EMBO/sd-character-level-ner huggingface dataset:
Figure 2A. Cdc20 binding assay in Xenopus egg extracts. The purified recombinant WT or Apc-loop500 mutant APC/Cs with mutations (1-T532A, 1-T539A, 1-T532A/T539A (1-2A) and 1-S558A) was incubated with APC/C depleted (ΔAPC) interphase extract (Inter) or ΔAPC anaphase extracts supplemented with non-degradable cyclin B (Ana) at 23˚C for 1 h. The APC/C was recovered with Apc3 monoclonal antibody (AF3.1) beads, and the bound proteins were analysed by SDS-PAGE and immunoblotting with indicated antibodies. B. Quantification of (A). The bar graph is quantification of bound Cdc20. The intensities of WT control in anaphase were arbitrarily set to 1.0. Error bars, SEM from three independent experiments. C. Plx1-binding deficient APC/Cs are less active in ubiquitylation assay than WT APC/C. The purified recombinant WT APC/C or mutant APC/C (1- 2A or 1-S558A) was incubated with ΔAPC anaphase extract and the recovered APC/C-Cdc20 complex was subjected to ubiquitylation assay (Fig S3). Ubiquitylation was quantified and the activity of WT at 45 min was arbitrarily set to 1.0. Error bars, SEM from three independent experiments. A representative result is shown in Fig S3. D. In vitro kinase assay of Apc3-loop using purified Plx1. The purified Apc3-loop (182-451 in Xenopus) fragment was incubated with Plx1 in the presence of ATP at 23˚C for indicated times, separated by SDS-PAGE and detected by Coomassie brilliant blue (CBB). E. In vitro phosphorylation by Plx1. Apc3-loop fragment, α-Casein, N-terminus of Cdc20 (N159) or MBP protein was incubated with purified Plx1 in the presence of [γ32P]-ATP at 23˚C for indicated times, separated by SDS-PAGE and detected by autoradiography and Coomassie brilliant blue (CBB) staining. F. Phosphorylation of Apc3-loop by Plx1 in the presence of [γ32P]-ATP. WT Apc3-loop fragment or its CDK-sites mutant (9A) was incubated with purified Plx1 in the presence of [γ32P]-ATP at 23˚C for indicated times, separated by SDS-PAGE and detected by autoradiography.
Fig.Figure 2Littermate control and δWD mice were challenged intranasally with IAV strain X31 (103 pfu). (A) Mice were monitored for weight loss at indicated time-points. (n = 8). Littermate control and δWD mice were challenged intranasally with IAV strain X31 (103 pfu). (B) Survival was assessed at indicated time points (n = 15). Littermate control and δWD mice were challenged intranasally with IAV strain X31 (103 pfu). (C) IAV titre in lungs was determined by plaque assay at 5 d.p.i. (n = 6). Littermate control and δWD mice were challenged intranasally with IAV strain X31 (103 pfu). (D) The presence of IAV antigen was assessed by IH at 7 d.p.i. (representative images from n = 6).
Figure 6A. Heat map depicting all human AML samples from the Haferlach study (Haferlach et al., 2010) whose transcriptomes resembled DN2-leukemia by a Spearman's rank correlation coefficient ≥ 0.5. The top 100 up- and downregulated gene signature of Myc/Bcl2+DN2-derived myeloid blasts was applied (see also Figure 3B). B. Hierarchical clustering of all FAB M2 AML samples from the Verhaak study (Verhaak et al., 2009) based of the Myc/Bcl2+DN2-derived myeloid blast top 100 upregulated (UP) gene signature (see Figure 3B). C,E. GSEA confirming enrichment of the Myc/Bcl2+DN2-derived myeloid blast top 100 UP (C) and pan-DC (Schonheit et al., 2013) (E) gene signatures in the human FAB M2 DN2-like AML samples as compared to all residual M2 AMLs from the Verhaak study (Verhaak et al., 2009). D. Relative transcript levels of the T cell receptor alpha locus (TRAC) in human DN2-like M2 AML compared to residual M2 AML patient samples from the Verhaak study (Wilcoxon rank-sum test, **=p≤0.01).
Figure 1Schematic drawing of S. cerevisiae RNAPII transcription active center. Trigger loop is shown in blue. TL-interacting Rpb2 domain is shown in beige. Proline 1018 (P1018, green) and gating tyrosine 769 (Y769, red) are highlighted. The schematic drawing is based on PDB: 2e2h [15]. Protein sequence alignment of RNAPII Rpb2 Y769 and P1018 regions in S. cerevisiae and A. thaliana. P979S and Y732F are the yeast equivalent point mutations in Arabidopsis. The color scheme indicates conservation from variable (blue) to conserved (red). Detection of NRPB2WT-FLAG, NRPB2P979S-FLAG and NRPB2Y732F-FLAG protein by western blotting in NRPB2WT-FLAG Col-0, NRPB2P979S-FLAG Col-0 and NRPB2Y732F-FLAG Col-0 plants. Untagged NRPB2 (Col-0) was used as a negative control. Histone H3 was used as an internal control and total protein level detected by stain-free blot was used as a loading control. Quantification was done by normalizing to the loading control and anti-H3 blot based on 3 independent replicates. Transmission rate of nrpb2-2 allele in nrpb2-2 +/- line (n=197) and nrpb2- +/- lines combined with homozygous NRPB2P979S-FLAG +/+ (n=280), NRPB2Y732F-FLAG +/+ (n=240) and NRPB2WT-FLAG +/+ (n=210), respectively. Fisher´s exact test was used as a statistic test, three asterisks denote p<0.001 between samples and n.s. stands for not significant. Image of homozygous mutant nrpb2-2 fully complemented by NRPB2WT-FLAG (top, NRPB2WT +/+ nrpb2-2 -/-) and partially complemented by NRPB2Y732F-FLAG (bottom, NRPB2WT +/+ nrpb2-2 -/-). Plants were grown for 4 weeks in soil. Scale bars represent 1 cm.
Figure 5A, B. CDF plots of (A) PTC+ and PTC-isoforms, (B) NMD+ and NMD- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot. C. Two possible models for UPF3A/3B-dependent and -independent NMD. Model 1 predicts that mRNAs (represented by wavy lines) from one set of genes (mRNA 1) undergoes UPF3A/3B-dependent NMD and those from another set of genes (mRNA 2) are targeted by UPF3A/3B-independent NMD. Model 2 posits that same mRNAs are targeted to both UPF3A/3B-dependent and -independent NMD. The number of arrows signify the probability/rate of NMD commitment via each branch. In Model 2, commitment to NMD is higher in the presence of UPF3 paralogs and lower in their absence. D, E. CDF plots of UPF3A/3B-independent (UPF3A/3B-indep., D) and -dependent (UPF3A/3B-dep., E) PTC+ isoforms and their respective PTC- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot. F. CDF plots of UPF3A/3B-dependent (UPF3A/3B-dep.), UPF3A/3B-independent (UPF3A/3B-indep.) NMD+ isoforms and NMD- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot.
Expression of pro‐fission proteins and Bnip3 induces muscle atrophy.Figure 5(A) Adult TA muscles were transfected with either DRP1, Fis1, DRP1 and Fis1 or mock vector. Muscles were collected 12 or 21 days after transfection and cross‐sectional area of transfected fibres, identified by immunofluorescence, was measured as described earlier (*P0.001) n=400. (B) Bnip3 or Bnip3 l expression for 7 days causes a 20% reduction of the cross‐sectional area. TA muscles were transfected with Bnip3, Bnip3l or mock vector. Cross‐sectional area of transfected fibres, identified by immunofluorescence, was analysed (*P0.001) n=500. (C) Quantification of LC3‐positive autophagic vesicles in adult muscles co‐tranfected with YFP‐LC3 and DRP1, Fis1 or DRP1/Fis1 expression plasmids or mock vector. (D) Mutations in BH3 domain of Bnip3 (Bnip3BH3mut) do not affect BNIP3‐mediated autophagy. Adult muscles were co‐transfected with YFP‐LC3 and Bnip3 or Bnip3BH3mut expression plasmids and LC3‐positive vesicles were quantified. (E) Bnip3‐mediated atrophy is not modified by mutating the BH3 domain (Bnip3BH3mut). Adult TA muscles were transfected with Bnip3 or Bnip3BH3mut expression plasmids and cross‐sectional area was quantified 7 days later and plotted as % of controls (*P0.001) n=440.
Figure 2 (A) Steady state levels of mitochondrial ribosomal structural subunits (MRPL11 and MRPS17) or assembly factor (C7orf30) of HeLa cells transfected with siRNAs for either NT or for LETM1 (siR1, siR2 or siR3). Vinculin and GAPDH are shown as loading controls. Data are expressed as means ± SEM of n=3 independent experiments for siR1 and siR2, and n=2 (MRPL11) or 1 (MRPS17 and C7orf30) for siR3  (B) Relative 12S (upper panel) and 16S rRNA (lower panel) levels in HeLa cells after LETM1 siRNA compared to NT, n=3 independent experiments  (C) Total lysates from HeLa cells treated with NT or a siRNA for LETM1 were separated on 100 mM NaCl, 10-30% isokinetic sucrose gradients and fractions analyzed by immunoblotting with antibodies to components of the large (39S) and small 28S subunit of the 55S ribosome. Immunoblots were quantified by ImageJ and the value for each fraction expressed as a percentage of the sum of all fractions. Data are expressed as mean ± SEM of n=3 independent experiments  (D) Relative mtDNA copy number estimated by qPCR. Data are expressed as mean ± SEM of n=3 independent experiments except for siR3 (n=2)  (E) The combined average mRNA levels of ND1, COII, COIII, Cyt b and ATP6/8 in HeLa cells treated with either NT or siLETM1 (siR1, siR2 or siR3). Data are mean values ± SEM, n=3 independent experiments
'-phosphopantetheine corrects markers of CoA, iron, and dopamine dyshomeostasis and mitochondrial dysfunction in Pank2 KO mice.Figure 6Relative quantification of Coasy mRNA from GP compared by treatment status using four compounds: 4'-phosphopantetheine (pPanSH), pantetheine, vitamin B5, and CoA. n=8 (WT-veh), 5 (KO-veh), 5 (KO-pPanSH), 4 (KO-all other intermediates). Correction of Coasy, Tfrc, Ireb2, and Drd1 expression in GP by 4'-phosphopantetheine over a range of doses. n=8 (WT-veh), 5 (KO-veh), 5 (KO-0.82), 4 (WT-5), 5 (KO-5), 5 (KO-8.2), 5 (KO-10). 5 (WT-20), 5 (KO-20) Relative quantification of COASY mRNA from human fibroblasts treated with pPanSH. n=3 for both genotypes. ECAR measured in cultured human fibroblasts by genotype and treatment status. Cells were treated for three days with 4'-phosphopantetheine (pPanSH) or vehicle (veh). n=3 for both genotypes.
Figure 4Development and symptom induction of Col-0, visp1-1, visp1-2, rdr6-15, and sgs3-1 plants to mock treatment or CMV-2blm infection at 21 dpi. Scale bar = 2 cm. Long-term systemic symptoms of Col-0, visp1-1, visp1-2, rdr6-15, and sgs3-1 plants inoculated with CMV-2blm at 50 dpi. Scale bar = 2 cm. Western blotting showing accumulation of CMV CP in systemically infected leaves at 14 dpi. Bottom values represent relative accumulation (RA) of CMV CP. RbcL served as loading controls. Northern blotting detecting accumulation of genomic RNAs and RNA3-derived vsiRNAs in systemically infected leaves at 14 dpi. Relative accumulation (RA) of gRNA3 was calculated from band densities.   Northern blotting analyzing accumulation of RNA3-derived vsiRNAs in the same samples as shown in panel D. Bottom values represent relative accumulation (RA) of RNA3-derived vsiRNAs.   Relative accumulation of vsiRNAs/gRNA3 ratios calculated from hybridization signal intensities of northern blotting in panel D. Data points above columns are means of three biological repeats. Error bars indicate SD. Letters indicate significant differences (ANOVA, P < 0.05). Accumulation of the CMV CP protein in inoculated leaves of Col-0, atg5-1, atg7-3, rdr6-15, and sgs3-1 plants with CMV-2blm at 4 dpi.
GO Biological Process enrichment analysis.Figure 2All 131 candidate proteins were used to identify over-represented GO Biological Process terms, which are represented in the following network. Novel processes 'translation' and 'peptide metabolic process' are outlined. The node size corresponds to the number of candidate proteins associated with a particular term. The node colour corresponds to the associated term"s p-value. The line thickness corresponds to the kappa score value to show interrelatedness as defined in the legend. Node position and line length were created arbitr Leading terms from (A) are represented by their associated proteins. 'Translation' node and FXR1 protein are highlighted. The node size corresponds to the p-value of a particular term, as defined in the legend. Node position and line length were created arbitrarily
The full complement of Mcm2‐7 is loaded during an unperturbed G1/S transitionCell cycle analysis by FACS of cells arrested in G1 by Dacapo overexpression followed by release back into the cell cycle for 13 h (top).Figure 2Cell cycle analysis by FACS of cells arrested in G1 by Dacapo overexpression followed by release back into the cell cycle for 13 h (top). Western blot analysis of Mcm2‐7 and Orc2 for the nuclear chromatin and cytoplasmic fractions of Mcm2‐7, Orc2, and Dacapo.
H.Figure 2A Venn diagram showing the overlap of H. influenzae genes whose expression is up-regulated or down-regulated by the presence of corticosteroids in sBHI medium (in vitro) or in the mouse model of infection (in vivo). Genes that are divergently regulated in these conditions are not depicted in this Venn diagram but can be found in the complete RNA-Seq dataset detailed in Supplementary Table S2. B COG map detailing significantly enriched or scarce functional categories expressed in vitro and in vivo during the presence of corticosteroids. C, D Comparison of relative fold changes between RNA-seq and qRT-PCR results in vitro (C) and in vivo (D) in the presence of corticosteroids. All qRT-PCR results were normalized using the Cts obtained for the 16S rRNA amplifications run in the same plate. The relative levels of gene transcripts are determined from standard curves. Values given are the mean and standard deviation of triplicate measurements (three biological and three technical replicates).<!-- ngIf: paper.panels[paper.currentPanelIdx].panel_id --><!-- end ngIf: paper.status != "created" --><!-- /#page-content-wrapper --><!-- /#wrapper -->
Figure 2Body weight. P, postnatal day; w, weeks. Error bars: SD. n=5-12 mice. Hindbrain vessel parameters. Vessel density; isolectinB4 vessel area normalized to WT mean of the litter. Hindbrain vessel parameters. EdU incorporation in ERG-positive ECs normalized to total ERG-positive ECs. P4-P7 retina vessel morphology. IsolectinB4 (IsoB4) in black; outer 20% of the vascularized area in pink. Scale bar, 250 µm. P6 insets; sprout morphology. Scale bar, 50 µm. Radial outgrowth. Distance between optic nerve and vascular front. P, postnatal day; error bars: SD; 2-way ANOVA p<0.0001; Bonferroni's multiple comparison test, *p<0.05. P4 n=3-5 retinas, one retina/mouse, P5 n=4-7, P6 n=9-9, P7 n=4-5. Retina vascularized area. P, postnatal day; error bars: SD; 2-way ANOVA p=0.0013. P4 n=7-9 retinas, one retina/mouse, P5 n=4-9, P6 n=9-9, P7 n=4-5. Retina vessel density in the retinal front. Quantification of the vessel area in the outer 20% of the vasculature (pink in D) (vessel area normalized to vascularized area). P, postnatal day; error bars: SD; 2-way ANOVA p=0.0054; Bonferroni's multiple comparison test, *p<0.05, ** p <0.01. P4 n=3-5 retinas, one retina/mouse, P5 n=4-6, P6 n=3-5, P7 n=4-5. Proliferation of retinal ECs. H. EdU incorporation in ERG-positive ECs normalized to total ERG-positive ECs, at P6. IsolectinB4 (IsoB4; white), ERG (red), EdU (green) and double-positive cells (yellow). Lower panel shows ERG/EdU merged staining alone with EdU signal masked by ERG signal. Scale bar, 50 µm; error bars: SD; unpaired T test, *p < 0.05. n=5-8 retinas, one retina/mouse. Retina sprout length. Sprout length from tip to base in P6 retinas; error bars: SD; unpaired T test, *p<0.05; n=3-5 retinas, one retina/mouse. Vessel stability. IsolectinB4 (IsoB4, green) and collagen IV (red) in P4 wildtype (WT) and Vegfr2Y1212F /Y1212F retinas. Arrows; collagen IV-positive empty sleeves. A; artery. Scale bar, 50 µm. Vessel stability. Collagen IV empty sleeves around main arteries in P4-P7 retinas, three fields/retina/mouse. Error bars: SD; 2-way ANOVA p=0.0580; Bonferroni's multiple comparison test, ** p <0.01. P4 n=7-9, P5 n=6-12, P6 n=3-5, P7 n=4.
GFP–Atg8 mutants were tested for their carboxy‐terminus processing, phosphatidylethanolamine conjugation and autophagic activity.Figure 6(A) GFP-Atg8 localization was determined using fluorescence microscopy (arrows depict pre‐autophagosomal structure, and arrowheads point to GFP within vacuoles). Cells were also tested for the appearance of autophagic bodies by using light microscopy. (B) Immunoblot analysis of different cell extracts was carried out using anti‐GFP antibodies (asterisk represents nonspecific band). (C) Atg8WT-HA, Atg8L50A-HA or Atg8Y49A-HA was transformed into Δatg8 and Δatg8Δatg4 double knockout strains and cell extracts were subjected to SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by immunoblot analysis using anti‐HA antibodies (lower panel; asterisk represents nonspecific band). (D) Atg8WT, Atg8L50A or Atg8Y49A was transformed into Δatg8 and Δatg8Δatg4 double knockout strains and grown under control or starvation conditions for 4 h. Cell extracts were subjected to 13.5% SDS-PAGE containing 6 M urea, followed by immunoblot analysis using anti‐Atg8‐N15 antibodies. GFP, green fluorescent protein; WT, wild type.
H2AQ105me fluctuates with the cell cycle and is a mark of proliferating cells.Figure 1A) Cell cycle profile of H2AQ105me. Logarithmically growing cells were arrested using alpha-factor for 2.5 hours. Upon release (t=0), samples were taken every 15 minutes and samples were analysed for H2AQ105me levels using western blotting. S-phase is indicated by the enrichment of H3K56ac. B) H2AQ105me levels upon arrest (2.5 hours) at different cell cycle stages. Treatment is given above the lanes. C) H2AQ105me levels upon entry of cells into stationary phase. D) H2AQ105me levels in various histone mutations targeting sites of well-known cell cycle-dependent modifications. E) H2AQ105me and H3K56ac levels in deletions of genes important for H3K56ac deposition F) Scheme of rDNA locus and indication of primer locations used in G-J. G-J) ChIP-qPCR for indicated antibodies after treatment with 5nM rapamycin for the indicated time points. Samples were either normalized to input or to the core histone. n=3, biological replicates, error bars are standard error of the mean. *, p<0.05, relative to t=0, based on unpaired, 2-tailed t-test K) ChIP-qPCR for Nop1-FLAG using anti-FLAG tag antibody. Samples were normalized using input. n=3, biological replicates, error bars are standard error of the mean. **, p<0.001, based on unpaired, 2-tailed t-test
Figure 2Variable selection and median canonical weight strength from bootstrap sCCA modeling in the CReATe PGB cohort. See Table EV1 for additional detail on genetic variants.
AP in Aβ endocytic generation in neurons.Figure 8(A) Normal APP and BACE1 endocytic trafficking diverge at early endosomes restricting Aβ generation. 1a. BACE1 endocytosis. 1b. APP endocytosis. 2. BACE1 recycling to the plasma membrane. 3. APP sorting to intraluminal vesicles. 4. APP delivery to the lysosome for degradation. 5. BACE1 cleavage of APP. 6. γ-secretase cleavage of APP-CTF (not represented). 7. Aβ generation.(B) In Bin1-depleted neurons, BACE1 accumulates in early endosomes raising Aβ generation in axons due to inhibition of local BACE1 recycling. Inhibition of recycling likely results from inefficient scission and exit of tubular BACE1 carriers from axonal early endosomes to which Bin1 preferentially associates.(C) In CD2AP-depleted neurons, APP accumulates in early endosomes raising Aβ generation in dendrites due to inhibition of local APP degradation. Inhibition of degradation likely results from impaired sorting of APP in dendritic early endosomes to which CD2AP preferentially associates. Inhibition of APP sorting away from the endosomal limiting membrane favours local APP processing.
ISG20 localizes to nucleoli after interferon treatment.Figure 4dHepaRG cells were infected with HBV at an MOI of 100 virions/cell and treated with 600 U/ml IFNα or 400 U/ml IFNγ from day 10 to 14 p.i. and ISG20 was stained by immunofluorescence. Primary human hepatocytes were infected with HBV at an MOI of 100 virions/cell and treated with 500 U/ml IFNα or 200 U/ml IFNγ from day 4 to 6 p.i. and ISG20 was stained by immunofluorescence. dHepaRG cells were infected with HBV at an MOI of 500 virions/cell, treated with 600 U/ml IFNα or 400 U/ml IFNγ from day 7 to 9 p.i. and stained by immunofluorescence for ISG20 and PML (C) or ISG20 and nucleophosmin (D). Primary human hepatocytes were infected with HBV at an MOI of 100 virions/cell, treated with 500 U/ml IFNα or 200 U/ml IFNγ from day 4 to 6 p.i. and stained for ISG20 and nucleophosmin. White arrowheads indicate double-positive nuclei.
Pathological changes in rhesus macaques infected with SARS-CoV-2.Figure 4.SARS-CoV-2.Eight adult rhesus macaques were inoculated with SARS-CoV-2 isolate nCoV-WA1-2020. Four animals were euthanized on 3 dpi, and 4 animals on 21 dpi. Upon gross examination, lungs showed focal areas of hilar consolidation and hyperemia (circles) on 3 dpi (a) and multifocal, random consolidation and hyperemia (circles) on 21 dpi (b). At necropsy, the percentage of the area of the lungs affected by gross lesions was estimated by a board-certified veterinary pathologist (c) At necropsy lung weight to bodyweight ratio was calculated as a measure for pulmonary edema. (d). The dotted line represents baseline ratio calculated from an in-house collection of rhesus macaque lung and bodyweights from animals with grossly normal lungs. Histological analysis was performed on tissues collected at 3 dpi (e-i). (e) Pulmonary vessels are surrounded by moderate numbers of inflammatory cells (arrows) Magnification 100x. (f) Alveoli are filled with small to moderate numbers of inflammatory cells (asterisks). Adjacent alveolar interstitium (arrows) is thickened by edema, fibrin and inflammatory cells. Magnification 400x. (g) SARS-CoV-2 antigen is detected by immunohistochemistry in type I pneumocytes. Magnification 400x. (h) Pulmonary vessels are bounded by inflammatory cells (arrowhead) and hyaline membranes (arrows) line alveolar spaces. Magnification 100x. (i) Hyaline membranes line alveoli (arrows). Magnification 400x. (j) SARS-CoV-2 antigen is detected by immunohistochemistry in type I pneumocytes (asterisk) and type II pneumocytes (arrow) as well as alveolar macrophages (arrowheads). Magnification 400x. (k) SARS-CoV-2 antigen is detected by immunohistochemistry in mediastinal lymph node. Magnification 400x. (l) SARS-CoV-2 antigen is detected by immunohistochemistry in macrophages and lymphocytes in the lamina propria of the cecum. Magnification 400x.