EMBO/sd-character-level-ner huggingface dataset:
(A, B) Analysis of gene classes associated with the homeodomain TF clusters. For each gene in the dataset, normalized, scaled expression in single cells was modelled as a function of homeodomain TF cluster identity, and significance of the association was determined using an F-test. Panel (A) depicts the number of genes with significant homeodomain TF cluster association falling into distinct gene classes. p-values were retrieved by a Fisher test. Panel (B) contrasts the p-values for homeodomain TF cluster association between Ig domain genes and other genes using a boxplot. See Methods, section Data visualization for a definition of boxplot elements. P values are from a two-sided Wilcoxon test. ***: p<0.005.
Model for p62-dependent cargo nucleation and autophagic degradation of poly-ubiquitinated proteins, and its crosstalk with the UPS
C. A heatmap generated by three independent biological replicates shows gene expression profiles of wild type and KAP114 knockout strains grown in the presence of 1.5 M NaCl. The Log2 (fold-change) values and the color scale are shown.
CAGE-seq data showing the transcription start sites of JARID2 in different cell lines. CAGE peak is mainly observed at JARID2 isoform-1 in most cell types. JARID2 gene structure is shown at the top.
G - J) Statistical analyses of mitochondrial transport parameters of five independent experiments shown in (D-G and Fig. EV3A-D). Each bar represents the mean (±SEM) of medians of single experiments for (G) run length and (H) speed distributions, and average (±SEM) (I) overall mitochondrial motility and (J) density of all five experiments. Values of fold change between control and Ttll1‑/- and Ttll7-/- conditions are indicated below the graphs. Full bars are for anterograde, and empty bars for retrograde transport events. Significance was tested using unpaired t-test. Average (G) run length as well as (H) speed showed no significant differences between control and Ttll1-/- and Ttll7-/- conditions. (I) The averages of overall motilities reveal an about 1.7-fold increase in overall mitochondrial motility in Ttll1-/- neurons, while no significant differences were found in Ttll7-/- neurons. (J) Mitochondrial density was unaltered between control and knockout conditions. Total number of mitochondria analysed from five independent experiments: control (1260), Ttll1-/- (1158) and Ttll7-/- (1191).
(E) Overall survival analysis of medulloblastoma patient based upon FBW7 expression level. Analysis was performed on 383 out of the 423 cases from which the survival data were available. Cohort was divided into high- (blue line) and low- FBW7 (red line) expressing subgroup using FBW7 median expression as group classifier. Statistical analysis was determined by using a LogRank test.
Bar plots representing enriched KEGG pathways among genes that showed significant changes at both transcript and protein levels in aging. Genes were grouped according to the four possible patterns of transcript and protein regulation, as visualized by their positions in the four quadrants shown in (D) and (E), respectively. Only pathways significantly enriched (FDR < 0.05) are shown. The complete list of enriched pathways is reported in Dataset EV4.
(A) An INS1 cell expressing mtPA‐GFP and co‐labeled with TMRE. The two mitochondria fused 20 s after photoactivation (arrow in '20 s'). Then, a voltage difference was established between the two poles (120 s) and they were later physically separated (120 s). The pattern is qualitatively similar to that shown in Figure 3Bi. Scale bar, 2 μm.
Figure 3. Mmi1 promotes transcription termination of nam1 non-coding gene and prevents nam1 read-through transcription from repressing the downstream MAPKKK gene byr2. (D) Microscopy images of, respectively, WT (h90), nam1-1 and nam1-1-Ttef cells, after induction of sexual differentiation for 24 hours. The percentage of sporulation and iodine vapor assays are shown at the bottom of the images. Scale bar, 10 µm.
(C) WT, Irgm2-/-, Casp11-/- and Irgm2-/-Casp11-/- BMMs were treated with LPS (1 µg/ml) and/or MCC950 for 24 h and IL-1β/LDH release was measured.
B. Control cells and cells treated with Dinaciclib (CDKi) were treated with SA and stained for GM130 (in gray). Insets, eIF3. Blue, nuclear DAPI staining. The graph shows quantification of Golgi objects in HeLa cells untreated or treated with SNS-032, Flavopiridol, or Dinaciclib for 150 min and then treated with SA (300 µM, 30 min). Mean ± s.e.m. of three independent experiments. ****p<0.0001, One-way ANOVA with Dunnett's multiple comparison test.
A, B. Tumors from CT26 tumor-bearing BALB/c mice treated with vehicle or TP-16 for 2 weeks were harvested, and tumor single-cell suspensions were analyzed for tumor-associated myeloid cells by flow cytometry analysis. Representative graphs and quantification of F4/80+MHC-II+ immunosuppressive myeloid cells (IMCs)-M1 macrophages (A) and F4/80+CD206+ IMCs-M2 macrophages (B) gated on CD45+CD11b+ myeloid cells (n = 5).
to h. Inhibitory activity of EK1C4 in cell-cell fusion mediated by the S proteins of Rs3367 (g)
(A, B) Western blot analysis of p62, ubiquitin (Ub), TDP-43 and p-TDP-43 in RIPA- and urea-soluble fractions from spinal cord (C5-C8) and brain of 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. Spinal cord: n=3; brain: n=4. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: *, p<0.05; **, p<0.01***, p<0.001, ****, p<0.0001.
A. Imaging of SPBs (Cnm67-RFP) and Spc72-GFP or Mpc70-GFP in PHSL1-CDC20 ama1∆ control cells and spo13 mutants. Top, time-lapse series. Bottom, meiotic events were quantified in cells synchronized in silico to SPB separation at entry into metaphase I (t = 0). Graphs show overlays of SPC72-GFP and MPC70-GFP strains. Data information: data are representative of two independent experiments.
(F) Relative Quantitative Real-Time PCR analysis of SUMF1, DERL1, ATF6, APEX1 and GPX1 mRNA transcript levels in ARPE-19 cells infected with either adenovirus expressing Null or TFEB-S211A (mean ± SD of the RNA fold change of indicated gene mRNAs normalized to actin mRNA from three independent experiments, students t-test, **p < 0.01, ***p < 0.001).
WT cells before and after calcium shift-induced differentiation (E) were treated with cycloheximide. Cell lysates were collected at 0, 30, 60, 90, 120, 180, and 300 minutes post treatment and subjected to immunoblotting with different antibodies as indicated.
F. Representative images of Sec24C localization at SGs (stained for G3BP) in TRAPPC3-KD and TRAPPC2-KD cells treated with SA. Depletion of the entire TRAPP complex (via TRAPPC3 depletion) or of only TRAPPC2 reduces Sec24C recruitment. Graph, quantification of Sec24C at SGs, calculated as in (E). Mean ± s.e.m., n = 40-60 cells per experiment, N = 3. ****p< 0.0001, One-way ANOVA with Dunnett's multiple comparison test. Data information: Scale bars, 10 µm.
D, E Hematoxylin and eosin and immunohistological staining with A6, HNF4, Sox9 and CD133 antibodies of tumor sections from xenografts dissected 20 or 30 days after injection with primary hepatocytes from P240 PR-SET7ΔHepA livers.
(C) Differentially expressed genes using RNAseq transcriptome analysis of CD31+ endothelial cells (ECs) sorted from sprouting EBs from Apelin STOP cells stimulated with VEGF (30ng/mL) and DMSO (-Apln) and repaired Apelin GO sister cells stimulated with VEGF and Apelin (1000nM) (+Apln). VEGF target genes and angiogenesis-related genes, predicted by Ingenuity Pathway Analysis (IPA) software, are indicated by bars on the upper axis of the heatmap. GO terms were analyzed by DAVID on-line software.
(A) L. pneumophila subpopulation proteomics. A. castellanii was infected (MOI 5, 42 h) with L. pneumophila JR32 (Ptac-mCherry-PflaA-gfp). After cell lysis, released intracellular bacteria were sorted by flow cytometry in mCherry-positive/GFP-negative and mCherry-positive/GFP-positive L. pneumophila subpopulations, and their proteome was determined and compared. Protein abundance in each subset is depicted as a volcano plot. Proteins enriched in the GFP-producing subpopulation have a positive log2 ratio (q-value).
Quantification of the wound area invaded in 24 hours (grey dots) for Epi cells expressing CTR, HOT, HOTΔP or HOTΔP (B), or Mes cells transfected with ASO CTR (control), ASO1 and ASO2 targeting HOTAIR (C), or Epi cells overexpressing CTR or HOT alone or together with LSD1 (LSD1-OE) (D). Bars correspond to Mean values and Confidence Interval (CI) of 95%. *** P-value < 10-4, ** P-value < 0.03 (Student t-test, N=48 for (B), N=6 for (C), N=30 for (D)).
HCT-116 or HT-29 cells were treated with 5mM 3-MA or 5μM chloroquine (CQ) for 30 min, and then with 2mM sodium butyrate (NaB) for 24 h. Representative Western blots of LC3-I and LC3-II expression were quantified by densitometry and normalized to GAPDH (ratio of LC3:GAPDH). The fold change from control is indicated as the mean ± SD of three independent experiments. One-way ANOVA was used for statistical analysis. ** p<0.01, compared to the respective control group. (A) HCT-116 cells treated with 3-MA and NaB;
C. Representative images for TIF quantification: co-localization between 53BP1 (green) and telomeres (red FISH probe) in U2OS or IMRB cells with or without ectopic hTR overexpression. White arrows indicate TIF. Quantification of TIF is on the right. A total of 110-170 nuclei were scored from three independent experiments. Each dot represents the number of TIF per nucleus. Data information: All scale bars: 5 μm. Data are shown as mean ± SD. , C, the red line marks the mean value. Statistical analyses were performed with Student's two-tailed unpaired t-tests with Welch's correction for normality of distribution, unless specified otherwise.
(G) Overview of residues affected by Mn2+ binding to YqgPNTD mapped onto its solution NMR structure. The view is oriented as the left view in panels (A and B).
ELISA analysis of IL-8 secretion in response to TNF stimulation (10 ng/mL) in healthy control or OTULING281R primary fibroblasts. Bars represent mean ± SEM (n=4).
WT and Mfn1/2 double KO were transfected with: GFP and the indicated plasmids. After 24 h, the transfected cells were sorted and plated for another 24 h. (J) SRC were calculated (n= 3 independent experiments). Data are presented as mean ± SEM.
A. Immunoblot analysis of cleaved GSDMD in culture supernatants and full length GSDMD, cleaved GSDMD and α-tubulin in the cell lysates of immortalized LPS-primed WT macrophages left uninfected (NS) or infected for 10-40 minutes with log phase S. typhimurium (MOI=50).
D. Model representing how RASSF1C expression in RASSF1A‑silenced breast cancer cells (MDA-MB-231) activates a signaling cascade involving SRC kinase, RhoGDI and culminates in RhoA activation and generation of amoeboid contractility and cancer stemness features. RASSF1C-driven amoeboid cancer stem cells contribute to alteration of the tumor microenvironment by rendering recipient cells (MCF7, T47D) more invasive and able to upregulate stem cell markers, due to EV-mediated communication.
(C) Quantification of different phenotypes manifesting in MN2a and MN3 after neuronal RNA interference or mis-expression of Ig genes (DIPgamma, DIPkappa, dpr11, dpr1) in comparison to control animals: MN2a axons projecting to the MHE muscle, representing the wild-type (wt) innervation pattern of MN2a (magenta); MN3 axons projecting to the MHD muscle, representing the wild-type (wt) innervation pattern of MN3 (cyan); MN2a or MN3 axons projecting to muscles other than the MHE or MHD termed wiring defects (dark grey); abnormal synaptic morphologies at MN2a or MN3 derived axon terminals termed terminal defects (light grey). Each experiment was performed in triplicates. Note, each genetic experiment was performed in parallel to an adequate control experiment using the same driver line crossed to a line that controls expression of either UAS-RFP or UAS-GFPRNAi. p-values between two genetic conditions were calculated by a two-sided Fisher test. * p < 0.05, **<0.01, *** p < 0.005.
(D) Quantification of the Western blot bands intensities of two independent experiments with the Adobe Photoshop program.
H&E stained sections of back skin from indicated mice treated with IMQ for 2, 3 or 5 days. Bright-field images, Magnification: 20x, Scale bar: 100 µm.
(B) Incidence of spinal ankylosis in PGIS model. n=5 per cage of total 3 cages per group, Fisher's exact test. (C) Quantitative analysis of structural parameters of spinal ankylosis by μCT analysis. n=5 per group, one‐way ANOVA, Bonferroni post hoc.
A) hnRNPA2 LC (AlexaFluor488-tagged, green) undergoes LLPS, while hnRNPF PLD (AlexaFluor555-tagged, red) does not. However, hnRNPF PLD partitions into hnRNPA2 LC droplets when mixed at a 1:1 ratio. Conditions: 20 µM indicated protein (~1% fluorescently tagged), 20 mM MES pH 5.5, 50 mM NaCl, 150 mM urea. Scale bar: 10 µm. B) At 300 µM, FUS LC (AlexaFluor488-tagged, green) undergoes LLPS, but at 200 µM hnRNPF PLD (AlexaFluor555-tagged, red) still does not undergo LLPS. When mixed at 300 µM FUS LC and 200 µM hnRNPF PLD, hnRNPF PLD does not partition into FUS LC droplets. Conditions: 300 µM FUS and 200 µM hnRNPF PLD (~1% fluorescently tagged), 20 mM MES pH 5.5, 150 mM NaCl, 150 mM urea. Scale bar: 10 µm.
Liver sections from control and CCl4- and CCl4/R-III-treated mice were immunohistochemically stained for TGF-β and F4/80. Scale bar, 50 μm.
E Yeast two-hybrid analyses of the interactions between DJA6 and chloroplast SUF components. Positive control, the interaction between murine p53 fused with GAL4 BD and SV40 large T-antigen fused with GAL4 AD; negative control, the coexpression of Human Lamin C fused with GAL4 BD and SV40 large T-antigen fused with GAL4 AD. The dilution ratios are indicated on the left.
CD11b+ CD11c+ dendritic cells were enriched from WT or Rab39a KO spleens via magnetic negative selection. Cells were fed with 3 µm biotin-ova-magnetic beads for 4 hours. Phagosomes were extracted, permeabilized and stained for the indicated proteins. For ROS measurements, phagocytosis was performed with 5 µM CellROX and the phagosomes were not permeabilized. For analysis, the background fluorescence of unstained beads was subtracted from the resulting phagosome gMFI and the fold change of target (dox/no dox) was calculated. Shown are three independent experiments combined. Error bars show SD between experiments. p values were calculated using two-tailed ratio-paired Student's t-test.
X-ray analysis of 7-months-old H2-c-fosLTR/Egfrwt and H2-c-fosLTR/Egfr∆Ob littermates. Scale bars: 1cm
(D) SMAD3 gain-of-function increases BRAFi-resistance. Determination of BRAFi half maximal inhibitory concentrations (IC50 values) for 501Mel cell lines (Log[Vem] (nM)). Parental 501Mel cells (n=5), 501Mel cells expressing dCas9 and HSF1-p65-MS2 (named here 501Mel 2+, n=5), the 501Mel 2+ cells expressing a control guide (backbone, n=5) and the 501Mel 2+cells overexpressing SMAD3 (n=3 biologically independent experiments). A representative experiment has been chosen. Dotted line is used to determine the IC50 values.
E. Cellular extracts from H1299 cells transiently transfected with 2 μg of each indicated plasmids were immunoprecipitated with rabbit polyclonal YAP antibody. Cell lysates derived from cells transfected with the empty vector were used as negative control of immunoprecipitation.
A Ribbon diagrams of the structure of rat Munc18-1 containing the K332E/K333E mutation, two orientations rotating 90° with respect to each other were shown. Two Munc18-1 K332E/K333E molecules in an asymmetric unit pack against each other through helix-helix interaction in domain 3a.
(A) Confocal microscopy images of untreated (UT) or treated with Ciliobrevin D (CilioD) or AZ82 or both treatments simultaneously (CilioD + AZ82) ECs and stained for endogenous EEA-1 (in green) and LAMP-1 (in red) to visualize EEs and LEs, respectively, and Draq5 (in blue) to highlight the nucleus. The yellow line is drawn to define cell periphery. Scale bar = 20 μm. On the right, inset panels to highlight respective perinuclear and peripheral area of the cell. Scale bar = 5 μm.
B. Chemical inhibition of Hsc70 activity in HEK293T cells overexpressing FLAG-DnaJC5 reduces extracellular α-synuclein levels as shown by dot blot. Intracellular levels are shown by Western blotDnaJC5 was detected by FLAG antibody. Quantification of extracellular synuclein levels is shown as average ± SEM, n=3, ***p<0.001 one-way analysis of variance with Tukey's multiple comparison post-hoc analysis.
D. Trophozoite stage infected erythrocytes were incubated with FM4-64 and DAPI to assess lipid uptake by 3D7 or PfCDPK7-KO parasites. Subsequently, FM4-64 associated fluorescence was visualized by live microscopy (top panel) and also analyzed by FACS and % change in FM4-64 uptake in KO parasites was determined (bottom panel) (mean± SEM, n=3; biological replicates, *p<0.05, t-test; Scale bar-1 μm).
The survival time (days) of cardiac graft in mice treated with DMSO, 2.0 mg/kg FK506 or 2.0 mg/kg CX5461. (n=5)
A) Spatial distribution of H3K9me3 in CD38-, CD33+ and CD19+ cells. For each population, two representative nuclei are presented. Inverted images of equatorial Z plane of DAPI (left panel) and H3K9me3 (right panel) are shown. Scale bar: 5 µm.
Flow cytometry of total back skin after 2, 3 and 5 days of IMQ treatment. Analyzed were Monocytes (CD11b+Ly6Chi) (G), and Neutrophils (CD11b+Ly6G+) (H). Graphs show immune cells as % of live, single cells. n = 10-21 (G), n = 4-25 (H); ≥ 2 independent experiments). Data information: Data are shown as mean ± SEM. P‐values were calculated by Bonferroni multiple comparison test Statistical significance: ns > 0.05, *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. See Appendix Table S3 for exact P‐values.
Based on the structures of apo-PfFNT and PfFNT-MMV007839, we propose that the PfFNT membrane protein is capable of picking up lactate ions from the parasite's cytosol, converting them to lactic acids and then exporting these acids into the extracellular space via a sequential displacement mechanism. We believe that residues lining the central channel are highly flexible and can quickly rearrange sequentially to contract and relax the channel for propelling the export of substrate across the membrane. This schematic diagram indicates that PfFNT shuttles lactate ions from the parasite's cytoplasm to the midway of the central channel. These ions will be converted to lactic acids, via proton transfer from H230, and then shuttled across the second half of the channel to the parasite's extracellular surface. Residue K35 contributes to form a transient binding site to bind lactate ion nearby to the cytoplasmic surface of the parasite. As soon as the second lactate ion arrives from the parasite's cytoplasm, the first lactate will be displaced and continue to propagate to the midway of the channel, where H230 is responsible for donating a proton to convert this lactate ion into lactic acid and open the constriction for further propagation. Residue K177 participates in forming a transient binding site, which binds lactic acid nearby the extracellular surface. A second ion enters this site will cause displacement and extrusion of lactic acid out of the parasite.
Figure 4 - Semi-quantitative prediction of mRNA log2 fold changes upon different signalling scenarios. A: Gene expression upon different stimulations was predicted based on fitted model parameters and measured pERK2 levels. Predictions were verified with gene expression time-course data.
D PAX7+ cells in skeletal muscle sections, demonstrating that satellite cells are less abundant in D233E patients than in controls (n = 3 muscles with 10-15 fields analyzed per muscle). Mean ± SEM; Mann-Whitney U test; Scale bar, 50 μm.
(d) PtdIns(3) Pdepletion inhibits Golgi-to-ER retrograde transport of VSVG-KDELR. HeLa cells were transfected with empty vector, wild-type MTMR3, the C413S mutant of MTMR3, or treated with wortmannin or rapamycin, and then the ER pattern of VSVG-KDELR was quantified. UT, untreated. Data are the mean±s.d.; n = 100 cells for each group obtained from three independent experiments; **P0.01.
(E) Schematic map of nine EWS mutants (left) and IP-western blot analysis (right). GFP-PARP1 and siPARG were transfected into HEK-293 cells with each EWS mutants plasmid. After H2O2 treatment, the cells were conducted to IP with anti-Flag antibody.
B J774A.1 macrophages were stimulated with live or fixed swollen conidia (MOI = 5) or zymosan (50 μg/ml), and NFAT translocation was assessed by confocal microscopy. NFAT is indicated in green, the nuclei are indicated in red, and AF conidia can be seen in pink. Live conidia were observed to stimulate sustained nuclear translocation compared to dead conidia or zymosan. Data represent mean ± SEM. Scale bar: 50 μm. Arrows indicate A. fumigatus or zymosan-positive cells.
(E) RALF23/34 promoted the growth of Pto DC3000 in phr1 mutants. Col-0 and phr1 mutant seedlings grown in LP media were root inoculated (by soaking) with a bacterial suspension (OD600 = 0.2) for 2 min, and the number of bacteria from individual root was quantified at 5 dpi. The data shown indicate the means ± SDs (n = 18, n refers to the number of roots per group). The different lowercase letters indicate statistical significance (one-way ANOVA). Data information: All experiments were repeated three times with similar results.
C, ChIP-qPCR for total RNA Pol II, pSer5 Pol II, and pSer2 Pol II at ERP70, GRP78, and a gene desert (Prom = gene promoter, Coding = downstream coding region - see Appendix Table S1 for primer sequences). Three independent experiments are represented as mean ± SEM. with significance measured by Student's t-test, *p<0.05, **p<0.01, ***p<0.005.
Study design. Adult (12-14 wph) killifish were treated with different proteasome inhibitors or vehicle control for 4 days. Proteasome activity and proteome changes were analysed in brains from treated and control fish.
D. Wt and ∆LE HUVECs co-cultured on fibroblast monolayers. Endothelial cells were identified either with an antibody against the endothelial cell marker PECAM-1 (left) or through expression of a nucleofected plasmid encoding the cytoskeletal marker Lifeact-GFP (right). Arrowheads indicate filopodia
Protein-scale validation: Comparison between predicted CS enrichment from leave-1-out validation to CS enrichment computed from all carbonylated peptides measured for E. coli (left) and D. radiodurans (right). Each point represents a different protein species. Predicted probability-weighted CS enrichment = (sum of carbonylation probabilities across training set sites)/(number of residues in corresponding peptides from experiments). Experimentally measured probability-weighted CS enrichment = (sum of empirical oxidation probabilities across training set sites)/(number of residues in corresponding peptides from experiments). The solid line is the fitted regression line, and dashed lines indicate the boundaries of the 95% confidence interval.
Dilution assay of wild-type or rev3Δ cells expressing BRCT3/4-SGS1 in the presence of 0.0025% MMS.
(A) Digitonin-solubilized mitochondria from doxycycline-treated 143B cells, COX1∆ and COX2∆ cybrids were analyzed by BN-PAGE followed by CI-IGA assays (upper panels) or immunoblotting (medium and lower panels) with antibodies against CI subunits NDUFA9 and NDUFS1. The identities of MRC complexes and SCs are as in Figure 1.
(G) RNA-seq was performed using RNAs from freshly isolated SCs (FISCs); scatter plot shows differentially expressed genes with a fold change >=2 (red dots) in YY1iKO vs Ctrl.
Solubilized mitochondria from MITRAC15FLAG-expressing cells were first subjected to native anti-FLAG immunoisolation (Total 0.1 %, Eluate 10 %, lane 4). Purified complexes were applied to anti-MITRAC12 immunoisolation (Eluates 100 %, lane 5). All samples were analyzed by SDS-PAGE and immunoblotting.
D Colonies number of p53+/+ and p53-/- HepG2 cells expressing control or SQLE siRNA. Number of colonies with a diameter greater than 10μm were quantified.
Lipids were extracted from EV secreted by adipocytes from lean (ND) and obese (HFD) mice (n=5) (left panel) or from human adipose tissue samples from patients with varying BMI (right panel) and fatty acid content was measured (n=15).