EMBO/sd-character-level-ner huggingface dataset:
Fig.Figure 7A-H. (A) Experimental design for the mouse model in Fig. 7A-H. p53+/+ and p53-/- C57BL/6N male mice (p53+/+ mice n=8;p53-/- mice n=6) were fed with HFD diet for 10 weeks and were administered PBS or terbinafine (80mg/kg) every day for 8 weeks. (B) Mice body weight of p53 +/+ (left) and p53-/- (right) mice. (C) Representative liver photos of mice (left), changes in liver weight (right), H＆E staining (D) and Oil-Red staining (E) of liver tissues are shown respectively. Total liver cholesterol concentrations (F) and triglyceride levels (G) of each group were examined. (H) SQLE mRNA expression of mice liver tissues by qRT-PCR. (I) Experimental design for the mouse model in Fig. 7I-O. p53-/- C57BL/6N male mice (n=7) were injected with a single dose of diethylnitrosamine (DEN) (25mg/kg) at two weeks and then fed with HFD diet at 4 weeks. Oral administration of terbinafine were given at 13 weeks old as indicated. Body weight (J) of mice are shown. p53-/- C57BL/6N male mice (n=7) were injected with a single dose of diethylnitrosamine (DEN) (25mg/kg) at two weeks and then fed with HFD diet at 4 weeks. Oral administration of terbinafine were given at 13 weeks old as indicated. liver/body weight ratio (K) of mice are shown. p53-/- C57BL/6N male mice (n=7) were injected with a single dose of diethylnitrosamine (DEN) (25mg/kg) at two weeks and then fed with HFD diet at 4 weeks. Oral administration of terbinafine were given at 13 weeks old as indicated. Shown are liver tumor incidence (L) and tumor numbers (M). (N) H&E (left), Ki-67 (middle) and Oil Red O (right) staining of livers of mice. (O) Total liver cholesterol concentrations of mice were examined.
Figure 11(A) Accumulation of autophagosomes and lysosomes in the spinal cord sections from a 5-month-old Tmem106b-/-Grn-/- mouse as shown by transmission electron microscope analysis. Scale bar = 1µm. Arrows: autophagosome; arrow heads: lysosomes; (a): axon. (B) Accumulation of myelin debris and amorphous inclusions in the microglia in the spinal cord sections from a 5-month-old Tmem106b-/-Grn-/- mouse as shown by transmission electron microscope analysis. Scale bar = 1µm. Arrows: myelin debris; arrow heads: dark amorphous inclusions; (m): microglia. (C) Western blot analysis of LC3-I and LC3-II in the spinal cord lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ****, p<0.0001. (D Immunostaining of TFE3 and IBA1 in the spinal cord sections from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. E) Immunostaining of TFE3 and IBA1 in the spinal cord sections from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. Nuclear signals of TFE3 in IBA1 positive microglia were quantified. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p<0.001, ****, p<0.0001. Scale bar = 10 µm.
Figure 1Model 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. rad9Δ cells fail to activate the Rad53 checkpoint in the presence of either the DNA alkylating drug MMS (0.02%) or the radiomimetic drug phleomycin (40μg/mL). Quantitative phosphoproteomics dataset showing phosphorylation sites enriched in cells lacking RAD9. Among the most highly enriched sites are Sgs1 T1269, Uls1 T540, Mec1 S1964, and 2 S-N sites in Rfa2. This response is similar in both the presence of 40μg/mL phleomycin (x axis) and 0.02% MMS (y axis). Note downregulation of Rad53 signaling (red dots) due to absence of RAD9. Pie chart showing that S/T-Q phosphorylation comprises a large fraction of rad9Δ-induced phosphorylation (71%), though only accounting for a small fraction (5%) of the entire dataset. Quantitative phosphoproteomics dataset showing that most phosphorylation events induced in rad9Δ cells are dependent on Mec1. These phosphoproteomic analyses were conducted in the presence of 0.02% MMS for 2 hours. Model depicting Mec1-dependent phosphorylation of Sgs1, Uls1, and Rfa2 in response to hyper-resection in rad9Δ cells.
Figure 5Pseudo-coloured scanning electron micrographs of individual outer and inner hair cell bundles from clarinet mice at P8 and P16, showing that gross morphology of OHC and IHC bundles is similar between Clrn2+/+ and Clrn2clarinet/clarinet mice. Representative images from the mid region of the cochlear spiral are shown and close-up views illustrate the three full rows, tallest (red), middle (blue) and short (yellow), of stereocilia in IHC and OHC hair bundles. At P8 and P16 (upper panels in A and B), the three stereocilia rows are observed in Clrn2clarinet/clarinet OHCs (A) and IHCs (B), although the shortest and middle row of IHC stereocilia appear less prolate compared to controls. (C,D) Distribution of individual stereocilia measures across genotypes at P8 and P16. The OHC stereocilia measurements at both P8 and P16 (C) show a significant difference in height of Clrn2+/+ stereocilia compared to Clrn2clarinet/clarinet in: e.g. for the shortest row at P8: Clrn2+/+: 0.6188 ± 0.0944 p.µm (n=27); Clrn2clarinet/clarinet: 0.2948 ± 0.1029 p.µm (n=27) (p<0.0001, Mann-Whitney ranks comparison), and at P16: Clrn2+/+: 0.579 ± 0.06179 p.µm (n=27); Clrn2clarinet/clarinet: 0.07282 ± 0.1626 p.µm (n=27) (p<0.0001, Mann-Whitney ranks comparison). Note the amount of value points equal to zero at P16. (D) Conversely, IHC stereocilia measurements at P8 and P16 did not show a difference between Clrn2+t/+ and Clrn2clarinet/clarinet in: for the shortest row at P8: Clrn2+/+: 0.8808 ± 0.1753 p.µm (n=27); Clrn2clarinet/clarinet: 0.9313 ± 0.1217 p.µm (n=27) (p=0.2244, unpaired t-test); and at P16: Clrn2+/+: 0.6784 ± 0.1171 p.µm (n=23); Clrn2clarinet/clarinet: 0.6063 ± 0.1855 p.µm (n=26) (p=0.2436, Mann-Whitney ranks comparison). Sensory hair cell bundle patterning and measurements in clarinet mice Pseudo-coloured scanning electron micrographs of individual OHC (left panels) and IHC (right panels) hair bundles from clarinet mice at P28. Clrn2clarinet/clarinet mutants have only two rows of OHC stereocilia, and the middle row of stereocilia is less uniform in height compared to controls. The middle and short rows of stereocilia in Clrn2clarinet/clarinet IHC bundles appear fewer in number, and heterogeneous in height. Scale - 2 µm.
Figure 3Cell size during starvation. Length and width of the cells are measured with phase-contrast microscopy and the volume is computed considering cell shape as a cylinder with two semi-spheres, as described in the graphical synopsis at the top (see also Table EV3 and Methods). Each measurement is an average of 200 cells. (A) Measured length and width of wild type cells starved in batch cultures and previously grown in the chemostat at different steady-state growth rates and of GlpK22 cells starved and previously grown in batch culture at μ = 0.9 h − 1 (see upper color legend). Note that, as shown in Schink et al. (2019), cell widths do not change from steady state growth to starvation, while lengths decrease. Both length and width increase exponentially with growth rate. (B) Starvation volume of the cells described in panel A, computed as explained in the graphical synopsis (see also Methods). In agreement with literature (Schaechter et al., 1958), it increases exponentially with growth rate (black line). Recycling yield and maintenance rate per cell volume. (C) Recycling yields and (D) maintenance rate measured as described in Fig. 2 are normalized per cell volume and plotted versus the previous growth rate of the cultures they refer to (see color legend at the top and Table EV3). The normalized yield is constant within the uncertainty. Maintenance rate increases significantly with a slope of (0.99±0.55) h, matching the increase of the death rate, (1.1±0.4) h, shown in Fig 2B. Solid black lines show linear fits on log transformed data, using weighted least square fits.
Figure 2(a) 20x snapshot of an ex-vivo slice culture of E10.5 spinal cord from Venus::HES5 heterozygous knock-in mouse, transverse section; delineated region (blue) correspond to data shown in (b-c). D- dorsal, V- ventral. (b) Spatial profile of Venus::HES5 intensity averaged over 2.5hrs with 0 distance representing the ventral end of kymograph; black line represents the trend in Venus::HES5 data across the domain produced using an polynomial order 6 (see Materials and Methods). (c) Detrended spatial profile of Venus::HES5 corresponding to data shown in (b). (d) Lomb-Scargle Periodogram analysis of detrended Venus::HES5 data in (c); horizontal line indicates Lomb-Scargle significance level p=0.0001; red arrowhead indicate significant peaks. (e) Auto-correlation analysis of detrended Venus::HES5 spatial profile in (c) with multiple peaks indicating spatial periodicity; significant peaks (red arrowhead) lie outside gray area indicating 95% significance based on bootstrap approach (see Materials and Methods) and non-significant peaks (black arrowhead). (f) Peak to peak distance in auto-correlation from detrended Venus::HES5 signal collected in apical regions of spinal cord between E9.5-E11.5; bars indicate mean and SD of individual slices from 3 independent experiments; Kruskal-Wallis test not significant, p=0.44. (g) Representative example of auto-correlation from detrended Draq5 nuclear signal with peak to peak distances indicative of inter-nuclear distance in live tissue; gray area denotes 95% confidence area for Draq5. (h) Peak to peak distance in auto-correlation of detrended Draq5 spatial profile in apical regions of spinal cord between E9.5-E11.5; bars indicate mean and SD of individual slices from 3 independent experiments; Kruskal-Wallis test not significant, p=0.3. (i) Schematic of multiple non-overlapping regions of interest identified as Apical, Intermediate and Basal in the spinal cord tissue; width of regions in the apical-to-basal direction was 15μm. (j) Peak to peak distance in auto-correlation of detrended Venus::HES5 spatial profile corresponding to Apical, Intermediate and Basal regions of spinal cord at E10.5; dataset is different from (h); markers indicate average distance per experiment with a minimum of 3 z-stacks per experiment and 2 repeats (left and right of ventricle) analysed per z-stack; bars indicate mean and SD of 6 independent experiments; Kruskal-Wallis test not significant, p=0.115; distances correspond to 4-5 cells considering the inter-nuclear distance in DV quantified in (h).
Effect of MIR376A overexpression on autophagy.Figure 2(A) MCF-7 cells were co-transfected with either MIR-CNT (control plasmid) or MIR376A and GFP-LC3 plasmid, and GFP-LC3 dot formation was analyzed. White arrows indicate clusters of the GFP-LC3 dots in cells. (B) Quantification of the experiments in A. MIR376A overexpression, but not MIR-CNT expression, blocked starvation (STV)-induced autophagy (mean ± S.D. of independent experiments, n = 4, ***p<0,01). NON STV, non-starved (C) Overexpression of MIR376A resulted in a decrease in the autophagic activity of MCF-7 cells. Starvation-induced conversion of LC3-I to LC3-II in MCF-7 cells was analyzed. Tests were performed in the presence or absence of E64d (10 µg/ml) and Pepstatin A (10 µg/ml) (E+P). LC3-II/LC3-I densitometric ratios were marked. ACTB was used as a loading control. (D) MIR376A blocked starvation induced SQSTM1 degradation in MCF-7 cells. ACTB was used as a loading control. SQSTM1/ACTIN densitometric ratios were marked.
Proposed mechanism for the MUTYH-initiated BER pathway.Figure 9MUTYH initiates the excision of the misincorporated adenine opposite 8-oxo-dG. The resulting 1-nt gap is then filled by Pol λ in an error-free (C) or error-prone (A) manner. Completion of the canonical short-patch (SP) pathway is futile as DNA ligase III cannot seal an 8-oxo-dG:dC base pair at the primer terminus. Thus, Pol λ promotes the long-patch (LP) extension past a correct base pair to complete error-free BER. Conversely, Pol λ is capable of stalling ligation (SP) or extension (LP) of an 8-oxo-dG:dA mispair, thus promoting its excision by proofreading. The resulting intermediate can then proceed through the error-free pathway.
Figure 1(A) cBioPortal was used to access and visualize TCGA data for MIG-6 (ERRFI1) gene expression in 81 cases of invasive carcinoma of basal-like breast cancer Cancer Genome Atlas, 2012(). Each column represents an individual sample. (B) Box plots show the MIG-6 (ERRFI1) gene expression in different breast tumor subtypes in the Servant dataset of 343 primary breast cancer carcinomas, analyzed using Illumina HumanWG-6_v3 Arrays. The gene expression levels are determined using the R2 Genomics Analysis and Visualization Platform (http://r2.amc.nl). In the box plot, error bars are the 95% confidence interval, the bottom and top of the box are the 25th and 75th percentiles, the line inside the box is the 50th percentile (median), and any outliers are shown as open circles. **p < 0.01, by Student's t-test. (C) Immunoblotting analysis for MIG-6 protein expression in various human breast cancer cell lines. (D) Representative images of histological analyses of MIG-6 in TNBC patients in low-grade (stage I) and high-grade (stage III) tumors. Scale bar, 200 µm. (E) Quantification analysis of MIG-6 expression in 85 cases of resected TNBCs. In the box plot, error bars are the 95% confidence interval, the bottom and top of the box are the 25th and 75th percentiles, the line inside the box is the 50th percentile (median). The p-value 0.011 is used for the comparison of all three groups, determined by the Kruskal-Wallis H test. (F) Kaplan-Meier plot analysis of the disease-specific survival of 85 TNBC breast cancer patients with low or high expression of MIG-6. (G) Kaplan-Meier plot analysis of the metastasis-specific survival of 85 TNBC patients with low or high expression of MIG-6. MIG-6 protein expression in the 85 TNBC specimens was determined by H-score and widely distributed. MIG-6 expression greater than or equal to the median is classified as "high," while expression less than the median is classified as "low."
Figure 6Model of neural progenitor cells behaviour during spinal cord regeneration in wild type (wt) and foxm1-/- tadpoles The blue circles correspond to sox2/3+ve cells (progenitors) and the orange circle to snap25+ cells (differentiated neurons)
Figure 1A. Schematic representation of human FAM111A domains and mutations that compromise FAM111A functions. The FAM111A N-terminus contains a functional PCNA interaction motif (PIP box; Alabert et al., 2014()). The FAM111A C-terminal trypsin-like protease domain contains a typical H385-D439-S541 catalytic triad Unger et al., 2013(), and binds the C-terminus of the SV40 Large T antigen Fine et al., 2012Tarnita et al., 2019(, ). We used an S541A mutation to disrupt the catalytic triad and inactivate FAM111A's trypsin-like protease activity. Finally, the KCS2 and OCS patient mutations are indicated in red boxes. See text and Unger et al., 2013() for phenotypic details. B. Confocal microscopy images of HeLa, RPE, and U2OS cell lines that were pre-extracted with Triton X-100 before fixed with formaldehyde and co-stained with DAPI and antibodies against PCNA and FAM111A. Scale bars: 10 μm C. U2OS cells were stained with antibodies against PML and FAM111A and imaged by confocal microscopy. Scale bars: 10 μm.
Figure 7A. CRISPR-Cas9 strategy to generate the Tg(kdrl:EGFP) rab13+/∆3'UTR zebrafish strain. The wild type (Wt) rab13 exon 8 is represented with its coding sequence in dark and the 3'UTR in clear boxes; the 5' and 3' gRNA-targeted regions are represented with green lines. Arrows: relative positions of the forward (f) and reverse (r) PCR primers used to identify animals with CRISPR-Cas9-mediated deletions (∆) in the rab13 3'UTR. B. Representative genotyping PCR demonstrates the band size shift in zebrafish harbouring a ∆482 rab13 3'UTR. Asterisk marks a heteroduplex formed between Wt and ∆482 rab13 3'UTR PCR amplicons. C. Detailed DNA sequence depicting nucleotide positions within the Wt and ∆482 rab13 3'UTR. D. RNAseq mapped reads depicting rab13 exon usage in Tg(kdrl:EGFP) rab13+/+ and rab13∆3'UTR /∆3'UTR zebrafish embryos. Coloured lines indicate SNPs. E. qPCR analysis of rab13 mRNA levels in individual 26-28 hpf clutch-matched sibling embryos (n≥9 embryos; ns: not significant; Kruskal-Wallis test with Dunn's correction). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively F. smFISH detection of rab13 and kdr mRNA in cultured GFP-expressing endothelial cells extracted from 48 hpf Tg(kdrl:EGFP) rab13+/+ and rab13∆3'UTR /∆3'UTR zebrafish embryos. Arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 10 µm (F). G. Polarisation Index (PI) of rab13 and kdr detected by smFISH in individual zebrafish cells (n≥8 cells; **P<0.01, ns: not significant; one-way ANOVA with Bonferroni's correction). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively H. rab13 PI plotted against respective kdr PI. The slope of the coloured lines represents the average rab13/kdr PI ratio; the dashed grey line represents a 1:1 ratio (n≥8 cells). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively
Figure 1Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (A) Box-plot of the enrichment of the RNAs identified by Mmi1 RNA-IPs coupled to high throughput sequencing. The log of the average enrichments obtained from two independent RNA-IPs is plotted. The enrichment is relative to the no antibody RNA-IPs conducted in parallel of Mmi1 RNA-IPs. The mRNAs and lncRNAs enriched at least two folds in both Mmi1 RNA-IPs are shown in blue and green, respectively. Crosses represent newly identified Mmi1 targets and dots known targets. Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (B) LncRNAs predicted to be targets of Mmi1 with a high confidence by our computational approach. Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (C) Surface representation of Mmi1 YTH domain. Area corresponding to conserved residues (according to the alignment shown in Fig EV 2A) and located at the surface are highlighted in green. Mutated residues in Mmi1 YTH domain are indicated in blue for the ones located within the aromatic cage, in purple for the ones surrounding the cage, and in red for the rest. Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (D) RNA-IPs showing the impact of Mmi1 YTH domain point mutations on Mmi1's binding to ssm4 mRNA. The lower part shows a Western blot monitoring the protein level of WT and mutant Mmi1 proteins in the cells used for the RNA-IPs. Loading was monitored using an anti-Tub1 (tubulin) antibody. Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (E, F) RNA-IPs showing the YTH-dependent association of Mmi1 to the lncRNAs identified in (A) and (B). Average fold enrichment is shown with error bars that indicate mean average deviations for three independent experiments for (D, E and F). Figure 1. Extensive identification of Mmi1 RNA targets by combining RNA-IP sequencing and computational approaches. (E, F) RNA-IPs showing the YTH-dependent association of Mmi1 to the lncRNAs identified in (A) and (B). Average fold enrichment is shown with error bars that indicate mean average deviations for three independent experiments for (D, E and F).
Figure 9A. AiryScan images of HeLa cells treated with SA for the indicated times and stained with GM130 (gray). Scale bar, 10 µm. The graph shows quantification of Golgi objects in SA-treated cells. Mean ± s.e.m. of three independent experiments. n=90-100. ****p<0.0001; ns: not significant, Student's unpaired two-tailed t-test. B. Control cells and cells treated with Dinaciclib (CDKi) were treated with SA and stained for GM130 (in gray). Insets, eIF3. Blue, nuclear DAPI staining. The graph shows quantification of Golgi objects in HeLa cells untreated or treated with SNS-032, Flavopiridol, or Dinaciclib for 150 min and then treated with SA (300 µM, 30 min). Mean ± s.e.m. of three independent experiments. ****p<0.0001, One-way ANOVA with Dunnett's multiple comparison test. C. Quantification of Golgi objects in cells plated at different percentage of confluency and treated or untreated with SA. Mean ± s.e.m. of three independent experiments. **p<0.001; ***p<0.0002; ns: not significant, One-way ANOVA with Dunnett's multiple comparison test. D. Quantification of Golgi objects in cells pre-treated with ISRIB (1 µM) for 3 h and then exposed to SA (30 min) in the presence of ISRIB. ***p<0.002, Student's unpaired two-tailed t-test. E. Electron microscopy images of cells treated (300 µM, 30 min) or untreated with SA. The arrow indicates the Golgi complex. Scale bar, 200 nm. F. AiryScan images of HeLa cells at steady state or exposed to SA for the indicated times. A Rab1-GTP specific antibody was used to monitor the pool of active Rab1, and GM130 to stain the Golgi complex. Insets, eIF3. Scale bar, 10 µm. The graph shows quantification of Rab1-GTP at the Golgi complex expressed as a percentage of the control. Mean ± s.e.m. of three independent experiments. *p<0.011, **p<0.002, Student's unpaired two-tailed t-test. G. HeLa cells transfected or not with WT GFP-Rab1B were left untreated or treated with SA and stained for GM130 and G3BP to monitor SGs. Dashed white line, WT GFP-Rab1B transfected cells. Scale bar, 10 µm. The graph shows quantification of Golgi objects in the different conditions. NT: non-transfected. Mean ± s.e.m. of three independent experiments. ****p<0.0001, Student's unpaired two-tailed t-test.