EMBO/sd-character-level-ner huggingface dataset:
Figure 2(A) Analysis of motor function in vaccinated GA-CFP mice and wild-type littermates in a beam walk assay. Average time to cross the beam from duplicate repeat measurements in consecutive weeks. Pairwise Wilcoxon rank sum test with Benjamini-Hochberg correction. All comparisons with WT-PBS and the TG-Ova-(GA)10 mice vs. TG-PBS comparison are depicted with * p<0.05, **, p<0.01. (B) Average number of drop-downs per mouse from all aggregated runs. Kruskal-Wallis test with Dunn's multiple comparisons. * p<0.05. TG-Ova-(GA)10 vs. TG-PBS p=0.0188. (C) Representative image of poly-GA aggregates in the anterior horn in spinal cord using immunohistochemistry. (D) Quantitative analysis of poly-GA aggregates in the spinal cord using immunohistochemistry. Images from complete spinal cord sections at 1 mm intervals. One-way ANOVA, Tukey's post hoc test, F(5,12)=1.625, p=0.2270. *** p<0.001, ns not significant. TG-Ova-(GA)10 vs. TG-PBS p<0.0001; TG-(GA)15 vs. TG-PBS p=0.2460. Scale bar indicates 100 μm. (E) Immunoassay of poly-GA from the insoluble fraction. One-way ANOVA, Tukey's post hoc test, F(5,24)=3.098, p=0.0269. ** p<0.001, ns not significant. TG-Ova-(GA)10 vs. TG-PBS p<0.0001; TG-(GA)15 vs. TG-PBS p=0.1975.
Figure 5Type VII collagen (COL7) labeling in WT dorsal skin sections (P1). Scale bar: 200 μm. ITGA6/COL4 (left, indicated by arrows) and L332 labeling (right, indicated by arrows) in the blistered skin of Col7a1-/- mice at P1. Scale bar: 100 μm. Schematic diagram of control, Col17a1-/-, and Col7a1-/- mouse skin splits. BM: basement membrane. Whole-mount AP staining of the blister roof epidermis from Col7a1-/- mice (right) and their littermate controls (left) at P1. Scale bar: 500 μm. Whole-mount AP staining of the blister roof epidermis from Col7a1-/- mice (right) and their littermate controls (left) at P1. Scale bar: 500 μm. K10/K14 (low magnification, left) and K14 (high magnification, middle and right) labeling of Col7a1-/- mouse (bottom) and littermate control (top) blistered skin at P2. Scale bar: 30 μm. Quantification of BrdU-positive cells per μm HF length (n=55 HFs from three control and 143 HFs from four Col7a1-/- mice). The data are shown as violin plots. Student's t-test. NS, no significance. Length of the major axis of keratinocytes in the regenerated epidermis (n=244 (control, L), and 132 (Col7a1-/-, L) cells from four mice, respectively) and in the surrounding intact epidermis (basal cells; n=200 (control, NL), 299 (Col7a1-/-, NL), from four mice, respectively). NL: nonlesional area. L: lesional area. The data are shown as violin plots. ****p<0.0001, one-way ANOVA test, followed by Tukey's test. NS, no significance. K10/K14 (left) and K14 (high magnification, right) labeling of WT blistered skin treated with CaCl2 (middle and bottom) or PBS (top) at P2. Scale bar: 30 μm. Quantification of BrdU-positive cells per μm HF length (n=83 (PBS), 95 (1.8 mM CaCl2), and 97 (9.0 mM CaCl2) HFs from four mice). One-way ANOVA test, followed by Tukey's test. NS, no significance. Length of the major axis of keratinocytes in the regenerated epidermis (n=433 (PBS, L), 451 (1.8 mM CaCl2, L), and 425 (9.0 mM CaCl2, L) cells from four mice) and in the surrounding intact epidermis (basal cells; n=311 (PBS, NL), 279 (1.8 mM CaCl2, NL), 302 (9.0 mM CaCl2, NL) cells from four mice). NL: nonlesional area. L: lesional area. The data are shown as violin plots. ****p<0.0001, one-way ANOVA test, followed by Tukey's test. NS, no significance.
Figure 13D-brain model, horizontal brain section illustrating transgenic human P301Ltau expression in the entorhinal cortex (green, EC) of the ECrTgTaumouse lines, and the propagation of transgenic tau to the dentate gyrus (DG). Tau composition in ECrTgTau and control mouse lines investigated. Immunostained horizontal sections show the expression of human P301Ltau in ECneurons in absence of endogenous mousetau (ECrTgTau-Mapt0/0). Fluorescence in situ hybridization of humantau mRNA combined with immunofluorescent labeling (Immuno-FISH) of humantau protein (huTau) verifies P301Ltau transgene expression in the EC. Scale bars 50 μm. Propagation of humantau protein to neurons in the DG (white arrows) in ECrTgTau-Mapt0/0 mice. Close-ups show DG neurons from three ECrTgTau-Mapt0/0 mice (DG I-III). Immuno-FISH proofs the absence of humantau expression in DG neurons, which have huTau protein but no humantau mRNA. Scale bars 50 μm. Immunostained horizontal sections of ECrTgTaumice show the expression of human P301Ltau in ECneurons in presence of endogenous mousetau. Close-ups show DGneurons from three ECrTgTaumice (DG I-III) and Immuno-FISH proofs the absence of humantau expression in these DGneurons. Scale bars 50 μm. Human P301Ltau propagation to DG neurons (white arrows) in presence of endogenous mouse tau in ECrTgTau mice. Scale bars 50 µm. Human (huTau, antibody Tau13) and total tau (hu+moTau, DAKO) levels in entorhinal cortex (EC) extracts from 18-month-oldmice show equal human P301Ltau expression in ECrTgTau and ECrTgTau-Mapt0/0 mice (p=0.201, n=3 mice/group, one-way ANOVA with Bonferroni correction) The number of human tau-positive cell bodies in the DG (p=0.58, n=4 sections and 3 mice/group) and human tau in hippocampal (HPC) extracts (p=0.14, n=3 mice/group) were similar in ECrTgTau-Mapt0/0 and ECrTgTau mice (two-tailed Student's T-test).
IGF1R inhibition increases the rate of retrograde axonal transport in an ALS mouse model A) The graph shows the average velocity of HcT-containing organelles in vivo in D72/73 SOD1G93A mice and wild type littermate controls.Figure 7The graph shows the average velocity of HcT-containing organelles in vivo in D72/73 SOD1G93A mice and wild type littermate controls. PPP (blue) treatment increased the transport rate of signalling endosomes in wild type and SOD1G93A mice compared to animals treated with vehicle control (grey) (WT control: cargo 371, movements 15,272, N=4 independent experiments; WT + PPP: cargo 388, movements 14,512, N=4 independent experiments; SOD1G93A control: cargo 322, movements 15,425, N=4 independent experiments; SOD1G93A + PPP: cargo 404, movements 17,643, N=4 independent experiments; P=2.24x10-12 (treatment), P=2.22 x10-16 (genotype), two-way ANOVA, Tukey's post-hoc test: all conditions *** P<0.005, boxplot shows median, first and third quartiles. Upper/lower whiskers extend to 1.5 * the interquartile range). PPP treatment does not alter the pausing of signalling endosomes (WT: 16.1 ± 1.5%, WT + PPP: 13.1 ± 1.5%; SOD1G93A: 16.6 ± 1.9%, SOD1G93A + PPP: 16.2 ± 2.1%; P=0.36 (treatment), P=0.32 (genotype), N=4 independent experiments for each condition, data shown are mean ± SEM. Treatment with PPP had no effect on Akt levels in the sciatic nerve (WT: Control-100 ± 8.6, PPP-91.5 ± 14.6%; SOD1: Control-101.4 ± 13.5%, PPP-117.6 ± 32.9%, P=0.81 (treatment), P=0.53 (genotype), two-way ANOVA, N=5 independent experiments, data shown are mean ± SEM, Appendix Fig S7D). Erk1/2 activation was down-regulated after treatment with PPP in the sciatic nerve of wild type and SOD1G93A mice (WT: control-100 ± 15.4%, PPP-64.4 ± 3.2%; SOD1: Control-78.0 ± 11.9 %, PPP-51.2 ± 8.2%, * P=0.013 (treatment), P=0.13 (genotype), two-way ANOVA, N=5 independent experiments, data shown are mean ± SEM, Appendix Fig S7D). Protein was normalised to GAPDH protein levels.
Figure 5A) Scatterplot comparing X-chromosomal genic H4K16ac MNase-ChIP-seq levels in early (stage 5-8) and late (stage 13-15) mixed-sex embryos. Genes are grouped by k-means clustering (k=3). The numbers of genes are cluster 1 = 979, cluster 2 = 364 and cluster 3 = 172. B) Log2 Fold Change (log2FC) of RNA-seq between female (F) and male (M) embryos at genes grouped as in A (cluster 1-3). C) Log10 distance between the middle of a gene and its nearest functional MSL2 DNA peak (cluster 1-3). Red line indicates median distance to the nearest peak. D) Comparison of cluster 1 (left) or cluster 3 (right) genes defined by H4K16ac MNase-ChIP-seq levels with constitutive and developmental genes
Figure 4A-E The JurkatTat LTR-luciferase cell line was treated with the EC50/4, EC50, EC50*4 of PH01 - PH05, alone or in combination with 300 nM SAHA, 100 nM Chaetocin, 1 µM Ionomycin, or 10 nM PEP005 as indicated. Luciferase activity was measured after 24 h, and the results are presented as percent activation relative to results from PMA treatment (percent activation for the EC50 of each compound are shown here).  F The JurkatTat LTR-luciferase cell line was treated with the indicated concentrations of PEP005 alone (upper panel) and in combination with the PH compounds (EC50) (lower panel). Luciferase activity was measured after 24 h, and the results are presented as percent activation described above. Data information: Mean and SE for the results are determined from three biological replicates (n=3) and technical duplicates. Statistical significance, derived from one-way ANOVA analysis is indicated as: *, P<0.05; **, P<0.005; ***, P<0.0005; ****, P<0.00005. The exact P-values are indicated in the Appendix Table S1.
Fig.Figure 2(A) Steady-state cleavage profile of endogenous MgtE processed by endogenous and ectopically overexpressed YqgP from the inducible Phyperspank promoter in living B. subtilis (BTM2 and BTM501, respectively, Table EV2), in minimal medium at low magnesium concentration (10 µM). Strain lacking YqgP (ΔyqgP, BTM78, Table EV2) was used as a control. Proteins were detected by immunoblotting with chemiluminescence detection. Data information: In all panels, endogenous full-length MgtE is indicated by a black arrow, and N-terminal cleavage product by red arrows. Endogenous MgtE was visualised by anti-MgtE(2-275) (α-MgtE) (B) The cleavage is efficiently inhibited by 1 μM STS736, a specific peptidyl ketoamide rhomboid inhibitor Ticha et al., 2017b(). Data information: In all panels, endogenous full-length MgtE is indicated by a black arrow, and N-terminal cleavage product by red arrows. Endogenous MgtE was visualised by anti-MgtE(2-275) (α-MgtE) and ectopic YqgP by anti-YqgP antibodies. (C) To map the cleavage site region within endogenous MgtE (second lane from the left, from strain BTM501), MgtE-derived reference fragments encoding first 300, 315, 330 amino acids as well as full-length MgtE (black arrow), were in vitro transcribed and translated. Mobility of the N-terminal cleavage product (red arrow) of MgtE on SDS PAGE was compared to the mobilities of the translated reference fragments. Data information: In all panels, endogenous full-length MgtE is indicated by a black arrow, and N-terminal cleavage product by red arrows. Endogenous MgtE was visualised by anti-MgtE(2-275) (α-MgtE) and ectopic YqgP by anti-YqgP antibodies. (D) Diagrammatic display of the mapping shows that YqgP cleaves MgtE in a periplasmic region between transmembrane helices 1 and 2 (red arrow).
Figure 7Schematic of the timeline of clinical disease in patient III.2 (see Appendix Clinical Description). Arrows indicate therapeutic interventions. d, day; mo, month; yr, year. Analysis of the blood cell chimerism in patient III.2 after HSCT. Short terminal repeat (STR) analysis was used to determine the percentage of donor cells in peripheral blood. Arrow indicates point of relapse. Photograph of patient III.2 at age ~10 years at an episode of inflammation caused by delayed etanercept administration. Arrows indicate the erythematous subcutaneous nodules (panniculitis). Model of the cellular effects of OTULIN deficiency in myeloid cells and fibroblasts in ORAS. Hyper-signalling and TNF secretion in myeloid cells as well as TNF-induced cell death of both haematopoietic cells and cell types with LUBAC downregulation, e.g. dermal fibroblasts, may contribute to the inflammation, pathogenesis, and clinical manifestation of ORAS.
Figure 5Figure 5. TGFβ signaling activity in smooth muscle cells in human left main coronary arteries with various degrees of atherosclerosis.(A&amp;amp;C&amp;amp;E) Representative images of immunofluorescence staining for TGF (red), p-Smad2 (red), or p-Smad3 (red) from patients with No/mild, moderate, or severe disease. Nuclei were counter-stained with DAPI (blue). Scale bar: 16 m.(B&amp;amp;D&amp;amp;F) Medial TGF area and percentage of medial p-Smad2, and p-Smad3 positive SMCs (***p<0.001 compared to No/mild disease; one-way ANOVA with Newman-Keuls post hoc test for multiple comparison correction).A full table of p-values for this figure is shown in Appendix Table S1.
Mitochondrial Morphology Is Affected in gba−/− Cells.Figure 5(A) Neurons and astrocytes were immunostained for cytochrome c and stained with Hoechst. Far left panels were additionally immunostained for GFAP and MAP2 to mark neurons and astrocytes. "A" in nucleus denotes astrocytes. Scale bar, 20 μm.(B) Mitochondrial morphology was blind counted from cells in (A) with neurons scored as MAP2 positive and astrocytes as GFAP positive. A "normal" morphology is classified as a mixture of fused and fragmented mitochondria that comprise a wild-type network. (n = 3; 100 cells counted/experiment). (C) Levels of morphology proteins from gba+/+, gba+/−, and gba−/− isolated mitochondria were analyzed via immunoblotting with the indicated antibodies. (D) Midbrain gba+/+, gba+/−, and gba−/− astrocytes expressing GFP-DRP1K38A were immunostained for cytochrome c and mitochondrial morphologies analyzed; concurrently cells were stained with TMRM and fluorescence intensity analyzed via confocal microscopy. Scale bar, 20 μm (n = 3, >15 cells/experiment). All data in this figure represent the mean ± SEM.
Paclitaxel blocks nascent transcription and significantly increases cleaved caspase 3 immunoreactivity in hair matrix keratinocytesA) Nascent RNA synthesis, as detected by ethynyl uridine (EU) incorporation, is blocked within clusters of nuclei in the hair matrix (arrows) following paclitaxel treatment (100 nM, 24h).Figure 3A) Nascent RNA synthesis, as detected by ethynyl uridine (EU) incorporation, is blocked within clusters of nuclei in the hair matrix (arrows) following paclitaxel treatment (100 nM, 24h). 20 µm scale. B) Quantitative analysis highlights a significant (p =<0.0001 [****]) decrease in the number of EU+ nuclei following 24h paclitaxel treatment. Welch's t-test performed using N of 11-12 hair follicles (HFs) from 3 patients. C) Representative dual fluorescence stain highlights how EU incorporation in the hair matrix is blocked within the pH3+ cell population that accumulates in response to paclitaxel treatment 10 µm scale. D) Cleaved caspase 3 expression in the hair matrix following 24h paclitaxel treatment. 20 µm scale. E) 100 nM paclitaxel treatment significantly (p = 0.0016 [exact] [**]) increases the number of cleaved caspase 3+ cells in the hair matrix after 24h. Mann Whitney U test performed using N of 16-18 HFs from 5 patients. Values plotted represent the mean number of positive cells counted per HF analysed. Error bars are standard error.
Figure 1IAPV-IRES diagram colored according to secondary structure motifs. Bottom, a closer view of the IAPV-IRES PKI highlighting its sequence, with base pairs indicated as well as the Variable Loop Region (VLR) and stem loop III (SL-III). Sucrose gradient UV profile of 60S/40S/IAPV-IRES reaction mixture after an overnight run. The peaks corresponding to 80S and 40S were used for RNA extraction and UREA-PAGE shown in the inset. Representative cryo-EM image where roughly half of the particles correspond to 40S (blue) and the other half to 80S (orange). Two classes with robust density for the IAPV-IRES where found in the 40S group. After classification, three classes with clear IAPV-IRES density and small differences in the conformation of the 40S where found in the 80S group.
The Munc18-1 domain 3a is essential for synaptic vesicle exocytosis.Figure 2A Representative traces (left), summary graphs of normalized frequency (middle) and normalized amplitude (right) of mIPSCs recorded from cultured cortical neurons that were infected with lentivirus expressing Munc18-1 WT or mutants, with or without Munc18-1 shRNAs (Control, n = 25; None, n = 17; WT, n = 17; QKAA, n = 18; KKEE, n = 16; P335A, n = 23; L348R, n = 21).
Figure 3BrdU labeling of blistered samples at P2. Scale bar: 100 μm. BrdU-positive cells are indicated by arrows. Blisters are indicated by stars. (Bottom) Quantification of BrdU-positive cells in the epidermis (left) and HFs (right) (n=4 biological replicates). The data are shown as the mean ± SE. *0.01 test, followed by Tukey's test. NS, no significance. α5 integrin (ITGA5) labeling at P2 (left image: section, right image: whole-mount). Scale bar: 100 μm. Blister edges (epidermal tongue) and HFs are indicated by arrowheads and arrows, respectively. Blisters are indicated by stars. Lineage tracing strategy. Sections of K14CreER:H2B-mCherry mice at P4. Scale bar: 100 μm. (Bottom) Quantification of mCherry-positive cells (n=3).. The data from individual mice are connected by lines. Student's t-test. NS, no significance. Whole-mount imaging of K14CreER:R26R-confetti samples at P4. Scale bar: 200 μm. Sections of Lrig1CreER:H2B-mCherry mouse skin at P4. Scale bar: 100 μm. (Bottom) Quantification of mCherry-positive cells (n=3). The data from individual mice are connected by lines. *0.01 test. Whole-mount imaging of Lrig1CreER:R26R-confetti mouse samples at P4. Scale bar: 200 μm.
Mitochondrial Physiology Is Affected in gba−/− Neurons and Astrocytes.Figure 3(A) Neurons and astrocytes from gba+/+, gba+/−, and gba−/− mice were stained with TMRM. The mean florescence intensity in mitochondria was analyzed via confocal microscopy (n = 3, >32 cells analyzed/experiment). (B) Neurons from gba+/+ and gba−/− bathed in TMRM containing recording solution and fluorescence intensity analyzed via confocal microscopy. After 1 min, 1 μM oligomycin was added followed by 1 μM FCCP (n = 5, three cells analyzed/experiment). (C) Neurons from gba+/+ and gba−/− incubated with 5 mM methyl pyruvate 5 min prior to imaging. Cells bathed in 25 nM TMRM and 5 mM methyl pyruvate containing recording solution and fluorescence intensity analyzed via confocal microscopy. After 90 s, 1 μM oligomycin was added, followed by 1 μM FCCP (n = 3, three cells analyzed/experiment). (D) As in (C), except cells were bathed in 10 mM methyl succinate, (n = 3, four cells/experiment). All data in this figure represent the mean ± SEM, *p < 0.05. Neurons from gba+/+ and gba−/− incubated with 5 mM methyl pyruvate 5 min prior to imaging. Cells bathed in 25 nM TMRM and 5 mM methyl pyruvate containing recording solution and fluorescence intensity analyzed via confocal microscopy. After 90 s, 1 μM oligomycin was added, followed by 1 μM FCCP (n = 3, three cells analyzed/experiment).
Subspecies co-occurrence and phylogenetic consistency.Figure 2Subspecies identified for M. smithii and B. vulgatus/dorei are shown in principle coordinate (PCoA) projections of the between-sample distances based on single nucleotide variations (see Methods). The first principal coordinate (PC) explains over 70% of the variation in both cases (panels A and C). Reference genomes have been projected into the same PCoA plots (marked with 'x' in A and C, see Methods). The numbers adjacent to the placed genomes correspond to those shown in parentheses next to NCBI taxonomy identifiers (leaves) on the phylogenetic trees in B and D, respectively. The sample density for each subspecies is highlighted by the histogram above and the total number of samples in which the species could be quantified is indicated in headers. Quantification of the frequency of each subspecies (bottom plot in A and C) reveals that for M. smithii only one sample has two subspecies co-occurring in one individual, while all the others have a single dominating one. In contrast, for B. vulgatus/dorei, co-occurrence is more commonly observed. Phylogenies reconstructed from the reference genomes (NCBI taxonomic identifiers, see Methods) are fully consistent with the SNP-based clustering. The representative genome for each species, relative to which genomic variants were called, is highlighted with a box. (E) In B. vulgatus/dorei, subspecies composition within each individual is generally stable over time, with a change of the dominant subspecies being rare even over a period of up to 1,000 days. An exception (highlighted by purple line) is seen for an individual, in which one dominant subspecies is replaced by another one after antibiotic treatment. The right hand panel summarizes subspecies frequency changes, underlining remarkable stability over time.
Specific combinations of homeodomain TFs are expressed in embryonic MNs during synaptic wiring.Figure 2(A) Heatmap depicting the expression of homeodomain encoding genes (columns) across n=537 single twitlow MNs for which spatial mapping information was available (rows). Rows and columns are arranged by hierarchical clustering. Normalized expression levels are color-coded. Arrows indicate selected clusters for follow up studies (see Fig 1D). Hox gene expression in individual cells as identified by scRNA-Seq is shown on the left by colored bars, clusters 1 to 60 expressing specific combinations of homeodomain genes are shown on the left. (B) Schematic drawing of a stage 17 Drosophila embryonic head, highlighting the position of selected MNs (MN2c, MN2a, MN4, MN3) and feeding muscles (LR, MHE, MHD) located in consecutive segments expressing different Hox proteins (Lab, Dfd, Scr). Each MN innervates a specific muscle by a FasII-positive axonal projection, projection A connects MN2a and the MHE muscle, while projection B connects the MN3 with the MHD muscle. (C) Visualization of the different MNs based on Dfd expression in MN2a and the MHE, which is innervated by a FasII positive axon emerging from MN2a (projection A), while the motoneuronal projections from MN3 (projection B) innervates the Dfd-negative MHD located just underneath the MHE (see also B). All MNs are highlighted by yellow circles. (D) Chart comparing the expression of eight homeodomain TFs in the four anterior MNs (MN2c, MN2a, MN4, MN3) as identified by scRNA-Seq (Seq) and immunohistochemistry (IF/HCR), with absence of expression color-coded in magenta and presence of expression in green. The genes were selected for validation, as they allowed an unambiguous distinction of the four anterior MNs according to the scRNA-Seq data. (E) Validation of the specific expression of the eight homeodomain TFs (Lab, Dfd, Scr, VVl, Lim1, Hth, Unc4 and Mirr) in MN2c, MN2a, MN4 and MN3 by immunohistochemistry or in situ HCR. For expression analysis, proteins or transcripts were detected with specific antibodies (Lab, Dfd, Scr, Hth, Vvl) or HCR probes (Lim1, unc4) using wild-type embryos. Mirr expression was detected by GFP antibody stainings using a GFP fusion line (mirr::GFP). The stereotypic position of MN2c, MN4, MN2a and MN3 was identified by the two axon projections A and B (labelled by FasII), which invariantly innervate the MHE (projection A) and MHD (projection B) muscles in wild-type embryos. MN2c and MN4 are the two MNs adjacent to MN2a. The four MNs are highlighted by yellow circles.
Figure 4(A) Scatter plot comparing polysome association score (defined as fold-change between abundance in polysome libraries vs. total RNA) and RDR6-dependent siRNA levels of TEs found de-repressed in ddm1 (brief description of RDR6 dependency). Quartiles of siRNA levels are confined by gray vertical lines. For comparison and reference, polysome association and RDR6-dependent siRNA levels of protein coding and non-coding transcripts are displayed as boxplots. Copia93 elements: EVD (AT5G17125) + ATR (AT1G34967), are circled. Inlet: Polysome association score of TEs in quartile 4, EVD mRNA isoforms are displayed separately. (B) Boxplots of RNA expression levels of TEs in ddm1 from the quartiles in (A). (C) ORF length of Ty1/Copia and Ty3/Gypsy elements expressed in ddm1 relative to their genomic length.