EMBO/sd-character-level-ner huggingface dataset:
Figure 1(A) In a mixed population, flies reach the end of a "pre-mortality plateau phase" (PMP) at an age of four weeks, where 90% of the flies are still alive. We define this age as their "midlife" point. At this stage, the rate of the population decline accelerates from 1% (plateau) per day in the previous 10 days to 3.5% per day in the following 10 days. Median survival=39 days, N=260. (B) Oxygen consumption rates (OCR) quantification show a decreased OCR in old whole heads compared to young flies. Data were normalized to 1-week-old flies (young flies). and N=14 young versus N=12 old. (C) At midlife, flies show a reduced physical activity compared to young flies. (D) Oxygen consumption rates (OCR) quantification show an increased OCR in midlife whole heads compared to young flies. Data were normalized to 1-week-old flies (young flies). N=21 young versus N=24 midlife. (E) Metabolite levels show increased levels of acetyl-CoA and citrate/isocitrate compound in midlife flies. N=6 per group. (F) Enzymatic activity of citrate synthase and ATPCL is increased in midlife flies. CS, citrate synthase (Kdn); ATPCL, ATPcitrate lyase. Data was normalized to young flies. N=8 young versus 9 midlife for CS and 6 young versus 7 midlife for ATPCL. (*P<0.05, **P<0.01 ***P<0.001). Error bars indicate the S.E.M. in all the graphs. Unpaired two tailed t-tests were used for calculating the p-values in B-F. All male flies were collected from a mixed male/female population.
Fig.Figure 7(A) Live imaging of C. elegans expressing TOM70::GFP in body wall muscle cells. Depletion of the UNC-59 or UNC-61 led to an increase in mitochondrial network connectivity as shown by quantification in (B). Insets represent a twofold magnification. Scale bar: 10 µm. (C) Live imaging of C. elegans body wall muscle cells expressing TOM70::GFP. Depletion of DRP-1 or UNC-61 caused an increase in mitochondrial elongation and network connectivity, which did not increase upon combination of DRP-1 and UNC-61. Insets represent a twofold magnification. Scale bar: 10 µm.
Figure 8A. Schematic of the full-length Srs2 protein shown as a bar. I - VI indicate Srs2 helicase motifs, K41 - a lysine residue required for ATP binding and hydrolysis, BRCv - BRC repeat variant motif, Rad51-BD - Rad51-binding domain, asterisks - sumoylation sites, PIM - PCNA-interacting motif, SIM - SUMO-interacting motif. Numbers below the protein indicate positions of amino acid residues within the Srs2 protein. B-D. The efficiency of DSB repair via SSA (B), de novo telomere addition (C) and BIR (D) in different alleles of SRS2. Average ± SD (n=3) is shown for each genotype in all experiments. Strains used: SSA: NK4691-4693; NK4805-4808; NK5104-5107; NK5066-5069; NK5062-5065; NK5058-5061; de novo t.a: NK1264; NK2375, NK2376; NK3332-3334; NK3308-3310; NK4217, NK4247; NK3353-3355; BIR: NK4070, NK4079; NK5321, NK5322; NK5536, NK5537; NK5450, NK5451; NK5452, NK5453; NK5454, NK5455. (E) E. Srs2 (1-783) is less active than Srs2 (1-910) in promoting PCNA loading in vitro. The assay was performed as shown in Figure 5E.
Schematic representation of the described metabolic imbalance in glycolytic muscle fibers of SOD1G86R mice.Figure 9Under normal conditions in WT mice, both glucose and lipids enter the cell and are used as cellular fuels. In this situation, both pathways are used and are driven by PDK4 according to needs and fuel availability.In the case of ALS, metabolic flexibility is lost because of chronically increased PDK4 and subsequent inhibition of PDH and PFK1 leading to glycogen accumulation. Increased lipid use through β-oxidation that can only function under aerobic conditions may underlie the greater endurance capacity in SOD1G86Rmice. With time, the cell produces more reactive oxygen species, thereby inducing cellular damage.Data information: CD36, CD36 antigen/fatty acid translocase, CPT1, carnitine palmitoyl transferase 1, FAs, fatty acids, FA-CoA, acyl-fatty acids, GLUT4, glucose transporter 4, LPL, lipoprotein lipase, PDH, pyruvate dehydrogenase complex, PDK4, pyruvate dehydrogenase kinase 4, PFK1, phosphofructokinase 1, ROS, reactive oxygen species. Drawing was performed with the website Somersault1824 (http://www.somersault1824.com).
Figure 6(A) Structures of two compounds identified as inhibitors of SERA6 autoprocessing and egress. (B) E64-d, MMV676881 and Compound 31 inhibit RBCM rupture and merozoite release despite normal PVM rupture, indicated by loss of a continuous ring of EXP2-mNeon signal (green) and RBCM poration (red ring indicating access and binding of phalloidin to the host RBC cytoskeleton) (reproducible in 2 independent experiments). P. falciparum EXP2-mNeon schizonts were allowed to reach the point of egress in the presence of C2 (1 µM), E64-d (10 µM), MMV676881 (2 µM), Compound 31 (2 µM) or DMSO (0.1% v/v; control) then examined by DIC and fluorescence microscopy. Scale bar, 5 μm. (C) Western blot comparing dose-response of E64-d, MMV676881 and Compound 31-mediated inhibition of maturation of SERA6-mTAP from SERA6-mTAP:loxP parasites (reproducible in 3 independent experiments). (D) Western blot of P. falciparum and P. knowlesi parasites showing that host RBC β-spectrin truncation during egress (red arrowhead) is inhibited by all three P. falciparum SERA6-maturation inhibitors (concentrations as in panel B), matching the egress inhibition in panel E (reproducible in 2 independent experiments). (E) Giemsa-stained thin films showing inhibition of rupture of P. knowlesi schizonts in human RBCs by E64-d, MMV676881 or Compound 31 (concentrations as in panel B; representative of 2 independent experiments). The increased space between individual merozoites still contained within the host RBC in parasites treated with E64-d, MMV676881 and Compound 31 (compared to C2-arrested parasites) suggests that PVM rupture has occurred. Note that P. knowlesi schizonts generally form fewer merozoites (~10-12) than P. falciparum schizonts. Scale bar, 5 μm.
Figure 6A. Number of differentially expressed (DE) genes between Irf8+/+ and Irf8-/- mice in several embryonic and adult MΦ cell populations. DE genes were identified by a one-way ANOVA model (|FC| > 1.5, FDR adjusted p-value < 0.05). The absolute numbers were normalized to the number of genes present in embryonic or adult cells. B. Venn diagrams of DE-genes between Irf8+/+ and Irf8-/- CD11bhi cells from adult or embryonic liver and kidney. Commonly up- (red area) and down-regulated (blue area) genes between cells derived from Irf8+/+ and Irf8-/- mice are shown. C. Venn diagrams of DE-genes for F4/80hi cells from adult or embryonic liver, kidney and brain. D. Gene Ontology (GO) network built on common DE genes in embryonic (left panel) and adult (right panel) F4/80hi (upper row) CD11bhi (lower row) cells from microglia, liver and kidney identified in at least two organs (identified in B and C). Red symbols represent GO terms associated with up-regulated genes in Irf8-/- compared to Irf8+/+ mice while blue edges indicate down-regulation. E. Quantitative qRT-PCR of selected genes in tissue MΦ from adult Irf8-/- and Irf8+/+ mice. Data are normalized to β-actin and GAPDH and expressed as ratio of the mRNA expression compared to microglia of Irf8+/+ mice or to liverCD11bhigh cells of Irf8+/+ mice and show mean ± s.e.m. Three mice per group were analyzed.
Figure 1Representative 3D microglia reconstructions showing morphological changes upon LPS injection within the first 48 hours. Scale bar: 10µm Morphological parameters quantification within 48 hours after LPS injection Two-photon microscopy experimental design Representative 3D microglia reconstructions from 5 and 15 months old mice showing microglia changes 2 and 10 days post LPS injection. Scale bar: 20µm Morphological parameters quantification for 5 and 15 months old mice after LPS injection
ATF6α C467 forms a Stable Mixed-disulfide Complex with the ERp18 Substrate-trapping Mutant HEK293T cells were co-transfected with the ERp18 substrate-trapping mutant and the indicated ATF6α constructs.Figure 4HEK293T cells were co-transfected with the ERp18 substrate-trapping mutant and the indicated ATF6α constructs. Cell were allowed to recover for 24 h post-transfection before being either left untreated (-) or treated (+) for 1 h with 5 µM TG to induce ER stress. ATF6α was immunoisolated from cell lysates with mouse anti-ATF6α, separated by SDS-PAGE under non-reducing conditions and ATF6α detected by western blotting using rabbit anti-HA. The blot confirms that ATF6α C618A forms a stable complex with ERp18 trapping mutant following ER stress. M, D and O refer to ATF6 monomer, dimer and oligomer respectively. *indicates positions of the ATF6-ERp18 mixed-disulfide complexes. HEK293T cells were co-transfected with GFP-ATF6α and ERp18 trapping mutant constructs as indicated. GFP-ATF6α complexes were immunoisolated using GFP-trap. Immunoisolated material was separated by SDS-PAGE under non-reducing conditions and silver stained to detect ATF6α disulfide-linked complexes. MS analyses confirmed that protein bands indicated by black arrows are a complex comprising ATF6α and ERp18, whilst bands marked as monomer (M) and oligomer (O) contain ATF6α only. Cartoon depicting the presumed composition of the ATF6α disulfide-linked complexes and dimers indicating their respective apparent molecular weight.
a,b) Control (a) or hh[ts2] (b) larvae were incubated at permissive temperature (18 °C) to the third instar stage, then cultured at non-permissive temperature (29 °C) in well-fed conditions for 24 h.f5(a,b) Control (a) or hh[ts2] (b) larvae were incubated at permissive temperature (18 °C) to the third instar stage, then cultured at non-permissive temperature (29 °C) in well-fed conditions for 24 h. Dissected fat body tissue was incubated in Lysotracker Red and DAPI and imaged unfixed. (c) Lysotracker Red-labelled fat body containing single-cell flipout clones (GFP positive) overexpressing patched. Fat body was dissected from well-fed larvae, incubated in Lysotracker Red/DAPI and imaged unfixed. (d) Confocal image of a GFP-positive patched-expressing clone, with mCherry-Atg8a expressed in all cells. Fat body was dissected from well-fed larvae and imaged after formaldehyde fixation. (e) GFP-marked flipout clones of CiCell-expressing cells. Fat body was dissected from well-fed larvae, incubated in Lysotracker Red/DAPI and imaged unfixed. (f) Confocal image of fixed mCherry-Atg8a expressing fat body containing a GFP-marked clone of CiCell-expressing cells. (g) Cells homozygous for the null costal2[2] allele (marked by lack of GFP) were generated by flp/FRT-mediated recombination in mCherry-Atg8a expressing fat body. Larvae were starved 4 h before dissection and fixation.
Expression of hTauAT leads to pathological conformation and aggregation of Tau in the hippocampus of aged mice.Figure 2A. Conformational change of Tau detected by ALZ-50 antibody immunoreactivity in stratum lucidum (asterisks) of area CA3 and somata in stratum pyramidale (arrowheads). B. Tau aggregation confirmed by Gallyas silver staining of NFTs bearing neurons in hetero- and homozygous hTauAT mice at 14 month of age compared to non-reactive control littermate mice. In homozygous hTauAT mice the extent of neurofibrillary tangles (NFTs) visualized by Gallyas silver staining is enhanced compared to heterozygous hTauAT mice (white arrowheads). The control shows no silver-reactive Tau aggregates. C. Western blot analysis using the pan-Tau antibody K9JA indicates sarcosyl-insoluble Tau species of human hTauAT (upper band) and mouse Tau (mTau, lower band). Note the enhanced Tau aggregation in homozygous hTauAT mice compared to heterozygous hTauAT mice and control mice.D. Quantification of (C). The ratio of hTauAT /mTau indicates a stronger aggregation in the homozygous hTauAT mice (~1.4) compared to heterozygous hTauAT mice (~0.7 (n=4 animals, error bars represent SEM). E. Electron micrograph of CA3 region of the hippocampus illustrating typical synapse with a perforated postsynaptic density (asterisks) in a control animal at 12 months. (ds) dendriticspine, (pt) presynaptic terminal and (m) mitochondrium.F. Example of a degenerating synaptic bouton (arrow) containing swollen synaptic vesicles in proximity to a large terminal with a perforated postsynaptic density (asterisks) in a transgenic animal at 13 months.G. Electron dense neuronal cytoplasm with dark nucleoplasm and various vacuoles (arrow) detected in CA3pyramidal neurons (arrow) at 13 months in transgenic animals in proximity to normally appearing neurons (asterisks), degenerating apical dendrite (d).H. Neuropil of a transgenic animal (13 months) with a degenerating neuritic profile (arrow).I. Degenerating dendrite (arrow) in a transgenic animal with darkened cytoplasm and abnormally distributed mitochondria (arrow).J. Degenerating dendrite containing electron-dense whorling membrane fragments (arrow) in proximity to normally appearing synapses (synapse with a perforated postsynaptic density, asterisks).
DMSs are induced by diverse beta- and alpha-CoVs.Fig 2.alpha-CoVs.2D-EM images from 100-nm thick sections of different mammal cells infected with (A) SARS-CoV (MOI 10, 9 hpi), (B) MHV (MOI 10, 8 hpi) and (C) HCoV-229E (MOI 5, 24 hpi). Both beta-CoVs (A,B) and the alpha-CoV (C) induce membrane modifications that include not only DMVs (asterisks) and CM, but also DMSs (white arrowheads). Scale bars, 250 nm.
Figure 1A. Schematic diagram depicting the recombinant ppαF-mEGFP substrate (upper panel) and purification strategy for the signal sequence-bound Sec complex (lower panel): Detergent-solubilized heptameric Sec complex (TM domains: green; cytosolic domains: cyan; detergent micelles: blue) FLAG-tagged on Sec62 was immobilized on anti-FLAG beads and incubated with molar excess of purified recombinant ppαF-mEGFP substrate. Substrate-bound Sec complex was eluted with 3C protease. B. SDS-PAGE of the reconstituted signal sequence-bound Sec complex stained with Coomassie Blue. C. Cryo-EM reconstruction as obtained after focused refinement of TM region. The map was segmented and color-coded by the individual Sec complex components. For clarity density for the detergent micelle was masked and the contour levels for the for Sec62 TMs and Sec71/72 densities are slightly lower. For the Sec62 cytosolic domain the map is low-pass filtered to 15 Å. D. Molecular model of the signal sequence-bound Sec complex. The model for the Sec62 N-terminal cytoplasmic domain (Sec62 domain) is derived from the crystal structure as determined in this work.
Figure 7A) Left panel: plasma total cholesterol in the different lipoprotein fractions of WT and Pkp2+/- mice fed a 3-month HFD (blue line) or a 3-month HFD+atorvastatin (red line). Right panel: plasma total cholesterol quantity in fractions 29-32, corresponding to low, very-low and intermediate-density lipoproteins, of WT and Pkp2+/- mice fed a 3-month HFD (blue line; n=7) or a 3-month HFD+atorvastatin (red line; n=9; Two-tailed Student's t-test). Data information: mean ± SEM. * p<0.05; ** p<0.01; *** p<0.001. B) oxLDL plasma concentration in WT and Pkp2+/- mouse samples, fed a 3-month HFD plus atorvastatin (n=8), compared to HFD (as in Figure 6B; Two-tailed Student's t-test). Data information: mean ± SEM. * p<0.05; ** p<0.01; *** p<0.001. C) Left panel: representative images of ORO staining of cardiac sections of Pkp2+/- mice, fed a 3-month HFD plus atorvastatin. Right panel: quantification of the percentage of ORO positive area (n=9) is compared to that in HFD (as in Figure 6C; Two-tailed Student's t-test). D) Representative images of PPARγ immunostaining (green) on cardiac sections of Pkp2+/- mice fed a 3-month HFD plus atorvastatin (n=9). Quantification is compared to the values of Pkp2+/- in HFD and relative to WT in CD (as in Figure 6D; Two-tailed Student's t-test). E) Representative images of MDA immunostaining (green) on cardiac sections of Pkp2+/- mice fed a 3-month HFD plus atorvastatin (n=9). Quantification is compared to the values of Pkp2+/- in HFD and relative to WT in CD (as in Figure 6E; Two-tailed Student's t-test). F) Representative images of CD36 immunostaining (green) on cardiac sections of Pkp2+/- mice fed a 3-month HFD plus atorvastatin (n=9). Quantification is compared to the values of Pkp2+/- HFD and relative to WT in CD (as in Figure 6F; Two-tailed Student's t-test). Nuclei are counterstained with Hoechst33342 (blue). Data information: mean ± SEM. * p<0.05; ** p<0.01; *** p<0.001. G) RV EF and FS percentages, RVID in systole and diastole of Pkp2+/- mice during (left panel) and after (right panel) 3-month HFD plus atorvastatin feeding (n=9). For comparison RV EF of Pkp2+/- mice fed a HFD is shown (as in Figure 6G; Two-tailed Student's t-test). Data information: mean ± SEM. * p<0.05; ** p<0.01; *** p<0.001.
Figure 1A. Representative fluorescence micrographs of HeLa cells treated with 250 μM lysosomotropic drug LLOMe or equal volume of DMSO (Ctrl) for 1 h before fixation and immunostained with Hoechst (blue), anti-CHMP4B (green), anti-GAL3 (red) and anti-LAMP1 (white) are presented. Cells treated with LLOMe show increased recruitment of ESCRT-III protein to lysosomes when compared to Ctrl cells. Number of foci per cell were quantified and are indicated as mean ± SD. Data from >86 cells per condition from three independent experiments. CHMP4B, GAL3, LAMP1 foci per cell (Ctrl versus LLOMe treatment): p=0.0398, p=0.0033, p=0.2400 (Student"s t‐test), respect Data information: Scale bars: 10 μm and 1 μm (inset) B. HeLa cells stably expressing CHMP4B-eGFP and mCherry-Galectin3 treated as in (A) and stained with CD63 antibody are shown. Number of foci per cell were quantified and are indicated as mean ± SD. Data is quantified from >87 cells per condition from three independent experiments. CHMP4B, GAL3, CD63 foci per cell (Ctrl versus LLOMe treatment): p=0.0111, p=0.0050, p=0.3793 (Student"s t‐test), respect Data information: Scale bars: 10 μm and 1 μm (inset)
Db-NP TRM cells from aged lungs are dysfunctional in protective immunity.Figure 5.immunity.A. PR8 virus infected young (filled triangles, Y) or aged (open circles, A) mice were treated with FTY720 daily starting at 60 d.p.i. per methods and materials. Then mice were infected with a lethal dose of X31 at 61 d.p.i. Survival (middle panel) and weight loss (bottom) as percent of pre-secondary infection weight were determined daily post secondary infection (d.p.2°i.). B. Db-NP-specific TRM cells (CD8+CD44HiCD69+i.v.CD90-Db-NP tetramer+) from PR8 infected young (n=18) or aged (n=12) mice were pooled and sorted for single-cell RNAseq analysis. GSEA of NF-кB signaling and inflammatory response. NES: normalized enrichment score, FDR: False discovery rate (middle and bottom panel). C. Violin plots of Bhlhe40, Cd3e, Lck, Junb, Fos, Fosl2, Nr4a1, Ifng and Tnf expression in young or aged Db-NP TRM cells. D. Seurat UMAP plots with clusters 0-3 of aged (left panel) and young (right panel) samples from scRNAseq data. E. Composition of aged or young TRM cells per cluster. F. Cluster-differentiated heat map (purple = lower relative expression, yellow = higher relative expression) of indicated genes. G. Representative flow cytometry plots of the production of IFN-γ and TNF in lung resident CD8+ T cells following 1 ng/ml NP 366-374 peptide stimulation. H. Percent of IFN-γ+ resident CD8+ T cells following stimulation with increasing amount of NP 366-374 peptide (0.01 - 10 ng/mL). I. Geometric Mean Fluorescence Intensity (gMFI) IFN-γ levels following of stimulation with increasing amount of NP 366-374 peptide. J. Percent of IFN-γ+ TNF+ resident CD8+ T cells following stimulation with increasing amount of NP 366-374 peptide (0.01 - 10 ng/mL). A are pooled data from 2 experiments. G-J are representatives of 3 experiments. * p<0.05 Student's two-tailed t-test with unequal variance.
Figure 1A. Whole chromosomes imaged by conventional TEM. Data information: Scale bars: 1µm B. Slice from a large tomographic volume; part of the carbon film surrounding a hole with vitrified ice containing the plates is indicated with an asterisk; the inset illustrates that the slice of a plate corresponds to a line in the x-y plane (perpendicular to the direction of the electron beam). Data information: Scale bars: 200 nm C-G Slices from different tomograms and the corresponding 3D segmentations showing plates with different sizes and shapes. In addition to a typical slice through the x-y plane (yellow), two slices through the x-z (red) and y-z (green) planes (orthogonal to the x-y plane) are shown in (C). Data information: Scale bars: 200 nm D), 100 nm (E-G), 50 nm (C).
Figure 3Detection of LL-37 expression in the engineered mDASCs by immunofluorescence Detection of LL-37 expression in the engineered mDASCs by real-time quantitative PCR Detection of LL-37 expression in the engineered mDASCs by Western blot Anti-Krt5 (red) and anti-P63 (green) immunostaining of WT- and LL-37-mDASC colonies. Scale bar, 70 μm. Stem cell colony-forming efficiency of WT- and LL-37-mDASCs during 5 serial passages. n=6. Representative 3D organoid culture of mDASCs with expression of type I alveolar cell markers (Aqp5 and Pdpn). Left panels, bright field imaging of 3D organoids. Right panels, immunofluorescence of organoid sections. Scale bar, 20 μm. Co-culture of bacteria with DASC shows the antimicrobial effects in dose-dependent manner. Initial additions of PAO1 were 0.1×, 0.5× and 1 × 104 CFU, respectively. Coculture duration, 6h. n=4. Error bars, S.E.M. MOI, Multiplicity of infection. Co-culture of bacteria with DASC shows antimicrobial effects in time-dependent manner. Initial additions of PAO1 was 1 × 104 CFU. MOI=1. n=3. Error bars, S.E.M. Preincubation of cells with anti-LL-37 antibody, but not IgG control, significantly reduced anti-PAO1 and anti-E.coli (J) effects of LL-37-mDASCs. Initial dose of bacteria was 103 CFU.
Figure 2A. UMAP visualization of scRNAseq data of SARS-CoV-2 infected colon- (left) and ileum-derived organoids (right). Triangles represent infected cells and colors represent the corrected targeted normalized expression of SARS-CoV-2 determined using the targeted scRNAseq data. B. Proportion of cells infected with SARS-CoV-2 for each cell type and corresponding boxplot of the normalized expression values of SARS-CoV-2 for each infected cell in each individual cell type in colon (left) and ileum (right) infected organoid samples. Data are color coded for mock, 12 and 24 hpi. The boxes represent the interquartile range, the horizontal line in the box is the median, and the whiskers represent 1.5 times the interquartile range. (Colon; Immature Enterocyte 2 12h n=15 & 24h n=47,Secretory TA 12h n=2 & 24h n=4,TA 12h n=7 & 24h n=21,Enterocyte 2 12h n=4 & 24h n=11,Immature Enterocyte 1 12h n=2 & 24h n=7,Stem Cells 12h n=1 & 24h n=3,Cycling TA 12h n=3 & 24h n=6,Enterocyte 1 12h n=0 & 24h n=4, Ileum; Immature Enterocyte 2 12h n=31 & 24h n=50,Secretory TA 12h n=1 & 24h n=1,Enteroendocrine cells 12h n=3 & 24h n=1,Cycling TA 12h n=8 & 24h n=15,TA 12h n=5 & 24h n=5,Enterocyte 1 12h n=9 & 24h n=4,Immature Enterocyte 1 12h n=2 & 24h n=8,Stem Cells 12h n=2 & 24h n=1) C. Dot plots of known entry determinants across cell types. The dot size represents the percentage of cells expressing the gene; the color represents the average relative expression across the cell type. Data are from mock-infected colon (left) and ileum organoids (right).