EMBO/sd-character-level-ner huggingface dataset:
C. Quantification of ubiquitin linkage peptides in the TNF-RSC. The box plot shows the relative abundance of K48, K63 and linear ubiquitin linkage-specific peptides in the TNF-RSCs isolated from TNF-α-stimulated (15 min) and control cells quantified by SILAC-based MS.
Representative images of analysed C5 P1 (left) and C5 P19 (right) NLS-3xmCherry stable cells. Mean intensity of fluorescence for cytoplasm and nucleoplasm for each cell are labelled. Scale bar, 20 μm.
D 20 nM siRNA targeting negative control (NC) and PKR were transfected into iBMMs for 48 h, the protein and mRNA expression level of PKR were tested by RT-qPCR and Western blot, respectively.
Growth inhibitory concentration (GI50) of CY and bendamustine in the NCI60 cell line panel.
(c) Left, FAK−/− cells stably re-expressing wild-type FAK, FAKY397F or FAKY4F-Y9F were fixed and stained for anti-FAK (red) and anti-pTyr-416-Src (green). Solid arrows indicate co-localization at adhesions and dashed arrows indicate active Src in autophagosomes. Scale bars, 20 μm. Right, lysates from these cells were also immunoblotted with anti-FAK and anti-actin antibodies.
D Statistical quantification of (C) showing the ratio of USP33+ cells in SOX2+, CA9+, or SOX2+/CA9+ cells in human primary GBMs. USP33 expression was detected in a fraction of GSCs (SOX2+) or CA9+ hypoxic cells, but the majority of the hypoxic GSCs (SOX2+/CA9+ cells) were USP33+, indicating that USP33 was induced in GSCs in response to hypoxia. (n = 5 sections; ***, p < 0.001; mean ± s.e.m.; two tailed unpaired t-test).
(A) Top: Representative images of In situ PLA performed between DDX5 and S9.6 (DNA-RNA hybrids) antibodies in BRCA2 deficient DLD1 cells (BRCA2-/-) or DLD1 stable clones expressing BRCA2 (WT) or BRCA2-T207A (T207A). Cells were fixed directly or 4h post-irradiation (6Gy). When indicated, cells were transfected/treated with RNase H1 (RH) prior to fixation. Single antibody controls in non-irradiated BRCA2 WT cells are shown. Scale bar indicates 10 µm. Bottom: Quantification of the number of PLA spots per nucleus. At least 500 cells were counted per condition from three independent experiments. For statistical comparison of the differences between the samples we applied a Kruskal-Wallis test followed by Dunn's multiple comparison test and the p-values show significant differences. The red line in the plot indicates the median and each symbol represents a single PLA spot. (B) Top: Representative images of In situ PLA performed between DDX5 and γH2AX antibodies in BRCA2 deficient DLD1 cells (BRCA2-/-) bearing BRCA2 (WT) or BRCA2-T207A (T207A). Cells were fixed directly or 4h post-irradiation (6Gy). When indicated, cells were transfected/treated with RNase H1 (RH) prior to fixation. Single antibody controls in non-irradiated BRCA2 WT cells are shown. Scale bar indicates 10 µm. Bottom: Quantification of the number of PLA spots per nucleus. At least 600 cells were counted per condition from three independent experiments. For statistical comparison of the differences between the samples we applied a Kruskal-Wallis test followed by Dunn's multiple comparison test and the p-values show significant differences. The red line in the plot indicates the median and each symbol represents a single PLA spot.
Protein levels of the validated SPPL2c substrates Membrin (F) were reduced using specific siRNAs. Non-targeting control siRNA (Ctr) served as negative control and overexpression of SPPL2c WT was used as a positive control. Non-transfected cells (-) or stably transfected but non-induced SPPL2c wt cells (n/i) served as additional controls for antibody specificity. Processing and maturation of ectopically expressed GnT-V and maturation of endogenous SPPL2a were monitored by Western Blotting. None of the substrates' knock down fully recapitulated the effect on GnT-V or on endogenous glycoproteins observed in SPPL2c overexpressing cells. Calnexin served as loading control and ectopic expression of SPPL2c WT and SPPL2c D/A was confirmed using a SPPL2c specific antibody.
Successful injections per minute for a novice user on the manual microinjection system, an experienced user on the manual microinjection system, and the Autoinjector.
(C, D) Quantification of cystine levels (nmol/mg protein) by HPLC-MS/MS in two different patient-derived cystinotic tubuloids in the absence of the drugs (NT) or upon treatment with cysteamine (100 μM), bicalutamide (35 μM) or cysteamine (100 μM)-bicalutamide (35 μM) combination treatment (n = 3). (E) αKG levels measured in patient-derived cystinotic tubuloids (CNTSPatient-1 and CTNSPatient-2) in the absence of the drugs (NT) or upon treatment with cysteamine, bicalutamide or cysteamine-bicalutamide combination treatment using metabolomics (n = 3).
(B) The detailed information of deleted sequences in various lncPSCA-knockout clones (MGC80-3: KO-C1 and KO-C3; HGC-27: KO-C14 and KO-C40).
(E) The C terminus of SLFN11 is required for its foci formation. SF268 cells were transfected with plasmids encoding Flag-tagged wild-type or mutant of SLFN11. Immunostaining experiments were performed 3 hr after CPT (1 µM) treatment using indicated antibodies. Scale bar, 10 µm.
(A) The level of ATG5 was detected in cell lines using western blot analysis. β -actin was used as internal controls.
B No correlation between length of combined repeats and age of onset in SCA8 patients, n=85, p=0.9847 or in the subset of SCA8 patients with CCG•CGG interruptions (int.), n=26, p=0.2096, linear regression analyses. Open circles indicate SCA8 patients with pure CAG repeat expansions. Red squares show average expansion size for individuals with two expanded alleles, individual allele repeat lengths: 137/177,110/320, 104/130, 96/109. Red triangles show average expansion size for individuals with two expanded alleles and CCG•CGG interruptions: 84/114, 92/100. Grey triangles indicate individuals with CCG•CGG interruptions.
E Quantitative RT-PCR analyses of the gene expression of femoral bone samples. Results are shown as mean ± SEM; n=6; *: p<0.05, **: p<0.01 and ***: p<0.001 by t test
Differences in viability of HeLa and CCNF K/O cells after treatment with specific Chk1i (LY2603618) at the indicated concentrations plotted on a log10 scale to measure differences in IC50.
(B) 293T cells were co-transfected with Flag-TRAF6 and Myc-Rv2626c and IP with αFlag or αMyc. WCLs were used for IB with αFlag, αMyc or αActin.
C. Quantification graph showing dynamics of Lysotracker recovery in control (siCtrl) and both TSG101 and ALIX depleted cells. HeLa cells stably expressing CHMP4B-eGFP were co-transfected with siRNAs against TSG101 and ALIX. 48 h post-transfection, cells were pre-treated for 20 min with 75 nM Lysotracker Deep-Red, which was used as a read-out. While the decrease in the number of Lysotracker spots is quickly recovered in siCtrl, simultaneous depletion of ALIX and TSG101 leads to a severe impairment in lysosomal repair. Data from >40 cells per condition from four independent live-cell imaging experiments are shown. Graph is normalized to the area occupied by the cells. Error bars correspond to 95% confidence intervals.
(I) Western blot analysis of cell lysates isolated from STAT5 wild type and knockout MEFs. **, p<0.01; ***, p<0.001.
A Metabolic Atlas pathway analysis of proteomic changes of RKO and IMT1-resistant RKO cells treated with 1 μM IMT1 for 96 hours. Data are expressed as average log2-fold change of controls (DMSO-treated RKO cells).
C57BL/6 mice were treated with mouse recombinant IL-33 or PBS daily for 5 consecutive days. (C, D) Representative FACS analysis showing the proportion of ILC2s (Lin-GATA-3+) in the CD45+ leukocyte compartment from the spleens (C) and kidneys (D) at day 3 after treatment in C57BL/6 mice receiving PBS (n=4) or IL-33 (n=6).
(G) Kaplan-Meier survival graphs of SCA1 mice with heterozygous knockout of either one or both kinases. The data of Msk1+/-, Rsk3+/-, and Msk1+/-; Rsk3+/- mice overlap those of wild-type mice. *P<0.05, Gehan-Breslow-Wilcoxon test, n = 15, 15, 12, 13, 22, 11, 20, 19 following the order of genotypes in the legend on top of the figure, respectively.
MAGMA gene-set analysis of the differentially expressed genes upon LEMD2 depletion in cortical neurons using the summary statistics from multiple GWAS datasets. Phenotypes are listed on the y-axis, EA (educational attainment), IQ (cognitive ability/human intelligence), SZ (schizophrenia), ASD (autism spectrum disorder), CAD (coronary artery disease), ADHD, (attention deficit hyperactivity disorder), CD (Crohn's disease), MDD (major depressive disorder), Stroke, T2D (type 2 diabetes), AD (Alzheimer's disease), OSD (obsessive-compulsive disorder). P-values are shown above each data point, which represent beta values (x-axis). Horizontal bars indicate error bars (SE). P-values in red survived Bonferroni multiple test correction of p < 0.0125 for the 4 tests (IQ, EA, ASD, and, SZ).
A, B X-gal staining showed NB-3/LacZ expression in the sham-operated (A) and injured (B) spinal cords from adult NB-3+/−mice.
signaling.A. OT-I T cells (CD90.1+) from young donors were adoptively transferred into young or aged C57BL/6 mice 1 day prior to infection with PR8-OVA virus.
B Fluorescent photomicrographs of HepG2 cells expressing AgHaloER (TMR-labeled, red). Endogenous PDI was immunostained (green) as an ER marker. Scale bar = 10 μm.
J Semi-quantification and comparison of Ki67 expression levels during E60, E70, and E90 stages. n = 3. Data information: Data represent the means ± SEM. *P < 0.05 (one-way ANOVA and Newman-Keuls post-hoc tests).
A mRNA expression of indicated components of the canonical Wnt/β‐catenin pathway in freshly isolated small intestinal crypts of 12‐ to 16‐month‐old G3 mTerc−/−mice and age‐matched mTerc+/+mice (n = 5 mice per group).
Regulation of Swi6 dynamics and the role of Swi6 in heterochromatin spreading, boundary formation, and repressionModel for the formation of a distinct heterochromatic domain. The spreading‐competent open conformation of Swi6 dimers is fully dispensable or acts redundantly with RNAi‐mediated spreading mechanisms in the formation of constitutive heterochromatin. The spreading of heterochromatin into neighboring euchromatin in the absence of DNA‐encoded boundary elements, such as TFIIIC binding sites, can be stopped by the spreading‐incompetent closed conformation of Swi6 dimers, RNA‐mediated eviction of spreading‐competent Swi6, or Epe1 activity. Swi6 molecules interact with H3K9me2 only transiently and exchange between free and RNA‐bound forms (2, 1, or 3, respectively; see also C). Removal of RNA from Swi6 constitutes a rate‐limiting step in the Swi6 exchange cycle (blue arrow) and contributes to tight repression of heterochromatin.In the absence of Swi6, H3K9 methylation is mediated by the RITS complex (Ago1, Chp1, Tas3) and can spread beyond natural boundaries via self‐associating Tas3. This might occur independently of siRNAs.In theory, Swi6 can exist in at least three kinetically distinct populations: 1) freely diffusible Swi6, 2) Swi6 bound to H3K9me2, and 3) Swi6 bound to RNA; 3 is the least and 1 the most mobile population. The blue arrow indicates the rate‐limiting step in the Swi6 exchange cycle. Under physiological conditions, most Swi6 molecules exchange between the RNA‐ and H3K9me2‐bound forms.
E Bisulfite sequencing of hCD45 exon 5 DNA from the WT- and Mut-hmC clones to confirm the persistence of methylation at the intact and mutated CTCF binding site following stable insertion into the CHO genome.
B. Wildtype or TRAPPII deleted cells were loaded with oleic acid and stained with bodipy 493/503 (green) and endogenous Rab18 by immunofluorescence (red). Bar = 10 μm.
F Strand-specific RT-qPCR analysis of antisense levels after 10 h of ABA treatment in 10-, 20- and 40-day-old Col-0 plants.
C. Time-lapse images showing the disassembly of Tpm domains. Filaments were saturated with 100 nM nGr-Tpm1.8 before the experiment and Tpm was removed from solution at time t=0 (the solution contains 0.6 µM unlabeled G-actin to prevent filament depolymerization). PE and BE indicate F-actin pointed and barbed end, respectively.
(B) The stiffness of back skin and forepaw palms from 10-wk-old WT and RDEB mice was measured with a micro-indentation stiffness measurement tool. N = 3 mice per genotype and 5-7 measurements per mouse. Individual data points, mean ± S.E.M. are shown, P = 0.0348 (back skin) and P < 0.0001 (forepaws) tested with unpaired t-test.
Transfer of α-syn fibrils is shown in neurons at 1 DIV. Cells were loaded in suspension with either Alexa-568 α-syn fibrils (red) or Alexa-488 α-syn fibrils (green) and cultured together. The insets (right panels) show a magnification of the area depicted in the expanded field image (left). Yellow arrows point to red and green α-syn puncta contained in the soma of a neuron. Yellow arrowhead points to a TNT-like connection.
The S. typhimurium SPI-1 TTSS-secreted protein SipB localizes to the mitochondria of infected macrophages. (A) Bone marrow-derived macrophages were infected with either wild-type S. typhimurium or the TTSS translocation-defective sipD mutant strain with a multiplicity of infection of 50. 3 h after infection, macrophages were collected and processed for immuno-EM using gold-labeled antibodies. SipB could be readily detected in macrophages infected with wild-type (A and B), but not in macrophages infected with the sipD mutant strain (C). Bars, 100 nm.
C. LINC00115 knockdown reduced ZEB1 mRNA expression in 1123 and 528 GSCs. Data information: , data are representative of three independent experiments. Error bars, ± SD. **, p < 0.01, by One-way ANOVA
C IF double staining of end-stage SCA8 BAC frontal cortex shows exclusive localization of polyGln (mouse α-Gln, red, bottom panel) in neurons (rabbit α-NeuN, green, bottom panel). In contrast, polySer (Rabbit α-SerCT, red, top panel) shows widespread accumulation in the frontal cortex including within neurons (mouse α-NeuN, green, top panel).
Quantification of proliferating Ki67-positive cells specifically in glomeruli (C), interstitium (D) and tubules (E) in Foxd1Cre::Pdgfrb+/J mice (black bars) and wt mice (white bars) of 6, 14, 25 and 35 weeks of age. Foxd1Cre::Pdgfrb+/J mice exhibited increased proliferation of glomerular and interstitial cells, whereas tubular epithelial cell proliferation was not altered. Data in C, D and E are shown as means ± SD of n = 3 animals per group.
Kaplan-Meyer survival curves of Nsmce2+/+ and Nsmce2SD/SD mice. The P‐value was calculated with the Mantel-Cox long‐rank test.
MDM were treated with 5μM ETO or 0.01μM CTH for 18h, lysed and immunoblotting performed to detect cell cycle/cell cycle arrest and DNA damage associated proteins.
Representative microscopic views of the myenteric plexus of Ndrg4+/+ and Ndrg4-/- murine colonic sections labeled with either TuJ1 and S100 (B, n=3) or HuC/D (C, n=6) did not reveal structural or organizational differences in the ganglionic network of Ndrg4+/+ and Ndrg4-/- mice. Scale bars, 100 µm. Quantification of the enteric neuronal cell number (HuC/D) shows a similar number of enteric neurons in the proximal and distal colon of Ndrg4+/+ and Ndrg4-/- mice (n=6).
WT and SNX10 KO Caco-2 cells were treated with indicated doses of OMVs for 24h. Protein expression of E-cadherin and SNX10 was determined by immunoblots (A) and quantified by ImageJ software (B) (n = 3 independent experiments). Data information: Data are means ± SD. One-way ANOVA followed by Bonferroni post hoc test was used for statistical analyzes. *p < 0.05; **p < 0.01; ***p < 0.001.
Migration of SCC13 cells plated on either de-cellularized matrix from Fb Act (clone 2) or Fb EV. N=6. The experimental setup is shown schematically above the graph.
(T) Loss of function of epg-7 does not ameliorate the degeneration of mec-4::gfp-labeled touch neurons caused by mec-4(u231).
C. DNA effects on Smc5/6 arm co-alignment as judged by CC-Cys cross-linking. As in (B) but also including 40bpDNA. Additon of plasmidDNA but not 40bpDNA reduces CC-Cys cross-linking in the Smc5/6 hexamer.
(G) Regression analysis showing that the signal intensity of Gadd45b mRNA in reactivating neurons at 48 hrs post treatment with LY294002 and WAY-150138 was inversely related to the signal intensity of viral UL36 mRNA. No significant relationship was detected for ICP27 or UL30 mRNAs. Each dot represents a single reactivating neuron (n=3 biological replicates). Data information: R and R square values were calculated using Correlation analysis by Prism 8.
In vitro crypt culture (day 8) from small intestine crypts isolated from mice with indicated genotypes. Arrows mark the crypt-like structure (E). The number of organoids per culture wells (n=4-5 mice per group). Two hundred crypts are seeded per well (F).
(A) Mean ± SEM body weight of ASMko and wt mice treated or not with Ca074Me at the indicated time during treatment (n = 7 mice per group).
C. Quantification of the colony size in methylcellulose of MDGI-silenced (sh1 and sh2) cells relative to the controls (Scr) that is set as 100 (n = 3). Data are represented as mean ± SD. ***P < 0.001, two-tailed, nonparametric Mann-Whitney's U-test.
B) Hierarchical clustering of the AGR2 modulator genes significantly deregulated in non-inflamed colonic mucosa from patients with Crohn's Disease (CD) versus healthy controls (C) (dChip software t-Test)
(E) AUC in mESCs expressing GFP, GFP-lncRNA-c1 and GFP-lncRNA-c2 wildtype construct (noBoxB, circles) or with a 5xBoxB cassette insertion 30 nucleotides upstream of the GFP start site (BoxB(-30), triangles). Comparison of AUC between construct with and withoux (BOxB(-30) paired two-tailed t-test p-value= 8.12X10-4, 0.011 and 0.002 for GFP, GFP-lncRNA-c1 and GFP-lncRNA-c2, respectively. Data is represented as mean±SD and Each point corresponds to the results of one independent biological replicate.
C) Cells expressing Cdc14-YFP and Cnm67-RFP were grown overnight and blocked in G2/M by using nocodazole prior phleomycin treatment (1μM). Samples were taken every 30 minutes to follow Cdc14 re-localization. The efficiency of the arrest was determined as in Fig 3A. Scale bar: 3μm. Graphs represent the percentage ± SD of cells with Cdc14nucleolar exclusion (left graph) and cells arrested in metaphase (right graph) from three independent experiments.
(B) GST-NCOA3 full-length (FL), GST-NCOA3 ΔN (1-408aa), GST-NCOA3 ΔS/T (409-921aa), GST-NCOA3 CBP (922-1161aa), and GST-NCOA3 ΔC (1162-1424aa) were constructed (upper panel).Pulldown assay with GST-NCOA3 FL or its protein fragments (ΔN, ΔS/T, CBP and ΔC) and His-UHMK1 were performed (lower panel).
Covariance models and parameters used to characterize oscillatory (KOUosc ) and non-oscillatory (KOU ) single cell expression.
(B) Venn diagram showing the overlap between the YAP signatures obtained in Oral SCC and Breast (YAP Signature 1) and CRC and HCC (YAP Signature 2) .(C
Representative images of pERK1/2-stained lung sections from KrasG12D mice treated with either vehicle (control, Ctl) or anti-IL-6R antibodies 1F7 or 25F10 over 6 weeks post Ad-Cre inhalation. Scale bar, 100μm. Quantification of pERK1/2-positive cells/high power field (HPF) in lungs of the indicated groups (n = 5 per group).
G Quantification of morphological parameters of experiments (n>100 cells from 3 independent experiments). Data information: In (G), data presented as boxplots showing the median, the first and the third quartile. Error bars show minimum and maximum values. (G) ***, P≤0.001; **, P≤0.01 *, P≤0.05 (One-way ANOVA, Tukey's multiple comparisons test).
Immunofluorescence microscopy analysis of the STK38L wild type and the R105W mutant display no clear difference in localization. Both the wild type and the R105W mutant display nuclear, cytoplasmic and plasma membrane localization. However, the MS-microscopy analysis suggests a more prominent endosomal localization with the R105W mutant. (key: the scale bar for the immunofluorescence images is 10 µm, and the color gradient on the MS-microscopy indicates the localization scores calculated by the MS-Microscopy tool.
Four-day-old seedlings of 35S:ARR12:YFP, 35S:ARR12S323A:YFP, and 35S:ARR12S323D:YFP were transferred to 1/2 MS medium supplemented with or without 50 mM or 75 mM NaCl. After three days of salt treatment, relative primary root lengths (B) were determined. After ten days of salt treatment, changes in survival rates (C) and fresh weights (D) were examined. Scale Bar, 1 cm.
BTH screen for interactions between TssA1 and T6SS components of interest. A graphical representation (bottom) of β-galactosidase activity from E. coli DHM1 cells producing the indicated proteins fused to the adenylate cyclase T25 or adenylate cyclase T18 subunits and images of corresponding spots on X-gal LB agar plates (top) are shown. The combination of T25/T18 fusion proteins are indicated as 25 or 18 followed by the name of the fused T6SS protein. T6SS proteins are abbreviated as follows: A1=TssA1, E1=TssE1, F1=TssF1, G1=TssG1 and K1=TssK1. The values shown on the y axis correspond to the activity in Miller units. In each case, average activity from two independent experiments is shown and error bars indicate the standard deviation (S.D.). Experiments were carried out in triplicate.
H mRNA expression of p16 gene normalized to GAPDH measured by RT-PCR from young and old WT and SirT7-/- fibroblasts (mean ± SEM; 3 samples per genotype).
A, B Development of X chromosome-containing female (A) and Y chromosome-containing male (B) M. polymorpha plants.
Development and pathogenic responses of Col-0, VISP1OE1, VISP1OE2, rdr6-15, and sgs3-1 plants to mock buffer or CMV-2blm infection at 21 dpi. Scale bar = 2 cm.
E) Representative TEM images of control and Mfn2KD C2C12 myotubes treated with NAC showing increased number of autophagosomes and mitochondrial alterations (n=3 independent experiments) (Scale bar: 2 µm).
RNA-seq analysis of Maf and Mafb expression in WT and DKO AMs, which were isolated by flow cytometry from mice in steady state (top) or from mixed BM chimeras (bottom).
Schematic depicting experimental design for Figures d-f: 27 month old INK-ATTAC mice were treated 4 times with AP20187 (or Vehicle), 3 days in a row, every 2 weeks (2-month-long treatment in total) and were sacrificed afterwards for analysis.
B) Expression of the 21U sensor (left) and DAPI staining (right) of gonad arms in the indicated genetic backgrounds. Gonads are outlined by a dashed line. The mCherry signal is represented in pseudo-colours [LUT fire (ImageJ)] to reflect differences in the intensity of the signal. Number of animals analysed and with indicated phenotype are given in the panel. Animals not showing the activation of the 21U sensor(+) were still silenced, and animals that did not show the silenced 21U sensor(RNAe) state were expressing weakly, comparable to the 21U sensor(+). Scale bar: 25 μm.
A-B. Involvement of filamentous cytoskeletal structures in BiFC foci polarization. Time-lapse micrographs of agarose-embedded cells expressing the Dsl1pVN•ε-COPVC BiFC combination at RT with fresh PM Glc+ura medium supply. (B) Microtubuli disruption through 24 μg/ml nocodazole did not affect polarization of the COPI•Dsl BiFC signals. Arrowheads: polarized signal, asterisks: unpolarized localization. Fluorescent images are displayed with inverted brightness values. Scale bar 10 μm.
C Gata4, Hand1 and SclChIP‐seq tracks with cardiac and hematopoietic gene regions show examples of three subgroups of enhancers-those bound by Scl, Hand1 and Gata4 (gray), Scl and Gata4 (orange) and those bound only by Scl (blue).
Crystal structure of AK2 (pdb entry 2C9Y). In the crystal structure, a disulfide bond between C42 and C92 is visible with about 50 % occupancy, while 50 % of the Cys42/92 residues are in the reduced state. This disulfide bond is far away from the active site of AK2. The figure was created using PyMOL.
Representative normalized FCS curve of Scc1-GFP at different cell cycle phases. Dotted lines indicate fitting of one-component anomalous diffusion models to the respective FCS curve.
Resting mitochondrial calcium levels in ShRNA MICU1 HeLa stable cells transfected with the indicated constructs and evaluated through ratiometric imaging of the mitochondrial targeted GCaMP6m (n=3 independent experiments; 38-50 cells)