EMBO/sd-character-level-ner huggingface dataset:
Figure 5Representative images and quantification of vacuolar morphology of late meristematic atrichoblast cells. PI (green) and MDY-64 (yellow) staining depicts cell wall and vacuolar membrane, respectively. (A) Vacuolar morphology of Col-0 control (n=52) and lrx3/4/5 triple mutants (n=48). Mann Whitney U test (***p < 0.001). scale bars: 5 µm. Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values. Representative images and quantification of vacuolar morphology of late meristematic atrichoblast cells. (B) 3-D reconstructions of PI-stained cell wall (red) and BCECF-stained vacuole (green) of late meristematic cells. Boxplot depicts vacuolar occupancy of the cell in Col-0 control (n=11) and lrx3/4/5 (n=10). Student´s t-test (***p < 0.001). scale bars: 5 µm. Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values. Representative images and quantification of vacuolar morphology of late meristematic atrichoblast cells. PI (green) and MDY-64 (yellow) staining depicts cell wall and vacuolar membrane, respectively. (C) Col-0 (n=40-44) and lrx3/4/5 (n=36) seedlings were treated with DMSO or 50 µM EGCG for 22 h on solid medium. Kruskal Wallis test followed by Dunn´s multiple comparison (b: p < 0.01, c: p < 0.001). scale bars: 5 µm. Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values. Representative images and quantification of vacuolar morphology of late meristematic atrichoblast cells. PI (green) and MDY-64 (yellow) staining depicts cell wall and vacuolar membrane, respectively. (D) Col-0 (n=40-48) and fer-4 (n=28-32) seedlings were grown on the surface or into the matrix of 2 % agar-containing solid medium. Kruskal Wallis test followed by Dunn´s multiple comparison (b: p < 0.05, c: p < 0.001). scale bars: 5 µm. Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values.
Figure 5A. Macrophages play a role in mediating shrinkage of lung cancer by Carfilzomib. TetO‐EGFR (T790M/Del19)/CC10-rtTA (TD) mice were fed with doxycycline for 3 months to induce lung cancer. Tumor burdens were then documented through computed tomography (CT) imaging before treatment (PreRx). After two-week treatment with saline (iv), Clodrosome (iv), Carfilzomib (iv), or Carfilzomib plus Clodrosome, mice were CT-scanned again (PstRx). Treatment effect was determined by comparing tumor-areas of PreRx and PstRx through ImagJ analysis. B. Statistics of the tumor burden in lung tissue. Data are means ± SD of three independent experiments. *p < 0.05, **p < 0.01 (student's t-test). C. Representative images of Hematoxylin and eosin (H&E) staining of the lung tissue obtained from different treatment groups. Expression of Ki-67 in lung tissues was detected by immunohistochemistry method. D. Statistics of the tumor area and the number of Ki67 positive cells in sections of lung tissue. Data are means ± SD of three independent experiments. *p < 0.05, **p < 0.01, ***p < 0.001 (student's t-test). E. Carfilzomib treatment promotes the infiltration of M1 macrophages. Tumor bearing TD mice were treated as indicated in (A) and euthanized. Lung tissues were dissected for evaluating M1/M2 populations through analyze the expression of CD80 and CD206 by flow cytometry. F. Statistics represent the proportion of CD80 or CD206 positive cells in lung tissue. Data are means ± SD of three independent experiments. **p < 0.01 (student's t-test). G. Carfilzomib treatment promotes the infiltration and activation of CD8+ T cells. Lung tissues of (E) were used for evaluating the infiltration of CD8+ T cells and their expression of CD69 by flow cytometry. H. Statistics about the proportion of CD8+ or CD69+ positive cells in lung tissue. Data are means ± SD of three independent experiments. **p < 0.01 (student's t-test). I. Genetic confirmation of role played by macrophages in mediating carfilzomib's tumor shrinking effect through immune reconstitution with bone marrow from CD11B-DTR mice. TD mice were irradiated with X-ray (8 Gy for 20 min), transplanted with 5×106 of bone marrows from CD11B-DTR mice. Immune reconstituted mice induced to develop lung cancer by doxycycline-diet. Mice were treated for 2 weeks with saline (iv), DT (ip), Carfilzomib (iv), or Carfilzomib plus DT. Tumor burdens were documented through CT imaging before and after treatment. J. Statistics of the tumor burden in lung tissues. Data are means ± SD of three independent experiments. *p < 0.05, **p < 0.01 (student's t-test). K, L. Carfilzomib shrinks tumor through modulating tumor microenvironment. EG7 cells were inoculated in wild-type or LyzM-cre;lsl-dTA to allow tumor xenograft to reach a volume of around 80 mm3. Mice were randomized for treatment (n=5) by saline or Carfilzomib for two weeks. The xenografts were dissected to photograph (K) or weigh (L) after treatment. Data are shown as mean ±SD and n indicates the number of biological replicates. *p < 0.05, ***p < 0.001 (student's t-test).
Fig.Figure 3(A) Hematoxylin and eosin (H&E, upper panels) and periodic acid Schiff (PAS, lower panels) staining of liver samples harvested from wild-type (WT) and AslNeo/Neo mice treated with TB-1 or vehicle. Scale bars: 500 µm. (B) Computational analysis of PAS staining (n≥4 mice/group). **p<0.01, *p<0.05 (One-way ANOVA). Data information: All values are shown as averages ± S.E.M. (C) Quantification of hepatic glycogen in vehicle (n=6)- and TB-1-treated AslNeo/Neo mice (n=12) compared to WT (n=5) controls. **p<0.01, *p<0.05 (One-way ANOVA). Data information: All values are shown as averages ± S.E.M. (D) Representative Western blotting bands and densitometric quantification of PYGL in livers of WT and AslNeo/Neo mice treated with either with TB-1 or vehicle (n=4 mice/group). *p<0.05 (One-way ANOVA). GAPDH was used as loading control. Data information: All values are shown as averages ± S.E.M. (E) Representative electron microscopy images of liver samples harvested from WT and AslNeo/Neo mice treated with TB-1 or vehicle. Scale bar: 900 nm.
68Ga]Pentixafor PET/CT and [18F]FDG PET/CT.Figure 3[68Ga]PentixaforPET/CT and [18F]FDGPET/CTA-D Maximum intensity projections (MIP) of [68Ga]Pentixafor (A) and [18F]FDGPET/CT (B) of a 68-year-old male with histologically proven multiple myeloma indicating the better lesion-to-background contrast for [68Ga]Pentixafor in the corresponding myeloma manifestations. Trans-axial views of the upper thorax (C) and the pelvis (D) underline the higher uptake values of the bone manifestations (yellow arrows) of [68Ga]Pentixafor compared to [18F]FDG.
Figure 1A RNA-Seq of naïve and TNFα-stimulated J-Lat 10.6 cells. Differentially expressed genes were filtered with log2FC of 1 and PvalueFDR cutoff of 0.05. Upregulated and downregulated genes were labeled as red and blue dots respectively. Representative genes were labeled aside corresponding dots. B RNA-Seq result as in (A). Significantly changed genes were sorted out and plotted as heatmap. SEC16A indicated unchanged gene. C The GFP-positive percentages of monoclonal sgCHAF1A and sgNT J-Lat 10.6 cell lines were shown in the top right corner of each flow cytometry figure. TNFα, SAHA and JQ-1 were used as supplements. D ChIP assay with antibody against CHAF1A was performed in J-Lat 10.6 cells. All the ChIP-qPCR DNA signals were normalized to siNC IgG of G5'. G5' represented cellular DNA and viral 5'LTR junction; A: Nucleosome 0 assembly site; B: Nucleosome free region; C: Nucleosome 1 assembly site; V5: Viral 5'LTR and gag leader sequence junction; E represented envelope; V3: Viral poly purine tract and 3'LTR junction; G3' represented viral 3'LTR and cellular DNA junction. E The statistical graph of the result in (C). F-I ChIP assays with antibodies against H3K9me3, H4K20me3, H3K4me3 and H3K9Acetyl were performed as in (D). Only 'C' position signals were showed and normalized to Input. J, K J-Lat 8.4 cells were treated with shCHAF1A lentiviruses and 5-aza-dC. The GFP-positive cells and HIV-1 LTR methyl-CpGs percentages of different groups were plotted in (J) and (K) respectively. L ATAC-Seq was performed in WT and CHAF1A-KO J-Lat 10.6 cells. The relative tag densities of the pseudotyped HIV-1 5'LTR integration site in each group were calculated. The highest tag density was set as 100. Figure showed 2kb range centered the 5'LTR integration site. Dashed line represented HIV-1 pseudotyped virus 5'LTR integration site. M ChIP assays with antibodies against CDK9 and Pho-Pol II were performed in siNC and siCHAF1A J-Lat 10.6 cells. ChIP signals in each group were normalized to Input.
Figure 1A. Immunostaining of TUJ1, DESMIN and GATA6 after six days of mESC differentiation towards ectoderm, mesoderm and endoderm. Bar: 50 μm. B. Scheme of the experimental approach to quantitatively capture gene expression changes during mESC differentiation towards the three germ layers at high temporal resolution. C. Venn diagram of genes with differential expression during mESC differentiation towards the three germ layers. D-F. Hierarchical clustering of mRNA expression of mESCs differentiated towards ectoderm (E), mesoderm (F) and endoderm (G).
Figure 4Indicated cell lines were treated as depicted in Figure 2, and labeled with bromodeoxyuridine (BrdU), harvested at indicated time points and utilized for FACS analyses Top: Data generated as described above in Figure 2 was compared to a separate microarray analysis in which the same cell line was exposed to 1uM palbociclib instead of veliparib. Cut-offs for comparison were a p value<0.05, and fold change of 1.5. Venn diagrams show the overlapping and non-overlapping genes of both down- (top) and up-regulated (bottom) genes in response to either treatment modality. Statistical significance was determine using the Chi-squared statistical test. Bottom: Genes found to be exclusively regulated by palbociclib, commonly regulated by palbociclib and veliparib, or exclusively regulated by veliparib were used for Gene Set Enrichment (GSEA) KEGG pathway analyses. Data indicate both FDR q value, where the darker colors indicates higher confidence (lower q). Numbers indicate q values. Blue arrow highlights the Homologous Recombination KEGG pathway
Graphical abstract.Figure 7In the intestinal epithelial cells (IECs) of the small intestine, a constitutive expression of interferon-stimulated genes (ISGs) is suppressed by the presence of dimer GR. During LPS-induced endotoxemia, LPS has indirect effects on the IECs: TLR4 binding on macrophages results in production of diverse cytokines, such as IFNs, IL1β and TNF. TNF performs its effects on IECs via binding to TNFR1. TNF induces the expression of ISGs, such as necroptosis mediators: Mlkl, Zbp1 and Ripk3. High expression of these mediators can potentially lead to cell death of the IEC and eventually lethality of the animal. When no (dimer) GR is present in the IECs, there is no dampening of the constitutive ISGs signature. We hypothesize that necroptosis proteins such as MLKL and ZBP1 are in this case "ready to use" and that TNFR1 signaling by TNF can directly lead to necroptosis, death of the cell and eventually lethality. This hypothesis still needs further investigation.
dEsyt is necessary for PLCβ-dependent modulation of ER-PM MCS.Figure 6(A) TEM images of a single ommatidium from photoreceptors of (i) dEsytKO- day 1 (iii) dEsytKO- day 14 flies reared in dark, scale bar: 1 µm except for (Ai): 2 µm (red asterisk indicates R7 photoreceptor). (A-ii, iv) Magnified image showing a single photoreceptor from the ommatidium image shown on the left. Scale bar: 200 nm. Boxes represent the origin boxes for magnification. M- Microvillar plasma membrane, S- Sub microvillar cisternae, MCS- Membrane Contact Site, P- Pigment granules. (B) Quantification of the number of MCS per photoreceptor, X-axis indicates the genotype and age of the flies and Y-axis indicates the number of MCS/photoreceptor. n=9 photoreceptors from 3 separate flies for R7. (C) TEM images of a single ommatidium from photoreceptors of (i) norpAP24;dEsytKO- day 1 (iii) norpAP24;dEsytKO- day 14 flies reared in dark, scale bar: 1 µm (red asterisk indicates R7 photoreceptor). (C-ii, iv) Magnified image showing a single photoreceptor from the ommatidium image shown on the left. Scale bar: 200 nm. Arrows indicate the SMC forming an MCS with the microvillar PM. (D) Quantification of the number of MCS per photoreceptor, X-axis indicates the genotype and age of the flies and Y-axis indicates the number of MCS/photoreceptor. (i) n=30 photoreceptors from 3 separate flies for R1-R6. (ii) n=9 photoreceptors from 3 separate flies for R7. (E) TEM images of a single ommatidium from photoreceptors of (i) rdgB9-day1 and (iii) rdgB9;dEsytKO - day 1 flies reared in dark, scale bar: 1 µm (red asterisk indicates R7 photoreceptor). (E-ii, iv) Magnified image showing a single photoreceptor from the ommatidium image shown on the left. Scale bar: 200 nm. (F) Quantification of the number of MCS per photoreceptor for R1-R6 in 1 day old dark reared wild type (from Figure 5B i), rdgB9 and rdgB9;dEsytKO flies. n=30 photoreceptors from 3 separate flies.
| PenG induces hydrogen peroxide production and the Fur iron starvation response.Figure 5(A) Total intracellular hydrogen peroxide (H2O2) levels were measured using AmplexTM Red Hydrogen Peroxide/Peroxidase Assay Kit and normalized to total cellular protein level (measured by QubitTM). Data are average values from three independent experiments, error bars represent standard deviation. Cat, catalase (1μg/ml). (B). To test PenG-mediated induction of Fur-regulated genes, S1 nuclease mapping assays were performed on the small RNA ryhB, the RyhB target sodB, hutA/B, coding for heme transport systems and vc2212, which encodes a component of a ferric citrate uptake system). Cells were grown to mid-exponential phase followed by exposure to H2O2 or PenG for the indicated duration. Numbers represent expression levels normalized to untreated control (averages from three independent replicates). White demarcation line between time points indicates that these data points were not adjacent in the original experiment but were cropped for presentation purposes. Source data is available as supplemental material. (C) To confirm the induction of ryhB transcript by PenG treatment, the native ryhB promoter was fused with msfGFP and introduced into WT and ΔvxrA mutant cells. Each strain was cultured until mid-exponential phase, when 1mM EDTA or 100μg/ml PenG were added for the indicated duration. Quantified GFP fluorescence intensities are presented with average values from 3 independent biological replicates (cell, n>500), error bars represent standard deviation. ∗∗∗∗ P<0.0001 (paired t-test).
Matrin3 and PTB splicing mapsMatrin3 crosslinking in Matrin3‐regulated pre‐mRNAs where position of crosslinked nucleotides was mapped onto the regulated exon and the 500 nucleotides upstream and downstream of its 3′ss and 5′ss, respectively, the upstream flanking exon and 500 nucleotides downstream of its 5′ss and the downstream flanking exon with 500 nucleotides upstream of its 5′ss.Figure 5A Matrin3 crosslinking in Matrin3‐regulated pre‐mRNAs where position of crosslinked nucleotides was mapped onto the regulated exon and the 500 nucleotides upstream and downstream of its 3′ss and 5′ss, respectively, the upstream flanking exon and 500 nucleotides downstream of its 5′ss and the downstream flanking exon with 500 nucleotides upstream of its 5′ss. The iCLIP tags were mapped onto silenced ASE (blue, n = 421), enhanced ASE (red, n = 187) and to control ASE (grey, n = 16,242), and percentage of occupancy is plotted. B Same as in (A) but using iCLIP tags obtained from PTBiCLIP and mapped onto PTB/nPTB‐regulated ASE, silenced ASE (blue, n = 729), enhanced (red, n = 820) and control ASE (grey, n = 14,599). C Matrin3 crosslinked nucleotides mapped onto PTB‐regulated ASE. D PTB crosslinked nucleotides mapped onto Matrin3‐regulated ASE.
Figure 4ISC (eGFP+ve) cells were FACS-sorted from Lgr5-DTReGFP embryos at E16.5 and subjected to RNAseq analysis. Heatmap of differentially regulated genes in HE and KO ISCs at E16.5. Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO) Compared Hallmarks for upregulated and downregulated genes in the transcriptome of E16.5 Lgr5 KOs vs E16.5 HEs, adult HEs vs E18.5 HE embryos and adult Lgr5-Cre cKO vs HEs. * Asterisks refer to given pathways for which differentially modulated genes were found upregulated and downregulated. Right panels: GSEA showing enrichment of the epithelial to mesenchymal transition (EMT) data set in E16.5 Lgr5 KOs vs E16.5 HEs, adult HEs vs E18.5 HE embryos, and adult Lgr5 cKO vs adult HE modulated genes. NES: Normalized Enrichment Score. Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO); Lgr5-DTReGFP E18.5 individual embryos (n=2 HE) and Lgr5-DTReGFP adult individual animals (n=2 HE); Lgr5-Cre/flox adult individual animals (n= 2 HE, 3 cKO). Expression levels of genes commonly downregulated in ISCs of Lgr5 KOs vs Lgr5 HEs at E16.5 and Lgr5 adult vs E18.5 HEs. RPKM: reads per kilobase of transcript per million mapped reads. Below: GeneOntology analysis of downregulated genes identified in the Epithelial Mesenchymal Transition Gene Set (Hallmark MSigDB collection). Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO); Lgr5-DTReGFP E18.5 individual embryos (n=2 HE) and Lgr5-DTReGFP adult individual animals (n=2 HE); Lgr5-Cre/flox adult individual animals (n= 2 HE, 3 cKO). Data are represented as means ± sem (C). Expression profile of Col1a1, Zeb2 and Cxcl10 genes detected by RNAscope in embryonic and adult intestines. Insets with higher magnification are depicted on the right of each corresponding picture, boundaries between epithelium and mesenchyme are shown with dotted lines and arrows point to epithelial expression.
Figure 5A) Gene expression of multiple cachexia-associated markers in gastrocnemius muscles of individual animals from Study 1 (n=5 for tumor-bearing groups; n=6 for tumor-free groups). Expression was determined by qRT-PCR and presented as described in the Materials and Methods (Geometric Mean ± Geometric STD). B) Androgen receptor (AR) mRNA expression in gastrocnemius muscles from Study 1. Statistics: p values provided in Appendix Table S5A-B. Dunnett's multiple comparison test. CEBPδ, n=4, insufficient sample to analyze all tumor-bearing GTx-024-treated animals.
Figure 5A Immunoblotting of subcellular fractions from serum-starved cardiomyoblasts for InsP3R, Akt and PP2a, as in Fig 3A. B Fractionation of crude mitochondrial fractions (containing mitochondria and MAM) from WT MEFs on a sucrose gradient (5-60%) and immunoblotting for relevant proteins. Fraction size: 200 µL. Representative of 3 independent experiments. C Immunoblotting for phosphorylated and total Akt or InsP3R protein in crude mitochondrial fractions from serum-starved WT and Nox4KO MEFs. FACL4 was used as a loading control for the MAM. InsP3R was first immunopreciptated and then the precipitate was immunoblotted for total InsP3R and for the phosphorylated Akt-substrate motif RXRXX(pS/T) (p-InsP3R). Representative immunoblots are shown at the top and mean data at the bottom. Cat = PEG-catalase. Nox4KO MEFs were transfected either with active Nox4 or a Nox4P437H mutant (Mut). n=3/group. D ROS levels indexed in MEFs using H2O2 specific HyPer probes targeted to the MAM (FACL4 HyPer) or the cytosol (Cyto HyPer). Imaging was performed after serum starvation for 12h. Representative photomicrographs of the fluorescence ratio are shown to the right and mean data for changes in fluorescence ratio presented to the left. The signal obtained using corresponding ROS-insensitive SypHer probes was used to correct for any pH-induced changes in fluorescence; the change in fluorescence ratio between HyPer and corresponding SypHer probe (ΔR) for each condition is reported. n=5 independent cell preparations/group, with at least 20 cells imaged/preparation. Scale bars: 10 µm.
H3K122suc is sufficient to stimulate transcription.Figure 4A Schematic representation of the IVT assay: chromatin assembly, density selection by sucrose gradient and in vitro transcription per se in the presence of 32P-rUTP. For details see material and methods. B In vitro transcription in the presence of GAL4-VP16 and p300, in the presence of no CoA, ac-CoA or suc-CoA. Shown is a representative autoradiogram of the IVT product. C Quantification of IVT reactions. Expression relative to no CoA is plotted. D In vitro transcription on unmodified chromatin or chromatin site specifically succinylated at H3K122. Shown is a representative autoradiogram. E Quantification of IVT reactions. Expression relative to transcription on unmodified chromatin is plotted.
Simplified metabolic network of the MiaPaCa-2 cell line as determined by proton NMR spectroscopy.Figure 7  The cell line is shown without and upon various treatment regimens (OMP, 5-FU or 5-FU+OMP combination). The nodes of this network symbolize metabolite signals, their colours correspond to relative signal intensity (when compared to an external standard) as indicated in the heatmap scale below. The signal intensity is linearly related to the intracellular concentration. The background of the nodes are left blank when the signal intensity is out of the range indicated by the heatmap scale. The lines between the boxes symbolize strongly simplified metabolic pathways. The colors of these lines indicate significant differences of the signal intensity ratios of the connected metabolites compared to the control group when orange (p<0.05), red lines indicate p<0.01. Upon OMP, the PC/Cho ratios are significantly lower compared to control. Furthermore the acetate/FACH2 ratio is significantly decreased in the OMP group. The latter also showed a higher CH = CH level, the ratio to FACH2 is, however, decreased. Upon 5-FU and 5-FU+OMP, similar changes could be observed. Furthermore, in contrast to ASPC-1 cells, the Ala/Gln/AMP pathway is also involved. Abbreviations: Gln - glutamine, Ala - alanine, PC - phosphatidylcholine, Cho - Choline. Lac1+FACH2 - methyl group signal of lactate and methylene groups of the fatty acids, Lac2 - methylene group of lactate, CH = CH - protons of methin groups of unsaturated fatty acids.