EMBO/sd-character-level-ner huggingface dataset:
A Cardiac function evaluated by echocardiography in mdx/CD38-/- mice: the dot plots show the left ventricular (LV) diastolic (A1) and systolic (A2) inner diameters and LV ejection (A3) fraction in 7-month-old WT (n=5), mdx (n=6) and mdx/CD38-/- (n=10) mice. Data information: : Each dot of the graphs represents a mouse. in duplicate After normality and variance comparison tests, significance was assessed using:A1 ANOVA followed by Fisher's LSD test; A2,A3 Kruskal-Wallis followed by Dunn's test; Values are expressed as means ± SEM. Significance: *p<0.05, **p<0.01, ***p<0.001.
(A) Intracellular detection of NOD2 (bold line in the histogram plot) was performed by flow cytometry using freshly isolated alveolar macrophages selected from a gate set on large granular bronchoalveolar cells (R1, dot plot). One representative experiment out of three experiments is presented.
PCA plot of single-cell transcriptomes from the indicated cells (left). Each dot represents a single-cell. All cells are classified into three groups (right). The two panels represent the same PCA coordinates.
C Food intake in 15-week-old male control and ad-FADDmice fed a HFD (n = 8 for each genotype).
(A) 786-0 cells expressing shGDH1 with restored expression of WT or ED GDH1 were supplemented with or without 500 μM methylated αKG for 48 hours, and then the cells were collected to extract total protein. WB was performed using the indicated antibodies.
Facial phenotypes of patient A at 3.5 years of age, showing coarse facial features, broad ear lobes, macroglossia and hypertrichosis.
(D) ATG16L1 knock-out HCT116 transfected with the indicated GST HA ATG16L1 were infected with Salmonella for 1 hour. Bacteria were stained using anti-LPS antibodies to analyze localization in addition to the autophagy marker LC3B. Representative immunofluorescent images of LC3B and LPS are shown (scale bars, 5μm and 1 μm). Quantification of bacteria undergoing autophagic clearance from 7 fields of view from a representative experiment is shown in the lower panel. Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test.
D) Southern blot of wild-type and spc110S36-91D mutant bearing the inter-chromosomal gene conversion assay depicted. Mid-log phase cells were HO-induced at 32ºC by adding galactose to the media. Samples were collected at different time-points and the genomic DNA was extracted. Preps were digested with EcoRI and analysed by Southern blot. Blots were hybridized with MATa-only and actin probes. Graphs show quantification of gene conversion, DSB induction and crossover vs non-crossover ratio. All data were normalized using the actin signal. Graphs represent the mean ± S.D. from three independent experiments. P values were calculated using a 2-tailed unpaired Student t test. Asterisk denotes an overexposed film to visualize the formation of crossover products.
B. Schematic of the genetically modified PARK15 gene locus located on chromosome 22.
(e) Western blot of cell lysates from stable inducible PC12 cells transfected with wild-type (Gln23; Q23) or mutant (Gln74; Q74) huntingtin shows that cells expressing mutant huntingtin had 31% (± 4.3% s.e.) less phosphorylated S6K1 (top) relative to total S6K1 (bottom) than cells expressing wild-type huntingtin. (f) Similarly, cells expressing mutant (Gln74; Q74) huntingtin had 30% (± 4.5% s.d.) less phosphorylated 4E-BP1 (top) relative to total 4E-BP1 (bottom) than cells expressing wild-type (Gln23; Q23) huntingtin. Expression of wild-type and mutant huntingtin was induced for 48 h (e,f). (g) Cells expressing mutant (Gln74; Q74) huntingtin also had lower levels of phosphorylated forms of transiently transfected FLAG-tagged 4E-BP1 than cells expressing wild-type (Gln23; Q23) huntingtin. The multiple bands in 4E-BP1 (f,g) are due to its different phosphorylated species.
(b) ELISA of anti-pneumovax IgG3 titers in serum 14 d after injection as in a. Results are presented as absorbance (A). *P 0.05, **P 0.01 and ***P 0.001 (Student's t-test).
HeLa cells were transiently transfected with N-terminally HA-tagged PLN (HA-PLN) and inactive (D/A) SPPL2c-myc The expressed proteins were visualised by indirect immunofluorescence via their HA and Myc epitopes.
L) Representative image of Mitotracker Red FM in CD25+/CD54+ NK cells and CD25-/CD54- NK cells. Scale bar: 20 μm.
F. Effect of ascorbate (Asc, 0.5 mM) on phosphatase inhibition in tunicamycin-treated H9c2 cells with overexpression or knockdown of Nox4 (Ad.Nox4 and Ad.shNox4, respectively). In control cells, ascorbate enhanced tunicamycin-stimulated increases in phosphatase activity. Phosphatase activity was lower in Nox4-overexpressing than control cells but was normalized by ascorbate to the same level as in control cells. In Nox4 knockdown cells, tunicamycin-induced increases in phosphatase activity were enhanced and ascorbate had minimal additional effect.
The ratio of translation between the TLS and CDS is calculated and compared between 1-to-1 homologs in the same tissue type across species.uORF activity is correlated across species. Scatterplots display the translation ratio comparison between the same transcripts (TLS length > 100nt, 1-1 mouse-human homology) in fibroblasts (BJF cells in human - sample bjf2, MEF cells in mouse - sample mef2wt) (B) and brain (samples hbrainwt and brainwt) (D). The correlation between species is not due to CDS signal correlation - scatterplots (C,E) display the translation ratio comparison between homologous transcripts (TLS length > 100nt, 1-1 mouse-human homology) in fibroblasts (B) and brain (D), maintaining CDS pairings while shuffling which TLS is associated with each CDS.
(D,E) Quantification of normalized MA currents in responding large DRG neurons (D, n=5) versus non-responding DRG neurons (E, n=3) before (black) and after (red) application of sumatriptan 10 µM to activate the Gi-coupled Htr1d receptors. *P<0.05, Repeated measures ANOVA with student's t-test no corrections. Data are shown as mean ± SEM.
Immunoblot analysis of ADAR1 p110, ADAR1 p150 and ADAR2 expression in various organs isolated from wild-type (WT) mice. The expression of GAPDH is shown as a reference.
The S values measured at standard conditions (30°C) indicate that, depending on the media composition (+Ura, -Ura, +5FOA), the formation of protein deposits can be neutral, deleterious or even advantageous for the cell as the function becomes non-essential, essential or toxic, respectively.
B - E Quantification of total axon length (WT, n = 13 neurons; Yme1l-/-, n = 13 neurons), total dendritic length (WT, n = 12 neurons; Yme1l-/-, n = 13 neurons), axonal branch points (WT, n = 12 neurons; Yme1l-/-, n = 13 neurons) and number of dendrites (WT, n = 12 neurons; Yme1l-/-, n = 13 neurons). Individual neurons originate from two independent preparations. Unpaired t-test, ns = not significant, *P ≤ 0.05.
Flow cytometric analysis of cells treated with TQS for 4 hours and stained with Annexin V (D) Data are means ± SEM of three independent experiments. *P<0.1, ****P<0.0001 (ANOVA).
HeLa cells were transfected with the indicated siRNAs (two control/non-targeting siRNAs and two PRMT1-specific siRNAs) and irradiated at 150 J/cm2 UVC or not irradiated. After 24 hours, the cellular distribution of endogenous p14ARF was determined by immunofluorescence (IF) staining using α-p14ARF antibody (red, endogenous p14ARF) and in the merge additionally DAPI (blue, nuclei/DNA). Representative IF results are shown for two conditions (siControl_4 and siPRMT1_1) in (A), with asterisks indicating exclusively nucleolar and arrowheads indicating not-exclusively nucleolar but additionally or predominantly nucleo-/cytoplasmic p14ARF localization. Scale bars: 15 μm. The subcellular distribution of p14ARF, as determined by IF, was quantified by cell counting (percentage of cells) for all conditions (B).
A Generation of two target site blocker (TSB) locked nucleic acid sequences: TSB1 and TSB2 (in blue), for the disruption of the miR-34a/Pdgfra interaction, indicating binding sites in the Pdgfra 3′-UTR, Kit 3′-UTR, and the Sirt1 3′-UTR (in black), alongside the miR-34a sequence (in red). The miR-34a seed sequence, and the seed-sequence binding site in the target mRNA 3′-UTR are indicated in bold, and brown, respectively.
H, I. Quantification of cilium disassembly and centrosomal AURKA levels after serum stimulation. RPE1 cells were transfected with control or PCM1 siRNA#1 for 48 h, serum starved for 24 h and treated with DMSO or 0.5 μM MLN8237 in serum stimulation medium for 2 h and 24 h. Cells were fixed and immunostained with antibodies against acetylated tubulin and gamma tubulin, and percentage of ciliated cells were quantified. x-axis indicates the hours after serum stimulation. (H) n>100 cells per experiment. Data represent mean value from three experiments per condition ± SEM. (I) n>95 cells per experiment. Data represent mean value from three experiments per condition ± SEM (***p < 0.001; ****p < 0.0001, Unpaired Student's t-test).
(s) Increase in bath [Ca2+](Rfura2) and [Ca2+]m (Ripcam) signals in response to CaCl2 (1 μM) and InsP3 (IP3, 7.5 μM) addition in permeabilized cells. Uncropped images of blots/gels are shown in Supplementary Fig. S6.
(A) Levels of KRAS, COUP-TFII, LDHA, and phosphorylated S6K (T389) in KRAS-silenced HCT116 and DLD-1 cells.
A HumanRPE‐1 cells stably expressing low levels of mannosidase II‐mApple were transfected with a TFG siRNA for 60 h. Cells were subsequently treated with brefeldin A (BFA) for 1 h, followed by a wash into fresh media and further incubation for 2 h in the absence of BFA, prior to fixation. Images shown are projections of 3D data sets (4 μm in z). Merged images with Sec31A in green and ManII in red are shown (representative of at least 15 cells analyzed). Scale bar, 5 μm.
(D) E14.5 cortices stained with antibodies against Ki67 (red) and phosphorylated-Histone H3 (PH3, yellow). Insets showing zoomed in view of cells in the VZ and SVZ. Scale bar = 100 μm.
I - L Western blots of in vitro kinase assays showing loss of phosphorylation in phosphomutants ARHGEF2 S122A (I Substrate levels are shown by coommassie staining underneath
A Cell culture timing schedule. Data information: S (standard medium), SF (serum free medium), q (queuine), Q (queuosine), G (guanine).
H. Representative immunoblot with anti-CerS2 antibody to determine CerS2 protein levels in shCtrl and ShCerS2-transduced 2B4 cells as in G. Filters were rehybridized with β-actin as loading control.
(I) A representative image from immunofluorescence analysis performed with anti-GFP and anti-Tbr1 antibody that shows retention of GFP positive cells below the Tbr1 layer in Tsc22d1 knockdown brain as compared to the control brain. The bar plot on the right side shows quantification of migrated GFP positive cells in control and Tsc22d1 depleted mouse brain with respect to the Tbr1 staining. y axis represent percentage of cells above or below the Tbr1 stain region. Error bars represent SEM from 3 independent biological replicates. * p<0.05, ** p<0.01, *** p< 0.001, Student's t-test.
A, B. Representative images and quantification of basal body levels of (A) AURKA and (B) phospho-AURKA (p-AURKA) in control and PCM1-depleted cells. RPE1 cells were transfected with control or PCM1 siRNA #1 or siRNA #2 for 48 h. Following 24 h serum starvation, cells were fixed and stained with the indicated antibodies. Centrosomal AURKA and p-AURKA fluorescence intensities were measured from maximum projections, and average means of the levels in control cells were normalized to 1. n>500 cells per experiment. Data for (A) AURKA and (B) p-AURKA represent mean value from three experiments per condition ± SEM (****p < 0.0001, Unpaired Student's t-test.) Scale bar, 10 μm
H Representative western blot showing RNF168, Flag-tagged H2AX (H2AX-FLAG) and endogenous H2AX (H2AX) protein levels from whole cell extracts in wt and junD-/- fibroblasts. Cells were first co-transfected with vectors encoding HA-tagged ubiquitin and Flag-tagged wild-type H2AX (WT), or K13-, K15-, K119-, or 9K-H2AX mutants. Flag-tagged H2AX proteins were next immunoprecipitated with Flag-specific antibody and incubated either with RNF168-specific antibody (Up) or H2AX-specific antibody (Down).
(D) Scatter plot generated from the analysis of the logarithmic heavy (H) to light (L) ratios in the x-axis and the reverse in the y-axis, in the two reciprocal labeling SILAC experiments (1 and 2) and anti-HA immunopurification of ∆4-CYB and WT cells expressing UQCR10HA.
A. Triplicate normalized fitness functions (*) for E. coli BW25113 strains harboring plasmid copies of tet(B)WT, tet(B)K183E,A290V,T326I (variant 6) and tet(B)F151I,F179L,T326A (variant 7) in TET and their corresponding least squares model fits (solid line) where both variants display decreased fitness in TET compared to WT.
C Enriched Gene Ontology (GO) of DEG in RNAi-ASCO1 seedlings as compared to WT, x-axis represent the -log10 FDR for the enrichment of each GO category over genome frequency.
(F) HEK293 cells overexpressing indicated constructs were treated and analysed as described in (D), with pRab10 analysed in the upper panel, and pRab8a in the lower panel.
C-terminus of IRF2BP2 interacted with VGLL4 by co-immunoprecipitation assay in HEK293T cells
D, Quantification of ER membrane length, plasma membrane length and ER/plasma membrane ratio using the EM pictures from C. Data information: Data are presented as mean values +/- SD. Statistical analysis: Unpaired t-test. Data reproducibility: n = 20 cells/condition.
(E) Loading of hsa-miR-let-7a, CoV2-miR-O7a.1 and COV2-miR-O7a.2 into AGOs as measured by stem-loop RT-qPCR and analyzed as a percentage of input from the immunoprecipitates (IPs) of either pan-AGO IP or control IgG IP from infected A549-ACE2 cells. Levels of miRNA were normalized for the percentage of infected cells.
B). RIF1 association with the Xist promoter assessed by ChIP-qPCR in two independent Rif1+/+ (Rif1+/+ +OHT, black) and two Rif1-/- (Rif1F/F +OHT, grey) female cell lines, at 2 days of EB differentiation (B). P1 and P2 indicate the two Xist promoters, 5' indicates a region 2 kb upstream of Xist TSS. Inter1 and 2 are two intergenic regions that serve as negative controls. Peak and cRAD represent two previously identified regions of RIF1 association (positive control). See Appendix Fig. S2C for primer positions within Xist. Mean ±standard deviation from 3 independent experiments (A) and 2 independent experiments (B). p calculated by Student's two-tailed, paired t test comparing RIF1 association in Rif1+/+ cells on Xist P2 and P1 versus 5'. *p ≤ 0.05, ****p ≤ 0.0001 and ns=not significant.
A LNCaP cells were implanted subcutaneously into nu/nu mice. Once tumors reached 5 mm in size, mice (n = 5 per group) were given nanoliposome-encapsulated control siRNA or STAMP2 siRNA as described in Materials and Methods. Tumor volumes were measured at the indicated time points. *P = 0.001.
G. v-WAT amounts of triacylglycerides (TAGs) and diacylglycerides (DAGs) (wt, n= 8; LowOXPHOS, n= 8). Data information: Bars are the mean ± s.e.m. of the indicated (n) mice/genotype. *p <0.05 when compared to wt by Student's t-test.
(b) Colocalization of GFP-LC3 dots and wild-type L. monocytogenes in S2 cells, quantified by confocal microscopy.
E Strains that lack HXT2 grow slower when coming from quiescence compared to WT.
(D) Data collected from the fluorometric measurements were analyzed as detailed in Materials and methods.
(D) Serum anti-C-peptide-immunoglobulins (coating: C-peptide) titers of mice immunized with cCP (n=9 for d14 and d28; n=5 for d49) and (G) anti-insulin-immunoglobulins (coating: Insulin) titers of mice immunized with complex native insulin (cInsulin, n=5) and control-immunized (CI: CpG only, n=3) measured by ELISA at indicated days. Dots represent individual mice. Mean ± SD, statistical significance was calculated by using Mann-Whitney-U test. (E, H) ELISpot assays showing CP-specific IgG (n=4 mice/group) (E) and insulin-specific IgG (n=3 mice/group) (H) producing splenocytes at day 14. Top lane showing representative images of wells. Mean ± SD, statistical significance was calculated by using Mann-Whitney-U test, *P < 0.05, **P < 0.01. : Schematic illustration of native insulin (cInsulin) and full length C-peptide (cCP) tetrameric polyvalent complexes.
(A) Immunofluorescent images of the mouse tibialis anterior muscle on the indicated days after CTX treatment. The images of anti-mouse ChIL probe for PolII-S5P (red) and anti-rabbit IgG for laminin (green) are shown. Scale bar: 20 µm.
(E) Representative images of hematoxylin and eosin-stained slides of lung metastatic nodules of MGC80-3 and HGC-27 with or without knockout of lncPSCA. Scale bar = 100 μm.
H&E staining of the liver, BAT and ingWAT from AAV-NC or AAV-ShQKI mice. (Scale bar represents 50 μm).
(A-B) CTLs exhibit distinct capacities to trigger calcium responses in contacted tumor cells. Mice with established B cell lymphoma expressing OVA and the Twitch-2B calcium indicator were adoptively transferred with GFP-expressing OT-I CTLs. Intravital imaging of the bone marrow was performed two days after T cell transfer. (A) Left. Two-photon time-lapse image and corresponding scheme showing representative CTLs triggering either limited (upper images) or numerous (lower images) calcium signals in 5 contacted targets. Red arrows mark tumor cells with elevated calcium. Scale bar, 5 µm. Right. The periods of contact for the indicated targets are shown as white boxes and periods of calcium elevation are shown in magenta. (B) Total number of distinct calcium fluxes triggered by individual CTLs in all contacted tumor cells during an imaging period of one hour. For a rigorous comparison, only CTLs which activity could be monitored for at least 1 h were included in the analysis. Data are representative of 4 independent experiments.
CTLs exhibit extensive differences in lytic activity in vivo. Mice with established B cell lymphoma expressing OVA and the caspase 3 reporter were adoptively transferred with LifeAct-GFP-expressing OT-I CTLs. Intravital imaging of the bone marrow was performed two days after T cell transfer. The frequency of CTLs engaged in lytic activity (induction of apoptosis in at least one contacted tumor cell) is shown (C) together with the frequency of lytic contacts within all CTL-tumor cell contacts recorded (D).
A. Immunofluorescence images of ICSI, SCNT-tdTomato+ and SCNT-tdTomato- embryos. Embryos approximately 26hr after activation were fixed and processed for immunostaining with antibodies to H3K27me3 and Gag protein. ICSI embryos produced by MERVL::tdTomato sperm from the littermates of male mice. The images are representative examples of the quantification shown in Fig 3B. Representative images from ≥ 128 embryos analyzed in five independent micromanipulations are shown. Scale bar, 20 μm. B. Percentage of 2-cell ICSI and SCNT embryos with strong H3K27me3 staining and moderate staining (left). Numbers of the total embryos analyzed from five independent micromanipulations are shown in the bars. Boxplots (right) for relative intensities of H3K27me3 from five independent experiments for each expression as in Fig 3A. Error bars, s.e.m., ***P < 0.001 by two-tailed Student"s  t
E Scatter plot of normalized transcript (mRNA) levels and antisense, 21nt siRNA levels for all TE families. Transposons generating somatic insertions are highlighted in red (LTR-elements) or blue (LINE-like), with a symbol size reflecting the somatic insertion counts.
B qRT-PCR analysis of Athila6A gag/pol steady‐state mRNA transcript levels in inflorescence and leaf tissue.
H. Immunoblot analysis of siRNA-treated HeLa cells that were exposed to indicated genotoxic agents and collected 1 h later.
Schematics illustrate the fly accessory glands and associated secondary cells, highlighting their acidic and non-acidic exosome-forming compartments. First panel shows male fruit fly and its accessory glands. Boxed region is enlarged in second panel, revealing secondary cells (SCs; black dots), with red line indicating the plane of section through the AG lumen, which is used to generate the transverse view through a SC and surrounding main cells within the epithelial layer in the third panel. The unusually large, acidic late endosomes and lysosomes (Rab7-positive; magenta) and non-acidic compartments, characteristic of SCs, which we demonstrate here contain intraluminal vesicles (ILVs; some of which are Rab11-positive; yellow), are labelled. The red line in the third panel shows the basal SC plane of section in the fourth panel and images in this figure.
(c) Single confocal sections from the Z-stack in figure 4B. Orange arrows show close LAMP1/Rab34 association.
B The expression of GA2-OX6 and GA20-OX1 in expanding leaf tissue (third leaf - 15 DAS), 8 h after transfer to DEX-containing medium to induce overexpression. The FC was calculated relative to control conditions.Data information: In B, data are presented as mean ± SEM, n = 3 independent experiments, * = FDR < 0.1 (mixed model analysis, user-defined Wald tests).
F The cellular ROS (superoxide) levels were determined (n=4) by DHE staining of NE4C cells treated with various HTL concentrations for 4 h. The ROS levels were normalized to those of untreated NE4C cells.
C57BL/6 mice received vehicle or LicoB (40 mg/kg) for 17 consecutive doses, once every two days for 34 days. Following that treatment, the serum levels were measured, along with the body weight (K) (n=8 mice per group).
Modulation of Rb protein in sh-TFEB ECs. Immunoblots of total lysates from scr-shRNA and sh-TFEB ECs probed with phospho-Rb and total Rb Abs. The bar graph shows the densitometric analysis of the immunoblotting expressed as % of sh-TFEB vs scr-shRNA and the ratio between phospho-Rb and total Rb in the different conditions
(E) Substitution of the STI-II sequence of UBQLN4 with that of UBQLN1 (designated as the 4-STI-II-1 mutant protein) abolished its high affinity to the IL-2Rα ΔSS client protein.
(H) Quantification of the phenotype in G. As individual vesicles could not be counted, quantification was done as the percentage of transfected cells showing redistributed GFP-LC3. At least 10 different fields were counted (about 400 cells). The experiment was repeated three times. Data are expressed as means ±s.d. of the triplicates.Source data for this figure is available on the online supplementary information page.
Heat map showing differential expression of significant TGF-β regulated genes in MoDC, MoLC and TGF-β-treated-MoDC of independent experiments from three donors (n=3). Fold change normalization to autologous MoDC was done on Log2-transformed normalized FPKM data and represented by Heat map. Row clusterization was applied based on (Log2) Fold Change values. Green and red shades correspond to increased or decreased gene expression levels respectively.
(B) Confocal microscopy of HeLa-Kyoto cells lipofected for 24 hrs with cDNAs encoding for GFP-DYRK3 and either an empty vector or mCherry-Hsp90 α and β. The upper panel shows endogenous Hsp90, stained with a specific antibody for total Hsp90; the lower panel shows exogenous mCherry-Hsp90 α and β. Scale bar is 10 µm.
D Sister chromatid exchange (SCE) events found per metaphase on Nsmce2+/+ and Nsmce2+/GT MEFs. ***P 0.001.
(C) Microglia isolated from wild type mouse pups were pre-incubated in full medium or starvation medium HBSS before addition of a pro-inflammatory stimulus (LPS followed by ATP). The autophagy blocker 3-MA was added for the final 1 h 45 min of the experiment. The concentration of the pro-inflammatory cytokine IL-1beta in the cell supernatant was determined by ELISA. Incubation with HBSS reduced IL-1beta release significantly while 3-MA treatment increased it; mean ± SEM, full medium n = 6, full medium LPS/ATP n = 6, full medium LPS/ATP + 3MA n = 3, HBSS n = 6, HBSS LPS/ATP n = 6, HBSS LPS/ATP + 3MA n = 6; two-tailed t-test *: p < 0.05; **: p < 0.01.
Principal components analysis of transcriptional profile similarity for individual and hybrid lysates with different mixing ratios for (b) E. coli + B. subtilis