EMBO/sd-character-level-ner huggingface dataset:
Figure 2A. U6A cells expressing wild-type or T387A STAT2 were treated with IFN-β (100 IU/ml). Cells were harvested after 4 h and total RNAs were analyzed by real-time PCR. Values are the means ± SD from three independent experiments. B. U6A cells expressing wild-type, T387A, or T387D STAT2 were treated with IFN-β (100 IU/ml). Cells were harvested after 4 h and total RNAs were analyzed by real-time PCR. Values are the means ± SD from three independent experiments. C, D. U6A cells expressing wild-type or T387A STAT2 were treated with IFN-β for 0, 4, 8, or 24 h. Total RNAs were analyzed by using an Illumina HumanHT-12 v4 Expression BeadChip array. The average signal for each probe was used to determine expression levels. Genes with average signals below 25 and detection P values greater than 0.01 in the untreated or treated cells were excluded from the analysis. Inductions of less than 2-fold were not scored. The Venn diagram shows the numbers of genes induced by 1.2 fold or more in U6A cells expressing T387A STAT2, relative to untreated control cells. The numbers in the table are fold changes calculated from the ratios T387A STAT2 treated / untreated and wild-type STAT2 treated / untreated.
Figure 6After SARS-CoV-2 infection, a local inflammation occurs, with increased pro-inflammatory cytokines (1). This promotes an interstitial increase of S1P, which in turn potentiates cytokine secretion by different cells (2). The exuberant local cytokine levels result in a systemic cytokine storm (3). This gives on to different alterations (4), including anemia (with impaired S1P synthesis/export) and acute phase response in the liver (with decrease in the negative acute phase proteins albumin and apoM, which act as S1P transporters). These alterations lead to a progressive drop of circulating S1P, with decrease in both apoM/S1P and albumin/S1P (5). The reduction of S1P in the systemic circulation correlate with COVID-19 severity (6) and patient outcome.
action.Figure 3A U2OS cells were transfected with the indicated siRNAs. Seventy-two hours later, cell lysates were prepared and proteins from lysates were subjected to western blot using the indicated antibodies. B U2OS cells were transfected as in A. Seventy-two hours later, total mRNAs were extracted and subjected to RT-qPCR for the indicated genes. C U2OS cells were transfected with increasing amount of plasmid DNA expressing NAT10. Proteins from whole cell extracts were subjected to western blot using the indicated antibodies. D U2OS cells were transfected with control or NAT10 siRNAs. Seventy-two hours later, cells were treated with cycloheximide (CHX) and harvested at the indicated time points. Proteins from cell lysates were subjected to immunoblot for the evaluation of NAT10 and p53 (upper panels). Beta-actin was evaluated as a loading control (lower panel). p53 half-life (t1/2) obtained from three independent experiments was presented as mean ± SEM at the bottom. E U2OS cells were treated with MG132 (10μM) for 4 hours after transfected with the indicated siRNAs. Proteins from cell extracts were detected by western blot for the indicated proteins. F HCT116 p53+/+ cells were transfected with the indicated constructs and treated with MG132 for 4 hours before harvest. p53 was immunoprecipitated with anti-p53 polyclonal antibody and immunoblotted with anti-Ub antibody. G p53 and Mdm2 double null MEF cells were transfected with the indicated constructs and treated with MG132 for 4 hours before harvest. Proteins from whole cell extracts were subjected to western blot using the indicated antibodies. H U2OS cells were transfected with vectors as indicated. Forty-eight hours later, cells were harvested and proteins from whole cell extracts were subjected to western blot using the indicated antibodies.
Figure 2Somatic copy number alterations in each individual Kras and Kras/Mad2 non-regressed tumours. 7 K non-regressed and 16 KM non-regressed tumours were sequenced. Focal deletion (DEL, green), Focal amplification (AMP, light green), whole chromosome gain (WCG, dark grey) and loss (WCL, light grey), partial chromosome gain (PCG, dark blue) and loss (PCL, light blue) and gross chromosomal rearrangement (GCR, red). Overlaying of the amplifications in chromosome 6 across multiple regions showing that all amplicons contained the cMet oncogene. Colour of the block corresponds to the segment mean (the degree to which a genome segment is lost (blue) or gained (red). Immunostaining of phospho-cMet in non-regressed tumours carrying or not the amplification in chromosome 6. Yellow numbers indicate the total number of cMet positive cells/total number of cells counted. Scale bar 100 µm.
Atg8 and Atg11 localization during pexophagy.Figure 3(A) Large phagophore membrane formation in WT and the Atg30 mutant cells monitored by GFP-Atg8 during pexophagy conditions. (B) Localization of GFP-Atg11 during pexophagy of methanol‐induced peroxisomes in cells expressing WT or mutant Atg30 proteins. White arrows indicate correct localization and yellow arrows indicate mislocalization, or in case of Atg8 localization, indicate absence of phagophore membrane elongation. Peroxisomes were labelled with BFP-SKL and vacuoles with FM4‐64. Scale bar, 5 μm. GFP, green fluorescent protein; WT, wild type.
Pri/proteasome processing of Svb is required for ISC/EB maintenanceA Schematic representation of the pri locus, with tested enhancers and location of the pri-Gal4 gene trap insertion.Figure 2Schematic representation of the pri locus, with tested enhancers and location of the pri-Gal4 gene trap insertion. Expression of priA, priJ or priH enhancers in the posterior midgut as seen by lacZ reporters (X-Gal staining, blue), and pri-Gal4 gene trap expressing GFP (green). Schematic representation of Svb maturation by proteasome processing, which is triggered by EcR-mediated expression of pri. esgts midguts expressing GFP alone (control), or expressing pri-RNAi, and quantification of GFP-positive cells (green). The graph also shows the number of YFP-positive cells in ISCts midguts expressing YFP alone (ctrl), or pri-RNAi (see EV2A). ISCts midguts expressing YFP alone (control), or expressing two non-overlapping EcR-RNAi, and quantification of the number of YFP-positive cells (yellow). The graph also plots the number of GFP-positive cells in esgts midgut expressing GFP alone (ctrl), or expressing EcR-RNAi#1, EcR-RNAi#2, and mcherry-RNAi as an additional negative control (see EV2B). esgts midguts expressing GFP alone (control), or expressing EcR-DN, and EcR-DN + pri. Samples were stained for GFP (green). The graph shows quantification of the number of GFP-positive cells in the different genotypes. Posterior midguts containing control and Ubr3 null MARCM clones (GFP, green). esgts midguts expressing GFP alone (control), or expressing Ubr3-RNAi, and Ubr3-RNAi + OvoB. Samples were stained for GFP (green). H' quantification of GFP-positive cells from H.
Figure 7Time-dependent binding of RG7716 is shown in pink, anti-VEGF-A/ANG-2 without modification of the Fc- part in red (wild-type), anti-VEGF-A/ANG-2 with modification of the FcRn binding site only in yellow (FcRn-), and anti-VEGF-A/ANG-2 with modification of the FcγR binding in grey (FcγR-).A) Shows SPR binding profile over time to immobilized FcγR-I, B) to immobilized FcγR-II, C) to immobilized FcγR-III, D) to immobilized FcRn. E) Summary data table of binding data for RG7716 in comparison to anti-VEGF-A/ANG-2 CrossMAbs without modifications in the Fc-part.
Figure 1A. Experimental approach for the detection of blood microRNAs that correlate with memory function in healthy humans. This cohort includes 132 healthy and young individuals (74 male and 58 females, age: 25.95 ± 5.1 years). Participants took part in cognitive tests and donated blood samples (PAXgene tubes). B. Weighted cognitive score of the 132 individuals shows the expected variability. Bar and Error bars indicates mean ± standard deviation. C. MicroRNAs having at least 5 reads in 50% of the samples were considered for downstream co-expression analysis. Co-expression analysis revealed 3 microRNA clusters that were significantly linked to weighted cognitive performance. Number of microRNAs in each module is given in parentheses next to module name. Co-expression modules are represented in rows, while each column refers to a phenotypic trait. Each cell contains the corresponding correlation coefficient and p-value (denoted inside parentheses). Color code represents Pearson´s correlation. Expressions of the modules are not correlated with sex, number of years at school or status of total education. D. The analysis of the experimentally validated mRNA targets of the microRNAs belonging to 3 clusters identified in (C). Downstream analyses on those genes reveal that they control pathways related to aging and age-related functions known to play a role in cognition. Venn diagram displays 23 of the top 30 significant pathways are common among three modules. Dot plot represents the top 23 common significant pathways across three modules. Size of the dot represents number of genes belonging to each pathway term while the color represents the statistical significance.
Comparison of mouse tissue staining following either PFA or glyoxal fixation.Figure 15A - B Confocal images showing staining of Olfactory Marker Protein (OMP) and ß3-tubulin along the dorsal aspect of the mouse olfactory epithelium. While sections from both types of fixative show OMP signal in the olfactory sensory neuron somata, their dendrites, and axons, the axon bundles (green arrow) located above the olfactory epithelium exemplify the clear signal-to-noise ratio benefits of glyoxal fixation versus that of the PFA-fixative. Immunostaining with the ß3-tubulin antibody stains the dendrites and axons in both PFA and glyoxal-fixed tissue, but strong staining of the cilia can only be observed in the glyoxal-fixed sections (B). C - D Confocal images depicting bundles of axons belonging to olfactory sensory neurons on the path toward the olfactory bulb. Identities of the axons are in part defined by the neuropilin-1 (Nrp1) and neuropilin-2 (Nrp2) expression levels, visualized here with antibodies raised against the two proteins. While complementary expression of the two molecules can be seen in the PFA-fixed sections (C), the glyoxal-fixed sections (D) exhibit profoundly improved signal-to-noise ratios for Nrp-1 (red arrows), and in the case of Nrp-2, also the segmentation of the axon bundle into varying levels of Nrp-2 (green arrows). E - F Confocal images of olfactory sensory neuron axons coalescing into glomeruli where they synapse with dendrites of olfactory bulb neurons. The axons of olfactory sensory neurons can be readily visualized with PFA staining (green) in the superficial olfactory nerve layer and terminating in glomeruli located below (green arrows). While sections fixed with either PFA or glyoxal display adequate staining levels, the signal distribution of the Immunostaining-fixed tissue appears more irregular (E), seemingly lacking the neurofilimentary morphology that appears preserved in the glyoxal-fixed sections (F). The glomeruli themselves are neuropil structures comprised primarily of olfactory sensory neurons forming synapses with dendrites of mitral/tufted cells as well as PFA of periglomerular neurons. Immunostaining with Vesicular Glutamate Transporter 2 (VGLUT2) allows visualization of these structures and is easily seen in the glyoxal-fixed section (F), while it appears the antigen was masked by PFA fixation as no signal above background can be seen in the PFA-fixed panel (red arrows in E). Note that a different polyclonal antibody for VGLUT2 from the same provider does provide signal with glyoxal, albeit weaker versus Glyoxal (inset). Staining with ß3-tubulin touts the benefits of glyoxal both due to the signal improvements in the case of the mild staining in the axons of the olfactory nerve layer that is only visible in the glyoxal-fixed tissue, but also in preserving tissue morphology as demonstrated by the dendritic processes inside glomeruli (blue arrows) and in the external plexiform layer located below the glomeruli.
Figure 4A) RNAscope in situ hybridisation analysis of TEAD1/2/4 mRNA expression from control (wild-type) and ApcMin mutant tumours from the small intestine (top) and colon (bottom). All three genes were strongly induced within the ApcMin mutant tumours, with TEAD2 being most strongly induced in colon ApcMin tumours (n=3 animals with multiple tumours within the small and large intestines). B) Q-PCR analysis of control and Apc5 mutant murine intestinal organoids in vitro, control and ApcMin mutant tumour samples in vivo, and control and Apcfl/fl knockout hyperplastic crypts in vivo. In all cases, TEAD1/2/4 mRNA expression was strongly elevated upon loss of Apc function, while TEAD3 mRNA expression was unaffected. (RNA was isolated from 6 individual tumours). C) Antibody staining for TEAD4 reveals a gradient of expression along the crypt-villus axis in both the small and large intestine, with uniformly high expression in colorectal adenomas, similar to SOX9.
a–c) We used quantitative real-time PCR to determine the expression patterns of ATG5 (a), ATG7 (b) and ATG16L1 (c) in various human immune and epithelial cell lines.figf2(a-c) We used quantitative real-time PCR to determine the expression patterns of ATG5 (a), ATG7 (b) and ATG16L1 (c) in various human immune and epithelial cell lines. ATG5 was broadly expressed in the cell lines studied (a), with between 1.5- and fourfold variations in expression level across the cell lines. ATG7 expression (b) was broadly comparable to that of ATG5, with the exception of THP1 cells, which showed 35-fold higher expression than SW480 cells. ATG16L1 expression (c) was also broadly similar to that of ATG5 and ATG7 (except for ATG7 expression in THP1 cells), with moderate variations across the cell lines tested (1.5- to 3.5-fold). (d) Expression of ATG16L1 in human primary immune cells. In a resting human immune cell RNA panel (Clontech), ATG16L1 showed a clear peak of expression in the T cell compartment, with CD4+ and CD8+ cells expressing high levels of transcript (15- to 20-fold more than control samples). We detected modest levels of ATG16L1 in CD19+ cells and low levels in CD14+ monocytes and unfractionated mononuclear cells. In all cases, we performed real-time quantitative RT-PCR reactions in duplicate and plotted the means; error bars represent 1 s.d. We normalized expression levels by comparison with GAPDH controls and plotted arbitrary relative expression units, where the SW480 or placental RNA expression equals 1 (for cell lines or primary cells, respectively). We isolated all RNAs from resting cells in the absence of stimulation or activation.
Figure 2(A) RNA affinity chromatography using the p53 5'UTR (5'p53) or a portion of the p47 5'UTR (5'p47) (depicted in (i)) and HeLa cytoplasmic extracts (CE), followed by western blot analysis (ii). (B) IP of in cellulo RNA-protein complexes (RIP) in HCT116 cells, followed either by RT-qPCR analysis. Bar plots represent the mean and the data of two independent experiments (i) or by western blot analysis (ii). The relative p53 mRNA levels for each IP sample were normalized to the corresponding IP IgG and to the corresponding input sample and were plotted relatively to the HPRT mRNA. (C) UV cross-linking of recombinant (Ku70/Ku80) with the in vitro transcribed 5'p53 with alpha 32P-GTP or alpha 32P-UTP (i). UV cross-linking of recombinant Ku70/Ku80 with the in vitro transcribed 5'p53 and the Ctrl (5'p53 antisense) with alpha 32PGTP (ii). (D,E) RNA affinity chromatography using the different RNA constructs depicted in (i), as described in A.
Figure 7Schematic view of a M. pneumoniae cell during cell division. The right cell compartment shows how protein homeostasis and quality control occurs in a minimal cell organism. Protein folding processes with the main chaperones involved are shown: MPN021 (DnaJ), MPN120 (GrpE), MPN331 (Tig), MPN434 (DnaK), MPN531 (ClpB), MPN573 (GroEL) and MPN574 (GroES). Translocation of proteins across the cell membrane through the Sec-translocation pathway is also shown, including the role of FtsH in regulating its proper assembly. Components of the Sec pathway are MPN184 (SecY), MPN068 (SecE) and MPN396 (SecD). Secreted and membrane-associated proteins containing signal peptides are delivered to the membrane by MPN210 (SecA) or co-translationally through the signal recognition particle MPN061 (SRP). All intracellular proteases and peptidases encoded in M. pneumoniae are also represented with their main functions. These include MPN671 (FtsH) and MPN332 (Lon) ATP-dependent proteases, and peptidases involved in peptide degradation such as MPN022 (Pip), MPN197 (PepF), MPN470 (PepP), MPN572 (PepA), and in protein processing and maturation, such as MPN186 (Map), MPN326 (Prp) and MPN293 (Lsp). Regulation of specific protease and chaperone genes through the MPN124 (HrcA) regulatory system is illustrated. Also the presence of a putative SPase-I like protein (not yet identified) and the Opp transport system are shown. The left cell compartment shows the major regulatory functions of Lon- and FtsH-controlling specific cellular pathways. Finally, essentiality of the genes involved in this model is shown as E, essential; F, fitness; NE, non-essential.
a) The scheme for designing monomeric (MutM) or stabilized (MutStab) mutants of the Beclin 1 CC domain.f4(a) The scheme for designing monomeric (MutM) or stabilized (MutStab) mutants of the Beclin 1 CC domain. Wild-type CC domain dimer is represented in the centre as two antiparallel colour bars. Each individually coloured segment on the two bars represents a single heptad repeat. The colour gradient is from blue at N-terminal to red at C-terminal. Two grey spheres are drawn for each coloured segment, indicating the a and d residues that form the dimer interface. The canonical a-d' pairings mutated in MutM constructs are coloured yellow and the imperfect a-d' pairings mutated in MutStab constructs are coloured red for charged residues or green for alanine residues. (b) The estimated molecular weight of Beclin 1 CC domain wild-type, MutM and MutStab constructs based on their respective sedimentation equilibrium profile (Supplementary Fig. S10). (c) Self-association pattern of wild-type, MutM and MutStab constructs of Beclin 1 in vivo. For each construct, both GFP- and Myc-tagged full-length Beclin 1 are co-transfected into HEK 293T cells and their self-association is probed by co-IP using GFP antibody for IP, followed by western blot with anti-Myc antibody. (d). Temperature-dependent CD profile of Beclin 1 CC domain wild-type and MutStab constructs at 220 nm.
Figure 4A Schematics of AB diblock copolymers with different lengths of blocks and examples of the microphases (sphere and cylinder) that they form. Different blocks are shown in different colors (magenta and cyan). B Schematics showing analogies between NEAT1_2 RNP (upper) and ABC triblock copolymer (middle), and a triblock copolymer micelle and a paraspeckle (lower). Different blocks consisting of RNA and the putative partner RBPs are shown in different colors (magenta, cyan, and green). The energetic contributions that are considered in the theoretical model (from i to iv) are also shown. They include i) the surface free energy of the core (B block) of the polymer micelle (the paraspeckle), ii) the excluded-volume interactions between the A and B blocks, which are energy cost in entering the A blocks into the core (B blocks), iii) the excluded-volume interactions between the A (or C) blocks in the shell, iv) the mixing free energy of thermal fluctuations that randomly distribute A (or C) blocks between the core and the shell (see the text for further details). C In the copolymer micelle model, B blocks are localized in the core and C blocks are localized in the shell. A fraction, α, of A blocks are localized in the shell, and the other fraction, 1-α, are localized in the core. D The fraction α of the A blocks in the shell versus the length of the A blocks (represented by the number of segments) of spherical paraspeckles in the steady state. The parameters used for the calculations are shown in the Materials and Methods.
Somatic retrotransposition occurs before and after the clonal expansion A A somatic insertion may arise in a normal tissue and be present in a fraction of cells of the tissue (red star).Figure 3A A somatic insertion may arise in a normal tissue and be present in a fraction of cells of the tissue (red star). If a second somatic event (yellow) inactivates the Notch pathway, the mutant cell (indicated in green) will initiate the clonal expansion amplifying somatic variants already present in its genome. Finally, any insertion that occurs after the clonal expansion (blue triangle) will be present in a subset of neoplastic cells. The graph represents theoretical allele frequencies of somatic variants obtained from the sequencing of clonal tissue samples. The allele frequency of a Notch inactivating event, marking the onset of neoplasia is represented with a green horizontal line. A somatic insertion with allele frequency higher than the Notch inactivating event was likely present in the tissue before the clonal expansion. In contrast, an insertion with allele frequency lower than the Notch inactivating event, likely occurred after the initiation of neoplasia and is thus subclonal. B The estimated fractions of cells containing an insertion for all somatic TE insertions identified in neoplastic samples. The onset of neoplasia is represented with a green horizontal line. Three samples (P45B, P51 and P21), where timing of the neoplasia onset could not be unambiguously estimated, were excluded from this analysis. C The distribution of somatic insertions with estimated cell fraction higher or lower than Notch-inactivating mutations for the most represented LTR-elements (rover and copia) and LINE-like I-elements. (p-values were calculated with Fisher's exact test, two-tailed, n= number of insertions)
Figure 1(A-F) Representative PAS-stained sections of the pons (A) and hippocampal (C) regions of the brain and heart (E) of one year old HOIL-1[C458S] and WT mice are shown. Scale bar = 100 μm. Arrow heads indicate α-amylase-resistant PAS-positive polyglucosan deposits. Graphs showing α-amylase resistant PAS scores of the pons (B) and hippocampal (D) regions of the brain and the heart (F) of HOIL-1[C458S] (red) and WT (blue) mice aged 0.5, 1.0 and 1.5 years. The number of biological replicates analysed at each age is indicated. The word zero highlighted in blue indicates that no α-amylase resistant, PAS-positive material could be detected in the WT mice. The error bars show mean + SEM. Statistical significance between the genotypes was calculated by using two-way ANOVA and Šidák's multiple comparison's test. **** denotes p<0.0001.
Expression of Bob1 is largely restricted to Tfh cells.Figure 1(A) Microarray-based transcriptome analysis of CD4+ T cell subsets from C57BL/6 mice. The heat map illustrates differentially expressed genes between CD4+CXCR5hiICOS+ Tfh cells, CD4+CXCR5-ICOS+ effector/memory T cells and CD4+CXCR5-ICOS- naïve T cells. Cells were purified from the spleen of mice seven days after immunization with NP-KLH with alum. Data are derived from three independent array analyses (10 mice/array) for each T cell subset. (B) Validation of microarray expression data for Bob1 mRNA by qPCR for the same CD4+ T cell subsets as described in (A). Data shown are derived from four independent experiments (mean ± SD). *, P < 0.05; unpaired Mann Whitney test.