EMBO/sd-character-level-ner huggingface dataset:
Immunostaining image of a cell containing autophagic bodies in the vacuole.Figure 7Immunostaining image of a cell containing autophagic bodies in the vacuole. The Δapg8Δpep4 cells expressing 3 × HA-Apg8p, TK116 cells, were shifted to SD(−N) medium for two hours. Cells were immunolabeled with anti-N mAb, 16B12, followed by 10-nm gold-conjugated goat anti-mouse IgG. AB, vacuole; N, nucleus; V, vacuole.
Fig.Figure 5A) In vitro phagocytosis of FAM-Aβ1-42 by wild type or PD-1-/- microglia for up to 6 h (mean +/-SEM of a technical quadruplicate, Student's t-test, ** p<0.01, *** p<0.001, representative result of an n=2 biological replicate). B) In vitro phagocytosis of FAM-Aβ1-42 by wild type microglia cultured in astrocyte-conditioned medium (ACM) from wild type or PD-L1-/- astroglial cultures (mean +/-SEM of a technical quadruplicate, Student's t-test, * p<0.05, *** p<0.001, representative result of an n=2 biological replicate) C) Flow cytometry analysis of microglia from wild type and PD-1-/- mice for the expression of CD36 and CD11b. D) Quantification of microglial in vivo phagocytosis in female APP/PS1 and APP/PS1 PD-1-/- mice at 8.5 month of age after intraperitoneal injection of methoxy-XO4 (biological replicates with n=5 for APP/PS1 and n=4 for APP/PS1 PD-1-/- mice, Student's t-test (t = 2.1808, df = 6.9829), * p<0.05). Data information: central bands represent median, boxes show interquartile range (IQR) and whiskers define the +/-1.5xIQR. E-G) Relative expression of the cell surface marker (E) CD36 (biological replicates with n=5 for APP/PS1 and n=4 for APP/PS1 PD-1-/- mice, ANOVA (DF=1, F= 0.002, p=0.94), Tukey's HSD, * p<0.05, *** p<0.001), (F) CD11b (biological replicates with n=5 for APP/PS1 and n=4 for APP/PS1 PD-1-/- mice) and (G) CD45 on methoxy-XO4+ versus methoxy-XO4- microglia in APP/PS1 and APP/PS1 PD-1-/- mice normalized to methoxy-X04-negative cells from APP/PS1 mice (biological replicates with n=5 for APP/PS1 and n=4 for APP/PS1 PD-1-/- mice) Data information: central bands represent median, boxes show interquartile range (IQR) and whiskers define the +/-1.5xIQR.
Figure 3A. Rescue experiments showing that ∆Hel-C but not ∆eTud restored piRNA biogenesis attenuated by endogenous Yb depletion. Flag-Piwi was expressed upon endogenous Yb depletion. B. The levels of transposon mdg1 Bars and error bars represent means ± SEM values of three independent experiments. p values were calculated by t-test. *: p < 0.05. C. Mapping of flam-piRNAs produced in the presence and absence of the Hel-C domain in OSCs. D. Mapping of tj-piRNAs produced in the presence and absence of the Hel-C domain in OSCs. E. Scatterplot showing changes in the abundances of transposon-repressing piRNAs and non-transposon-repressing piRNAs in the presence and absence of the Hel-C domain. Orange and blue dots indicate the number of normalized piRNA reads mapped uniquely to transposons in the reverse orientation and coding genes in the sense orientation, respectively. F. The relative enrichments of RNAs coimmunopurified with WT Yb and ∆Hel-C. Bars and error bars represent means ± SEM values of three independent experiments. In addition to tj, three genic piRNA sources that were characterized in previous studies (dm/Myc [59], c-Fos/kay [60], and CG9257 [34]) are also shown. rp49 was used as a negative control. p value was calculated by t-test. ***: p < 0.001. G. Summary of requirements of Hel-C and eTud domains of Yb in Yb body formation and transposon-repressing and non-transposon-repressing piRNA production.
Pathways inferred to be involved in mitochondrial DNA copy number maintenance and homeostasisSchematic diagram of the cell, showing categories of identified genes in the positives list (in dark blue), and their possible links to a ROS (or membrane potential, Δψ) surveillance mechanism, orchestrated by ATP synthase.Figure 6Schematic diagram of the cell, showing categories of identified genes in the positives list (in dark blue), and their possible links to a ROS (or membrane potential, Δψ) surveillance mechanism, orchestrated by ATP synthase.
The levels of miR-133b are increased in Cx43-containing extracellular vesicles.Figure 4A-D. EV-producing cells expressing or not Cx43 (HEK293Cx43+ or HEK293Cx43-) were transiently transfected with shRNAs targeting hnRNPA2B1, hnRNPQ or non-target shRNAs, for 48 h. miR-133b levels were assessed in EVCx43+ and EVCx43- (A; n=6-12 biological replicates) and EV-producing cells (B; n=4-9 biological replicates). miR-509-3p levels were assessed in EVCx43+ and EVCx43- (C; n=6-15 biological replicates) and EV-producing cells (D; n=4-9 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs. E-H. HEK293Cx43+ or HEK293Cx43- were transiently transfected with hnRNPA2B1-GFP, GFP-hnRNPQ or GFP alone, for 24 h. miR-133b levels were assessed in EVCx43+ and EVCx43- (E; n=4 biological replicates) and EV-producing cells (F; n=3 biological replicates). miR-509-3p levels were assessed in EVCx43+ and EVCx43- (G; n=4 biological replicates) and EV-producing cells (H; n=3 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs.
Figure 6Survival analysis of low and high expressers of SHLD2 in a cohort of 24 patients affected by Triple Negative Breast cancer (TNBC). Data are represented as Kaplan-Meyer curves with expression classified as low and high. Relapse-free Survival (Basal Subtype) of low and high expressers of SHLD2 obtained from the KM-plotter database. Data are represented as Kaplan-Meyer curves with expression classified as low and high. Schematic incorporating SHLD2 and SHLD1 as REV7 effectors in the NHEJ pathway and modulators of DNA repair pathway choice.
Figure 6Schematic view of celiac disease pathogenesis. The P31-43 peptide from the gluten-associated protein gliadin is generated in the gut lumen and interacts with the NBD1 domain of CFTR, if the domain is in its inactive conformation. P31-43 binds to specific residues of NBD1 of inactive CFTR, competing with ATP binding, thus blocking CFTR function as an anion channel. The inhibition of CFTR disrupts cellular proteostasis through two effects (i) TG2 activation and (ii) BECN1 complex inhibition. This accessorily recruits TG2 to a tripartite complex that stabilizes P31-43 binding to CFTR, thus worsening CFTR inhibition. P31-43-mediated CFTR inhibition leads to impaired endosomal trafficking, cytoskeleton disassembly, inflammasome activation resulting in IL-1β secretion, NF-κB activation and consequent IL-15 production. Stressed enterocytes stimulate local inflammation and immune responses against immunodominant gliadin peptides, in particular peptide P55-87, in the context of HLA-DQ2/DQ8, thus triggering celiac disease. This pathogenic cascade may be theoretically interrupted at two levels, at the apex by CFTR potentiators that prevent P31-43 binding to CFTR (but are poorly active if they are added after P31-43 addition) or by reconstitution of cellular proteastasis by inhibiting TGase or activating the BECN1 complex.
Figure 2A) Acetylation tracks for H3K9/14ac ChIP-seq (on the left) and corresponding FPKM values by RNA-seq (on the right) for representative genes in YC and OC FAPs B) Graphs showing RNA levels for the representative genes shown in (A) measured by qPCR; C) Graphs showing the H3K9/14 acetylation levels for the representative genes shown in (A) measured by ChIP-qPCR. D) Acetylation tracks for H3K27ac ChIP-seq (on the left) and corresponding FPKM values by RNA-seq (on the right) for representative genes in young and old mdx FAPs E) Graphs showing RNA levels for the representative genes shown in (D)) measured by qPCR; F) Graphs showing the H3K27 acetylation levels for the representative genes shown in (D) measured by ChIP-qPCR. G) Representative images of the EdU staining in freshly isolated YC and OC FAPs following EdU in vivo exposure for 3 days (EdU in red/DAPI in blue). Scale bar = 25 μm. H) Graph showing the percentage of EdU positive cells for the staining shown in (G). I) Representative images of the LMNB1 staining in freshly isolated YC and OC FAPs (LMNB1 in green/DAPI in blue). Scale bar = 25 μm. J) Graph showing the relative quantification of LMNB1 fluorescence intensity normalized for nuclei number,in the staining shown in (I). K) Graph showing the relative expression of Lmnb1 in YC and OC FAPs measured by qPCR. L) Representative images of the γH2AX and KI-67 staining in freshly isolated YC and OC FAPs (γH2AX in green/KI-67 in red/DAPI in blue). Scale bar = 10 μm. Magnification in the insert (scale bar = 3 μm) shows γH2AX positive CCF in OC FAPs. M) Graph showing the percentage of cells positive for γH2AX positive CCF, for the staining shown in (L). N) Graph showing the percentage of cells positive for KI-67 for the staining shown in (L). O) Graph showing the relative expression of Ki67 in YC and OC FAPs measured by qPCR.
Figure 6A Scheme of the bem1 mutants used for imaging. B Global average MSD curves of mEOS-Cdc42 in the strains indicated at the Pole (P) and Non-Pole (NP) of cells. Trajectories longer than 6 frames were analyzed. Number of trajectories analyzed: BEM1 (n = 11 cells: Non Pole: 1814 tracks; Pole: 706); bem1 bc-14E px (n = 10 cells: Non Pole: 1793 tracks; Pole: 908); bem1 bc-14E (n = 13 cells: Non Pole: 1714 tracks; Pole: 975). Error bars display s.e.m. C D coefficients of mEOS-Cdc42 in the strains indicated (in box-plots displaying the median (line), the 25-75 percentiles (box) and the mean (cross)), which were compared using a non-parametric, two-tailed Mann-Whitney rank sum test. D SR-Tesseler images of mEOS-Cdc42 nanocluster organization in BEM1 (5312 localizations shown in image) and bem1 bc-14E px cells (3739 localizations shown). Insets show mEOS-Cdc42 after 491 nm widelfield laser excitation to identify the cell pole. Scale bars: 2 μm. A zoom of the pole region shows the organization of the detected nanoclusters, circled in light blue, in the strains indicated. Scale bar in the zoom: 60 nm. E Distribution of nanocluster area at the pole (P) and non-pole (NP) regions of BEM1 (diameter NP: 59 nm ± 1 nm (s.e.m); P: 74 nm ± 3.2 nm) (n = 16 cells. NP: 570 clusters; P: 162 clusters) and bem1 bc-14E px cells (diameter NP: 59 nm ± 1.5 nm (s.e.m); P: 57 nm ± 2.4 nm) (n = 15 cells. NP: 421 clusters; P: 141 clusters). Data are presented as scatter dot-plots displaying the median as a line and the 25-75 percentiles. Data were compared using non-parametric, two-tailed Mann-Whitney rank sum test. F Active Cdc42-GTP levels were quantified in the strains indicated using a gic2(1-208)-yeGFP probe. Values are mean ± SD for n = 30 cells observed over 2 experiments. Data were compared using a Mann-Whitney test.
Figure 2A. Experimental design of TPA2. B. Hierarchical clustering of the phosphorylated sites differentially quantified in BT549 transfected with HA-FGFR1c, 2b, or 4 and stimulated for 8 or 40 min. with Enkamin-E, FGF10, or FGF1, respectively. Early Signalling and Recycling Receptors clusters are highlighted in light and medium blue, respectively. The intensity of phosphorylated sites is presented on the logarithmic scale with intensity below and above the mean color-coded in blue and red, respectively. C. STRING-based and Cytoscape-visualized network of the phosphorylated proteins belonging to "endocytosis" (clusters medium blue in b). The diamond shape represents phosphorylated proteins found in TPA1. Kinases are highlighted in burgundy. The border is color-coded based on the substrate motifs. D. Experimental design of TPA3. E. Hierarchical clustering of the phosphorylated sites differentially quantified in T47D stimulated with FGF10 and depleted or not of TTP or RCP. The clusters for TTP Adaptors, RCP Adaptors or Recycling Adaptors are highlighted in orange, brown, and light green, respectively. The intensity of phosphorylated sites is presented on the logarithmic scale with intensity below and above the mean color-coded in blue and red, respectively. F. STRING-based and Cytoscape-visualized network of phosphorylated proteins belonging to the Recycling Adaptors cluster (light green in E) and found in TPA1. Kinases are highlighted in burgundy. The border is color-coded based on the substrate motifs. G. Venn diagram showing the phosphorylated proteins belonging to "establishment of localization" identified in TPA1-3 (left). STRING-based and Cytoscape-visualized network of the 22 proteins identified by the 3 TPAs (centre). Phosphorylated sites quantified on EGFR (right). T693 is highlighted in yellow. Lysates from (H) T47D, BT20, and HA-FGFR2b-transfected BT549 stimulated or not with FGF7, FGF10, EGF, and TGFα for 40 min.; (I) breast cancer organoid cultured from the PDX tumour BB6RC37 and grown for the last 24 hours as indicated (J) control or 40 min. FGF10- or TGFα-stimulated T47D left untreated or depleted of TTP, followed or not by transfection with siRNA resistant Flag-TTP (Flag-TTP*) or depleted of RCP followed or not by transfection with siRNA resistant RCP-GFP (RCP-GFP*) were immunoblotted with the indicated antibodies. **, non-specific band (J).
Figure 1A Diagram for three constructs expressing MAVS-Region III C-terminally tagged with GCN4-derived peptides, whose sequences are presented in bold. B Recombinant MAVS-Region III-dimer (lanes 1-4), trimer (lanes 5-8) or tetramer (lanes 9-12) were subjected to IRF3 dimerization assay respectively in vitro. Increasing doses of recombinant MAVS-Region III were used and shown in Fig EV1C. Immunoblotting analysis was performed following Native-PAGE for the reaction mixture. C pcDNA3-based constructs expressing MAVS-Region III-dimer, trimer and tetramer were transfected into HEK293T cells respectively. ISG54 induction were measured thirty-six hours after transfection by quantitative PCR (qPCR). D Recombinant MAVS-Region III-dimer or tetramer were immunoprecipitated with anti-FLAG M2 beads with or without a preincubation with S100 from HEK293T cells following an experimental procedure outlined in Fig EV1G. The IP products were resolved in SDS-PAGE and a specific protein band pulled-down with MAVS-Region III-tetramer was indicated by an arrow. TRAF3IP3 was identified in the specific band by mass spectrometry. E Protein samples as described in (D) were subjected to immunoblotting analysis. The TRAF3IP3 band was indicated by an arrow and the asterisk indicated nonspecific bands F pcDNA3-FLAG-TRAF3IP3 (full-length and truncated forms) and pcDNA3-HA-MAVS were transfected into HEK293T cells, which were harvested thirty-six hours post transfection. Co-IP experiments were performed with anti-HA antibody, followed by immunoblotting. G Human cells, including THP1, HeLa, HEK293, HEK293T as well as Traf3ip3-/- HEK293T, were lysed and subjected to immunoblotting to examine TRAF3IP3 expression.
Figure 3(A) Quantification of the structures found on Bax wild type (purple) and on Bax 1-2/L-6 (grey) overexpressing cells. Data show the total number of structures in all the measurements. n (Bax wild type)= 13, n (Bax 1-2/L-6)=11.(B) Cumulative distribution plots of GFP-Bax wild type (purple) and GFP-Bax 1-2/L-6 (grey) showing differences in amplitude and frequency. Each plot represents a single cell. Thick lines represent average cumulative distributions for all the single cells transfected with GFP-Bax WT or mutant GFP-Bax 1-2/L-6.
Figure 3(A) Schematic showing the expression domain of the transcription factor Twist on the ventral side of the Drosophila embryo along the anterior-posterior axis (top: lateral view; bottom: cross section). (B) Schematic showing the genetic network that induces actomyosin contractility at the apical surface of mesodermal cells. The transcription factors Twist and Snail regulate expression of the G-protein coupled receptor (GPCR) Mist, its ligand Fog and the Gα Cta, as well as T48, which recruits the RhoA activating factor RhoGEF2 to the apical surface. Fog-mediated activation of Mist triggers RhoGEF2 activity through Cta and thus induction of actomyosin contractility. (C) Schematic of the optogenetic system employed to activate Rho signaling. RhoGEF2-CRY2 is cytosolic in the dark and interacts upon photo-activation with blue light with its binding partner CIBN which is anchored at the plasma membrane. (D, E) Still frames of a movie showing endogenously tagged mVenus::βH-spectrin in the cross section of a gastrulating wild type (D) and twist mutant (E) embryo imaged using two-photon microscopy. The top frame corresponds to the time point where an initial bending of the apical surface was observed, the middle frame was taken 2 min and the lower frame 3 min afterwards. Scale bars, 30 µm. (F, G) Confocal images showing apical βH-spectrin (endogenously tagged mVenus::βH-spectrin) in a wild type (F) and twist mutant (G) embryo. Scale bars, 20 μm. Medio-apical βH-spectrin fibers observed in wild type embryos were absent in twist mutant embryos. (H-Q) Confocal or two-photon microscopy images of the apical surface of an embryo mounted with the dorsal side facing the objective and co-expressing endogenously tagged mVenus::βH-spectrin (green, H, K, M, P), the myosin-II marker Sqh::mCherry (magenta, I, N), and the optogenetic modules as explained in (C). The apical surface is shown before photoactivation (H-L) and 1 min after photoactivation (M-Q). Panels (J, O) show a merge of βH-spectrin and myosin-II and the dashed rectangle indicates regions shown in (L and Q) at higher magnification. Panels (K, L) and (P, Q) are zoom-ins into the region indicated in (J) an (O), respectively. Scale bars, 20 μm (H-J, M-O). 2.5 μm (K, L, P, Q). (R) Quantification of apical βH-spectrin upon optogenetic stimulation of Rho signaling. The graph shows the mean intensity of βH-spectrin (green) at the apical surface over time as the fold change relative to the initial time point (before photo-activation). The semi-transparent region indicates the standard deviation and dots indicate individual data points (n = 5 embryos). (S-T) Two-photon microscopy images of apical βH-spectrin (green) 1.5 min after optogenetic stimulation of Rho signaling in embryos that were previously injected with water (S) or the ROCK-inhibitor Y-27634 (T). Dashed boxes indicate photo-activated cells. Y-27634-injected embryos did not undergo apical constriction and did not accumulate βH-spectrin upon photo-activation, while water-injected embryos constricted and showed increased βH-spectrin levels. Scale bars: 10 µm.
Figure 5(A) 15S rRNA levels are increased in the suppressor clones. Total RNA was isolated from the replacement strains (Sc+Sc-CCM1 and Sc+Sb-CCM1), two nuclear suppressor strains (Sc+Sb-CCM1D400N and Sc+Sb-CCM1E375Q) and one mitochondrial suppressor strain and then subjected to quantitative PCR analyses. Relative mRNA abundance was calculated by normalizing the 15S rRNA level to the ATP6 mRNA level. Graph was plotted using data from five independent repeats for each strain and p values were calculated by unpaired, two-sided student t-test. Error bars indicate S.D. ***, p value < 0.001. **, p value < 0.01. Asterisks in black, comparing Sc+Sc-CCM1 with others. Asterisks in gray, comparing Sc+Sb-CCM1 with others. (B) The steady-state level of mtDNA-encoded proteins is increased in the suppressor clones. Protein extracts from the replacement and suppressor strains were hybridized with antibodies against G6PDH, Cox1, Cox2 or Cox3.
Figure 2A-B) NK cells were activated with IL-2 or IL-15 for two days in the presence or absence of PGE2 (1µM) and analyzed for A) the levels of phosphorylated S6 (pS235/pS236), STAT3 (S727), STAT5 (Y694), Akt (S473) (n=4, biological replicates) and B) 16 categories of phosphorylation array showed. Red box indicates category 1 (pS6+, pSTAT3+, pSTAT5+, pAKT+). C) Relative changes in frequency of NK cells expressing pS6 in the presence and absence of PGE2 (n=4, biological replicates). D) Flow cytometry analysis of PDE4A in the presence or absence of Torin-1 (1µM) (left, n=7, biological replicates) with representative histograms (right). E) NK cell-mediated cytotoxicity of K562 cells by 4-hour chromium-release assay of two-day cytokine activated NK cells in the presence or absence of Torin-1 (1µM) and PGE2 (1µM) (n=6, biological replicates). E:T ratio=5:1. F, G) (F) Flow cytometry analysis of pS6 and (G) 4-hour chromium-release assay of PGE2-treated NK cells against K562 measured after 48 hours treatment with Roflumilast (PDE4i, 1µM) (n=3, biological replicates) E:T ratio=5:1.
Figure 1(A) Superior cervical ganglia (SCG) excised from stage E21 embryos were dissociated and plated. Treatment with the anti-mitotic agents fluorouracil (5-FU) and aphidicolin over a period of five days allows further enrichment for non-dividing cells (i.e. post-mitotic neurons). SCG cultures were subsequently infected with HSV-1 at a multiplicity of infection (MOI) of 1.5 in the presence of 100 μM acyclovir (ACV, an inhibitor of viral DNA replication) to allow the establishment of HSV-1 latency. Following removal of ACV, latently-infected cultures were maintained for up to two weeks prior to treatment with PI3K inhibitor LY2940002 (LY) to induce reactivation. Uninfected, latently-infected, and reactivating SCG cultures subsequently processed for scRNA-seq using the 10X genomics Chromium Single-Cell 3' v2 Reagent Kits. scRNA-seq of eight discrete SCG cultures using v2 chemistry yielded 28,346 cells passing filter Clustering of cell types by UMAP reveals four discrete cellular populations classified according to specified markers for neurons (Prph, Tubb3), fibroblasts (Col3a1, Fn1), satellite glial cells (Aif-1, Cd68), and Schwann cells (Sox10, S100b). scRNA-seq of eight discrete SCG cultures using v2 chemistry yielded 28,346 cells passing filter Clustering of cell types by UMAP reveals four discrete cellular populations classified according to specified markers for neurons (Prph, Tubb3), fibroblasts (Col3a1, Fn1), satellite glial cells (Aif-1, Cd68), and Schwann cells (Sox10, S100b). (D) smFISH images showing LAT RNA in Ntrk1-positive neurons. SCG-derived cultures were infected with HSV-1 in the presence of ACV and allowed to establish latency over 7 days before being processed for smFISH using probes for HSV-1 LAT (green) and neuronal marker Ntrk1 (TrkA) (red) or fibroblast marker Col3a1 (red). Signal intensities for the LAT probe were quantified in neurons and fibroblasts and plotted by ImageJ. The percentage of LAT-positive cells were quantified and displayed as bar graphs with mean ± SEM. Left: 3 biological replicates, signal intensities of 50 cells were quantified for each replicate. Middle: 3 biological replicates, signal intensities of 30 cells were quantified for each replicate. Right: the blue and red dots represent the number of biological replicates done for quantification of each cell type. Scale bar, 10 μm. Data information: P values equal to or less than 0.05 were considered significant, asterisks denote statistical significance (****, p<0.0001). P values are calculated using two-tailed unpaired Student's t test. P values > 0.05 were not significant (ns).
Figure 6A Scheme of the mathematical model. Integrated pAKT and ppERK obtained from our kinetic model were linked by linear regression analysis to measured cell-cycle indicator. Similarly, cell-cycle indicator and integrated pS6 were linked to measured proliferation by linear regression analysis and model selection. B Linear regression fit for the respective cell-cycle indicator of experimental data. Data points represent mean ± standard deviation, N=3. Solid lines represent the linear regression fit. C Simulated integrated pS6 response versus simulated cell-cycle indicator of mCFU-E, BaF3-EpoR and 32D-EpoR cells upon 5 U/ml Epo stimulation and single inhibitor treatment at indicated doses D Linear regression modeling and model selection revealed that while proliferation of mCFU-E cells is best described by integrated pS6 only, for 32D-EpoR and BaF3-EpoR cells proliferation correlates mainly with cell-cycle indicator. Proliferation was measured, integrated pS6 and cell-cycle indicator were simulated with our mathematical model. The linear regression model selection is based on Akaike's information criterion. The respective correlation is given. For details, see Appendix N and O.