EMBO/sd-character-level-ner huggingface dataset:
The symbiosis genome of S.Figure 2(A) Schematic representation of the plant infection screen that was used to map the S. meliloti symbiosis genome. Tn5 transposon mutant pools were selected for their ability to establish symbiosis with M. truncatula. After selection, Tn5 mutants recovered from root nodules were identified by TnSeq. (B) Genome map visualizing the distribution of essential symbiosis genes among the three S. meliloti replicons. Symbiosis genes are plotted as lines on the chromosome (grey) and the mega-plasmids pSymA (blue) and pSymB (green). (C) Functional classification of essential symbiosis genes located on the chromosome (grey), pSymA (blue) and pSymB (green).
a, b, d, Western blots from flies expressing the indicated transgenes.figf3a, b, d, Western blots from flies expressing the indicated transgenes. a, Steady state levels of AR52 protein are reduced in flies overexpressing Drosophila HDAC6, but are elevated in flies in which atg6 or atg12 has been knocked down. b, Western blots showing the temporal profile of AR52 protein monomer and high molecular weight aggregate levels after a brief pulse of expression. AR52 protein became detectable by 2.5 h after treatment with RU486, reached a peak at 10 h, and then slowly decayed. c, A logarithmic plot of AR52/actin ratios was used to determine the line of best fit by regression analysis (y = Ae-Kx). R2 = 0.9117 (AR52 - DHT), R2 = 0.7808 (AR52 + DHT), R2 = 0.9719 (HDAC6 + (AR52 - DHT)), R2 = 0.9644 (HDAC6 + (AR52 + DHT)). Half-life was determined by the slope of the best fit line with the equation t1/2 = 0.693/K. Half-life of AR52 in vivo was reduced ∼2-fold in flies co-expressing Drosophila HDAC6 and did not differ significantly in the presence (broken lines) or absence (solid lines) of DHT. Plots of the mean AR52/actin ratios are shown in Supplementary Fig. S12. d, Flies co-expressing Drosophila HDAC6 showed a nearly identical profile of induced expression as in b, but AR protein decayed at an accelerated rate. Exogenous Drosophila HDAC6 was detected by immunoblot against the V5 epitope.
Proteasome activity shows differential decline with aging across tissues and sexes.Figure 3A-D Comparison of chymotrypsin-like activity from female (n=9) and male (n=10) mice in young (3-5 months old) or older (10-15 months old, female (n=6) and male (n=7)) groups. Each point indicates a single mouse. A) Tissues that did not show significant decline, B) Tissues that show significant decline in females only, C) Tissues that show significant decline in males only or D) in both males and females. Each central line and error bar indicate mean +/- SEM of a biological replicates (n=9 young females, n=6 older females, n=10 young males, n=7 older males). P values obtained by unpaired two-tailed students t-test comparing young and older samples are indicated. E-F) Summary Venn diagrams indicating tissues that had significantly different chymotrypsin-like (E) or trypsin-like (F) activity, when comparing young and older mice. Arrows indicate the direction of change (up and down indicate increase and decrease respectively) in female (blue arrows) or male (red arrows) mice.
Figure 6(A) A549 cells were transfected with empty vector (VE) and vector contains Ras-G12V for 24 hours, followed by a 4-hours infection with P. aeruginosa ΔSTY or ΔTY. Cell lysates were evaluated by immunoblotting. (B) A549 cells were transfected, for 24 hours, with empty vector (VE) and vectors contain Ras-G12V or Ras-G12V&R41K followed by a 4-hours infection with P. aeruginosa ΔSTY or ΔTY. Cell lysates were evaluated by immunoblotting.
Schematic representation of ZIKV by targeting the cross-talk between inflammasome and type I IFN signaling.Figure 8ZIKV nonstructural proteins NS1 enhances inflammasome activation to benefit its infection by recruiting USP8 to cleave K11-linked poly-ubiquitin chains from caspase-1 at Lys134. NS1-mediated stabilization of caspase-1 further promotes the cleavage of cGAS, thus inhibiting type I IFN signaling as well as antiviral innate immunity.
Figure 3TNFR1+/+ (n=9) and TNFR1-/- mice (n=11) were treated with 12.5 mg/kg LPS and lethality was monitored. P-values were analyzed with a Fisher's exact test. TLR4fl/fl mice (n=7) and TLR4VillinKO (n=9) mice were treated with 12.5 mg/kg LPS and lethality was monitored. P-values were analyzed with a Fisher's exact test. TNFR1fl/fl mice (n=13) and TNFR1VillinKO (n=10) mice were treated with 12.5 mg/kg LPS and lethality was monitored. P-values were analyzed with a Fisher's exact test. Venn diagram of LPS- and TNF-upregulated genes in IEC, as identified by RNA-seq (n=3). HOMER motif analysis was performed on the 692 overlapping genes. Motifs with the highest rank and their p-value and q-value are displayed. TNFR1+/+ and TNFR1-/- mice (n=4-6) were treated with 12.5 mg/kg LPS. Ileum was isolated and gene expression was measured via qPCR. Fold changes are shown on the graph. TNFR1fl/fl and TNFR1VillinKO mice (n=4-6) were treated with 12.5 mg/kg LPS. Ileum was isolated and gene expression was measured via qPCR. Fold changes are shown on the graph.
Figure 1A) Cartoon of Coronavirus PLpro activities. PLpro is encoded as one of various domains of the 1900 amino-acid non-structural protein nsp3, and is thought to have three functions: (i) cleaving the viral polyprotein to generate mature nsp1, nsp2 and nsp3; (ii) hydrolysing ubiquitin chains important for inflammatory responses, and (iii) removing interferon-stimulated gene 15 (ISG15) modifications from proteins, reversing antiviral responses. B) Schematic of ubiquitin binding sites in SARS PLpro, which binds Lys48-triubiquitin via S2, S1, and S1' ubiquitin binding sites, and hydrolysis occurs between ubiquitin molecules bound at S1 and S1'. C) Time course analysis of triubiquitin (2 µM) hydrolysis using 250 nM SARS2 PLpro, resolved on a Coomassie stained SDS-PAGE gel. Linkage specific cleavage of Lys48-linked triubiquitin to di- and monoubiquitin resembles SARS PLpro activity (Békés et al, 2015; 2016). See Source Data for uncropped gels, and Appendix Fig S1B-D for gel-based cleavage quantification. D) Overview the catalytic efficiencies of PLpro. A fluorescence polarisation (FP) assay was used to derive the catalytic efficiencies (kcat/KM) of PLpro for the depicted substrates. Catalytic efficiencies were calculated from data shown in Appendix Fig S1A, as described in Methods. Substrate preference is indicated by x-fold activity relative to Ub-TAMRA cleavage. E) Crystal structure at 2.7 Å resolution of SARS2 PLpro with subdomains coloured in shades of blue, bound to ubiquitin propargylamine (Ub-PA, orange). Catalytic triad residues are shown in ball-and-stick representation, and a Zn ion is indicated as a grey sphere. Also see Appendix Fig S2 and Table 1. F) Crystal structure at 2.9 Å resolution of SARS2 PLpro (blue) bound to ISG15 C-terminal domain propargylamide (ISGCTD-PA, salmon). Also see Appendix Fig S2 and Table 1.
Partially decoupled regulation of transcriptional dynamic parameters inferred from protein and RNA measurements Summary of Hsp12-GFP dynamics single mutant screen.Figure 2Summary of Hsp12-GFP dynamics single mutant screen. 68 mutants were divided into three groups: increased/decreased/did not change the total GFP produced. Each group was independently hierarchically clustered. The values shown are the Z-Scores of each parameter: ton- response onset time; production rate; total open time - length of transcriptional window (toff − ton); Basal GFP - GFP levels measured before exposure to stress; Delta GFP - amount of GFP produced throughout the experiment (Max GFP - Basal GFP). The dynamic parameters are regulated by partially independent mechanisms. Mutant strains can be roughly divided to three groups: affecting total open time, affecting production rate and affecting both. Outline of mRNA-Seq experiment. 16 yeast strains were grown to mid-log phase, exposed to 0.4M KCl and sampled in the indicated time points after exposure to stress. mRNA levels of HSP12 (Y axis) as a function of time (X axis) in six representative strains. Comparison of RNA levels to protein levels. X axis is the sum over the HSP12 mRNA counts (see D). Y axis is the maximum over the Hsp12-GFP values. The red line indicates the best linear fit. Comparing the total open time parameter inferred from mRNA data (X axis) to the one inferred from protein data (Y axis). production/transcription rates. Time-lapse microscopy of Hsp12-GFP in response to stress (0.4M KCl). Examples of raw images (top) and traces of individual cells (bottom). Traces are colored according to their basal GFP level. Scatter plot showing the production rate estimated from single traces vs. the production rate estimated from the population average. Each point represents a different yeast strain.
Figure 1Representative confocal z-stack images of co-immunostaining for β-galactosidase (green) and CAMKII (red, upper) or GAD67 (magenta, lower) in neurons from the brains of Cdc50a knockout-first allele (Cdc50a lacZ/+) mice. Scale bar, 20 μm. Survival rates of control and Cdc50a cKO mice after oil or 4-OHT injection (n = 5 for each group, P*** = 0.0003). Schematic diagram of the experiment. Mice of both genotypes were sacrificed 13 days after oil or 4-OHT injection. Representative confocal z-stack images of cleaved caspase-3 (cCas3, red)- and Thy1-CreERT2, -EYFP (green)-expressing cells from control and Cdc50a cKO mice. Scale bar, 20 μm. Schematic diagram of behavioral tests for measuring audiogenic seizures (0: normal behavior, 1: wild running, 2: seizure, and 3: respiratory arrest and death) following auditory stimuli. Bar graphs showing audiogenic seizure scores following auditory stimuli (5, 10, 15, 20, 40 kHz or white noise (WN) at 70, 80, 90, or 100 dB) in control (E) and Cdc50a cKO (F) mice (n = 8 for each group). Representative confocal z-stack images showing cFos (magenta)-positive neurons from control and Cdc50a cKO mice (CTX: cortex, HP: hippocampus, and IC: inferior colliculus). Scale bar, 20 μm. Bar graphs showing the relative area of cFos-positive cells in the brains of control and Cdc50a cKO mice (n = 5 for each group, **P = 0.0030, n.s., not significant).
E.Figure 4A.) Construct used to express the E. coli DPCK protein with a C-terminal mCherry tag in the cytosol of the PfMev parasite line. B.) Live epifluorescence microscopy of the PfMev EcDPCK-mCherry line. This parasite line expresses api-SFG (green) and EcDPCK-mCherry (red) with DAPI marking the nuclei (blue). D.) Live epifluorescence microscopy of the PfMev EcDPCK-mCherry Δdpck line. This parasite line expresses api-SFG (green) and EcDPCK-mCherry (red) with DAPI marking the nuclei (blue). Data information: All microscopy images represent fields that are 10µm long by 10µm wide. C.) Genotyping PCR confirming the deletion of the endogenous DPCK using primer pairs E.) Attempted PCR detection of the ldh, sufB, and cox1 genes from the nuclear (N), apicoplast (A), and mitochondrial (M) genomes, respectively. We were successful in amplifying sufB from the PfMev EcDPCK-mCherry Δdpck parasite line grown under continuous supplementation with 50μM mevalonate, indicating retention of the apicoplast organellar genome.
Figure 8A Images of coronal sections of layer Vsensorimotor cortex from NB-3+/+ and NB-3−/−mice after SCI. Corticospinal neurons were retrogradely labeled with Fluorogold (FG), and coronal sections were co-stained with p-mTOR (A) (arrowheads).B Quantification of fluorescence intensity of p-mTOR in FG-labeled corticospinal neurons in (A). *p < 0.05, and **p < 0.01; one-way ANOVA followed by Bonferroni post-test. The intensities of more than 300 corticospinal neurons from 3 mice in each group were quantified. C Images of coronal sections of layer Vsensorimotor cortex from NB-3+/+ and NB-3−/−mice after SCI. Corticospinal neurons were retrogradely labeled with Fluorogold (FG), and coronal sections were co-stained with p-S6 (S240/244) (C) (arrowheads).D Quantification of fluorescence intensity of p-S6 (S240/244) in FG-labeled corticospinal neurons in (C). *p < 0.05, and **p < 0.01; one-way ANOVA followed by Bonferroni post-test. The intensities of more than 300 corticospinal neurons from 3 mice in each group were quantified. E-H Western blot analysis and quantification of the expression of p-Akt/Akt (E and F) and p-S6 (S240/244) (G and H) in sensorimotor cortex from NB-3+/+ and NB-3−/− mice after SCI. *p < 0.05, and **p < 0.01; one-way ANOVA followed by Bonferroni post-test. Data were analyzed from 3 independent experiments each including 3 mice per group. I, K, M, O Expression of Akt (I), p-Akt (K), p-mTOR (M), and p-S6 (S240/244) (O) in NB-3+/+ pyramidal neuron-astrocyte co-cultures. The astrocytes were transfected either with NB-3-Myc or a control vector. The dashed lines outline the astrocytes. The asterisks indicate the NB-3-expressing astrocytes.J, L, N, P Quantification of fluorescence intensity of Akt (J), p-Akt (L), p-mTOR (N), and p-S6 (S240/244) (P), respectively, in pyramidal neurons of the co-cultures in (I, K, M, and O). n.s., not significant, and *p < 0.05; one sample t-test. The intensities of more than 300 pyramidal neurons from 6 independent experiments in each group were quantified.
Transcriptional regulation of micV A) Alignment of micV sequences, including the promoter regions, from various Vibrio species.Figure 1Alignment of micV sequences, including the promoter regions, from various Vibrio species. The -35 box, -10 box, the TSS, the highly conserved potential seed region, and the rho-independent terminator are indicated. Lower part: Consensus motif of E. coli σE-dependent promoters. V. cholerae wild-type and ΔrpoE strains carrying the indicated plasmids were grown to early stationary phase (OD600 of 1.5) and induced with L-arabinose (0.2% final conc.). Expression of MicV and VrrA was monitored on Northern blots. 5S rRNA served as loading control. V. cholerae wild-type, ΔvchM and ΔvchM ΔrpoE strains harboring PmicV::mKate2 plasmids were grown in M9 medium. Samples were collected during various growth phases and analyzed for fluorescence. V. cholerae wild-type and ΔrpoE strains carrying PmicV::mKate2 plasmids were cultivated in LB to exponential phase (OD600 of 0.4) and treated with ethanol (3.5% final conc.), or water. Fluorescence was determined 180 min after ethanol treatment and mKate2 levels of the mock-treated samples were set to 1. V. cholerae wild-type and ΔrpoE strains carrying PvrrA::mKate2 (E) plasmids were cultivated in LB to exponential phase (OD600 of 0.4) and treated with ethanol (3.5% final conc.), or water. Fluorescence was determined 180 min after ethanol treatment and mKate2 levels of the mock-treated samples were set to 1. V. cholerae wild-type, ΔmicV, ΔvrrA or ΔvrrA ΔmicV strains were grown in LB to OD600 of 0.2 and treated with ethanol (3.5% final conc.). After 5h of treatment, serial dilutions were prepared, recovered on agar plates and CFU / ml were determined.
Figure 4Mice were treated with IFNα (1.45μg/50μl), IFNλ (2.6μg/50μl) or Veh Ctrl (50μl PBS), and whole lungs were taken at 18hrs post treatment for global analysis by Illumina.SingleColor.Mouse WG-6_V2_0_R0_1127 microarrays. Samples (n=5) were normalized to the median of the vehicle control group and filtered for a fold change of 1.5, yielding 553 genes differently regulated between treatments (One way ANOVA, P<0.01, Benjamini-Hochberg multiple test correction), of which 429 genes are upregulated. K means clustering revealed six gene clusters, one of which encompassed genes primarily induced by IFNα4 (A), while the remaining clusters contained genes upregulated by both IFNα4 and IFNλ2 (B). The two clusters of genes were analysed by Ingenuity Pathway Analysis (IPA) (C,D).
Figure 2A. Schematic of the genetic de novo telomere addition assay used in B. Cells with a galactose-inducible HO-cut are grown on YP agar with raffinose prior to plating appropriate dilutions on YPD (no DSB induction) to score cell titre, and YP with galactose to induce HO expression and DSBs. DSB repair via de novo telomere addition leads to URA3 loss and the ADH4-MNT2 locus becoming part of terminal restriction fragments containing telomeres, which can be assayed by Southern blotting. Triangle represents the HO site. B. Srs2 requirement in de novo telomere addition in cells with and without functional HR. All strains are pif1-m2. Strains used: NK1264; NK2375, NK2376; NK2014, NK2015; NK2451, NK2452; NK2012, NK2013; NK2457, NK2458; NK2363, NK2364; NK2469; 2369, NK2370; NK2473-2475. C. Schematic of the qPCR assay used in D to monitor (TG1-3)n addition to DSBs. Triangle represents HO site, blue arrows - qPCR primers. D. Dynamics of (TG1-3)n addition monitored by qPCR through a time-course experiment (asynchronous populations). The Y axis shows a fold increase in de novo telomere-specific PCR product relative to the background levels at 0 h and normalised against an internal control (ARO1 locus). Average ± SD (n=3) is shown for each time-point of each genotype. Strains used: NK3292, NK3293; NK4670, NK4671; NK4112, NK4113; NK4114, NK4115; NK3292 est2∆, NK3293 est2∆; NK4232, NK4233. E. Schematic of the qPCR assay coupled with PsiI digestion used in F to quantify ssDNA/dsDNA ratio at the de novo telomere addition locus. Numbers indicate positions of PsiI restriction sites and qPCR primer sequences relative to DSBs. Blue arrows represent qPCR primers, dashed lines - telomeres. F. Comparative analysis of ssDNA/dsDNA at de novo telomere addition loci in SRS2 and srs2Δ during a time-course experiment (synchronised populations). The Y axis shows a fold increase in de novo telomere-specific PCR product relative to the background levels at 0 h and normalised against an internal control (ARO1 locus). Average ± SD (n=3) is shown for each time-point of each genotype. Top set of error bars represents SD in relative increase of the de novo telomere-specific PCR product (as in panel D) while the lower set of error bars corresponds to quantifications of ss/dsDNA fractions. Strains used: NK3292, NK3293; NK4670, NK4671.
Figure 2A. Osmotic stress induces YAP nuclear translocation. HEK293A cells were serum starved for 1 hr followed by 0.2 M sorbitol treatment for 1 hr. YAP/TAZ (red, upper panels) or YAP (red, lower panels) were stained with two specific antibodies. DAPI (blue) was used to visualize cell nuclei. Scale bar: 20 μm. Quantification of more nuclear (N > C) or more cytosolic (N < C) YAP signal is determined with randomly chosen fields. B. Osmotic stress induces TAZ nuclear translocation. YAP knockout (KO) HEK293A cells were serum starved for 1 hr followed by 0.2 M sorbitol treatment for 1 hr. TAZ localization was determined by immunofluorescence staining with the YAP/TAZ antibody (red). Scale bar: 20 μm. C. Osmotic stress induces a transient YAP nuclear translocation. HEK293A cells were serum starved for 1 hr followed by 0.2 M sorbitol treatment for the indicated time points. D. Osmotic stress induces YAP target gene expression. Wild type (WT) or YAP/TAZ double knockout (Y/T KO) HEK293A cells were serum starved for 1 hr and treated with 0.2 M sorbitol for 4 hr. mRNA levels of CTGF and CYR61 were measured by quantitative RT-PCR and normalized to GAPDH control. Data are presented as mean ± SEM. *p < 0.05 (two tailed student's t-test, n = 3). E. Osmotic stress decreases YAP and 14-3-3 interaction. HEK293A cells were transiently transfected with Flag-YAP and Myc-14-3-3, and were serum starved for 16 hr. Cells were then treated with 0.2 M sorbitol for the indicated time points. Myc-14-3-3 was immunoprecipitated and the associated Flag-YAP was detected by Western. Data are presented as mean ± SEM. *p < 0.05 (two tailed student's t-test, n = 3).
Neurons form functional TNT-like structures.Figure 7Representative confocal images of co-cultured donor (D, labeled with DiI) and acceptor (A, labeled with CTG) neurons treated or not with 200 ng/mL of Wnt5a, 200 ng/mL sFRP-2 or 200 ng/mL Wnt5a plus 200 ng/mL sFRP-2 for 4 h. Yellow arrows point to DiI-labeled vesicles inside acceptor neurons. Percentage of acceptor neurons containing DiI-labeled vesicles after being co-cultured with donor neurons and incubated for 4 h with the indicated treatments. Primary cortical neurons at 1 DIV were fixed and labeled with MAP-2 (green), β-III-tubulin (red) and WGA (white). The inset shows a magnified image of the area depicted in the merged panel. Yellow arrowheads point out TNT-like structures. Transfer of α-syn fibrils is shown in neurons at 1 DIV. Cells were loaded in suspension with either Alexa-568 α-syn fibrils (red) or Alexa-488 α-syn fibrils (green) and cultured together. The insets (right panels) show a magnification of the area depicted in the expanded field image (left). Yellow arrows point to red and green α-syn puncta contained in the soma of a neuron. Yellow arrowhead points to a TNT-like connection. A TNT-like connection containing Alexa-488 α-syn positive puncta is found in neurons at 1 DIV stained with phalloidin (white) and DAPI (blue). The insets (right panels) show the 3D reconstruction of the area depicted in the expanded field image (left).
Figure 2A Representative STED super-resolution images of WT and MIC10 KO HAP1 cells immunostained with MIC60 or MIC10 antibodies (top panel) and TOMM70 (middle panel). Bottom panel shows merged images. Arrowheads show colocalization of MIC60 and TOMM70 punctae. Scale bar 500 nm. B Quantification of median interpunctae distance (IPD) per mitochondrion between MIC60 or MIC10 punctae in indicated cell lines represented by boxplots. Boxplots show median and interquartile range from 25 to 75 percentile and whiskers represent minimum and maximum value. Median IPD from n = 10-16 mitochondria (from 2 independent experiments) are shown as data points in the boxplots. ns, not significant, unpaired Student's t-test. C Scheme shows MIC60 marking the nascent sites of CJs formation independent of MIC10 and presence of contact sites in WT and MIC10 KO HAP1 cells shown by colocalization of MIC60 and TOMM70.
Figure 1(A) Chromatin features mapped here displayed differences between CLL (patient CLL1) and an NBC donor (H7) as shown for the TCF4 locus, which encodes for a transcription factor from the E protein family. Based on the increased H3K4me1, H3K27ac and ATAC signal, two predicted enhancer loci were marked that became active in CLL. Note that the y-axis for RNA-seq is scaled differently for CLL (8000) and NBCs (100) to visualize that the TCF4 gene was not completely silenced but lowly expressed also in NBCs as evident also from the H3K36me3 mark. Light grey depicts active chromatin region and dark grey the confined enhancer locus coinciding with an open chromatin region. (B) Chromatin segmentation of co-occurring histone modifications by ChromHMM yielding a model with 12 chromatin states. The indicated emission parameters for the contributions of individual histone marks and the average amount of each state (Mb) for CLL and NBC samples is given. (C) Chord diagram representation of genome wide chromatin state changes. The amount of chromatin change is proportional to the size of the segments with each tick representing 4 Mb of chromatin. (D) Distribution of ~24,400 annotated differentially accessible regions (ATAC-seq) in NBC and CLL samples according to the chromatin state annotation. In total 7,605 annotated regions gained an ATAC-seq signal in CLL, while it was lost at 16,790 loci. (E) Part of the computed B cell gene regulatory network showing TCF4 and its deregulated target genes as well as some of the adjacent nodes. The GRN was used to calculate the activity of regulators like TCF4 based on their target gene expression. Color code: TFs, red; target genes, grey; chromatin modifier, blue.