EMBO/sd-character-level-ner huggingface dataset:
TIMM50 and the import machinery A Schematic structure of the human mitochondrial protein import machinery showing the components of the translocase of the outer (TOM) and inner membrane (TIM23-PAM and TIM22).Figure 1A Schematic structure of the human mitochondrial protein import machinery showing the components of the translocase of the outer (TOM) and inner membrane (TIM23-PAM and TIM22). B Human TIMM50 isoforms (top), TIMM50L and TIMM50S, consist of three domains: a mitochondrial targeting sequence (MTS) that directs the protein to mitochondria, a trans membrane domain (TMD) and a presequence binding domain (PBD) that contains an active phosphatase FCP1-like domain. Isoform TIMM50L also contains a nuclear localization signal (NLS). Phylogenetic alignment of the human protein region containing the substitutions found in the affected individual is shown below. Altered residues in the affected subject are boxed in red and its position marked in relation to conserved domains. Abbreviations are as follows: Hs, H. sapiens; Pt, P. troglodytes; Bt, B. taurus; Mm, M. musculus; Rn, R. norvegicus; Xt, X. tropicalis; Dr, D. rerio; Dm, D. melanogaster; Ce, C. elegans; Sc, S. cerevisiae. C TIMM50S levels in primary and immortalized skin fibroblast from control (C1-4) and mutant TIMM50 (Pt). SDHA and ETHE1 are shown as loading controls. D qPCR quantification of TIMM50 transcript levels in control and TIMM50 mutant fibroblasts. Data are shown as mean ± SD, n = 4.
Figure 7Figure 7. Model for the function of Ψ42 and Ψ44 during spliceosome assembly. In wild-type, Ψ42 and Ψ44, the surrounding nucleotides, and perhaps the whole BSL structure (Perriman Ares, 2010), stimulate the interaction of U2 with Prp5 (perhaps through SF3b) and activation of Prp5's ATPase activity, resulting in a conformational change and Complex A formation. In the snr81Δ pus1Δ mutant, the absence of Ψ42 and Ψ44 leads to a U2 local structural change. The lack of Ψs coupled with the local structural change negatively impacts Prp5 binding and Prp5's ATPase activity. Consequently, Complex A formation or spliceosome assembly becomes less efficient.
a, Protein extracts from drpr null (w; drpr&Dgr5/drpr&Dgr5) pupae at puparium formation (0 h) and wild-type (Canton-S) salivary glands 6 h, 12 h and 14 h after puparium formation, analysed by western blotting with anti-Drpr antibody.figf1a, Protein extracts from drpr null (w; drpr∆5/drpr∆5) pupae at puparium formation (0 h) and wild-type (Canton-S) salivary glands6 h, 12 h and 14 h after puparium formation, analysed by western blotting with anti-Drpr antibody. b, Samples from control animals (+/w; +/drpr∆5), n = 12, and drpr null mutants (w; drpr∆5/drpr∆5), n = 47, analysed by histology for the presence of salivary gland material (red circles) 24 h after puparium formation. c, Quantification of data from b and d. d, Samples from control animals (+/w; +/UAS-drprIR), n = 11, and those with salivary gland-specific knockdown of drpr (fkh-Gal4/w; UAS-drprIR/+), n = 19, analysed by histology for the presence of salivary gland material (red circles) 24 h after puparium formation. e, Control animals (+/w; +/UAS-drpr-IIR), n = 9, and those with salivary gland-specific knockdown of drpr-I (fkh-Gal4/w; UAS-drpr-IIR/+), n = 20, analysed by histology for the presence of salivary gland material (red circles) 24 h after puparium formation. f, Quantification of data from e. g, Samples from drpr null animals (+/w; +/UAS-Drpr-I; drpr∆5/drpr∆5), n = 9, and those with salivary gland-specific expression of Drpr-I (fkh-Gal4/w; UAS-Drpr-I/+; drpr∆5/drpr∆5), n = 20, analysed by histology for the presence of salivary gland material (red circles) 24 h after puparium formation. h, Quantification of data from g.
Figure 1A) Representative specimen of colorectal (CRC) primary tumour stained with haematoxylin/eosin/saffron (HES), or antibodies against E-cadherin or Vimentin. i) The blue, orange and pink dotted lines highlight the normal mucosa, the submucosa and the muscularis propria respectively. Red dotted line highlights the neoplastic tissue. Black arrowheads indicate the direction of invasion. Boxed regions ii and iii show high magnification of normal colonic glands (ii) and the CRC invasive front (iii). Scale bar: 2 mm and 500 μm. B) Representative images of histological sections of normal colon and primary CRC stained for EpCam and Villin. Boxed regions i, ii and iii are high magnifications of the luminal cavity of normal colonic gland (i) and colorectal carcinoma glands (ii and iii). Aarrowheads point to the apical pole enriched in villin. Scale bars: 50 μm. (C) Graph presenting the percentage of the tumour area displaying a glandular architecture from a cohort of 16 patients
Figure 2(A) A3A co-precipitates with CCT complex subunits. U2OS and HepaRG cells with dox-inducible A3A-HA transgenes were treated with dox prior to immunoprecipitation of HA. HA immunoprecipitates were analyzed by immunoblot with antibodies for HA and subunits of the CCT complex. (B) Immunoprecipitation of CCT. IP of the CCT complex using antibodies to endogenous CCT subunits was performed in lysates from U2OS-A3A (top) and HepaRG-A3A (bottom) cells after dox treatment. Immunoblot analysis with probes for A3A-HA and indicated subunits of CCT with IgG as a control is shown. (C) A3A interacts with CCT in leukemia cells. HA immunoprecipitation in hematopoietic cell lines with inducible A3A-HA was analyzed by immunoblot. HA, CCT1, and CCT5 antibodies were used to evaluate co-precipitation of CCT subunits with A3A. (D) The CCT-A3A interaction occurs in breast cancer cells. HA (top) and CCT (bottom) immunoprecipitation in the MDA-MB-231 cell line with inducible A3A-HA expression was analyzed by immunoblot. Anti-HA and anti-CCT1 antibodies were used to evaluate reciprocal co-IPs.
DOT1L-mediated H3K79 methylation is associated with gene activity in B cells and indirectly promotes repression of PRC2 target genes.Figure 7A. Integrative analyses of differentially (FDR < 0.05) expressed transcripts from naïve and activated Dot1L-deficient B cells (left panel) with H3K79me2 ChIP values from WT naïve and activated B cells (right panel). B. The distribution of mean H3K79me2 amongst different gene sets (6A, left panel) from activated and naïve B cells depicted by box plots. Boxes in Box plot indicate Inter quartile range (IQR) and whiskers show 1.5 IQR of highest and lowest quartile. Central horizontal line within the bars represent median of the TMM normalized H3K79me2 counts + 1 values of the respective genes for each condition. Results represent the data generated from three biological replicates for each group. C. Differential (FDR < 0.05) expression of Ezh2 and Cdkn1a as indicated by counts per million after TMM normalization from WT and Dot1L-KO activated B cells. Data was generated from three independent biological replicates for each genotype. Bars and error bars indicate mean ± SD. Statistical significance is indicated by FDR after the Benjamini-Hochberg multiple testing correction performed by edgeR package using R language. D. H3K79me2 methylation at the Ezh2 locus from WT activated and naïve B cells, as determined by reads per genomic content (RPGC). Data represent three independent biological replicates. E. Correlation between expression of Ezh2 and Dot1L as depicted by TPM in different mature B-cell subsets; B1: B1 cells, MZB: marginal Zone B, FOB: follicular B, GCB: germinal Center B, SPLPB: spleen plasma blast, SPLPC: spleen plasma cells) and Bone Marrow (BMPC: Bone marrow plasma cells) A20: Germinal Center like cell lymphoma cell line. Correlation shown by scatter plot. F. Coverage plot of H3K27me3 from naïve B cells (Frangini et al., 2013) and H3K79me2 (from WT activated and naïve B cells) flanking 4 kb around transcriptional start sites (TSS) for genes upregulated in KO (KO Gain) or non-differential Expression Matched genes. Coverage was calculated as reads per genomic content cutoff at the 0.995th quantile and rescaled to a maximum of 1. Black boxes indicate the relavant B cell population for comparing the distribution of H3K27me3 and H3K79me2 for the indicated gene sets obtained from the differential gene expression analysis of Dot1L-proficient and deficient B cells.
Figure 6Figure 6. No autophagy inhibition (A-C) and no mitophagy defect (D-E) in patient fibroblasts. A. Immunoblot of LC3B-I/-II expression in fibroblasts of patient 2 (1,2), patient 1 (3,4) and control individual (5,6) in absence (-) or presence (+) of chloroquine (CLQ). B. Quantitative analysis of LC3B-II/β-tubulin ratio from immunoblots (n=3). C. Quantitative analysis of LC3B-II + CLQ/ LC3B-II - CLQ ratio from immunoblots (n=3). D. Confocal images of fibroblasts derived from a control, patient 1 and patient 2. Boxed regions are enlarged. Scale bar: 20µm. E. Bar graph showing ratios of fluorescent intensity of mitochondria delivered to lysosomes relative to that of mitochondria present in the cytosol (FL lyso/FL mito ). Statistical analysis were performed on mean ± SEM using Student's t-test (two-sided).
Figure 3(A) Clustering analysis for upregulated and downregulated genes in BY4741 nat4Δ (NCR, 2% glucose) and wild-type (CR, 0.1% glucose) strains. Gene ontology was calculated by DAVID software (version 6). GO categories with enrichment scores of p < 0.05 are shown. (B) Venn diagram showing statistically significant overlap (83 genes) between upregulated genes in nat4∆ cells (138) and wild-type cells grown in CR conditions (914). Significance of overlap between the two sets is shown (p = 4.19 x10-13; calculated using hypergeometric test [phyper]). The most relevant GO categories from the overlapping genes are indicated in the table on the right. (C) Gene expression analysis of selected upregulated stress-response genes (according to results in 3A) in BY4741 wild-type and nat4∆ strains grown under NCR and CR conditions. Expression levels were normalized to TAF10, whose expression remains unchanged. Error bars, SEM of 3 independent experiments. p-values were obtained comparing results to wild-type under NCR conditions, and calculated by unpaired two-tailed Student's t-test: * p ≤ 0.05; ** p ≤ 0.01. (D) Gene expression analysis showing fold induction levels (Log2) of selected genes comparing BY4741 wild-type and STE5p-NAT4 strains under NCR (2% glucose) and CR (0.1% glucose) conditions. Expression levels were normalized to TAF10, whose expression remains unchanged.
Figure 2(a-b) Plots as in Figure 1, showing changes in Lamin B1 DamID signals upon CRISPRa activation of NLGN1 (a) and SOX6 (b). Control cells were treated either without sgRNA or with one of various sgRNAs targeting promoters on different chromosomes. Vertical green dotted lines mark the position of the sgRNA target sequence. (c) Domainograms showing regions with reduced NL interactions around 12 genes individually activated by CRISPRa. Genomic regions are aligned by the respective sgRNA target positions, and oriented so that the activated genes are all transcribed from left to right. (d) Color key of domainograms in a-c. Increases in NL interactions (red) are not shown in (c).
Figure 3Experimental design. Germ nuclei isolated from empty vector or ints-11 RNAi-treated nematodes were fractionated into chromatin-bound and nucleoplasmic fractions. RNA corresponding to each fraction was purified and used as input for short capped RNA libraries. Length distribution of chromatin-bound and nucleoplasmic piRNA precursors in wild type N2 nematodes, calculated from two merged replicates. Length distribution of piRNA precursors generated from loci with weak and strong AT content enrichment downstream of the 21U-RNA in wild-type nematodes, calculated from two merged replicates. Distributions of log2 fold change in piRNA precursor abundance in nucleoplasmic and chromatin fractions relative to N2 empty vector controls, for N2 ints-11 RNAi, tfiis empty vector, and tfiis ints-11 RNAi nematodes in two replicates. Significance for each distribution to be different from no change was tested using a two-tailed paired Wilcoxon rank sum test, with all p-values<2.2e-16. Boxplots show the interquartile range with a line at the median; the whiskers extend to the greatest point no more than 1.5 times the interquartile range. Length distributions of nucleoplasmic and chromatin-bound piRNA precursors in N2 empty vector, N2 ints-11 RNAi, tfiis empty vector, and tfiis ints-11 RNAi nematodes. Length shifts in nascent RNA in tfiis mutants are indicated with dashed vertical lines and arrows. The length distributions were calculated from two merged replicates (see Appendix Figure S2 for the length distributions in each replicate). Distribution of the position of the ~28 nt (F) and ~48 nt (G) nascent RNA peaks in 2000 bootstrapped subsamples of 3000 precursors. Sampling probability was weighted by precursor abundance.
Ultrastructural characterization of late compartment segregation along the perinuclear/peripheral axis.Figure 3A-D. Correlative light and electron microscopy (CLEM) on A. untransfected (WT) HeLa cells harbouring endogenous CD63 labeled with GFP as compared to those ectopically expressing B. HA-RILP, C. HA-SKIP or D. both HA-RILP and HA-SKIP. Left panels: wide field fluorescence images of fixed cells showing endogenous GFP-CD63 (green) and SiR-lysosome-stained endosomes and/or lysosomes (red). Cell and nuclear boundaries are demarcated with solid and dashed lines respectively, zoom insets highlight regions selected for EM imaging. Middle panels: overview electron micrographs of perinuclear (PN) and peripheral (PP) cell regions selected for further analysis. Various endolysosomal subtypes are designated by arrowheads: MVBs (white), lysosomes (black), endolysosomes (yellow) and abnormal/enlarged endolysosomes (red). Right panels: graphical representations of endosomal distribution under the indicated conditions based on ultrastructural characterization.
a, Protein extracts from drpr null (w; drprDgr;5/drprDgr;5) pupae at puparium formation (0 h) and from the fat bodies of wild-type (Canton-S) third-instar larvae were analysed by western blotting with anti-Drpr antibody.figf4a, Protein extracts from drpr null (w; drprDgr;5/drprDgr;5) pupae at puparium formation (0 h) and from the fat bodies of wild-type (Canton-S) third-instar larvae were analysed by western blotting with anti-Drpr antibody. Third-instar larvae were either fed or starved for 4 h. b, We either fed Wild-type (Canton-S) third-instar larvae or starved them for 4 h, and dissected fat bodies, stained them with anti-Drpr antibody, and imaged them for Drpr (green). We stained nuclei with 4′,6-diamidino-2-phenylindole (DAPI) (blue). c, We starved third-instar larvae expressing GFP-Atg8a in all cells, and drprIR specifically in dsRed-marked clone cells (hsflp/w; UAS-drprIR/+; hsGFPAtg8a, act,cd2, FRT > Gal4, UAS-dsRed/+), for 4 h. We dissected larval fat bodies and imaged them for GFP-Atg8a (green) and dsRed (red). d, Salivary glands of animals expressing GFP-Atg8a in all cells, and drprIR specifically in dsRed-marked clone cells (hsflp/w; UAS-drprIR/+; hsGFPAtg8a, act,cd2, FRT > Gal4, UAS-dsRed/+), dissected 14 h after puparium formation. Imaged for GFP-Atg8a (green) and dsRed (red). We stained nuclei with Hoechst (blue).
Fig.Figure 3(A) Schematic representation of the clearance experiment. (B) Purified KB-AT-23-fus and KB-hFX-11-fus were given intravenously to wild-type C57B6 mice (10 mg/kg). At indicated time-points, blood was collected and residual protein was measured. Plotted is residual protein versus time after injection. Green circles: KB-AT-23-fus; Red circles: KB-hFX-11-fus. (C) Schematic representation of the tail vein transection (TVT) assay performed in F8-/- mice. Ø 2.3mm: size of the diameter of the tail at the location of the TVT; 0.5mm: depth of the cut performed on the mouse tail. (D) Graph reporting the volume of blood loss (µL) in treated mice (n=4-9 per group) observed during 30 minutes post TVT. Dosing was 10 mg/kg for KB-AT-23 and 1 mg/kg for FVIIa. The grey area represents the range of blood loss in FVIII-treated mice (33-245 μL), which is similar to that of wild-type C57BL/6 mice (49-308 μL; Johansen et al. 2016).
Figure 1Left - Single-level electron micrograph images of zymogenic chief cells (ZCs) after 24h vehicle or high-dose tamoxifen (HDT) treatment from FIB-SEM 3D tomography. G = representative secretory granules; N = nuclei. Scale bar, 2μm. Right - Stacked EM images rendered into 3D projections using Amira software. Cells outlined by dashed yellow line. Representative immunofluorescence images of stomach unit bases at homeostasis, 6 hour, and 24h HDT stained with GIF (red, granules) and LAMP1 (green, lysosomes) Scale bar, 25μm. Stomach unit base outlined by dashed white line. Representative TEM images of normal and injured ZCs (scale bar, 2μm). Right (insets)- higher magnification images of boxed regions from left show emergence of double-membraned autophagic vesicles engulfing mature granules, mitochondria, and rough ER 24h after HDT injury. Scale bar, 500nm. Arrowheads mark vesicular degradation events in the cell lacking double membranes. Cells outlined by dashed yellow line. Graph of the number of zymogenic chief cell granules per cell in vehicle vs. 24h HDT treatment. Each data point=total granules in a cell in a single TEM section with cells from 2 separate mice plotted together (each cell is a data point; cells from the same mouse are grouped by color shade). Red line indicates mean across all the mice. Graph of the number of degradation events scored as in D. A degradation event was counted if electron dense-cargo or organelles were surrounded by a single membrane (lysosome) or double membrane (autophagosome). Red line indicates mean across all the mice. Representative TEM images of normal and injured acinar cells. Scale bar, 2μm. Right (insets)- higher magnification images of boxed regions from left show emergence of double-membraned autophagic vesicles engulfing mature granules, mitochondria, and rough ER 24h after cerulein (CER) injury. Scale bar, 500nm. Arrowheads mark degradation events without double membranes. Graph of the number of acinar cell granules per cell in vehicle vs. 24h CER treatment. Each data point=total granules in a cell in a single cell counted from one mouse. Red line indicates mean. Graph of the number of degradation events scored in vehicle vs. 24h CER treatment. Each data point=total events in a cell in a single cell counted from one mouse. Red line indicates mean. mRNA expression by qRT-PCR of Rab5, Rab7a, Rab7b, and Rab9. Significance determined by one-way ANOVA, Tukey post hoc. Each data point represents the mean of triplicate technical replicates from a single mouse, n=3-4 mice in independent experiments. Error bars denote standard deviation.
Fig.Figure 6Amphetamine-induced rotation scores. The ipsilateral net rotation values of individual animals transplanted with differentiated mutant (n=7) and corrected (n=6) pt-hiPSCs are depicted. Significant differences from the mutant cell-transplanted at each post-transplantation time point are at *p<0.05 or **p<0.001. Cell engraftments measured by the integrated fluorescent intensities in the animals grafted with DiR-labeled pt and corrected hiPSCs. *p<0.05. Overviews of hNCAM+/TH+ cell grafts at 8 weeks post-transplantation. Insets, TH+ DA neuron morphology in grafts shown with high magnification. Co-expression of the mDA neuron-specific FOXA2, LMX1A, NURR1, DAT in TH+ DA cells generated by the corrected pt-hiPSC transplantation. Cell engraftments measured by the integrated fluorescent intensities in the animals grafted with DiR-labeled pt and corrected hiPSCs. *p<0.05. Total number of TH+ cells in the graft (TH+ numbers/mm3) per animal.
Figure 3 Note the accumulation of profoundly altered mitochondria in Cox15sm/sm muscles (white arrows), possibly as a result of partially digested organelles within endolysosomes. Black arrows indicate examples of normal mitochondria. In rapamycin-treated Cox15sm/sm animals only a few of these structures are present, which can be detected also in rapamycin-treated WT samples. The bar corresponds to 1136 nm (4400X)
Figure 6Comparison of tumor-derived (human, left) and stroma-derived (mouse, right) differentially expressed genes in a pro-invasive (Ren13) and non-pro-invasive (Ren50) Ren-PDOX tumor models, obtained from species-specific RNAseq analysis. Venn diagrams illustrate gene expression differentials and overlap between Ren13 and Ren50 tumor types. Tumor specific (human) enriched gene sets in Ren13 and Ren50 Ren-PDOX tumors, after GSEA analysis from RNAseq data. Gene sets most significantly enriched in Ren13 or Ren50 are indicated in the table (left), including their normalized enrichment score (NES), p-value and false discovery rate (FDR q-value). Heatmaps illustrate expression levels of the genes responsible for the enrichment of KRAS signaling up and down in Ren13 and Ren50, respectively (right). Venn diagram comparing differentially expressed genes in the KRAS signature among Stage (blue), T (yellow) and M (red) from the TCGA KIRC primary tumors cohort. Only significant (FDR-adjusted p-value < 0.05) age- and gender-corrected correlated genes are included. 19 genes are listed separating upregulated (red) and downregulated (green) in more advanced/aggressive tumors. Validation of candidate gene expression in unique series of 39 RCC patients (GSE29609), where microvascular invasion (MVI) and renal vein involvement (RV) are specifically annotated. Progressive invasion relates to the three progressive degrees of invasion toward the vena cava in this series: 1st, no invasion; 2nd, microvascular invasion; and 3rd, renal vein involvement. The gene expression is shown for each variable and condition in box plots representing median, Q1/Q3 and max/min value whiskers, *p < 0.05 **p < 0.01 by Mann-Whitney test.
Figure 3Time line of the experiment and experimental groups: 8 month-old mice were injected 3 times (1 per week) with Vehicle (WT mice, WT VEH, saline), Vehicle (THY-Tau22 mice (TAU VEH), CSP 500 μg /mouse) or Molecule (THY-Tau22 mice (TAU MOL), CSP-TTK21 500 μg/mice). One sub-group of WT mice was left in their Home cage (WT VEH_HC) and the other groups of mice (WT and THY-Tau22) were subjected to a 3-day spatial training (Learning). RNA extracts were isolated from the dorsal hippocampus, one hour after the last training (n=5/group) Volcano plot showing that 2756 genes are differentially regulated between THY-Tau22 and WT mice during learning. The log2(Fold-Change) was estimated by DESeq2. FDR<0.05 and |log2 Fold Change| > 0.2. Red dots correspond to genes with adjusted p-value <0.05. Numbers in the corners represent the number of down-regulated (left) and up-regulated (right) genes. C Heatmap representing expression of z-score of the 2756 deregulated genes in all experimental conditions. Color-coding was performed according to the z-score of the normalized reads counts divided by gene length. Clustering was performed using the Unweighted Pair Group Method with Arithmetic mean method and the Pearson"s distance. Groups: WT VEH_HC (n=3), WT VEH (n=2); TAU VEH (n=2); TAU MOL Volcano plot showing that 1756 genes are differentially regulated between treated-THY-Tau22 and WT mice during learning. Same parameters as in B E Venn diagram showing the rescue of the transcriptome in learning mice, by comparing differentially regulated genes before (TAU VEH vs. WT VEH) and after (TAU MOL vs. TAU VEH) the treatment for all genes with an adjusted p-value <0.05 F, G Volcano plots showing differentially regulated genes by the molecule in THY-Tau22 mice (F) and by learning in WT mice (G). Same parameters as in B H Fold changes for every significant pathology-regulated gene (TAU VEH vs. WT VEH) condition are plotted for down-regulations (top) and up-regulations (bottom) separately (Adjusted p-value <0.05). Functional annotation performed with DAVID for GOTERM_Biological Process and their significance are shown on the right before (green) and after (red) treatment. Significantly regulated pathways with -log10(Benjamini p_value) <0.05 are given