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D and H. Quantification of at least five (D) or seven (H) independent replicates of experiment shown in B/C and F/G, respectively. Uridylation signal intensity for substrate S1 (indicated in B and F) was corrected for adenylation activity and normalized to wild-type 2 min time point. Data represent mean SEM. P-values were determined using Student's t-test. * p<0.05, ** p<10-2, *** p<10-3, **** p<10-4.
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Amount of GS-MQ by LC-MS (green line, left axis) and NAC-MQ (purple line, right axis) over time after incubation of GS-MQ with NAC (n = 2). Values on y-axes are not comparable because GS-MQ and NAC-MQ have different response signals on MS. Data information: Indicated values are assessed by LC-MS. Data are represented as mean ± SEM. See also Appendix Figure S4.
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A, Immunoblot analysis of protein lysates from ARPE-19 cells over-expressing FLAG-tagged C. elegans HLH-30 wild-type or mutated HLH-30(C284A) mutant. Samples were run under non-reducing conditions.
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(C) With increasing stress levels, the steady state level of σV activity increases, as observed experimentally. Bars correspond to the mean ± s.d. (N=100 simulations for each lysozyme stress level).
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(I) Kaplan-Meier survival curves of mice shown in panel H. Statistics: Gehan-Breslow-Wilcoxon test.
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(C) Nuclear extracts of U2OS cells stably expressing FLAG-tagged TIP60WT or TIP60S90A, or FLAG-tagged chromodomain mutants TIP60F50A, TIP60Y47A, TIP60Y44F or the empty vector (vec) were subjected to fractionation into nucleoplasm (nuc.) and chromatin (chr.) fraction. Both fractions were analysed by Western blotting
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I-K Quantification of the effect of indicated MMS22L mutations on RAD51 foci in U2OS cells treated with 50 nM CPT for 1 h (I; n = 3), 50 nM CPT for 18 h (J; n = 3) or 5 µM ETP for 1 h followed by 3 hours incubation without the drug (K; n = 3). Graphs represent averaged median values; error bars indicate SEM. Statistical analysis according to one-way ANOVA with Bonferroni post-test; *** P ≤ 0.001; ** P ≤ 0. 01; ns, not significant. Representative immunofluorescence images are shown in (H), Figures EV6G and EV6H, respectively.
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C) IAV infection following acid bypass is comparable between control and δWD MEFs. IAV was bound on ice for 1 h, and warmed at either neutral pH (6.8) or low pH (pH 5.0) for 2 min, followed by incubation in STOP medium containing NH4Cl for 18 hours. Cells were fixed and stained for NP and Hoechst, imaged by automated confocal microscopy and maximum intensity projection images analysed to quantify viral infectivity. The results from N=3 independent experiments (5,000-10,000 cells quantified per experiment), and the means are shown. Scale bar; 500 µm.
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(I) IDH1 K224 deacetylation suppressed cellular ROS levels in HCT116 cells. ROS was determined in cells under non-stressed condition or exposed to menadione. *P<0.05 and **P<0.01 Data information: All results were expressed as mean ± SD of three independent experiments (n ≥ 3 per experimental condition). For figure I, statistical significance was assessed with the two-way ANOVA followed by Tukey's post hoc test. *P<0.05 and **P<0.01. n.s. = not significant.
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(d) EBER1 5'-pppRNA detection using splint-ligation. EBV-WT- or EBV-ΔBRLF1-harboring HNE1 cells were cotransfected with empty vector, BRLF1 or BRLF1 L578A, BRLF1 plus BZLF1, or BRLF1 L578A plus BZLF1 for 48 h. The total RNAs were extracted, and 5 μg of each RNA was subjected to splint-ligation with FAM-labeled probe to quantify the 5′-monophosphorylated EBER1 and total EBER1 RNA. The ligation products were separated using urea-PAGE, visualized by a fluorescent scanner and analyzed using ImageJ software. The ratio of 5'-pRNA density to total RNA density and the relative 5'-pppRNA level were calculated for three independent experiments.
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Number of Kit+ cells per IAHC increases following αDll4 antibody treatment. Each dot represents one cluster. Quantification on confocal images. Statistical analysis: Mann-Whitney U test. ****p< 0.0001.
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Coomassie stained SDS-page showing purified serum IgM of complex InsA peptide (cInsA) immunized and CI mice under reducing (+ β-ME), and non-reducing conditions. Representative of two independent experiments.
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(F) H&E staining, Sirius red staining, and KLF10 immunofluorescence staining of liver sections from NAFL and NASH patients. n=3.
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(b) Effects of CerS1 and C18-ceramide induction on the lipidation of Flag-tagged wild-type, LC3BI35A, LC3BF52A and LC3BG120A proteins were examined by western blotting. Noninduced cells (− tet) were used as controls. β-actin was used as a loading control. Full blots can be found in Supplementary Figure 13.
|
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Deletion of MIG1 in ρ0 snf1∆ cells rescues ∆ψm. Cells were cultured to mid-log phase and stained with 125 nM TMRM for FACS analysis
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(G) Morphology of MEFs expressing B-Rafwt or B-RafAVKA in the presence or absence of TAg.
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(A) Sanger sequence trace showing homozygosity for the c.469C>T mutation, predicting a stop codon in exon 6 of GRK2 (arrow).
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J Modulation of podocyte-specific marker expression in primary podocytes by KLF10 overexpression. Ectopic overexpression of KLF10 in primary podocytes significantly repressed various podocyte-specific markers, but conversely increased KDM6A expression. *P < 0.05 versus the empty vector control (Wilcoxon two-sample test; n = 3).
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B The m-fold predicted folding free energy (ΔG) of hairpin structures of pure CAG and CGG interrupted repeat tracts with different configurations. Filled symbols show sequences also used for UV melting analyses. Grey dotted line indicates ΔG of pure (CAG)8.
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(C) Box plots showing testicular expression from the bulk RNA-seq data (biological replicates, n = 5) of SC- and LC-specific genes extracted from the single-cell RNA-seq data Expression levels are normalized to average expression in WT for each gene.
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A Differential clustering based on secretagogin (Scgn), neuropeptide, hormone and hormone receptor mRNA expression. Secretagogin‐expressing(+) neurons typically contained corticotropin‐releasing hormone (Crh) and Nr3c1 mRNA transcripts.A1 Clusters of gene transcripts from 130 cells reveal the phenotypic segregation of PVN neurons. Increasing mRNA copy numbers were depicted by a color gradient from deep blue (not detected) to red (high numbers). Secretagogin+ neurons are indicated by red arrows.
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(B) TSC2−/−, p53−/− MEFs stably reconstituted with wild-type raptor or S722A/S792A mutant raptor were treated with 2 mM AICAR for the indicated times. Cell lysates were prepared in RIPA buffer and analyzed by immunoblotting with the indicated antibodies. The levels of p62 are listed relative to those of untreated WT raptor cells, which were set as 1.
|
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E To measure secretion of Asm by platelets, tumor cells and platelets were co-incubated for 30 s, the samples were pelleted, the supernatants were acidified, and the Asm activity was measured. All Asm activity measurements were performed in the presence of 100 μM Zn2+.
|
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(G) Cells were transfected with siRNAs as indicated, followed by further transfection with CA-Rab8, incubation in serum-starvation media for 12 h, and immunostained for acetylated-tubulin. Representative fluorescent images of GFP-Rab8 Q67L (green), acetylated-tubulin (red), and DNA (blue) are shown. Scale bar, 10 μm. (H) Quantification of the percentage of GFP -positive ciliated cells (only those cilia having both GFP-Rab8 and acetylated-tubulin on cilium were considered for quantification). Data represent mean ± SD (n = 3 experiments), 200 GFP positive cells were scored per condition per experiment, *P < 0.05, Student's t-test.
|
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A Distribution of Scl binding sites relative to TSS in Scl‐bound activated or repressed genes shows that majority of Scl binding sites locate away from TSS. Chi‐square test was used to assess differences in the distribution.
|
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(E) Co‐immunoprecipitation of Bcl‐XL and WT or mutant Beclin‐1. HeLa cells were transfected with the indicated constructs, followed by immunoprecipitation of Flag‐tagged Bcl‐XL and immunochemical detection of Beclin‐1.
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A. 293T-GFP1-10 and -GFP11 cells (1:1 ratio) were co-transfected with S, ACE2, TMPRSS2, IFITM or control plasmids. Cell fusion was quantified by measuring the GFP+ area by high-content imaging after 18h. (B and C) or analyzed over time by video microscopy (D and E).
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STED super-resolution microscopy showing colocalization of endogenous polyUb proteins (FK1) and PML-NBs in PML-GFP HeLa cells treated with HS at 42˚C for 2 h. Scale bars: 5 µm.
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I) Secretion of AGR2 wild-type (wt), E60A and ∆45 mutant as determined by Western blot. eAGR2, extracellular AGR2; iAGE2, intracellular AGR2.
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(B) FP titrations showing the binding of R126E CaM to PSD-95 peptides, either WT (blue) or E17R (black).
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DNA and crRNA sequence used for experiments with a full target and multiple PAMs. DNA sequence is shown for the single-target single-PAM construct and schematic representation is shown for multiple-PAM containing constructs.
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Blot for peptide-enriched GRB2 and PI3Kp85. HDMEC total lysate incubated with indicated immobilized peptides followed by immunoblotting for GRB2 and PI3Kp85.
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Pyridostatin (PDS) was administered intravenously (i.v.; 7.5 mg/kg/day) and NU-7441 was administered intraperitoneally (i.p.; 10 mg/kg/day), over the indicated periods of time. Vertical dashed line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 6 mice. Error bars represent SEM. P values were calculated at day 24 using an unpaired two-tailed t-test N.S. P> 0.5; **, P ≤ 0.01; ****, P ≤ 0.0001.
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H qRT-PCR analysis of Ifng gene expression in naïve wildtype or Peli1-KO OT-I CD8 T cells that were either not treated (-) or stimulated for 6 h (+) with anti-CD3 plus anti-CD28 in the presence (+) or absence (-) or rapamycin.
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Quantitation of the % of cells with polyUb proteins (FK1) sequestered in nuclear foci. HeLa cells were treated with OP-puro (25 µM) and heat shock (HS) at 42˚C for 2 h. Then, cells were either immediately fixed or let to recover for 3 h in drug-free medium (control), with VER (40 µM) or Eeyarestatin I (5 µM). Number of cells counted/condition: 593 - 1016 in three independent experiments; statistical significance via One-way ANOVA; p = 10-3, ± s.e.m.
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C-C') Representative images showing that Hh.N.EGFP (which cannot undergo cholesterol modification) are found as puncta on the surface of NBs (yellow arrows) when overexpressed in neighbouring cortex glial cells (NP2222-GAL4>).
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(A-D) Cryo-EM maps of eEF3 bound to non-rotated ribosomal species with isolated densities for the 60S, 40S and eEF3 (colored as in Fig.1), as well as the A- (pale yellow), P- (red) and E-tRNA (blue). The eEF3 ligand is binding the ribosome in the pre-translocational (PRE) state termed as (A) PRE-1 (A/A‑, P/P‑tRNA) and (B) PRE-2 (A/A-, P/E-tRNA) as well as to the post-translocational (POST) version named (C) POST-2 (P/P-, E/E-tRNA) and (D) POST-3 (P/P-tRNA).
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E. Telomeric silencing assay at TEL7L in WT, sir4Δ, sir3T557I cells, cells overexpressing SIR3 (oeSIR3) or sir3T557I (oesir3T557I). Growth on 5-FOA plates reflects telomeric silencing.
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(J) Within accessibility-increased cis-regulatory regions in the late phase (brown dot in Fig 3E), 192 regions showed more than 2-fold increases in H3K27ac levels in CD48+ progenitor cells than in maintained HSCs (Venn diagrams). The GSEA plot represents the enrichment of the gene set related to these H3K27ac-increased regions within differentially expressed genes between CD48- HSCs and CD48+ progenitor cells. NES and q values represent normalized enrichment scores and FDR, respectively.
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E. Speed of ookinetes of the different lines. Numbers of analysed parasites are shown above the graph. Data pooled from three independent experiments (biological replicates). Violin plots show median (line) and quartiles (dashed lines).
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Co-depletion of STN1 and BRCA2 significantly impairs DNA replication. Scale bar: 50 µm. Results were from three independent knockdown experiments. In each experiment, >180 nuclei were analyzed per sample.
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C Fraction of expressed genes (genes with non-zero counts in DESeq2) were calculated which exhibit individual or combinations of differential gene expression (DGE), differential transcript usage (DTU) and/or alternative splicing (AS) events in the indicated conditions using the respective computational analysis (cutoffs are indicated). AS and DTU events were collapsed on the gene level. For DGE, p-values were calculated by DESeq2 using a two-sided Wald test and corrected for multiple testing using the Benjamini-Hochberg method. For DTU, p-values were calculated by IsoformSwitchAnalyzeR using a DEXSeq-based test and corrected for multiple testing using the Benjamini-Hochberg method. For AS, p-values were calculated by LeafCutter using an asymptotic Chi-squared distribution and corrected for multiple testing using the Benjamini-Hochberg method.
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(C) Cells stably expressing GFP-p62 display a cytoplasmic punctuate localization of GFP-tagged p62 similar to endogenous p62. Video microscopy of live cells demonstrated that the small, faint bodies (thin arrows) displayed directed migration, whereas the majority of the larger, intense bodies (thick arrows) were nonmigratory (Videos 1 and 2, available at http://www.jcb.org/cgi/content/full/jcb.200507002/DC1). A still image from Video 1 is shown here.
|
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D Epo-induced phosphorylation of EpoR, AKT and ERK of mCFU-E and BaF3-EpoR cells. Above each panel the number of growth-factor deprived cells examined per time point is indicated as well as the concentration of Epo applied for stimulation. To the left the position of the molecular weight marker is indicated in kDa and arrowheads indicate the position of the protein of interest. For the detection of the EpoR, 5x106 mCFU-E cells were stimulated with 2.5 U/ml Epo and 5x106 BaF3-EpoR cells were stimulated with 5 U/ml Epo. Cells were lysed, subjected to immunoprecipitation with anti-EpoR and were analyzed by immunoblotting using either anti-pTyr (pEpoR) or anti-EpoR (EpoR) antibodies. For the detection of AKT, mCFU-E cells were stimulated with 2.5 U/ml Epo and BaF3-EpoR cells were stimulated with 5 U/ml Epo. Per time point cellular lysates equivalent to 5x105 mCFU-E cells and 1x106 BaF3-EpoR cells were analyzed by immunoblotting using anti-pAKT and anti-AKT antibodies. For the detection of ERK, cells were stimulated with 50 U/ml Epo. Per time point cellular lysates equivalent to 8x105 cells were analyzed by immunoblotting. Immunoblot detection was performed with chemiluminescence utilizing a CCD camera device (ImageQuant).
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] |
I Basal and insulin-stimulated glucose uptake in control and FADD deficient primary isolated adipocytes. Data shown are from one experiment (n = 4 for each genotype), representative of a total of two independent experiments. Results are means ± SEM. *P = 0.0073 (Student's t-test).
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A RUNX1 expression levels in human CD34+ cells grown in pro-MK medium in a time course were measured by real-time PCR (n=4, mean ± SD).
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(B) Cox6a2 expression was effectively abolished in Cox6a2-/- PV+ interneurons. In addition, Cox6a2 knockout led to a decreased expression of Gad1 and Gad2 genes (n= 4 WT, 6 Cox6a2-/-). Two-tailed unpaired Mann-Whitney tests.
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We treated 30-day-old Mecp2 KO mice (n=10) and Mecp2 KO/HTTSA mice (n=10) with 5mg/kg FK506 three times a week by intraperitoneal injection and assessed them in various behavioral tests. (F) Forelimb strength of FK506-treated KO, FK506-treated KO HTTSA and vehicle-treated KO mice assessed by the grip strength test at P40 and P60 (Mann-Whitney test). Data information: *p < 0.05, **p < 0.01, ***p < 0.001, ns = not significant. Data are means ± SEM.
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(F) Cells treated with control shRNA and PPM1G specific shRNAs were lysed and blotted against specific antibodies.
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A. Schematic representation of human Nup358-IR region and the constructs used in this study. IR, internal repeats; SIM, SUMO-interacting motif; 1, 2, SIM1 and SIM2. Amino acids substituted in Ubc9 mutant are indicated with red asterisks.
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(D) Immunohistochemical staining of STXBP4 and YAP were performed in a kidney cancer tissue microarray, where the indicated regions in the box were shown three times enlarged. Brown staining indicates positive immunoreactivity. Scale bar, 100 μm.
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The representative FACS plots show the frequency of CD31+CD34+ EPCs at day 5 with or without SRSF2 depletion by administration of DOX from day 2.5 to 5.
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C-E. Cell cycle analyses by flow cytometry using BrdU/PI double staining show increased replication arrest in HUWE1-depleted 8988T cells in the absence of exogenous DNA damage treatment. C. Representative flow cytometry profiles of control and HUWE1-knockdown cells. R1-labeled region indicates mid and late S-phase cells (BrdU-positive, >2N DNA content), while R2-labeled region indicates S-phase arrested cells (BrdU-negative, DNA content between 2N and 4N). D. Quantification of S-phase cells. Percentage of cells in R1 region is shown. Bars represent the average of three independent experiments. Error bars indicate SD. P-value is 0.0014. E. Quantification of S-phase arrested cells. Bars represent the fold increase in the percentage of cells in R2 region, normalized to siControl-treated cells. The average of three independent experiments is shown. Error bars indicate SD. P-value is 0.0135.
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Gid9 (gray) subunits of the yeast structure are shown in the same orientation as the hGID complex. D. Spatial arrangement of yeast Gid4 with respect to WDR26 is shown in context of the hGID complex.
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F) Western blot analysis of Ub-K48 proteins in the soluble fractions of spinal cord lysates from mice plus or minus heat shock. G) Quantification of F. Each central line and error bar indicate mean +/- SEM of a biological replicates (n=3 biological replicates per group) Data information: * indicates p<0.05, ** indicates p<0.005, and *** indicates p<0.0005 by unpaired two tailed students t-test comparing male and female samples or samples with or without heat shock.
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(C) HEK293T cells were transiently transfected with Myc-tagged PAQR3. At 24 h after transfection, the cells were treated with normal medium (NM)，amino acid starvation (AS) or glucose starvation (GS), HBSS solution, or rapamycin (Rapa, 50 nM) for 4 h respectively. The cell lysates were then used in IP and IB.
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B, Example of a TOPflash reporter assay used to screen for DUBs regulating Wnt signalling. Cells were transfected in triplicates with the single siRNAs against the indicated DUBs or the positive control ZNRF3, and stimulated with control or Wnt3a conditioned media.
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A) mRNA fold-changes of Id1, endogenous (mouse) and transgenic (human) Zrf1, pluripotent markers Cdh1 and Oct4, the neural markers Pax6, Sox1, Olig2, HoxB1 and the epiblast/mesodermal marker T in control ESCs, Id1-Flag ESCs, or Id1-Flag ESCs transiently over-expressing Zrf1. Self-renewing conditions (d0), and day 3 and day 5 of neural differentiation were analyzed. SD is representative of three independent experiments. *P < 0.05 and ** P < 0.01 (paired t-test) represent comparison with Ctrl ESCs at the corresponding time point.
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Survival of yw flies, PGRP-LE112 flies, flies treated with Atg5-directed RNAi (hml-Gal4>Atg5IR) and control flies carrying hml-Gal4 (hml-Gal4>GFP), after injection of wild-type L. monocytogenes (a), Δhly L. monocytogenes (b) or E. carotovora (c) into adult flies. *, P 0.01 (Wilcoxon-Mann-Whitney test): P = 0.0024, Atg5-directed RNAi versus control (a), P = 0.0007, PGRP-LE112 versus control (a); P = 0.0055, PGRP-LC7454 versus yw (c). Data represent the average of four independent experiments.
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(B) Survival curve of humanized mice infected with 105 GRU EBV wt (n = 13), EBV S379A (n = 11) or EBV S457A/T465V EBV (n = 9).
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16HBE cells were stably infected with pSUPER, pSUPER expressing shCdc42, shARHGEF18, shSOS1 hairpins 1-3. All data are representative of 3 independent experiments. (c) Quantification of tight junction phenotype. >500 cells were counted per sample/experiment, across n=3 independent experiments (dots indicate individual data points). Error bars denote mean ± SEM. *, p = 0.0199; **, p = 0.0041; **** p = 0.0001.
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(F) Comparison between the effect of single factor knockdowns on ESC maintenance (n=4 independent experiments) and EpiSC resetting using experimental results
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MMP was monitored by TMRE fluorescence at every 1 h. FCCP (200 µM) and antimycin A (50 µM) were used as pretreatments for 30 min. Data were normalized by basal state of WT A549 cells (B-D) Data at 1 h (C), 5 h (D are presented as mean ± SEM; n = 4 (B-D) biological replicates, ****p < 0.0001, **p < 0.01, *p < 0.05 by paired T-test (C), or one-way ANOVA followed by Dunnett's multiple comparison test (D
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PARP1 and OAS1 compete for the 2'-hydroxyl of the terminal ADPr of PAR (shown in purple), which may result in "capping" of PAR chain termini with adenylates. The 2'-hydroxyl of the terminal adenylate (shown in red) can be further modified by OAS1 (OAS1 typically adds 2-3 AMPs), but presumably not by PARP1. 2'-positions modified by PARP1 are shown in blue. Besides the terminal ribose, PARP1 also attaches ADPr to the 2'-hydroxyl of the second ribose moiety of ADPr (shown in blue in parentheses), producing a branched PAR structure. We propose that 2-5A capping of PAR by OAS1 results in shorter and potentially more branched PAR chains (bottom).
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nanoCAGE sequencing was applied to determine transcription start sites in shERα BM67 cells. The number of detected transcription start sites (peaks) and RefSeq transcripts when sampling increasing number of RNAseq reads are indicated to evaluate the complexity of nanoCAGE RNAseq libraries.
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C-F Cell morphology of strains DWA350 and DWA307 following growth in LB at 30°C (C and D) and at 42°C in LB + 0.5% w/v xylose (E and F). Arrowheads indicate minicells. Cell membranes were stained with FM5-95. Insets show the corresponding phase contrast light microscopy images. Scale bar, 5 μm.
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(A) Schema of the analysis of gene expression in islets isolated from control larvae and larvae subjected to β-cell ablation. β cells were ablated by exposing nitroreductase (NTR)-expressing transgenic larvae to metronidazole (MTZ) from 3-4 dpf. Islets were then isolated, and their RNA extracted and analyzed by microarray. Out of the 470 genes that were upregulated more than 50%, 33 genes encoded proteins that harbored a signal peptide for secretion (according to the algorithm of SignalP). Excluding genes that encode enzymes or proteins with a transmembrane (TM) domain, we selected 11 genes for overexpression studies in zebrafishlarvae (C-E).
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E After transfection with the indicated siRNAs, cells from (D) were cultured for 2 weeks. The colonies formed were stained and photographed.F The area of the colonies in (E) was quantitated using an image analysis system and represented as percentage of the total area of the plate. *P = 0.024.
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F-H Viability assessment of RKO (F), MiaPaCa-2 (G) and HeLa (H) cells treated with DMSO, IMT1 alone and in combination with FG4592. Data are expressed as mean values ± SD of n=6, 5, 6 independent experiments for RKO, HeLa and MiaPaCa-2, respectively. Statistical significance was calculated with one-way ANOVA. Paired IMT1 vs IMT1 + FG4592 comparisons: RKO: **p<0,0028, MiaPaCa-2: **p= 0,0011, HeLa: *p= 0,0029.
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(D) Pull-Down of GST-CTC but not GST-CTD or GST-CTE (middle IB) by immobilized MBP-β2AR C-terminus (left) but not MBP alone (right), all of which were present at comparable amounts (bottom and top IBs, respectively). GST fusion proteins were detected by an anti-GST antibody and MBP fusion proteins by an anti-MBP antibody.(E) Quantification of (D) (***p<0.001, ANOVA).
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A Immunoblot analysis of the indicated phosphorylated (p-) and total proteins in whole-cell lysates of freshly isolated CD8 T cells from wildtype (WT) or Peli1 KO (KO) mice (6 weeks old). Data are presented as a representative blot (left) and summary graphs of densitometric quantifications of the indicated proteins (presented as phosphorylated/total protein ratio) based on three independent experiments.
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H. Frequency (in percentage) of pre-miR-181a-1 colocalization with vesicles double positive for organelle markers. Each data point corresponds to one axon. Total number of puncta, axons and independent experiments analyzed: 745 puncta, 23 axons, n=5 (CD63/pre-miR-181a-1/Rab7a), 577 puncta, 18 axons, n=3 (CD63/pre-miR-181a-1/LysoTracker). Values are median with interquartile range. Abbreviations: ns, not significant; CD63, CD63-eGFP or CD63-mRFP; Rab7a, Rab7a-eGFP or Rab7a-mRFP; pre-miR-181a-1, cy3-pre-miR-181a-1 or cy5-pre-miR-181a-1.
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] |
Volcano plots displaying the genes that are differentially expressed in immature enterocytes 2 upon SARS-CoV-2 infection of colon organoids. infected vs. mock infected cells The statistical significance (-log10 adjusted p-value) is shown as a function of the log2 fold change. MAST tests were used to generate P‐values, bonferroni multiple hypotheses correction was used to compute FDR values. Labeled dots in blue in all panels are gene names of selected differentially expressed genes between the compared two populations. Labeled dots in red in all panels are gene corresponding to interferon if detected.
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A TFIISmut shows upstream splice site selection. The splicing was assessed by RT-PCR and capillary electrophoresis in 3‐week‐old soil grown plants. The chart represents the average relative contribution of the mRNA forms found in the total pool of amplified products. The error bars represent ± SD (n = 3). To the right of the charts, the structures of the examined transcripts are shown. The black boxes, white boxes and black lines represent constitutive exons, alternative regions and introns, respectively. The black arrows show the locations of the primers. Representative splicing assays are shown.B Directionality of splice site selection in TFIISmut. For each type of alternative splice event, the black and white boxes show the contributions of opposite direction splicing events. The numbers represent the percentage of splice events supporting the direction of the splice site event change (also shown on horizontal axis). The numbers on the right‐hand panel represent the number of affected splicing events versus total number of splicing events analysed. The white bars represent downstream 3′ and 5′ splice site selection (3′SS/5′SS), exon skipping (ES) and intron retention (IR), while the black bars represent upstream 3′/5′ splice site selection (3′SS/5′SS), exon inclusion (ES) and intron splicing (IR).
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(D) Representative images of lungs, livers, intestines, and kidneys from mice 8 weeks after orthotopical injection of 22Rv1-M cells transfected with either Scramble-shRNA or ESM1-shRNA. Scale bar: 0.5 cm. Tumors were removed and weighed. Quantitative summary of tumor luminescence in different metastases measured in photons/second are shown.
|
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B. Ponatinib inhibits LPS-mediated cytokine release in THP1 macrophages in vitro. Data information, data are shown as the mean of three technical replicates. Error bars denote SEM.
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(B) MIA Paca-2 cells were transfected with HA tagged ArfGAP1 or RFP1 (control) for 4 days and then cell numbers were counted. Six replicated wells were counted each group. Columns represent Mean ± SEM. Student's t-test *P = 0.028.
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A Theoretical calculation of the rescaled radius of paraspeckles versus the rescaled transcription rate for the case in which the A and C blocks were deleted by CRISPR/Cas9 in the steady state. The graph is derived by assuming that NEAT1_2 is produced at a constant rate. The produced NEAT1_2 RNPs diffuse in the solution and the free diffusion is hindered by the attractive interactions between NEAT1_2 RNPs with the interaction parameter χ (we used χ = 1.0). NEAT1_2 was degraded at the constant rate k0. The radius was rescaled by the length scale $\sqrt{D/k_{0}}$ and the transcription rate was rescaled by the inverse time scale k0(D/k0)3/2/v0.
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(D) Treatment with 1,25D3 enhances co‐immunoprecipitation of p27KIP1 with CDK4 in U937 cells. Extracts of U937 cells were probed for p27KIP1 and CDK4, and immunoprecipitated with an anti‐CDK antibody and probed for p27KIP1 co‐immunoprecipitation.
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A-D. EV-producing cells expressing or not Cx43 (HEK293Cx43+ or HEK293Cx43-) were transiently transfected with shRNAs targeting hnRNPA2B1, hnRNPQ or non-target shRNAs, for 48 h. miR-133b levels were assessed in EVCx43+ and EVCx43- (A; n=6-12 biological replicates) and EV-producing cells (B; n=4-9 biological replicates). miR-509-3p levels were assessed in EVCx43+ and EVCx43- (C; n=6-15 biological replicates) and EV-producing cells (D; n=4-9 biological replicates). Data information: p-values were derived by Mann-Whitney test. Bars and error bars indicate mean ± SD in all graphs.
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(I) RNA ISH showing the co-localization between circLMP2A and miR-3908 in SNU-4th cells. circLMP2A probes were labelled with Cy3, and miR-3908 probes were labelled with FITC. Nuclei were stained with DAPI.
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(B) A standard uptake reaction was performed. After 70 min of incubation, the vacuoles were reisolated, washed, and treated with protease. The vacuoles were reisolated again, resuspended in reaction buffer without luciferase, and incubated for the indicated times at 27°C. Aliquots were withdrawn to assay the total luciferase remaining. As a control, luciferase was incubated in reaction buffer for the same periods of time and assayed for activity.
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(B) Diagram showing the percentage of up- and down-regulated genes in the RNA-seq experiment comparing NTC vs. shB DVL3 (left panel) and EV vs. DVL3-WT (right panel) in MDA-MB-468 cells.
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(b) Upper panel: Representative images of BOEC colonies from PBMC cultivation 10 days post-seeding. Dotted line in each image outlines a BOEC colony. Lower panel: Stabilized BOEC cultures after passaging of colonies (scale bar, 250 µm). (c) Proliferation doubling time for NAFLD and healthy BOECs based on passages 2 and 3. Sample sizes are n = 9 healthy, n = 7 NAFLD; with 3 biological replicates per donor. Box-whisker plots indicate median (middle line), 25th, 75th percentile (box) and the lowest/ highest data points (whiskers). ns, not significant (t-test).
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Cell cycle analysis by flow cytometry of BT474 and BTRH cells (50,000 events) treated with EV20/MMAF (10 nM) for the indicated times.
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E A working-model for the feedback regulation of synaptic activity. Prolonged neuronal excitation downregulates VSP34-mediated synthesis of endosomal PI(3) P. PI(3) P depletion causes the activation of Calpain 2 and Cdk5, resulting in repression of SV recycling, neurotransmission and kinetic impairment of SV endocytosis to limit SV re-supply and downregulate neuronal network activity.
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(J) Myeloid subtype (CD11b+Gr1mid), and c-Kit positivity inside myeloid fraction in BM (n = 3-5).
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MoLC were transfected with control (siCTR) or S100A9-specific (siS100A9) siRNA and checked for S100A9 expression by RT-qPCR (left) and western-blot (right). Shown is a representative experiment out of six. RT-qPCR data were represented as means of duplicates ± SD.
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(A) Cartoon representation of the NHE9 homodimer shown from the extracellular-side in the endosomal lumen (left), and along the membrane plane (right). Ion translocation 6-TM core transport domains (blue), dimerization domains (orange) and linker helix TM7 (grey), are coloured as in Fig. 1E with the respective helices numbered.
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A. RT-PCR products with divergent and convergent primers showing circularization of has_circ_0079480 and has_circ_0087391. cDNA, complementary DNA; gDNA, genomic DNA.
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C, D Quantification of the mitochondrial number and morphology in patient 1 (C) and the Mbtps1-cKO mouse model (D). (C) Left panel: n = 13 biological replicates of normal individuals, n = 10 biological replicates of patient 1. Middle and right panel: n = 121 biological samples of normal individuals and patient 1. (D) Left panel: n = 23 biological replicates of Mbtps1-loxP mice; n = 15 biological replicates of Mbtps1-cKO mice. Middle panel and right panel: n =113 biological replicates of Mbtps1-loxP mice and Mbtps1-cKO.
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G-J Time-controlled knock-down of metabolic enzymes in the dorsal compartment of ubi-AT1.03NL wing discs using the apGalts driver. Images of FRET efficiency in control (G), apGalts>PfkRNAi (H), apGalts>GapdhRNAi (I), and apGalts>Glo1RNAi (J) wing discs after RNAi induction for 48 h (G), 120 h (H, J), and 93 hours (I). A rainbow colormap is used to indicate the FRET efficiency levels. Scale bars = 50 µm. K Line graphs showing the FRET efficiency in the ventral and dorsal compartment of individual control (n=27), apGalts>PfkRNAi (n=7), apGalts>GapdhRNAi (n=10), and apGalts>Glo1RNAi (n=6) wing discs. Loss of Pfk, Gapdh or Glo1 in the dorsal compartment of the wing disc reduces the levels of ATP. Paired t-test, ns= not significant, **p≤0.01, ***p≤0.001.
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Analysis of p62/SQSTM1 levels in patient and control fibroblasts transduced with control or VPS16-expressing lentivirus under basal conditions and after 2 hours of serum-starvation.
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ChIP analysis of naïve WT or Stat4-KO CD4+ T cells cultured under Th0 or Th17 conditions in the absence or presence of LIF for 3 days. The cells were restimulated with IL-6 or LIF for 30 minutes, crosslinked with formaldehyde and immunoprecipitated with the anti-STAT3 antibody, followed by the amplification of the immunoprecipitated DNA by quantitative PCR with the p1-p10 primer pairs. The results are presented relative to the amount of input DNA.
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(h-k) Representative TEMs of wild-type and hlh-30 animals after 24 h starvation. IEC, intestinal epithelial cell; EPI, epidermis; BB, brush border; GON, gonad; BWM, body wall muscles, aj, apical junction; ld, lipid droplet. Scale bar, 2 μm.
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WT and C2βD1212A/D1212A mice were subjected to tMCAO followed by 24h of reperfusion. (A) Gene expression of TNFα, IL-1β and IL-6 in the cortex and basal ganglia (B. ganglia). The mRNA levels are given as the fold change normalized to rps29 relative to the corresponding contralateral (healthy) hemisphere. Data represent mean ± SEM (n=8-10 mice per group; *p=0.05; **p<0.01, Unpaired t-test with Welch's correction). Data represent mean ± SEM (n=5-7 mice per group; **p<0.01; Mann-Whitney test).
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G. The final circadian periods of Cry1-/- SCN slice double-transduced in complementary reverse orders did not differ between each other, p=0.7.
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(B) Convertase labeled perimCherry/cytoGFP bacteria (Green) exposed to C5b6MAC or Conv-MAC. Conditions were similar to those in (A), however C9-Cy5 was used to detect MAC pores (Red). 100 nM of C5 and C6 or C5b6 were used in combination with 100 nM C7, 20 nM C8 and 100 nM C9-Cy5. Conv + C5b6MAC and conv-MAC images were taken in separate experiments in which laser settings were adjusted to the staining intensity of C9-Cy5 to properly visualize pore distribution. Scale bars = 3 µm.
|
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(A) Nuclear extracts of murine intestinal crypts were immunoprecipitated with anti-SRCAP antibody or rabbit IgG followed by ADASDS-PAGE, sliver staining and mass spectrometry.
|
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(E) Immunoblot analysis of BBS4 expression in the brain lysates of Bbs4+/+, Bbs4GT/GT, and Bbs4KO/KO mice. β-actin staining served as a loading control. A representative experiment out of two biological replicates is shown.
|
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