EMBO/sd-character-level-ner huggingface dataset:
Figure 7(A)-(C) The scattering profiles (A), the PDDFs (B) and the dimensionless Kratky plots (C) of 3'SLs from DENV2 (cyan), ZIKV (red), WNV (blue) and WNV-3'SLM (438UAG441A→438GUC441U) mutant (green). The inset in (A) shows the guinier regions of the respective scattering profiles with linear fit lines. (D) The ab initio shape envelopes of the 3'SLs of DENV2 (left), ZIKV (middle) and WNV (right), WNV-3'SLM (green). The atomic models from de novo structure modeling by Rosetta except for 3'SLM of WNV are superimposed onto the respective envelopes. The back-calculated scattering profiles of the de novo atomic models are fitted to the respective experimental scattering profiles in (A). (E) Illustration of the three binding sites (orange asterisks) of WNV- 3'SL to eEF1A (pink ellipse), the potential pseudoknot is also indicated with red dash line. (F) The structure of ribosome-bound eEF1A (PDB: 5LZS) is compared with the envelope and atomic model of WNV- 3'SL side by side. (G) Sequence alignment of DENV2-, ZIKV- and WNV- 3'SL. The sequences involved in the potential pseudoknot between the sHP and long SL of WNV 3'SL were indicated with # sign at the top.
Figure 5Figure 5. The anaphase rDNA loop is condensin dependent.(A) FACS profiles and representative DAPI-stained cells of cells blocked in anaphase, in the absence of condensin (smc2-aid cdc15 +IAA and cdc14) or topoisomerase 2 (top2-aid cdc15 +IAA). Figure 5. The anaphase rDNA loop is condensin dependent. (F) Distribution of intra-chromosomal contacts of a cen-proximal rDNA flanking region (highlighted in grey) with the rest of chr12 in smc2 cdc15, top2 cdc15, and asynchronous (asyn) cells. Pink arrowheads point at the right arm anaphase loop. Figure 5. The anaphase rDNA loop is condensin dependent. (B - D) Log-ratio of contact maps. Yellow arrowheads: inter-centromere contacts. The pink arrowhead points at the right arm anaphase loop on chr12. Insets display magnification of the chr12 ratio map. (C) Ratio-map between (bottom left) cdc14 and smc2-aid cdc15 +IAA cells and between (top right) cdc14 and cdc15 cells. Figure 5. The anaphase rDNA loop is condensin dependent.(B - D) Log-ratio of contact maps. Yellow arrowheads: inter-centromere contacts. The pink arrowhead points at the right arm anaphase loop on chr12. Insets display magnification of the chr12 ratio map. (D) Ratio-map between (bottom left) top2-aid cdc15 +IAA and cdc20 cells and (top right) top2-aid cdc15 -IAA and top2-aid cdc15 +IAA cells. Figure 5. The anaphase rDNA loop is condensin dependent. (E) 3D representations of the contact maps from smc2-aid cdc15 +IAA, cdc14, and top2-aid cdc15 +IAA arrested cells. The right (XIIR) and left (XIIL) arms of chr12 are highlighted in red and blue, respectively. Figure 5. The anaphase rDNA loop is condensin dependent. (F) Distribution of intra-chromosomal contacts of a cen-proximal rDNA flanking region (highlighted in grey) with the rest of chr12 in smc2 cdc15, top2 cdc15, and asynchronous (asyn) cells. Pink arrowheads point at the right arm anaphase loop. Figure 5. The anaphase rDNA loop is condensin dependent. (G) Normalized contact frequencies between the left rDNA flanking region (50 kb) and the rest of the genome in cdc14, cdc15 and smc2 cdc15. Yellow arrowheads point at a subset of centromeric positions.
A screen for telomere associated proteins in yeast A) Schematic representation of the quantitative interactomics approach to identify proteins binding to the S.Figure 1A) Schematic representation of the quantitative interactomics approach to identify proteins binding to the S. cerevisiae telomeric sequence. Abbreviations: MS: mass spectrometry B) Volcano plot of quantified proteins. Log2 fold change was determined as the difference between the mean LFQ intensity of the four replicates of telomeric to control sequence and p-values were calculated with a Welch t-test. Proteins above the threshold p=0.05, s0=1, c=0.5 (dashed line) are considered enriched. Abbreviations: LFQ: Label free quantification C) Gene ontology enrichment analysis of the telomere-sequence associated interactors. Analysis was performed using the PantherDB.org overrepresentation Test. Fisher's exact test was subjected to Bonferroni correction. D) Heatmap of LFQ intensity of proteins enriched at DNA baits. Telomere interactors are indicated on the right side of the heatmap. Color code indicates measured log2 LFQ intensities in the telomere pull-down. RNA binding proteins are marked with a black box on the left side of the figure. Abbreviations: LFQ: Label free quantification RBP: RNA binding protein E) Critically short telomeres arise after 90 population doublings in the absence of telomerase (tlc1). Genomic DNA was extracted at indicated population doublings and digested with XhoI. A radioactive probe was used to recognize telomeric DNA in a southern blot. Abbreviations: PD: population doubling. F) tlc1 cells reach senescence at PD 80-100. %viability of indicated strains after propagation in YPD is indicated at different population doublings n=3. Asterisk indicates population doubling used in G) to determine binding of Npl3 to short telomeres by TAP-ChIP. 3 independent spores from the indicated genotypes were used. Population doublings are counted from germination of meiotic products and hence begin at approx. PD40. Abbreviations: TAP: tandem affinity purification tag G) Npl3-TAP associates strongly to short telomeres. Cross-linked samples from indicated strains were used in a TAP-ChIP. Enrichment at telomeres was determined by quantitative PCR on indicated telomeres. Data represents mean % input +/- SEM n=3 (paired t-test one tailed *p<0.05, **p<0.01). PD90 refers to 90 population doublings in the absence of TLC1 (telomerase RNA subunit). The no tag control serves as an indicator of non-specific background signal. Abbreviations: TAP: tandem affinity purification tag, PD: population doubling.
Figure 5Electron microscope images of mitochondria from SH-SY5Y e, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted Representative immunoblot of isolated mitochondria from the indicated groups treated with / without trypsin and probed for HSP60, ATP5a and TOM20. Bar graphs represent mean ± SEM of the ratio of densitometric levels of the indicated proteins (with : without trypsin) from at least 3 independent experiments Electron microscope images of mitochondria fro MEF WT, MEF PINK1 K as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted Representative immunoblot of isolated mitochondria from the indicated groups treated with / without trypsin and probed for HSP60, ATP5a and TOM20. Bar graphs represent mean ± SEM of the ratio of densitometric levels of the indicated proteins (with : without trypsin) from at least 3 independent experiments Electron microscope images of mitochondria fro Hela an e, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted Representative immunoblot of isolated mitochondria from the indicated groups treated with / without trypsin and probed for HSP60, ATP5a and TOM20. Bar graphs represent mean ± SEM of the ratio of densitometric levels of the indicated proteins (with : without trypsin) from at least 3 independent experiments Electron microscope images of mitochondria fro Drosophila thoracic muscle, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments For flies, more than 200 mitochondria from each group were counted from 5 different experiments Representative immunoblot of isolated mitochondria from the indicated groups treated with / without trypsin and probed for HSP60, ATP5a and TOM20. Bar graphs represent mean ± SEM of the ratio of densitometric levels of the indicated proteins (with : without trypsin) from at least 3 independent experiments
Figure 6The C2, DSL domains and N-terminal EGF repeat in Delta (cyan) and the ligand binding region (EGF11-13) of Notch (magenta) are renditions from the structures obtained (Figure 1), other regions of the molecules are represented not to scale. The amino acids in the β1-2 loop of Delta are highlighted in yellow (A). (A) The interaction of Delta (cyan) in trans with the Notch receptor (magenta) is augmented by the C2 domain, possibly through contacts of the β1-2 loop (yellow), with the "receiving" cell membrane, to yield highest levels of signalling (black arrow; green indicates ligand induced cleavages). Phospholipid contacts from β1-2 loop in the same cell could also influence cis-interactions between Delta and Notch in the same cell. (B) A deletion of 5 amino acids within C2 domain β1-2 loop (no yellow) disrupts phospholipid interactions but does not prevent Delta from interacting with Notch. Activation of Notch signalling is weakened (grey arrow) and phenotypes from transheterozygous combinations suggest that cis-interactions between Delta and Notch are also modulated.
Figure 5Mice were superinfected as described in Fig 3A. (A) Bacterial load as determined by enumeration of cfu in BAL following administration of αIL-17 or αIL-22 blocking antibody. Control wild-type and T-bet-/- groups were administered with IgG isotype control antibody Data information Dat are combined from two independent experiments (n = 8-12 mice per group) All data are represented as mean ± S.E.M. Statistical significance was determined with Kruskal-Wallis test followed by Dunn"s multiple comparisons test n.s. = not significant Mice were superinfected as described in Fig 3A (B) T-bet-/- mice were administered αIL-17 or IgG isotype control antibody every other day from day -2 post-secondary bacterial infection and monitored for survival Data information: Dat are combined from two independent experiments (n = 8-12 mice per group) All data are represented as mean ± S.E.M. Statistical significance was determined wit logrank test in (B Mice were superinfected as described in Fig 3A (C) Absolute neutrophil counts in the lungs following administration of αIL-17 or IgG isotype control antibody, as determined by flow cytometry Data information Dat are representative of two independent experiments with 3-4 in (C mice per group All data are represented as mean ± S.E.M. Statistical significance was determined wit unpaired-students t-test in (C Mice were superinfected as described in Fig 3A (D) Pneumococcal cfu in BAL following αLy6G antibody mediated neutrophil depletion. Control T-bet-/- mice were administered with IgG isotype control antibody Data information: Dat are combined from two independent experiments (n = 8-12 mice per group) All data are represented as mean ± S.E.M. Statistical significance was determined wit Mann-Whitney U test in (D Mice were superinfected as described in Fig 3A (E) mRNA expression of antimicrobial peptides in lungs following administration of αIL-17, IL-22 or IgG control antibody, as determined by qPCR Data information Dat are representative of two independent experiments wit 4-6 in (E) mice per group. All data are represented as mean ± S.E.M. Statistical significance was determined wit one-way ANOVA followed by Tukey"s multiple comparisons test in (E). n.s. = not signif
Figure 1The nanoconjugate contains a fusion protein [T22-GFP-H6 -composed of the peptide T22 as a CXCR4 ligand, a green fluorescent protein and a Histidine tail - bound to the payload drug Three to four pentameric oligonucleotides (approximately 20 molecules) of the antitumor drug 5-Fluoro-2'-deoxyUridine (FdU), named oligo-FdU, are conjugated to the T22-GFP-H6 targeting vector using a linker. T22-GFP-H6-FdU chemical synthesis: T22-GFP-H6 is first covalently bound to the 6-Maleimidohexanoic acid N-hydroxysuccinimide ester linker through its amino groups in the external lysines (Hermanson et al, 2013). The thiol-functionalized oligo-FdU (oligo-(FdU) 5-SH) (see Appendix Fig S1) is then reacted with T22-GFP-H6 functionalized with maleimide (Michael reaction). High and constitutive expression of CXCR4 in the membrane of SW1417 CRC cells as measured by flow cytometry. Lack of human SDF-1α release from cultured SW1417 CRC cells, as measured by ELISA, whereas human control 1BR3.G fibroblasts express high SDF-1α levels, after 48h or 72h of growth in culture. (N=2 experiment in duplicate) Nanoconjugate internalization in CXCR4 overexpressing (CXCR4+) SW1417 CRC cells after 1 hour exposure at 1µM, as measured by fluorescence emission using flow cytometry. (N=3 experiments in duplicate) Significant difference at p= 0.002 between T22-GFP-H6-FdU and AMD3100+T22-GFP-H6-FdU groups Intracellular trafficking of T22-GFP-H6-FdU in CXCR4+ SW1417 cells by confocal microscopy after exposure at 1µM for 24 h. The green staining corresponds to GFP containing nanoconjugates and the red staining corresponds to plasma cell membranes stained with a red dye (CellMask™), whereas cell nucleus was stained in blue with hoescht. The insets show detail of the intracellular localization of nanostructured, fluorescent entities, in an isosurface representation within a three-dimensional volumetric x-y-z data field Linearized T22-GFP-H6-FdU dose-response trend line representation compared with unconjugated free oligo-FdU exposure. Antitumor effect was measured as CXCR4+ SW1417 cell viability by MTT after 72 h exposure as the described concentrations. (N=3 experiments in duplicate) Reduction of cell viability determined by optical microscope images of SW1417 cells exposed to 1µM T22-GFP-H6-FdU for 48 h, as compared to T22-GFP-H6 or free oligo-FdU. (N=3 experiments in duplicate; Scale bar, 100µm).
Concomitant macrophage accumulation and in situ switch from M1 to M2 phenotype with blood vessel abnormalities during glioma growth.Figure 3A. MHCII and MRC1 immunohistochemistry on a section of 3-5 weeks growth glioma implanted in ROSAmT/mG::Pdgfb-iCre mouse. M1 macrophages, preferentially located in hypoxic area, are abundant at 3 weeks and their number decreases at 5 weeks. M2 macrophages, preferentially located around blood vessels, are present at a low level at 3 weeks and their number increases at 5 weeks.Scale bars: A: 200µm; B. Macrophage quantification during glioma growth (n=5 mice per group). Statistical analysis: B. one-way ANOVA followed by multiple comparisons Tukey's test; C. MHCII and MRC1 macrophage population FACs analysis in 2, 3, 4 and 5 weeks glioma (subsets in gated CD11b+ cells) (n=3 mice per group). D. Correlation analysis of M2 like macrophages accumulation (MRC1 positive) with vessel dysmorphia over glioma growth (n=12 mice). Statistical analysis: D. Spearman correlation test;Scale bars: D: 70µm; E. MRC1 immunohistochemistry on 3 weeks growth glioma in ROSAmTmG::Pdgfb-iCre mouse following MHCII-FITC labeled IV injection at 6 or 24h (5µm depth stack). Note the segregation of MRC1 and MHCII cell labeling at 6 hours and the overlapping of these two markers at 24 hours (n=5 mice per group). Statistical analysis: E. t-test. Error bars: E: 50µm.
CLIP-signature of established breast cancer driver kinases.Figure 4(A) Subset of cell line-specific drivers that were identified as rCCS genes in this study. Highlighted entries indicate that the gene was identified as a rCCS gene in that modality. (B) Proportion of the rCCS genes identified by CLIP and supported by the various data modalities, relative to the average number of genes profiled for each modality in all cancer cell lines (n=1047). Boxes represent the interquartile range, notch in each box represents median value and whiskers the range of the values. (C) Proportion of ER+ and ER- breast cancer cell lines that have ESR1 as a rCCS gene. P-value was calculated with the Fisher's exact test. (D) The data modalities that supported the rCCS status of ESR1 and the proportion of cell lines having that evidence in the ER+ cell lines (n=20). (E) Proportion of HER2+ and HER2- breast cancer cell lines that have ERBB2 as a rCCS gene. P-value was calculated with the Fisher's exact test. (F) The data modalities that supported the rCCS status of ERBB2 and the proportion of cell lines having that evidence in the HER2+ cell lines (n=17). (G) Benchmarking the performance of CLIP to identify well-known breast cancer driver genes. True positive (TP) fraction of unique cancer driver genes (n=201) for the three defined breast cancer subtypes as identified by CLIP and alternative approaches based on differential analysis in each specific modality alone, and using the latent factor-based Multi-Omics Factor Analysis (MOFA+) methods for data integration.
Figure 2(A)-(D) The scattering profiles (A), pair distance distribution functions (PDDFs) (B), dimensionless Kratky plots (C) and Porod-Debye plots (D) of the complete sfRNAs of DENV2 (cyan line), ZIKV (red line) and WNV (blue line). The fine features of P1 in the scattering profiles in (A) arise from helical interstrand pair-distance correlation. The PDDF profiles in (B) were calculated using GNOM (qmax=0.3). The dimensionless Kratky plot and Porod-Debye plot for ZIKV xrRNA1 (red dashed line) were included in (C) and (D) for comparison, indicating that the structures of sfRNAs are more extended and open than that of ZIKV xrRNA1. (E) The ab initio shape envelopes of the complete sfRNAs shown in three views. The spatial resolution of the envelopes is 21 Å.
Figure 2(A) mtDNA NGS of MitoA fibroblasts (MitoA FB at passage 5) and MitoA-derived hiPSCs (passages 7-9); n=13.(B) mtDNA NGS of MitoB fibroblasts (MitoB FB at passage 3) and MitoB-derived hiPSCs (passages 5-11); n=12.(C) mtDNA NGS of MitoC fibroblasts (MitoC FB at passage 7) and MitoC-derived hiPSCs (passages 5-11); n=11.GPMs are represented by black diamonds at the specific mtDNA positions; small black diamonds denote mutation load between 1 and 10%, medium black diamonds 10 to 40%, and large black diamonds > 40%. Red diamonds: point mutation A3243G (MELAS causing disease mutation). Numbers beside diamonds indicate the specific mutation load at that position.
Oxidized phospholipids are potent inhibitors of the pro-inflammatory response of myeloid cells.Figure 1A, B BMDCs were treated with OxPAPC or DPPC (40 μg/ml) for 60 min followed by R837 stimulation (5 μg/ml). (A) Supernatants were harvested after 18 h, and concentrations of IL-6 and IL-12 were quantified by ELISA. One-way ANOVA adjusted by Dunnett's multiple comparisons test. Mean ± SD of triplicate determinations from > 3 independent experiments are shown. A, B BMDCs were treated with OxPAPC or DPPC (40 μg/ml) for 60 min followed by R837 stimulation (5 μg/ml). (B) mRNA was harvested after 2 h, and expression of IL-6 and IL-12 was measured by real-time PCR and normalized to G6pdx. Unpaired two-tailed t-test. Data (mean ± SD) are representative of three independent experiments. C Bioactive OxPAPC mixtures were obtained by various oxidation protocols from highly pure PAPC. Periods of oxidation were 24 h for CuSO4 (10 μM), 48 h for FeSO4 (10 μM), and 72 h for air. BMDCs were treated for 60 min with lipids prior stimulation with R837 (5 μg/ml) for 18 h. Cytokine concentrations in supernatants were quantified by ELISA. One-way ANOVA adjusted by Dunnett's multiple comparisons test. Data represent mean ± SEM of triplicate determinations. D PAPC (40 μg/ml) oxidized with CuSO4 (10 μM) for the indicated times was used for treatment of BMDCs prior to R837 (5 μg/ml) stimulation and measurement of IL-12 secretion. Mean ± SEM of triplicate determinations from three different oxidation series are shown. E, F Treatment of BMDCs with the indicated concentrations of CuSO4-oxidized PAPC suppressed IL-6 (E) and IL-12 (F) secretion triggered by a variety of different TLR agonists. After OxPAPC treatment for 60 min, BMDCs were stimulated for 18 h with LTA (500 ng/ml), Poly I:C (50 μg/ml), LPS (10 ng/ml), R837 (5 μg/ml), and CpG (100 nM). Cytokine concentrations in the supernatant were quantified by ELISA. Data are shown as mean ± SD of triplicate determinations from three independent experiments and were analyzed by one-way ANOVA adjusted by Dunnett's multiple comparisons test. G-I Splenicdendritic cells were treated with OxPAPC or DPPC (40 μg/ml) before co-culturing with naïve transgenic SMARTA CD4T cells in the presence of the specific peptide gp61. (G) After 4 days of cell culture, T-cell polarization was assessed by intracellular staining for the cytokines IL-4 (Th2) and IFN-γ (Th1). (H) Bar graphs represent the frequencies of IL-4- and IFN-γ-producing T cells after 4 days of co-culture with OxPAPC-treated and DPPC-treated splenicdendritic cells. Bars represent mean ± SD of duplicate experiments. *P ≤ 0.05 by unpaired two-tailed t-test. (I) IFN-γ production in supernatants of SMARTA CD4T cells (stimulated with 1,000 nM gp61) and co-cultured with OxPAPC- and DPPC-treated splenicdendritic cells for 4 days. One-way ANOVA adjusted by Dunnett's multiple comparisons test. Bars represent mean ± SD.
stabilizes R-loops.Figure 3A-B) Npl3 associates to telomeres in early S. A) Cell cycle profiles of indicated strains. Cells were synchronized in G1 with alpha-factor for 2.5h and released into the cell cycle at 30°C in pre-warmed medium supplemented with the indicated HU concentrations. B) Npl3-TAP associates strongly to telomeres in early S (250 mM HU). Cross-linked samples from indicated strains were used in a TAP-ChIP. Enrichment at telomeres was determined by quantitative PCR on indicated telomeres. Data represents mean % input +/- SEM relative to cells arrested in alpha factor n=3 (paired t-test two tailed *p<0.05, **p<0.01 Abbreviations: ns: not significant HU: hydroxyurea. *p<0.05, **p<0.01 C) NPL3 over expression stabilizes telomeric R-loops. The indicated strains were grown on 1% raffinose 2% galactose to induce NPL3 over expression. Cross-linked samples were subjected to DRIP. DNA-RNA hybrids were immunoprecipitated using the S9.6 antibody. R-loop levels were determined by quantitative PCR on indicated telomeres. Data represents mean % input +/- SEM relative to 250 mM HU eV n=3 (paired t-test two tailed *p<0.05, **p<0.01). Abbreviations eV: empty vector control, oE: over expression HU: hydroxyurea. *p<0.05, **p<0.01 D) Deletion of NPL3 decreases telomeric R-loops. The indicated strains were crosslinked and subjected to DRIP. DNA-RNA hybrids were immunoprecipitated using the S9.6 antibody. R-loop levels were determined by quantitative PCR on indicated telomeres. Data represents mean % input +/- SEM n=3. Specificity of S9.6 antibody was determined treating a fraction of the samples with RNase H. E-G) NPL3 stabilizes R-loops. E) R-loop dot blot. The indicated strains were grown on 1% raffinose 2% galactose for 72h and subsequently released into 1% raffinose 2% galactose or 2% glucose medium for 6 PDs. R-loop levels and dsDNA levels were determined using the S9.6 antibody and anti-dsDNA antibodies. Specificity of the S9.6 antibody was confirmed by treatment with RNase H. Loaded genomic DNA content is indicated at the bottom of the figure. F) R-loop dot blot quantification. Data represents R-loop signal as the S9.6 antibody signal relative to corresponding dsDNA signal n=3 (unpaired t-test two tailed *p<0.05). G) Serial dilutions of indicated strains were assayed on 1% raffinose 2% galactose media. Plates were imaged after 72h incubation at indicated temperatures. Abbreviations: V: empty vector control, oE: over expression, ds: double-strand,