EMBO/sd-character-level-ner huggingface dataset:
Cilia localisation of wild-type and mutant Smo.Figure 6A Wild type 18hpf embryos injected with mRNA encoding GFP-tagged mSmo (green) showing localisation to the PC of myotomal cells labeled with anti-Acetylated tubulin (AcTub; red), stimulated in response to Shh injection (n = 4). Differences in PC distribution are due to morphological changes in the myotome induced by ectopic expression of Shh as revealed by the distribution of nuclei (DAPI stained; blue). Scale bar, 10μm. B Notochord cells of wild type embryos expressing GFP tagged wild-type and mutant forms of mSmo. Note the localisation to the PC (labeled with anti-AcTub; red) in each case (n=4 for each sample). Scale bar, 10μm. C MZgrk2 18hpf embryos injected with mRNA encoding GFP-tagged wild type mSmo or mSmoSA (green) showing localisation to the PC (labeled with anti- AcTub; red) in myotomal cells. More Smo is localised to the PC in MZgrk2 mutants compared to wild type (panel A). Scale bar, 10μm.
Identification of the human-associated clade from Streptococcus suis population.Figure 1Correlation of the Maximum-likelihood tree with genetic and phenotypic classification/clustering. Maximum-likelihood tree was constructed using genome-wide SNPs of 1634 S. suis isolates. Tip nodes are colored based on the host source (human in red; diseased pig in yellow; healthy pig in green). From inside to outside: the first ring represents BAPS clustering; the second ring represents the country source. Human-associated Clade (HAC) are colored in red, with Diseased-pig Clade (DPC) in yellow and Healthy-pig Clade (HPC) in green. Phylogenetic relationship is consistent with BAPS clustering and correlates with host source. Most isolates in BAPS2, BAPS5, BAPS6 were obtained from healthy pigs. The majority of isolates in BAPS7 and BAPS8 were obtained from patients and diseased pigs, respectively. Phylogenetic tree (unrooted) showing three important clades (HAC in red; DPC in yellow; HPC in green).
Figure 5(A, B) Role of the Lqs system for PflaA expression in intracellular L. pneumophila. A. castellanii was infected (MOI 5, 48 h) with L. pneumophila JR32, ∆lqsA, ∆lqsR, ∆lqsS, ∆lqsT, or ∆lqsS-∆lqsT harboring Ptac-mCherry-PflaA-gfp, and (A) fixed and analyzed by confocal microscopy (representative 3D reconstructions, scale bars: 10 µm), or (B) lysed, fixed and analyzed by flow cytometry. (C-F) Role of the Lqs system for LCV escape and cytosolic localization of L. pneumophila. (C, D) A. castellanii or (E, F) D. discoideum was infected (MOI 5, 48 h) with L. pneumophila JR32, ∆lqsA, ∆lqsR, ∆lqsS, ∆lqsT, or ∆lqsS-∆lqsT harboring Ptac-mCherry-PflaA-gfp, fixed and treated with an anti‐ubiquitin antibody. Amoebae containing bacteria decorated with ubiquitin were quantified by confocal microscopy. Representative images of (C) A. castellanii (scale bars: 10 µm) or (E) D. discoideum (scale bars: 5 μm) infected with L. pneumophila JR32 escaping or not from the LCV are shown. The percentage of amoebae containing ubiquitinated bacteria was quantified by counting the total number of infected cells and the number of ubiquitinated cells: (D) JR32: n = 482; ΔlqsA: n = 834; ΔlqsR: n = 572; ΔlqsS: n = 729; ΔlqsT: n = 1469; ΔlqsS-ΔlqsT: n = 693; (F): JR32: n = 136; ΔlqsA: n = 201; ΔlqsR: n = 303; ΔlqsS: n = 183; ΔlqsT: n = 534; ΔlqsS-ΔlqsT: n = 180. (G, H) D. discoideum producing the LCV/PtdIns(4)P probe P4C-GFP and cytosolic-mCherry was infected (MOI 5, 48 h) with L. pneumophila JR32, ∆lqsA, ∆lqsR, ∆lqsS, ∆lqsT, ∆lqsS-∆lqsT, or ∆flaA harboring Ptac-mCerulean. Representative images of (G) D. discoideum infected with L.-pneumophila JR32 in intact cells with intact LCV (18.5%), lysed cells and lysed LCVs (60.2%), intact cells with lysed LCVs (15.5%) and lysed cells with intact LCVS (5.8%) are shown (scale bars: 5 µm). (H) The percentage of amoebae with intact LCVs was quantified by counting the total number of infected cells and the number of cells with intact LCV membrane: JR32: n = 426; ΔlqsA: n = 468; ΔlqsR: n = 344; ΔlqsS: n = 325; ΔlqsT: n = 287; ΔlqsS-ΔlqsT: n = 289; ΔflaA: n = 248.
PTX-mediated changes in synaptic genes.Figure 7Schematic representation of significantly changing genes (compartment RNA-sequencing) associated with excitatory synapses. Genes differentially expressed in only one compartment are highlighted with either yellow (processes compartment) or blue (somata compartment). The direction of change is illustrated as symbol shape (circle = sign. downregulated genes, triangle = sign. upregulated genes). miR-34 family binding sites in sign. downregulated genes are marked with a dashed line.
Figure 1(A) The intraerythrocytic state of P. falciparum illustrating the localization of PfFNT within the parasite's plasma membrane. (B) Cryo-EM density map of pentameric PfFNT viewed from the parasite's cytoplasm. The five protomers of pentameric PfFNT are colored yellow, cyan, orange, slate and purple. (C) Ribbon diagram of the 2.56-Å resolution structure of pentameric PfFNT viewed from the parasite's cytoplasm. The five protomers of pentameric PfFNT are colored yellow, cyan, orange, slate and purple. (D) Ribbon diagram of pentameric PfFNT viewed from the parasite's membrane plane. The five protomers of pentameric PfFNT are colored yellow, cyan, orange, slate and purple. (E) Ribbon diagram of pentameric PfFNT viewed from the extracellular side of the parasite. The five protomers of pentameric PfFNT are colored yellow, cyan, orange, slate and purple. (F) Structure of a protomer of PfFNT. This ribbon diagram is colored using a rainbow gradient from the N-terminus (blue) to the C-terminus (red).
Figure 2A, B The overlap of upregulated (A) and downregulated (B) ageing-regulated differentially expressed genes (Age-DEGs) in the worm and the analysed tissues. The number and ratio of Age-DEGs are shown in the corresponding Venn diagrams. Hypergeometric test. C The overlap of Age-DEGs among tissues. D The number of common upregulated (left) and downregulated (right) Age-DEGs drops with the increase of analysed tissues. The x-axis denotes the numbers of analysed tissues.
GABAergic neuron defects in zebrafish chd7 mutant brain.Figure 2A. Structural illustration of 5 dpf zebrafish brain from dorsal (top) and lateral (bottom) view (OB: Olfactory bulb, Tel: Telencephalon, OT: Optic tectum, CB: Cerebellum, HB: Hindbrain). B. 5dpf dlx5a/6a transgenic line showing GFP+ GABAergic neurons are reduced in chd7-/- mutants (bottom) in comparison to controls (top) in both dorsal (left) and ventral (right) view. C-H Total number of GABAergic neurons (GFP+ cells) in (C, D) the optic tectum (OT) and cerebellum (CB) regions of 5 dpf wild-type and chd7 mutant fish (n=16; ****p<0.0001; Student's unpaired t-test), (E, F) the hypothalamus (hyp) region (n=10; *p=0.0182; Student's t-test) and (G, H) the telencephalon (tel) (n=7; *p=0.0347; Student's t-test). I. Treatment of control (dark grey) and mutants (light grey) with GABA agonists Baclofen (N=3, n=24; ns, p=0.1427; Student's t-test) and Muscimol (N=3, n=24; ns, p=0.3987; Student's t-test) showing recovery of hyperactive locomotor activity in chd7-/- mutants (vehicle: N=3, n=24, **** denotes p<0.0001; Student's t-test). J, Functional analysis of GABAergic signalling shows increased responsiveness to GABA antagonist PTZ in both onset and overall locomotor activity (n=24; ****p<0.0001; one way ANOVA). K. Average locomotor activity between 2 dpf controls (black) and chd7-/- mutants (red) shows increased activity after 3 mM PTZ exposure (n=24; ***p<0.001; two-way ANOVA).
Structural mobility of an inter-layer GluN1 protruding loop during rolling.Figure 5Left, localization of interface 1 between GluN1 ABD and GluN2B NTD. This interface involves a GluN1 specific loop that protrudes from GluN1 ABD upper lobe towards GluN2B NTD lower lobe. Right, Initial and final frames of the fitting presented in Fig 4 at interface 1. The two pairs of residues targeted for cysteine mutations GluN1-N492/GluN2B-S188 and GluN1-K495/GluN2B-N192 are shown as spheres linked by a dotted line colored black and red, respectively Evolution of Cα-Cα distances of the two pairs of residues GluN1-N492/GluN2B-S188 and GluN1-K495/GluN2B-N192 during the fitting MK-801 inhibition kinetics. On-rate constants (kon) of inhibition by 10 nM MK-801 on wild-type (WT) and mutant receptors. All values are normalized to that obtained for WT GluN1/GluN2B receptors
Rap2b knockdown does not affect Hla-induced autophagy.Figure 5(A) HeLa cells were cotransfected with Rap2b siRNA and GFP-LC3 (right panel) or irrelevant siRNA and GFP-LC3 (left panel). Forty-eight hours after transfection, they were incubated for 2 h in starvation medium (Stv), with 50 ng/µl of rapamycin (Rapa) or treated for 4 h with 10 µg/ml of α-hemolysin (Hla). Cells without any treatment were used as control (Ctr). Cells were analyzed by confocal microscopy. Images are representative of two independent experiments. (B) Quantification of the percentage of cells presenting LC3 puncta upon incubation under the different conditions. Data correspond to two independent experiments (n = 50 cells/condition). (C) Upper panel: The knockdown of Rap2b was determined by Western blot as indicated in Materials and Methods. Lower panel: The band intensities of two independent experiments were quantified with the Adobe Photoshop program, and normalized against tubulin. * p<0.05 (paired Student's t-test). (D) HeLa cells were cotransfected with GFP-LC3 and Rap2b siRNA or an irrelevant siRNA and incubated for 4 h with complete medium in the absence (Ctr) or presence of 10 µg/ml of α-hemolysin (Hla), with 50 ng/µl of rapamycin (Rapa) or subjected to starvation conditions (Stv) for 2 h. Afterwards, cells were lysed with sample buffer and the samples were subjected to Western blot analysis using a rabbit anti-LC3 and the corresponding HRP-labeled secondary antibody, and subsequently developed with an enhanced chemiluminescence detection kit. These data are representative of two independent experiments. (E) The band intensities of two independent experiments were quantified with the Adobe Photoshop program, and normalized against tubulin. * p<0.05 (paired Student's t-test).
Figure 4A. Quantitative phospho-proteomics workflow. B. Volcano plot of the mass spectrometry data from the experiment in A C. List of proteins containing phosphorylation sites more abundant in cells expressing CDKL5NLS-WT versus KD, with phosphorylation sites having PTM score probabilities > 75% (peptides with a 100% PTM score probability are shaded in grey). Phosphorylation sites with a R-P-X-[S/T]-[A/G/P/S] motif are highlighted in red. D. Protein-protein interaction network of putative CDKL5 substrates from Table EV1. Confidence levels are based on the STRING database v11.0 combined score with following bins: 150-400: low confidence (blue), 400-700: medium confidence (gold), 700-900: high confidence (not encountered in this dataset), >900: very high confidence (black). P-value was calculated as 0.00068. E. Analysis of GO terms. Significance cut-off was set as α = 0.01 with at least 3 proteins identified in the respective group. GO term enrichment factor expresses the relative over-representation of the GO term within the group of proteins containing a phosphorylation site that is more abundant in WT compared with KD compared with the group of all proteins.
a, The production of LC3-II.figf2a, The production of LC3-II. Gapdh was used as a loading control. b, c, Punctate GFP-LC3 fluorescence in WT MEFs but not in Atg5-/- MEFs. b, Representative photographs. c, Graphical presentation of the percentages of WT MEFs and Atg5-/- MEFs with punctate GFP-LC3 fluorescence. b, c, Punctate GFP-LC3 fluorescence in WT MEFs but not in Atg5-/- MEFs. b, Representative photographs. c, Graphical presentation of the percentages of WT MEFs and Atg5-/- MEFs with punctate GFP-LC3 fluorescence. d, The same GFP-LC3-transfected Atg5-/- MEFs were assessed by IF and by EM. The magnified photo is the area indicated by the squares. Arrows indicate AVs. e, Atg5-/- MEFs were incubated without (NT) or with etoposide and immunostained with an anti-Lamp2 antibody (green). Nuclei were counterstained (red). The percentages of cells with punctate Lamp2 immunostaining are shown (means ± s.d., n = 4). f, Microarray analysis of the Atg5-/- MEFs during treatment with etoposide. g, h, Induction of Ulk1 in the etoposide-treated Atg5-/- MEFs was assessed by qPCR (g) and by immunoblotting (h). i-l, Atg5-/- MEFs were transfected with the siRNAs related to the Ulk1 complex (i, j) for 24 h and treated with etoposide for 18 h. Induction of macroautophagy was assessed by Lamp2 IF (i, k) i-l, Atg5-/- MEFs were transfected with the siRNAs related to the Ulk1 complex (i, j) for 24 h and treated with etoposide for 18 h. Induction of macroautophagy was assessed by EM (j, l). i-l, Atg5-/- MEFs were transfected with the siRNAs related to the PI(3) K complex (k, l) and a beclin 1 plasmid (k) for 24 h and treated with etoposide for 18 h. Induction of macroautophagy was assessed by Lamp2 IF (i, k). i-l, Atg5-/- MEFs were transfected with the siRNAs related to the PI(3) K complex (k, l) for 24 h and treated with etoposide for 18 h. Induction of macroautophagy was assessed by EM (j, l).
Figure 1A Expression of transcripts coding for PI3K subunit genes in pDCs (n =12 biological replicates). In the boxplot, the middle, the bottom, and the top of the box represent the median, the 1st quantile and the 3rd quantile, respectively; the height of the box is given by the difference between the 3rd and the 1st quantiles (IQR, interquartile range); the whiskers length is 1.5 times the interquartile range. Data points beyond the whiskers represent values more extreme than 1.5 times the interquartile range above or below the 3rd or the 1st quantile, respectively. B Selectivity of PI3K inhibitors used in this study. C Kyn levels in culture supernatants of pDCs incubated for 24 h with medium alone (Ctrl) or IFN-γ after 1−h pretreatment with PI3K inhibitors. D Real-time PCR analysis of Ido1 and Tgfb1 transcripts in pDCs stimulated for 18 h with TGF-β, in the presence or absence (Ctrl, control) of catalytic PI3K inhibitors, normalized to the expression of Gapdh and presented relative to results in untreated cells (dotted line, 1-fold). E In vivo suppression of the activity of HY-pulsed CD8− DCs in combination with a minority fraction (5%) of pDCs conditioned in vitro with TGF-β (or medium) for 24 h in the presence or absence (Ctrl) of catalytic inhibitors as in C. Analysis of skin reactivity of recipient mice to the eliciting peptide at 15 days is presented as change in footpad weight (experimental versus control footpads). F Real-time PCR analysis of Ido1 and Tgfb1 transcripts in pDCs transfected with p110α-, β-, δ-specific, or negative control (nc) siRNA and stimulated for 18 h with TGF-β, normalized to the expression of Gapdh and presented relative to results in unstimulated cells (dotted line, 1-fold). G In vivo suppression of the activity of HY-pulsed CD8− DCs in combination with a minority fraction (5%) of pDCs transfected with siRNA as in (F) and conditioned in vitro with TGF-β (or medium) for 24 h. Analysis of skin reactivity of recipient mice to the eliciting peptide at 15 days is presented as change in footpad weight (experimental versus control footpads).
Figure 3Luminex analytes from WT CHIKV-infected joint cell lysates are categorized based on fold change states (up, down at 2 dpi relative to mock, and 6 dpi relative to 2 dpi. The numbers in the heatmap represent Log2 fold changes of analytes or genes. Analytes in complete or partial agreement with corresponding gene expression values derived from RNA-sequencing (RNA-seq) data appeared predominantly in the (A) up then down state (Mock to 2 dpi, then 2 dpi to 6 dpi, respectively), (B Top canonical pathways discovered by Ingenuity pathway analysis (IPA). Corresponding associated transcripts in acute antiviral and cell signaling canonical pathways are presented as a heatmap showing the Log2 fold change. The study analytes and transcripts in the RNA-seq data from wild-type CHIKV-infected and mock-infected samples in the same states were used. (C, Luminex analytes from WT CHIKV-infected joint cell lysates are categorized based on fold change states no difference (ND)) at 2 dpi relative to mock, and 6 dpi relative to 2 dpi. The numbers in the heatmap represent Log2 fold changes of analytes or genes. Analytes in complete or partial agreement with corresponding gene expression values derived from RNA-sequencing (RNA-seq) data appeared predominantly in the (D) up then ND state (Mock to 2 dpi, then 2 dpi to 6 dpi, respectively). † indicates analyte involvement in the canonical pathways. Differences in analyte concentrations during attenuated CHIKV infection are indicated in the checkbox. Yellow represents lower while green represents higher concentrations relative to WT CHIKV. E) Top canonical pathways discovered by Ingenuity pathway analysis (IPA). Corresponding associated transcripts in acute antiviral and cell signaling canonical pathways are presented as a heatmap showing the Log2 fold change. The study analytes and transcripts in the RNA-seq data from wild-type CHIKV-infected and mock-infected samples in the same states were used. F)
Figure 4A. Anti-HA Western blots for each protein targeted for disruption with a detectable band corresponding to the expected product size. 100 nM rapamycin and 2.5 mM glucosamine were added to induce protein depletion for either one cycle (LDH1) or three cycles (Lipin and HAD4). Anti-PfBiP was used as the loading control. B. Growth of DiCre-3D7 transgenic lines following LDH1, HAD4, and Lipin depletion with 100 nM rapamycin and 2.5 mM glucosamine was assessed relative to uninduced parasite cultures. The untransfected DiCre-3D7 parasite line was used as a negative control. Data are presented as the mean ± standard error of the mean (SEM) from three independent replicates. C. Untargeted LC-MS analysis of LDH1 depletion (one cycle of rapamycin and glucosamine treatment) indicated minimal but selective metabolic changes. m/z feature intensities are plotted as the log2 ratio of treated/untreated and the Benjamini-Hochberg corrected P values across six biological replicates plotted as -log10(P). Below, LDH1 substrate and product (pyruvate and lactate respectively) abundance plotted as the ratio of treated/untreated from biological replicates (mean±SEM) and the parental DiCre line presented as the negative control. D. Loss of Lipin (PF3D7_0303200) leads to accumulation of various lipid species (three cycles of rapamycin and glucosamine treatment). Data are presented as the mean log2 fold change Lipin depleted (treated) enriched trophozoite-stage iRBCs to untreated controls from three to six biological replicates (± SD). The schematic depicts the proposed lipid phosphatase activity of Lipin. E. Loss of HAD4 leads to increases in intracellular levels of several nucleotides and intermediates in lower glycolysis. Data are represented as the mean log2 fold change of enriched trophozoite-stage iRBCs treated for three cycles compared to untreated controls from three/four biological replicates. Three nucleotide-nucleoside pairs are depicted in the top inset panels, HAD4 disruption leads to accumulation of the nucleotide-monophosphate and depletion of the nucleoside. The schematic depicts lower glycolysis and triose-phosphate interconversion, with the corresponding metabolite levels following HAD4 disruption depicted in the lower right inset. F. Phosphatase activity against the generic substrate pNPP of wild type HAD4, catalytically inactive HAD4D29A, and a no-enzyme (No Enz.) control, presented as the mean ± SEM (three biological replicates). G. Inhibition of HAD4 phosphatase activity by inorganic phosphate. Phosphatase activity against the generic substrate pNPP as the mean ± SEM from three independent experiments. The inorganic phosphate IC50 of HAD4 is 2.1 ± 0.21 mM. H. Substrate specificity of HAD4. Substrates are divided into nucleotide phosphates (black) and other metabolites such as sugar phosphates and vitamins (white). Presented is the enzyme activity from three independent experiments mean ± SEM). Substrate abbreviations are listed in methods.
Fig.Figure 5A to F Mice were vaccinated three times with AAV-vectors or two times with WIV and then challenged with a lethal dose of homologous influenza virus (Cal/7/9) (A, B; n = 5) or two different lethal doses of the heterologous PR8 strain (C, D; n = 6 and E, F; n = 7). Survival was monitored over a 14-day period and is depicted as Kaplan-Meier plot (A, C, E). Weight loss was determined during the 14-day period, which is shown in relation to the weight at day 0 (B, D, F). Mean ± SE. Statistical significance between negative control group (AAV-GFP) or WIV group (E) and each vaccine group was determined using Log-Rank (Mantel-Cox) test (*p<0.05, **p<0.01).
Follicle cell divisions are biased towards tissue expansion but not interphase cell shape.Figure 4A) Cartoon demonstrating how the tissue expansion angle is determined B) i) Planar division orientation is initially random in the follicular epithelium, with a significant bias towards the egg chamber elongation axis evident at stage 6 (asterisk, p = 0.0031, Wilcoxon Signed Rank Test, Theoretical Mean of 45; p = 0.0218 when comparison to a randomly generated list of the same size). Number of cells analyzed: stage 2/3 n=16, stage 4 n=27 stage 5 n=30, stage 6 n=40. ii) Quantification of the angle of tissue expansion as calculated by vector addition of the minor and major axis of egg chambers. Number of egg chambers analyzed: stage 2/3 n=10, stage 4 n=15, stage 5 n=15, stage 6 n=10. iii) Quantification of cell elongation angles (as shown in E) with respect to the chamber elongation axis by stage from live egg chambers. Number of cells analyzed: stage 2/3 n=18, stage 4 n=49 stage 5 n=64, stage 6 n=97. Bars represent mean and standard deviation C) Planar division orientation at Stage 6 correlates with tissue expansion in Fat2-shRNA and Pak-shRNA egg chambers. Mann Whitney test w1118 versus Pak shRNA p = 0.0094. Neither the Fat2-shRNA nor Pak-shRNA distributions are stastically different from random (Wilcoxon Signed Rank Test, Theoretical Mean of 45). Number of cells analyzed: w1118 n =97, Fat2-shRNA n=44, Pak-shRNA n=39. Egg chambers analyzed: w1118 n=40, Fat2-shRNA n=21, Pak-shRNA n=21 D) Neighboring cells can form new attachments underneath (basal to) a mitotic cell that has moved apically. Scale bars = 5 μm. Thin yellow lines in the XZ reconstructions indicate the z-position of the two XY focal planes E) Workflow for determining follicle shape shapes. Segmentation of an egg chamber with an aspect ratio of 1.5 reveals that follicle cell elongation is usually perpendicular to the elongation axis of the egg chamber. Cell outlines were marked with Basigin::YFP. Scale bars = 5 μm F) Live confocal imaging shows that the long axis of a follicle cell at interphase does not predict the orientation of division. Long axis orientations at the timepoints shown were determined as in (E). Scale bars = 5 μm. G) The interphase long axis does not correlate with the division angle in both the follicular epithelium (FE) and embyronic neuroectoderm (ENE). n=10 cells (FE), 18 cells (ENE)