amino acid sequences of toxin S-subunits depicting (A) Mut1 (∆112-117) and (B) Mut2 (∆130-134) domains, based on ClustalW alignment. C. Viability of primary human PMNs following incubation with mutant toxin pairings using the viability dye CellTiter. Bars indicate Mean ± SEM, with n = 3 donors. D-F. Viability of primary humanPMNs following incubation with WT or mutant toxin pairings. Insert: 2 μg per lane of purified recombinant toxins visualized by Coomassie blue staining using a 12% SDS-PAGE gel. Amut1 = HlgAmut1, Bmut = HlgBmut, Cmut1 = HlgCmut1, Smut1 = LukS-PVmut1, Fmut = LukF-PVmut. Bars indicate Mean ± SEM, with n = 4 donors (D), n = 4 donors (E), and n = 5 donors (F).