EMBO/sd-character-level-ner huggingface dataset:
Figure 1A Immunoblot of PPAR-α and Tubulin (control) (top) in WAT from WT and FADD-D mice with relative quantification (bottom). Data are expressed as mean ± SEM from three independent experiments. *P = 0.0035 (Student's t-test). B Immunostaining of PPAR-α expression in WAT from WT and FADD-D mice (Scale bars = 50 μm). Shown are typical results from four different fields and three different experiments. C Quantitative real time PCR for PPAR-α and PPAR-α target genes, using RNA from epididymalfat from 10-week-old male WT and FADD-D mice fed a SD. Data are expressed as mean ± SEM from two independent experiments (n = 6 total for each genotype). *P = 0.0022, **P = 0.0083, ***P = 0.0107, #P = 0.0011, ##P = 0.0037 (Student's t-test). D ChIP assay of CPT1b promoter in adipocytes isolated from WT, FADD-D and ad-FADDmice. Soluble chromatin from adipocytes was immunoprecipitated with control mouse IgG or antibodies against PPAR-α. The experiments were performed in triplicate. E ChIP assay of CPT1b promoter in adipocytes isolated from WT and FADD-D mice. Soluble chromatin from adipocytes was immunoprecipitated with control mouse IgG or antibodies against FADD. The experiments were performed in triplicate. F PPAR-α and RIP140coimmunoprecipitate in WT but not FADD knockout or FADD-D MEFs. PPAR-α was immunoprecipitated (IP) from the cell lysates of WT or FADD knockout MEFs. Data shown are representative of three independent experiments having similar results. G PPAR-α and RIP140coimmunoprecipitate in WT but not FADD knockout MEFs upon WY-14,643 stimulation. Ligand-dependent interactions were examined in the presence of 100 μM WY-14,643 where indicated. Data shown are representative of three independent experiments having similar results. H Coimmunoprecipitation analysis of FADD and RIP140 in 293T cells. As indicated, lysates from the cells transfected with plasmids encoding Flag-RIP140, HA-FADD-A or HA-FADD-D were subjected to immunoprecipitation with an anti-Flag antibody. FADD-A and FADD-D were detected using an anti-HA antibody. Data shown are representative of three independent experiments having similar results. I Coimmunoprecipitation analysis of FADD and PPAR-α in 293T cells. As indicated, lysates from the cells transfected with plasmids encoding Flag-FADD-A, Flag-FADD-D or HA-PPAR-α were subjected to immunoprecipitation with an anti-Flag antibody. PPAR-α was visualized by anti-HA. Data shown are representative of three independent experiments having similar results. J Left, the putative complex of FADD (yellow) and PPAR-α (colorful) by molecular modeling is portrayed in ribbon representation. Middle, the residue S194 of FADD and PPAR-α residue K448 are shown in sphere representation, which is immediately proximal and capable of hydrogen bonding interactions. Right, the key residue D194 of FADD-D and PPAR-α residue Q445, K448, K449, R465 are shown in sphere representation, which is immediately proximal and capable of salt bridging interactions.
The SCAN-B MutationExplorerThe SCAN-B MutationExplorer web-based application for interactive exploration of mutations, andtheir association with clinicopathological subgroups and overall survival.Figure 8The SCAN-B MutationExplorer web-based application for interactive exploration of mutations, and their association with clinicopathological subgroups and overall survival. As an example, generation of the image used in Fig 2 is shown.
Figure 8Schematic depiction of the proteolytic process of coronaviral replicase protein 1a and 1ab by proteases PLpro/NSP3 (labeled red) and 3CLpro (labeled blue). PLpro/NSP3-mediated cleavage generates NSP1, NSP2 and PLpro/NSP3 proteins ending in the diGly motif. The cleavage sequences of indicated viruses are shown. Stability analysis of FL SARS-CoV NSP1 and NSP2 proteins with or without DNKLHDC2 treatment. We were unable to analyze NSP3 due to its large size (214 kDa). Relative stability analysis of GAPDH C-terminally tagged with the last 12 residues of indicated proteins with or without DNKLHDC2 treatment by GPS assays. The -3, -4 or -5 residue of SARS-CoV NSP proteins was mutated to Ala (A) as indicated. The experiment was done in triplicate using three independently prepared viruses to express DNKLHDC2. Data are presented as the mean value of GFP/RFP +/- standard deviation from triplicate experiments. Global protein stability profiling of GPS reporter cells expressing random peptide libraries ending with a diGly motif or the last six residues of SARS-CoV NSP1 protein with or without DNKLHDC2 treatment.
GaMTs are more polarized and contain less intersections A.Figure 4A representative image of MT networks extracted from MT STORM image of an HRPE cell. Red line: GaMT; Green line: non-GaMT. Yellow circle: intersection. Blue circle: intersections formed by GaMTs and non GaMTs. Scale bar: 5 μm. Rose-plot presents the orientation of GaMTs and non-GaMTs. Red: GaMTs; Green: non-GaMTs. Box-whisker plot presents the projections of GaMTs and non-GaMTs to the leading edge direction. (Data were pooled from 3 independent experiments and n= 36 cells). The ends of the whiskers are set at 10% and 90% of the entire population, **p < 0.01, unpaired t-test. Box-whisker plot presents the intersection counts of GaMTs and non-GaMTs. (data are pooled from 3 independent experiments and n= 36 cells). The ends of the whiskers are set at 10% and 90% of the entire population, ***p < 0.001, unpaired t-test.
Cross-reactivity of antisera raised against SARS-CoV structural and non-structural proteins.Fig. 4. Cross-reactivity of antisera raised against SARS-CoV structural and non-structural proteins.Selected antisera previously raised against SARS-CoV nsps and structural proteins cross-react with corresponding SARS-CoV-2 proteins. SARS-CoV-2-infected Vero E6 cells (m.o.i. of 0.3) were fixed at 12 or 24 h p.i. For immunofluorescence microscopy, cells were (double) labelled with (a) a rabbit antiserum recognising nsp4 and a mouse mAb recognising dsRNA; (b) anti-nsp4 rabbit serum and a mouse mAb directed against the N protein; (c-e) rabbit antisera recognising against nsp3, nsp13 and the M protein, respectively. Nuclear DNA was stained with Hoechst 33258. Bar, 20 µm.
CXCR4 expression in MM patient bone marrow.Figure 1Flow cytometric evaluation of CXCR4 surface expression using an anti-CXCR4-PE antibody. Left: positive patient; right: negative patient; representative data are shown. The gating strategy is depicted in Supplementary Fig S1. Representative histograms revealing the magnitude of CXCR4 expression in myeloma cells as compared to the indicated bone marrow cell subtype. Median fluorescence intensity of surface CXCR4 expression relative to isotype control (n = 7-10 patients). Horizontal bars indicate mean of all individual patient values; asterisks indicate statistical significance (plasma cells vs B cells: P = 0.0082; plasma cells vs T cells: P = 0.0091; plasma cells vs CD34+ cells: P = 0.011; plasma cells vs monocytes: P = 0.0423; Student's t-test to compare mean plasmacell relative expression with mean relative expression of each further indicated cell subtype). MM patients judged positive for CXCR4 expression were selected for this analysis. Representative MM bone marrow staining of a patient positive for MM CXCR4 expression: hematoxylin and eosin (H&amp;amp;E) staining. Immunohistochemistry for CD138, CXCR4, light chain kappa, and light chain lambda.
Figure 5Representative images of Masson's trichrome staining of lung sections from F-LARP6 KO and F-LARP6/F-CRTH2 double KO (F-DKO) mice 14 days after bleomycin challenge; Scale bar, 100 μm. , Quantification of collagen content in mouse lung sections after bleomycin challenge. #P < 0.05 vs saline group (two-way ANOVA); saline groups, n = 4 each, bleomycin groups, n = 7-8. Hydroxyproline content in lungs from F-LARP6 KO and F-DKO mice treated with bleomycin. #P < 0.05 vs saline group (two-way ANOVA); saline groups, n = 4 each, bleomycin groups, n = 8 each. Western blot analysis of Collagen (Col) Ⅰ and Ⅲ expression in lung tissues from F-LARP6 KO and F-DKO mice 14 days after bleomycin challenge. Representative images of Masson's trichrome staining of liver sections from F-LARP6 KO and F-DKO mice 4 weeks after CCl4 challenge; Scale bar, 100 μm. Quantification of collagen content in mouse liver sections after CCl4 challenge. #P < 0.05 vs mineral oil group (two-way ANOVA); mineral oil groups, n = 4 each, CCl4 groups, n = 8 each. Hydroxyproline content in livers from F-LARP6 KO and F-DKO mice treated with CCl4. #P < 0.05 vs mineral oil group (two-way ANOVA); saline groups, n = 4 each, CCl4 groups, n = 8 each. Western blot analysis of Collagen Ⅰ and Ⅲ expression in liver tissues from F-LARP6 KO and F-DKO mice 4 weeks after CCl4 challenge. Representative images of Masson's trichrome staining of heart sections from F-LARP6 KO and F-DKO mice 21 days after ISO challenge; Scale bar, 50 μm. Quantification of collagen content in mouse heart sections after ISO challenge. #P < 0.05 vs saline group (two-way ANOVA); saline groups, n = 3 each, ISO groups, n = 7 each. , Hydroxyproline content in hearts from F-LARP6 KO and F-DKO mice treated with ISO. #P < 0.05 vs saline group (two-way ANOVA); saline groups, n = 4 each, ISO groups, n = 8 each. Western blot analysis of Collagen Ⅰ and Ⅲ expression in heart tissues from F-LARP6 KO and F-DKO mice 21 days after ISO challenge. , Schematic diagram of the working model of CRTH2-mediated collagen homeostasis in fibroblasts.
FUS is a bicistronic gene A, FUS gene bicistronic annotation, with the canonical FUS CDS (in blue, +1 frame) and altFUS CDS (in green, +2 frame) represented on the FUS canonical transcript (ENST00000254108 or NM_004960).Figure 1A, FUS gene bicistronic annotation, with the canonical FUS CDS (in blue, +1 frame) and altFUS CDS (in green, +2 frame) represented on the FUS canonical transcript (ENST00000254108 or NM_004960). Sequence length proportions are respected, the scale bar corresponds to 300 nucleotides. B, Genome browser view of FUS gene. The five most abundant transcripts in the brain are shown in the 'Transcript' track. Transcripts predicted coding by the OpenProt resource are coloured in blue, and in grey if predicted non-coding. The 'Protein' track contains all predicted protein products. The known FUS protein (ENSP00000254108) and its isoform (ENSP00000369594) are coloured in green. The novel predicted altFUS protein (IP_243680) and its isoform (IP_243691) are coloured in red. C, PhyloP nucleotidic conservation scores are represented in grey across the FUS mRNA (ENST00000254108). The noise reduction after FFT (Fast Fourrier Transformation) is outlined in blue. The average PhyloP score on the bicistronic and the monocistronic region are represented as dotted red lines. The position of the FUS CDS is represented by a blue rectangle, and that of altFUS CDS by a green rectangle. D, Alignment (Clustalω) of altFUS protein sequences in Human (Homo sapiens), Chimpanzee (Chimp. - Pan troglodytes), Rat (Rattus norvegicus), Mouse (Mus musculus) and Dog (Canis lupus familiaris). Residues are coloured based on their identity across species, from white (not conserved) to red (conserved in all species). E, Ribo-seq data over the FUS gene from the Gwips portal. Initiating ribosome reads are indicated by blue bars, and elongating ribosomes footprints are indicated by the blue curve. The graph captures the beginning of the FUS gene with FUS and altFUS methionines indicated by blue arrows. The genomic positions are indicated relative to the start of exon 1. Genome browser view of FUS gene, centered on altFUS. The 'Transcript' track contains the beginning of the canonical FUS transcript (ENST00000254108) in blue. The 'Protein' track contains the beginning of the FUS protein (green) and the whole altFUS protein (red). In F, the 'Peptide' track contains all the peptides identified by the OpenProt resource using the classical spectrum-centric approach. The peptides sequences are indicated and are unique to altFUS or its isoform Genome browser view of FUS gene, centered on altFUS. The 'Transcript' track contains the beginning of the canonical FUS transcript (ENST00000254108) in blue. The 'Protein' track contains the beginning of the FUS protein (green) and the whole altFUS protein (red). In G, the 'Peptide' track contains all the peptides identified by a peptide-centric approach. The peptides indicated matched better to at least one spectrum than any known protein, and are coloured in yellow if they matched better than any known protein with any PTM The peptides sequences are indicated and are unique to altFUS or its isoform.
Murine hepatitis virus infection alters hepatic and splenic immune responses in female Ly6eΔHSC mice.Figure 4.mice.a-e, Transcriptomic analysis from Ly6efl/fl (WT) and Ly6eΔHSC (KO) mice. a-b, Heat maps displaying significant changes (mean RPKM > 0.5; fold change > 2; FDR ≤ 0.05) in liver (a) and spleen (b). Dendrograms are normalized read data (row z-score) clustered with complete linkage method employing Spearman Rank correlation distance measurement. c, Pathway analysis of KO versus WT. Up-(red) or down-regulated (blue) pathways indicated by activation z-score. Numbers show significantly dysregulated genes as percentage of total gene number included in pathway. d-e, Expression of select genes in liver (d) and spleen (e). f-g, Immune cell counts from liver (f) and spleen (g). h, Infection of cultured splenocytes. For a-e, n=3. For f-g, n=8 MHV-injected, n=4 PBS-injected from two pooled experiments.
Co-translational insertion of N-in membrane protein EmrD.Figure 3Time course of EmrD135 translation. Translation was monitored by SDS-PAGE as in Fig 2A. Time course of EmrD(-) 135 translation. Kinetic model of EmrD synthesis. Ribosome stalling (peptide P1) is modeled at EmrD48.   Kinetic model of EmrD(-) synthesis. Stalling (peptide P1) is modeled at EmrD(-) 48.   Stopped-flow time courses for translocon insertion of TM1 of EmrD (black) and EmrD(-) (blue) with mRNA constructs of varying chain length (50 to 135 aa).The FRET acceptor (Atto655) was placed at the N-terminus of the nascent peptide, the donor (Atto488) at position 111 (donor-in) of SecY. The results of global fitting are indicated (red lines). Intrinsic fluorescence intensities (IFIs) calculated for EmrD (black) and EmrD(-) (blue). Error margins (shaded areas) are calculated using the Fitspace algorithm Stopped-flow traces for co-translational insertion of LepB94 (red, from Fig 2), EmrD135 (black, from Fig 4E), and EmrD(-) 135 (blue, from Fig 4E), rescaled according to the translation efficiency.
Figure 1Schematic representation of Stx17 and PGAM5. 293T cells were transfected with a plasmid encoding FLAG-Stx17 wild type (WT) or the indicated constructs. At 24 h after transfection, cell lysates were immunoprecipitated (IP) with anti-FLAG M2 beads, and analyzed by IB using antibodies against PGAM5 and FLAG. Five percent of lysates was analyzed as input. HeLa cells stably expressing FLAG-Stx17 WT or the K254C mutant were fixed and subjected to PLA using antibodies against FLAG and PGAM5. Scale bar, 5 μm. Values are means ± SEM (n = 3). ***P<0.001 as compared with WT (paired Student's t-test). MBP or the MBP-Stx17 constructs attached to amylose resin were mixed with GST-PGAM5, and the proteins bound to the resin were separated by SDS-PAGE and blotted onto PVDF membranes. The blots were detected by an anti-GST antibody (upper panels) or stained with Coomassie Brilliant Blue R-250 (lower panels). Ten percent of the proteins used for each experiment was analyzed as input. Asterisks and double asterisk may represent MBP dimers and degradation products. 293T cells were cotransfected with plasmids encoding FLAG-Stx17 WT and the indicated PGAM5-GFP constructs, and analyzed 293T cells were cotransfected with plasmids encoding FLAG-Stx17 or Stx18 and the C-terminally GFP-tagged transmembrane domain of PGAM5（amino acids 1-35）constructs, and analyzed
Figure 9Structures. In 2-5A, ATP and several AMPs (two are shown) are connected by (2'-5') phosphodiester bonds (highlighted in red) by OAS1. In PAR, ADPribose (ADPr) units are connected by (2'-1") glycoside bonds between ribose moieties (highlighted in blue) by PARP1. In PAR-2-5A. PAR can be used by OAS1 as an acceptor for addition of AMP residues to the 2'-hydroxyl of the terminal ADRr, which prevents PAR chain elongation by PARP. PARP1 and OAS1 compete for the 2'-hydroxyl of the terminal ADPr of PAR (shown in purple), which may result in "capping" of PAR chain termini with adenylates. The 2'-hydroxyl of the terminal adenylate (shown in red) can be further modified by OAS1 (OAS1 typically adds 2-3 AMPs), but presumably not by PARP1. 2'-positions modified by PARP1 are shown in blue. Besides the terminal ribose, PARP1 also attaches ADPr to the 2'-hydroxyl of the second ribose moiety of ADPr (shown in blue in parentheses), producing a branched PAR structure. We propose that 2-5A capping of PAR by OAS1 results in shorter and potentially more branched PAR chains (bottom). High PARylation in response to extensive DNA damage leads to accumulation of cytoplasmic PAR, which promotes initiation of parthanatos (cell death through AIF translocation and/or other mechanisms). OAS1 suppresses PARylation and thus prevents the accumulation of PAR to toxic levels and NAD+ depletion/energy collapse, promoting DNA repair and cell survival.
regulates the expression of chemokines via modulating JAK/STAT signaling (A) ELISA was performed to detect the secretion of cytokines TNF-α, IL-1, IL-6 and CXCL15 in Socs6+/+ and Socs6-/- BMDMs during Mtb stimulation.Figure 5(A) ELISA was performed to detect the secretion of cytokines TNF-α, IL-1, IL-6 and CXCL15 in Socs6+/+ and Socs6-/- BMDMs during Mtb stimulation. Data are shown as the mean ± s.e.m. of n = 3 biological replicates. (B) Phosphorylation states of STAT1 in response to Mtb stimulation in Socs6-/- BMDMs were examined by western blotting. Fludarabine treatment concentration was 10 μM and the treatment time was 24 hours. Representative blots from n = 3 biological replicates are shown. (C-F) Relative expressions of chemokines CCL5, CXCL10, ICAM1 (C), and Caspase 3, Caspase 7, Caspase 8 (F) in Mtb-stimulated Socs6+/+ or Socs6-/- BMDMs were detected by qRT-PCR. Data are shown as the mean ± s.e.m. of n = 3 biological replicates. Cluster analysis of clinical samples. Heatmaps showed relatively high (red) or low (green) expression levels of Socs6 and inflammatory factors in PBMCs from healthy individuals (n=27) (D) and TB patients (n=34) (E).
Fig.Figure 1(A) Microchamber that allows the isolation of axons within a corticostriatal network and live-cell imaging of axonal BDNF-mCherry transduced into mouse primary cortical neurons. Data information: Scale bars = 20 µm. (B) Representative kymographs and quantification of anterograde, retrograde, mean velocity, and linear flow rate of BDNF-mCherry-containing vesicles in cortical neurons transfected with siMecp2 (n= 753 vesicles/ 81 axons) or siControl (siCtl) (n= 894 vesicles/ 94 axons), inducing significant silencing of Mecp2 (3 independent experiments; unpaired t-test). Data information: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001 Data are presented as the means ± SEM. (C) Quantification of anterograde, retrograde, mean velocity, and linear flow rate of BDNF-mCherry trafficking into cortical neurons obtained from WT (n= 753 vesicles/ 81 axons), HTTSA (n= 812 vesicles/ 81 axons), or HTTSD (n= 787 vesicles/ 82 axons) homozygous knock-in mice in which S421 of HTT was replaced by an alanine (HTTS421A/S421A or HTTSA), mimicking the absence of phosphorylation, or by an aspartic acid (HTTS421D/S421D or HTTSD), mimicking constitutive phosphorylation (3 independent experiments; one-way ANOVA test with Tukey's multiple comparisons). Data information: , ***p < 0.001, ****p < 0.0001, ns = not significant. Data are presented as the means ± SEM. (D) Cell viability in WT (n=3), HTTSA (n=1), or HTTSD (n=2) neurons measured by MTT assay. No differences were observed between the different groups (3 independent experiments; one-way ANOVA Kruskal-Wallis test, p=0.5701 Data information: ns = not significant. Data are presented as the means ± SEM. (E) Kymographs and quantification of anterograde, retrograde, mean velocity, and linear flow rate of BDNF-mCherry axonal trafficking into WT (n= 894 vesicles/ 94 axons), HTTSA (n= 812 vesicles/ 82 axons), or HTTSD (n=787 vesicles/ 94 axons) cortical neurons transfected with siCtl or siMecp2, which significantly silenced Mecp2 (3 independent experiments; one-way ANOVA with Tukey's multiple comparisons). (F) Cell viability in WT, HTTSA, or HTTSD neurons transfected with siCtl or siMecp2 measured by MTT assay (WT siCtl: n=3; WT siMecp2: n=3; HTTSD siMecp2: n=3; HTTSA siMecp2: n=2). No differences were observed between the different groups (3 independent experiments; one-way ANOVA Kruskal-Wallis test, p=0.5701) Data information: Scale bars = 20 µm. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns = not significant. Data are presented as the means ± SEM.
Figure 3A HeLa cells were labelled with MitoTracker Red CMXRos, treated with cytochalasin D for 30 min, then fixed and labelled for endogenous SEPT7 for confocal microscopy. The scale bar represents 0.5 μm. See also Fig EV3A. B HeLa cells were infected with S. flexneri for 4 h 40 min, labelled with MitoTracker Red CMXRos, fixed and labelled with antibody for endogenous SEPT7 for quantitative confocal microscopy. The scale bar represents 1 μm. C HeLa cells stably expressing SEPT6-GFP were transfected with Mito-BFP for 24 h, infected with Shigella-mCherry for 4 h 40 min, and processed for CLEM. SEPT6 is shown in green, mitochondria in red, and Shigella-mCherry in blue. Septin cages identified by fluorescent light microscopy (FLM) were processed for TEM. The right-most image is enlarged from the boxed region in the TEM image, and shows the bacterium (Sf) surrounded by a double membrane of autophagy (Au) and the mitochondrial membrane (Mt). The scale bar represents 1 μm. See also Fig EV3B. D HeLa cells stably expressing SEPT6-GFP were transfected with Mito-BFP for 24 h, then infected with Shigella-mCherry for 2 h for live confocal microscopy. Time frame sequence shows a septin cage assembling around Shigella. Mitochondria (circle) support sites of septin ring assembly around the bacterium. Each frame was acquired every 2 min. The scale bar represents 1 μm. See also Movie EV1. E HeLa cells were treated with control (CTRL), Drp1, or Mfn1 siRNA for 72 h. Whole cell lysates were immunoblotted for Drp1 or Mfn1 to show the efficiency of depletion. GAPDH was used as loading control. siRNA-treated cells were infected with S. flexneri for 4 h 40 min, then fixed for microscopy and stained for endogenous SEPT7 for quantitative confocal microscopy. Graph represents the mean % ± SEM of Shigella inside SEPT7 cages from at least 4 independent experiments per treatment. Student's t-test, ** = p <0.01; *** = p<0.001.
Reduced kainate-evoked inward currents in the absence of SEZ6.Figure 3(A) Left: Current trace resulting from whole-cell voltage-clamp recordings at a holding potential of -70 mV in a CA1 pyramidal neuron in a WT mouse hippocampal slice (P15). The current was recorded in the presence of 10 µM bicuculline, 20 µM GYKI53655 and 30 µM APV in the ACSF. Perfusion of the recording chamber with 10 µM kainate and 100 µM 2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide (NBQX) are indicated with green and blue bars, respectively. Right: Analogous experiment in a SEZ6KO mouse (P15). (B) Summary of the experiments in A. Bar graph illustrates mean charge with standard error of the mean carried by the inward currents (measured as area under the curve, AUC) for the two genotypes at P15 (WT 46.6 ± 0.5 nC (n=10 cells), SEZ6KO 30.8 ± 0.5 nC (n=9 cells), *p=0.0375 Mann-Whitney-U-test).