EMBO/sd-character-level-ner huggingface dataset:
Schematic cartoons showing the proposed mechanism underlying the Hippo signaling pathway regulation of cervical cancer progression.Figure 12Schematic cartoons showing the proposed positive feedback loop in cervical cancer cells. Data in this study support the existence of an autocrine loop involving EGF-like ligands/EGFR pathway/Hippo pathway/EGF-like ligands in regulating the proliferation and motility of cervical cancer cells, which plays a critical role in cancer progression. Under normal conditions, low levels of EGF-like ligands such as TGF-α and AREG are not sufficient to activate EGFR. The inactive EGFR ensures the activation of Hippo signaling pathway, which in turn results in ubiquitination-dependent degradation of YAPprotein. In cervical cancer tissues, especially the advanced-stage cancer tissues, the elevated nuclearYAPprotein stimulates the expressions of TGF-α and AREG, which in turn activates the EGFR, leading to suppression of LATS1 and MOB1 phosphorylation. Dephosphorylation of LATS1 and MOB1 results in the dissociation of LATS1/2-MOB1 complex, leading to inactivation of the Hippo pathway and subsequent activation of the growth-promoting co-activator YAP. Activated YAP induces expression of growth factors such as TGF-α and AREG to drive cervical cancer growth. YAP-induced growth factors such as TGF-α and AREG complete the autocrine loop by activating EGFR and YAP to drive the proliferation of cancer cell and the production of growth-promoting factors in cervical cancer cells. HPVE6 protein maintains YAPprotein level in the HPV-infected normal and cancerous cervical cells by preventing YAP from proteasome-dependent protein degradation.Schematic cartoons showing the clinical relevance of the proposed positive feedback loop in cervical cancer. Multidimensional cancer genomics data analysis indicates that very high frequency of alterations has been observed in genes involved in the Hippo/YAP/EGFR positive feedback loop in cervical cancer (we acknowledge The Cancer Genome Atlas (TCGA) Data Portal for the datasets and the cBioPortal for Cancer Genomics for the online analysis tools).
Figure 6Example sites prone to carbonylation. (A) DRA0302_P252, (B) DR0099_P51, and (C) b0911_K411; and example robust site (D) b3313_P69. Data information: All atoms of central RKPT side chains are shown, with carbonylatable atomic site in red (predicted and measured carbonylated) or black (predicted and measured not oxidized) and labeled with the 1-letter code of the containing amino acid. Positive (blue) and negative (pink) charges within 8Å are labeled. Carbonylatable lysine sites (purple) within 8Å are labeled. Molecular surfaces within 5Å of the central CS are dark gray. See also Fig EV3.
Light-activated proton pump mitochondria-ON (mtON) is expressed in mitochondria.Figure 1Schematic depicting the targeting strategy to localize mtON to the mitochondrial inner membrane (IM). The electron transport chain (ETC) complexes generate the endogenous mitochondrial PMF by proton pumping, represented by the + and - across the IM. Mitochondrial ATP synthase utilizes the PMF to convert ADP to ATP. The N-terminal mitochondria target sequence from the IMMT1 protein shown in red; GFP shown in green. In response to light, mtON pumps protons from the mitochondrial matrix to the intermembrane space (IMS). Confocal images demonstrate overlap of GFP tagged mtON with MitoTrackerTM Red CMXRos stained C. elegans hypodermal mitochondria. Scale bar 10 µm. Immunoblot comparing the cytosolic supernatant and the mitochondria-enriched pellet of isolation fractions. GFP-tagged mtON migrates at the predicted molecular weight of 82 kDa accounting for the mitochondria-target sequence, the proton pump, and GFP. mtON is observed only in the mitochondrial fraction compared to marker proteins HSP60 (mitochondria) and actin (cytosol). All blots are from the same lanes on one membrane.
Proteomics show TCA/OXPHOS upregulation in low STAT3 human FFPE- PCa A.Figure 3A. STAT3 immunohistochemistry- staining of low STAT3 and high STAT3 PCa samples. Red arrows indicate transformed PCa glands, black arrows indicate pre-transformed normal prostate glands. Scale bar = 100µm. # = sample-IDs. B. Significantly enriched KEGG pathways in low STAT3 versus high STAT3 groups. Dotted line: adj. p-value = -log10(0.05). C. Significantly enriched Hallmark gene sets in low STAT3 versus high STAT3 groups. Dotted line: adj. p-value = -log10(0.05). Red = up-regulated, blue = down-regulated. D. Simplified scheme of the TCA cycle and associated metabolic pathways. TCA cycle = Tricarboxylic acid cycle, PDC = Pyruvate dehydrogenase complex, PDK = Pyruvate dehydrogenase kinase.
Figure 4A) Example genomic region of DNA binding by MSL2 (DNA), and chromatin binding of MSL2 (Chrom.), MOF and H4K16ac MNase-ChIP-seq profiles in early (stage 5-8, orange) and late (stage 13-15, purple) mixed-sex embryos. Called peaks/regions are represented as boxes above the tracks. Graph represents pooled IP/Input signal of 3 biological replicates. B) Size distribution of X-chromosomal MOF and H4K16ac regions, which are present in both early and late embryos. P-value (Wilcoxon rank sum test) is indicated. Total number of regions are 459, 443, 854 and 400, respectively. C) Average composite plots of MOF MNase-ChIP-seq centered at Transcription Start Site (TSS) or Transcription Termination Site (TTS) in early or late embryos for X-chromosomal genes (total=1515). Graph represents average IP/Input signal of 3 biological replicates. Shaded area indicates the 95% confidence interval across sites. D) Average composite plots of H4K16ac MNase-ChIP-seq centered at TSS or TTS in early or late embryos for X-chromosomal genes (total=1515).
Figure 5Figure 5. Mmi1- and RNAi-mediated silencing of pericentromeric DNA transcription alternate during the progression of the cell cycle. (A) ChIPs assessing the localization of Mmi1 to pericentromeric DNA in WT and clr4∆ cells. Figure 5. Mmi1- and RNAi-mediated silencing of pericentromeric DNA transcription alternate during the progression of the cell cycle. (B) ChIPs showing the localization of Mmi1 (dashed line) and H3K9me2 (black line) to the pericentromeric nam5/6/7 DNA regions during the progression of the cell cycle. Cell synchronization was achieved by using cdc25-ts cells (see experimental procedures for more details). Cell synchronization was monitored by measuring the percentage of cells with a septum (right part). Figure 5. Mmi1- and RNAi-mediated silencing of pericentromeric DNA transcription alternate during the progression of the cell cycle. (C) RT-qPCRs monitoring the levels of nam5/6/7 (left part) and dg (middle part) lncRNA populations during the cell cycle. Average fold enrichment is shown with error bars that indicate mean average deviations (n=3) for (A, B and C). Figure 5. Mmi1- and RNAi-mediated silencing of pericentromeric DNA transcription alternate during the progression of the cell cycle. (D) RT-PCRs monitoring the accumulation of nam7 lncRNAs and nam7-L read-through transcripts in G2/M and G1/S phases from synchronized cells as in (B). Red arrow heads point to the expected PCR products. The other bands are non-specific PCR products. From the scheme: black arrows, primers used for the reverse transcriptions; black lines and red numbers, regions amplified by PCR.
Figure 2Heat map (Pearson's correlation) of differentially expressed genes between the blistered (regenerated) and control WT dorsal skin epidermis at P2 (n=3). GO analysis of differentially expressed genes in the regenerated epidermis. Scatter plots of differentially expressed genes in the regenerated epidermis. The red dots represent upregulated genes, and the blue dots represent downregulated genes. The gray dotted lines indicate |logFC|>1. Hair canals in the regenerated (lesional) and nonlesional epidermis at P4 (indicated by asterisks). Scale bar: 300 μm. Quantification of hair canals in the lesional, nonlesional, and unaffected littermate control epidermis at P4 (n=5 biological replicates). The data are shown as the mean ± SE (littermate control) or connected with lines showing individual mice. *0.01 test, followed by Tukey's test. HF morphogenesis stages at P4 in lesional, nonlesional, and unaffected littermate control skin (n=5 biological replicates). Whole-mount imaging of the blistered skin of ins-Topgal+ mice at P2. Scale bar: 500 μm.
a) Expression of lipl genes in well-fed mxl-3(ok1947) and mxl-3(tm2580) young adults normalized to same age well-fed wild-type (WT) worms shows that mxl-3 loss of function is sufficient to induce lipl-1 to 3 and lipl-5.figf3(a) Expression of lipl genes in well-fed mxl-3(ok1947) and mxl-3(tm2580) young adults normalized to same age well-fed wild-type (WT) worms shows that mxl-3 loss of function is sufficient to induce lipl-1 to 3 and lipl-5. Mean ddCts+s.e.m. are depicted. n = 6 independent experiments for lipl-1 to lipl-5, and n = 4 independent experiments for lipl-6 to lipl-8. (b) L4 larvae were fasted and RNA was extracted at the indicated times. Mean ddCts+s.e.m. show that the response mxl-3 orchestrates is transient. Time 0, n = 6 independent experiments; time 3-12 h, n = 4 independent experiments; time 18-24 h, n = 2 independent experiments. (c) Immunostainings of well-fed or 6 or 12 h fasted MXL-3::GFP young adults are presented. Quantification of GFP-positive nuclei relative to total intestinal nuclei (4,6-diamidino-2-phenylindole, DAPI) of two independent experiments shows that MXL-3 transiently delocalizes from the intestinal nuclei during fasting. (d) ChIP-quantitative PCR (ChIP-qPCR) analysis of well-fed and 6 h fasted mixed-stage worms expressing MXL-3::GFP presented as Ct in αGFP immunoprecipitated DNA normalized to input DNA and relative to a mock promoter region (CACTAT site −88 of ama-1 gene) shows that MXL-3 vacates the lipl promoters during early fasting. Three sets of primers surrounding CACGTG target sites found up to 500 bp of the ATG of the lipl-1 and lipl-3 genes were used. A representative experiment is presented; see raw data of two independent experiments in Supplementary Table S9. (e) Wild-type or lipl-1(tm1954) lipl-3(tm4498) double mutant animals grown on control RNAi plates were transferred as L4 larvae to control or mxl-3 RNAi plates, incubated for 12 h at 20 °C, and processed for total FAMEs; as a reference, an aliquot of wild-type young adults on control RNAi bacteria was fasted for 6 h. FAME quantification (mean percentage of fed wild type ±s.e.m.) shows that acute mxl-3 inactivation, as fasting, reduces fat stores in a lipl-dependent manner. n = 3 independent experiments. NSD, P-value>0.05.
Figure 4Volcano plot displaying DEGs in starved cct3A(RNAi) planarians compared to controls at 72hR (q-value < 0.05). Y-axis indicates the negative log10 of the false discovery rate (FDR) (q- value). X-axis indicates the beta values (b), a biased estimator of the fold change. For better visualization, 13 dots with -log10 (q-value) > 20 are not displayed. This includes cct3A with q = 0. Notice that when down-regulating cct3A in starved planarians, xbp1, atf6, bip-1 and a repertoire of ER chaperones are down-regulated, whereas dnajb9, a repressor of the UPR, and other ccts are up-regulated. Relative expression of xbp1 and atf6 related to gfp control at 72 hours and 13 days of regeneration during either starving or feeding conditions in cct3A(RNAi) animals. The graph shows that cct3A RNAi down-regulates xbp1 and atf6 specifically during starvation at 72hR. n = 3 replicates (5 planarians each) per time point. The graph shows that both cct3A RNAi down-regulates xbp1, atf6 and bip-1 specifically at 72hR during starvation in X1 stem cells. 50 planarians per replicate (3 replicates) were used to obtain the X1 population (stem cells in S and G2/M). Live images show that xbp1/atf6(RNAi) planarians in starved conditions form a minimal blastema when compared to controls while at the feeding condition most of them can regenerate as controls. The remaining planarians in the starved condition are dead by the time point of regeneration shown. In the feeding condition, the remaining planarians at 8-10dR are either dead (13/145) or have a tiny blastema and died or regenerated later (40/145) while at 21-27dR are dead. Mitotic numbers during different time points of regeneration in starved conditions for xbp1/atf6 RNAi and controls. n ≥ 7 planarians per time point. Mitotic numbers in feeding conditions for xbp1/atf6 RNAi and controls. n ≥ 9 planarians per time point. Maximum projections of representative regenerating trunks after FISH for smedwi-1 in starved conditions. The dashed line delimits the body of the planarian. Relative expression of smedwi-1 related to controls at 13 and 20 days of regeneration of xpb1/atf6 RNAi in starved conditions. n = 3 replicates (5 planarians each) per time point. TUNEL maximum projections of representative blastemas from regenerating trunks in starved conditions. The dashed line delimits the body of the planarian. The graph shows the number of TUNEL+ cells per mm2 at the same time points in anterior (A) and posterior (P) blastemas. n ≥ 6 planarians per time point. Quantification of the percentage of stem cells in different mitotic phases and the percentage of defective mitotic figures in 72hR anterior blastemas of xbp1/atf6 RNAi and controls in starved conditions after double immunostaining with anti-tyrosine-tubulin and anti-H3P (****P < 0.0001, ***P < 0.001, *P < 0.05, n.s. indicates not significant using two-sided Chi-square test); n ≥ 5 planarians. Representative images are shown. Arrows indicate abnormal organization or number of spindle poles. j8 displays asymmetrical distribution of chromosome content.
Analysis of differentially expressed genes during spinal cord regeneration (A) Twenty spinal cords of NF50 tadpoles were isolated at 0, 1 and 3 day post amputation (dpa) and pooled for RNA sequencing.Figure 1(A) Twenty spinal cords of NF50 tadpoles were isolated at 0, 1 and 3 day post amputation (dpa) and pooled for RNA sequencing. (B) Genes with a |log2(FC)|>1 and p-adj<0.01 were used for hierarchical clustering. For each cluster, the gene list was uploaded on Fidea (http://circe.med.uniroma1.it/fidea/) (D'Andrea et al, 2013). The five most significant enrichment of GO (biological processes) terms are shown, and the -log10(p_value) with Bonferroni correction is shown. (C) The dataset was uploaded on the Ingenuity Pathway Analysis software (Qiagen). Genes with a |log2(FC)|>1 and p_adj<0.01 were considered. The software identified upstream regulators based on the changes in expression levels of known dowstream targets. Each upstream regulator is attributed a z-score, corresponding to the negative log of the p-value derived from the Fisher's Exact test. (D) Changes in the expression of foxm1 and known downstream targets in the whole tail comparing day 0 and day 3 (WT_d0d3) and in the spinal cord comparing day 0 and day 1(SC_d0d1) and day 0 and day 3 (SC_d0d3). The whole tail dataset was obtained from (Chang et al, 2017). (E) Tadpoles at NF50 were amputated, fixed at the indicated time and then processed for whole mount in situ hybridisation using a probe specific for foxm1. The two last panels show transverse section in the non-regenerating spinal cord (nr) and the regenerate at 3dpa. The red circle highlights the spinal cord and the asterisk the notochord. (F) Total RNA was isolated from regenerating tails at indicated time points post amputation, reversed transcribed into cDNA and analysed for foxm1 expression by qPCR, using ef1α as a reference gene. The graph represents the mean +/- SD of three independent experiments. One-way ANOVA with Dunnett's multiple comparisons test was used. * p=0.0149
Figure 3(A) Quantitative real-time PCR analysis of mature let-7 family in control and FRS2 knockdown HASMCs. SNORD47 was used to normalize the variability in template loading. Histogram of qRT-PCR results are three independent experiments. (B) Upper panel: Immunoblots of SM-calponin, phosphorylated Smad2 (p-Smad2), and TGFR1 expression in control and FRS2 knockdown HASMCs transduced with or without let-7b lentiviruses. Blots are representative of three independent experiments. Bottom panels: Band intensities of SM-calponin and p-Smad2 were normalized to GAPDH or Smad2 and expressed as a fraction of a control value. (C) Phase-contrast and immunofluorescence staining of smooth muscle markers (red) in HASMCs. Nuclei were counterstained with DAPI (blue). Scale bar: 12 m. Images are representative of three independent experiments. (D) HASMCs were cultured in the growth medium (M231 + SMGS) at day 0 then switched from growth conditions to differentiation medium (M231 + SMDS) for 8 days. Quantitative real-time PCR analysis of mature let-7 family in HASMCs. SNORD47 was used to normalize the variability in template loading. Histogram of qRT-PCR results are three independent experiments. (E) Control and FRS2 knockdown HASMCs were cultured in the growth medium (M231 + SMGS) at day 0 then switched from growth conditions to differentiation medium (M231 + SMDS) for 6 days with or without let-7b lentiviruses. Immunoblots of smooth muscle markers, phosphorylated Smad2 (p-Smad2), and TGFR1 expression in control and FRS2 knockdown HASMCs with or without let-7b lentiviruses. Blots are representative of three independent experiments.
Figure 4A. Illustration of the promoters of HSP70.3, HSP70.4 and HSP90.1. Relevant regulatory motifs and promoter regions that were assessed in ChIP experiments (C) or in vitro DNA-binding studies are shown with purple and grey lines, respectively. B. Relative expression changes of HSP70.3, HSP70.4 and HSP90.1 in bes1-D as compared to wild-type following heat shock. 14-day-old plants were exposed to 45°C for 60 minutes, expression was analyzed by qPCR and the results were normalized to UBC. Data show the mean ±SD. n=3 biological replicates measured in 3 technical repeats. Significant differences as compared to wild-type at 45°C, calculated by Student's t-test, are shown (*P≤0.05). C. ChIP to determine BES1-CFP enrichment on the promoters of HSP70.3, HSP70.4 and HSP90.1 following heat stress. 35S:BES1-CFP and wild-type plants grown at 21°C were either left untreated or treated with 45°C for 60 minutes. BES1-CFP was immuno-precipitated with α-GFP beads. Fragments were quantified in the precipitates with qPCR and the ratios of samples with antibody to without antibody were calculated. TA3 (70.3p and 90.1p) or 5s rRNA (70.4p) were used for normalization. UBQ5 served as an internal control. Data show the mean ±SE. n=3 biological replicates measured in 3 technical repeats. Significant differences as compared to wild-type at 21°C, calculated by Student's t-test, are shown (*P≤0.05; **P≤0.01; ***P≤0.001).
Figure 8Left: Inhibitory GlyRs (dark blue), GABAARs (light blue), and gephyrin scaffolds (red) are organized in sub-synaptic domains (SSD) and are aligned with presynaptic release sites (green), forming trans-synaptic nanocolumns (dotted boxes). Right: Increased network activity differentially affects the numbers of GABAAR complexed (light blue pentagons) and the phosphorylation status of gephyrin (phospho-S270 domain, dark red), while GlyRs and total gephyrin levels are largely unaffected.
Figure 5A. Anti-HA detection of AMR1 3'-HA tagged in the presence or absence of 100 nM rapamycin and 2.5 mM glucosamine for three cycles. Anti-PfBiP was used as a loading control. B. Relative parasitemia was assessed for the untransfected DiCre 3D7 parental line and transfectant parasite lines with AMR1 under inducible disruption. Rapamycin/glucosamine treatment began on cycle zero and parasitemia determined by flow cytometry and compared to identical lines that were left untreated. Data represents the mean relative parasitemia ± SEM from three biological replicates (y-axis) across seven replication cycles (x-axis). C. Metabolite profile following three cycles of rapamycin and glucosamine treatment. The abundance of isoprenoid biosynthestic intermediates (1-deoxy-xylulose-5-P (DOXP), methyl-erithritol-4-P (MEP), methyl-erithritol-cyclo-2,4-PP (MEcPP), and isopentyl-PP), and hemoglobin-like peptides are presented as the mean log2 fold change from four biological replicates (±SD).
A subset of mitochondria have reduced fusion capacity.Figure 1(A) INS1 cells were transduced with mtPA‐GFP (green) and stained with TMRE (red). mtPA‐GFP distribution is shown immediately (within 2 min) after photoactivation (area indicated by a dashed square) and in the plateau phase of mtPA‐GFP spreading (45 min). Mitochondria that did not exhibit GFP FI decay (less than 5%) are marked by arrows. Upper scale bar, 10 μm; lower scale bar 5 μm. (B) Fusion events result in the spread of mtPA‐GFP across the mitochondrial population, leading to its dilution and a decay in GFP FI value (n=16). (C) The relative difference in TMRE FI between non‐fusing mitochondria and fusing mitochondria, calibrated against the whole‐cell average. (D) Primary β‐cells expressing mtPA‐GFP were photoactivated in seven different regions (squares) and imaged after 2 min and again after 2 h of incubation. Scale bar, 10 μm. *P0.001.
A) The efficiency of knockdown and overexpression of Hsp.Figure 4(A) The efficiency of knockdown and overexpression of Hsp. HeLa cells were transiently transfected with Hsp70 plasmid or Hsp70 siRNA for 72 h. Lysates were subjected to Western blot analysis with anti-Hsp70 antibody. Values are the mean±SE of three independent experiments. *P<0.05, **P<0.01 (vs control). (B) Hsp70 had no effect on Htt-552 levels. HeLa cells were transiently transfected with Hsp70 plasmid, vector control or Hsp70 siRNA for 72 h and Htt-552 for 48 h. Lysates were subjected to Western blot analysis with anti-Htt 2166 and anti-Hsp70 antibodies. Values are the mean±SE of three independent experiments.