EMBO/sd-character-level-ner huggingface dataset:
D-E) From one time-course experiment, ions, cytosolic proteins and total protein were extracted in parallel samples. The presented experiment is representative of 3 separate time-course experiments that were carried out (N=3). Representative experiment shown (n=4 technical replicates for [K+], n=3 technical replicates for the other traces). Blue lines highlight the antiphasic relationship between oscillations in cytosolic protein and potassium concentration. Mean±SEM, p-values from RAIN, red lines are fits by a damped cosine compared with a straight line (null hypothesis). Parallel PER2::LUC recordings were also performed and plotted as a phase marker.
PI uptake assay from IFNγ-primed or untreated THP-1 ΔCASP-1 cells transfected with indicated siRNA and infected with STm-GFP for 4 h. Area under the curve (AUC) from real-time assay plotted as mean ± SEM from n = 3 independent experiments. Schematic on right shows overview of the pathway leading to caspase-1 and caspase-4 activation.
representative images (F) of body composition from male mice after 11 weeks of AKG supplementation (n = 9 per group).
(p-r) Cytospins of vaginal fluids from IL-17F-deficient (p), IL-17A-deficient (q) and C57BL/6 (r) mice intravaginally infected two days before with C.albicans SC5314 blastospores. Note the presence of hyphae in the vagina of IL-17F-deficient mice after May-Grünwald-Giemsa staining (scale bars, 20 μm). Shown is one representative experiment out of three.
wild-type (WT) (n=6) or Stat4 knockout(Stat4-KO) (n=6) mice receiving intraperitoneal injection of PBS or LIF during challenge with 3% DSS. Macroscopic changes in the colon of the mice on day 10 of colitis induction Comparison of the colon length in the mice on day 10 of colitis induction
(h) Cells of the indicated genotype were starved for the indicated times. Viability was determined as in e,f. Data represent mean ± s.e.m. of five independent experiments.
(A) Scheme of parallel analysis of codon effects (PACE). Codon tag reporter mRNAs were pooled as a library and coinjected into fertilized zebrafish eggs. Embryos were collected at 2 and 6 hpf and subjected to RNA-Seq analysis. Reads mapped on each codon tag region were quantified to calculate each codon's effect on mRNA stability.
(D) Fluorescent microscopy indicates that both Red1‐GFP and Red1H637I‐GFP form nuclear dots. Bars, 2 μm.
(B) Phenotyping of the same mice, presented in the same order, inoculated i.n. with 0.3 × 105 TCID50 of SARS-CoV-2 at the age of 5-7 wks and viral RNA content was determination in the indicated organs at 3 dpi by conventional E-specific qRT-PCR. Red lines indicate the qRT-PCR limits of detection.
The domestication of the PIF/Harbinger DNA transposon gave rise to two host genes, IDAP1 and IDAP2, which encode a putative DNA transposase and a myb-like DNA-binding protein, respectively. IDAP1 and IDAP2 form a complex in the nucleus where they cooperatively recognize target loci with TE-like structures and recruit the histone acetyltransferase IDM1 to these target loci. Since a previously identified protein MBD7, which recognizes highly methylated regions, also regulates IDM1 targeting, the joint action of MBD7, IDAP1 and IDAP2 may facilitate the targeting of the IDM1 complex to specific loci with multiple epigenetic features. The IDM1 complex then acetylates H3K18 and H3K23 at those loci and facilitates active DNA demethylation mediated by ROS1.
Representative H&E-stained histological sections of ear and skin tissue of Malt1fl/fl K5cre+/+ CARD14E138A+/+ and Malt1fl/fl K5creTg/+ CARD14E138ATg/+ mice (scale bar represents 100 μm).
Flow cytometry analysis of HeLa and TRIM16KO cells stained with Annexin-V/Propidium Iodide (double staining), untreated or treated with (C) As2O3 (2.5 µM, 4h)
A Up, Representative western blot from whole cell extracts showing H2AX protein levels in wt and junD-/- fibroblasts (Left) or in wt and Nfe2l2-/- fibroblasts (Right). Two representative clones, with their corresponding controls, are shown per genotype. H2B was used as negative control. Down, Bar plot showing H2AX protein levels as assessed by densitometry analysis of western blots (as shown above). n ≥ 3 independent experiments.
(C) Single and multiple COX regression analysis of HNSCC data sets from the TCGA for high risk (HR) of patients' death as a function of levels of HSD17B7 expression, either as a single variable or after adjusting for gender, ethnicity, age or all three together. Only HNSCC samples from patients of White (Caucasian) versus Black ancestries were used for this analysis. Cox proportional hazards regression model was fitted with the R function coxph.
E Cytocochleograms representing the percentage of surviving hair cells in four cochlear regions located at 1.1, 2.6, 3.5 or 4.1 mm from the cochlear apex provided from saline-treated p53wt mice (black bars), CDDP-treated p53wt mice (green bars) or p53-/- mice (blue bars), after 5 days (n=5 per group). Data are expressed as mean ± SEM. Kruskal-Wallis test followed by post hoc Dunn's test (**P ≤ 0.008, p53wt+CDDP, d5 vs. p53wt+saline, d5 or p53wt+CDDP, d5 vs. p53-/- + CDDP, d5).
ISCts midguts expressing YFP alone (control), or expressing two non-overlapping EcR-RNAi, and quantification of the number of YFP-positive cells (yellow). The graph also plots the number of GFP-positive cells in esgts midgut expressing GFP alone (ctrl), or expressing EcR-RNAi#1, EcR-RNAi#2, and mcherry-RNAi as an additional negative control (see EV2B).
D) Western blot analysis showed an upregulation of cytochrome C in the cytoplasmic fraction after bortezomib treatment.
Eight-week-old male WT and DOCK5-/- mice were fed a standard diet (SD) or high-fat diet ( HFD) for 3 months. Locomotor tolerance.
(C-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa cells. Cells were treated with (C) 0.5 nM LLO for the indicated times. Levels of PI incorporation by untreated cells were subtracted from all LLO-treated samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p<0.5, **p<0.01, ***p<0.001.
(B) Top, cells were lysed after 3 h exposure to infectious agents or at the completion of the infection phase. Intracellular mycobacteria were harvested and assayed for mycobacterial growth at day 0 and day 7. Bottom, MDM were harvested and stained for mycobacterium. Histograms are shown for a representative donor.
C Colonization patterns of GFP-Pst DC3000 (AvrRpt2) in wild-type and palQ plants after PA and CA pretreatments. Data information: Leaves were inoculated with GFP-labeled bacteria at 108 cfu/ml for 2 days. M, mock; PA, piperonylic acid; CA, coniferyl alcohol; IS, infected site; UIS, uninfected site. White dash lines indicate the boundary between IS and UIS. Scale bars, 100 μm
Immunoblotting analysis of proteins in control and Rab22A-, BLOC-1-, BLOC-2-depleted HeLa cells. *, non-specific bands. Protein band intensities were quantified and indicated on the gels.
Confocal whole-mount immunofluorescence analysis (WM-IF) of Kit+ cells in wild type and Sl/Sl E10.5 AGM (32-36sp). Images are 3D projections from 400μm-thick Z stacks, and are representative of 14 wild type and 11 Sl/Sl embryos analyzed. Total numbers of Kit+ cells (white) in the dorsal aorta were quantified and showed a significant reduction in Sl/Sl compared to wild type (p=0.008). CD31+ vasculature is shown in green. Arrowheads: hematopoietic cell clusters. Scale bars: 100μm. Quantification of WM-IF in (A), showing absolute numbers (±SD) of clusters of indicated size and separately shown relative to location. A total of 7 wild type and 7 Sl/Sl embryos were counted.
Boxplots showing fold changes in the histone mark association of piRNA target or non-target TEs based on ChIP-seq upon Piwi-KD (Definition of piRNA target and non-target TEs are described in Fig EV1E). Boxplot whiskers, box, and central band show maximum, third quartile, median, first quartile, and minimum, respectively (n=10 for piRNA target TEs, n= 80 for non-piRNA target TEs). P-values were calculated by Wilcoxon rank-sum test.
(C) Analysis of the artificial piRNA levels in DDX43-knockdown BmN4 cells. Left: Artificial piRNA and Flag-Siwi were detected by northern blotting and western blotting, respectively. Right: Quantification of artificial Siwi-piRISC formed by the ping-pong cycle pathway. Data represent the mean+/- standard deviations, n = 3 independent experiments. *p < 0.05 as determined with the t-test.
H. pDPC or a plasmid containing M.HpaII crosslinked to ssDNA (pDPCssDNA) (Larsen et al, 2019) was incubated with SUMO E1 and E2 enzymes and SUMO, in the presence or absence of recombinant xPIAS4. Samples were recovered by DPC pull-down and blotted against M.HpaII as in (A).
DNA fiber analysis of HCT116 cells with STN1 knockdown with and without mirin treatment.
Expression pattern of canonical markers used for identifying bladder cell types.
A Venn diagramm representing overlap of hCFU-E proteome from three independent healthy donors. In total 6,925 proteins were quantified
(H) Exogenous MHCI presentation of synthetic SKL8 peptide pulsed on XBP1fl/flIRE1fl/fl treated or not with 4µ8C, XBP1ΔDC IRE1truncDC and XBP1ΔDC BMDCs assessed with the B3Z T cell hybridoma. Bar graphs depict mean ± S.E.M (n=3 mice, one representative experiment from 2 independent experiments). Unpaired Student T-test, *: p<0.05, ns (p>0,05) when p values are not identicated.
(g) Brain lysates from mice expressing mutant huntingtin (Tg) or control (Cont) littermates were immunoprecipitated with antibody to mTOR and immunodetected with an antibody recognizing the polyglutamine tract (IC2). Htt, huntingtin
D) The velocities of several UIS4‐ or IBIS1‐positive features [tubules (left), elongated membrane clusters (center) and vesicles (right)] were measured over time, and the peak velocity of each was plotted. Plotted data was derived from multiple imaged infected cells: For IBIS1‐positive tubules data is derived from three infected cells and for UIS4‐positive tubules from 13 infected cells. Elongated membrane cluster speeds were analyzed in at least five infected cells for both UIS4 and IBIS1, and vesicle speeds were analyzed in at least 12 different cells for both protein markers.
A. Gene structure of ApoER2 exons 18-20 and the resulting RNA and protein products. Boxes are exons and lines represent introns. Diagonal lines represent splicing.
E) Representative images of prometaphase chromosomes from HeLa cells co-transfected with H2A.Z.2 siRNA and each of the constructs in D (green). Scale bar: 5μm. F) Quantification of the percentage of cells with micronuclei from experiment (E). The error bars represent the SD of three biological replicates (Control si N=887; H2A.Z.2 si N=1005; H2A.Z.2 si + wt N=760; H2A.Z.2 si + KR N=479). Data sets were statistically analysed using Chi-square test.
(B) B16Bl6 tumor growth after daily p.l. treatment with 7µg mTNF in C57BL/6J wild-type (WT), TNF-R1-/-, conditional TNF-R1 reactivation knockout (p55cneo/cneo), or p55cneo/cneo mice with Cre expression in endothelium (Flk1Cre) or all cells (DelCre). Tumor growth is shown as mean TSI + SEM (n = 7 for WT and Flk1Cre, 8 for DelCre, 9 for TNF-R1-/- and 10 for p55cneo/cneo). The line under the graph represents the treatment period.
(d) The stable Atg5 knockdown H1299 cells was further transfected with a control plasmid, Flag-FoxO1(WT), or Flag-FoxO1(ΔDB), and the percentage cell loss was quantified by flow cytometry at 48 h after transfection. Data in d are means ± s.d. (n = 3).
b, Mean phase durations in RPE, U2OS, and H9 cell lines. Error bars represent standard deviations.
(I-K) B6 BMDMs were transfected with miR-342-3p inhibitor or Socs6 siRNA, followed by stimulation with Mtb or z-VAD (20 μM) for 24 hours. Cell death mechanisms (I), cell viabilities (J), Mtb growth rates (K) were analyzed respectively. Data are shown as the mean ± s.e.m. of n = 3 biological replicates.
D) Schematic (top panel) illustrating the requirement for SAM transport across the mitochondrial inner membrane by Sam5 for PC production by Pmt in the mitochondrial matrix (MM). Lipids can be produced by the Kennedy pathway (red) independent of Sam5 activity. Transposon insertion maps generated in the UCSC genome browser for SAM5 for the library where PC is produced in the MM in either KennedyON or OFF conditions (bottom panel).
Representative images of small intestine crypt culture (day 2). Arrows mark the surviving cysts (C). Quantification of numbers of cysts per culture well (D)(n=4-5 mice/genotype).
A U2OS cells were transfected with the indicated siRNAs. Seventy-two hours later, cell lysates were prepared and proteins from lysates were subjected to western blot using the indicated antibodies.
Overexpression of WT OGA, but not catalytic-inactive OGA mutant, abated the O-GlcNAc levels of TDP-43. OGA protein levels were examined by immunoblotting.
G-J. New synaptic formations (VGlut1+) from regrowing axons are shown beyond the lesion site after injection of AAV-HDAC3mut. (G) Scale bar 200 μm, (H-J) High magnification insets depict co-localization of Dextran and vGlut1 staining. Scale bar 50 μm.
G. Quantitation of LAMP-1 gold particles per lysosome. VPS41S285P/R662* lysosomes have significantly less LAMP-1 then control and parental cells. >53 Lysosomes per condition were quantified. Similar results were obtained for LAMP-2 (Appendix Fig S2).
(D-E) Genome-wide distribution of BRG1 around all PRBs or PRBs associated to up, down or non-regulated genes (Panels D and E, respectively). The overlapping between PRBs and BRG1 is also shown (Panel D, inset).
A, Representative images of mouse small intestinal organoids generated with empty (Non-edited) or USP42gRNA containing CRISPR-concatemers, and cultured for 3 days in matrigel with the indicated growth factors, or the Wnt secretion inhibitor IWP-2. EN, EGF and noggin. Note that knockout of Usp42 (Usp42 gRNAs) rendered the organoids insensitive to RSPO1 withdrawal. Scale bar = 1 mm.
(B) Cells were treated with DOX to induce Xist expression for 1h and time-lapse imaging was performed with images acquired every 15 min. Maximum intensity projection images are shown with elapse time (hh:mm). Arrowheads mark Xi accumulating Xist RNA. Scale bar = 5 μm.
B) CAL27 cells transduced with doxycycline-inducible shRNAs targeting ADAR1 or GFP (negative control) were treated with doxycycline and transfected with two independent siRNAs targeting LGP2 (siLGP2 #1 or #2) or a control siRNA (siCtrl). To determine cell confluency at 120h post-transfection, cells were fixed, stained with Crystal Violet, and imaged. Images of a representative experiment are shown (n=3). C) Crystal Violet was extracted from stained cells (B) and the dye intensity was quantified using a colorimetric assay (OD590). OD590 values of doxycycline-treated cells were normalized to the OD­590 values of untreated cells. Quantification of data from three independent experiments is shown as mean ± s.d.. Statistical analysis was performed using ordinary two-way ANOVA with Tukey's post hoc test. ns, not significant; *, p<0.05; **, p<0.01; ****, p<0.0001.
Box plots showing Log2 FC ERS/Control in mouse liver (3 mice per group) (H) for LIVER-ID genes, UBQ genes and other genes. Box plots are composed of a box from the 25th to the 75th percentile with the median as a line and min to max as whiskers. One-way ANOVA with Welch's correction and Dunnett's Modified Tukey-Kramer pairwise multiple comparison test was used to assess statistical significance, *P < 0.05.
A-B Rectal temperature was measured at 24°C (A), and rectal temperature was monitored for 6 hours during acute cold exposure at 4°C (B) in Cdk4flox/flox (n=9) and Cdk4flox/flox Ucp1-Cre mice (n=9).
(b) Schematic of serum treatment of GC-1 cells. On day 1, cells are transfected with PPRE and luciferase normalization plasmids. Serum is mixed in culture medium at 10% concentration and exposed to cells on day 2. Cells are harvested 24h later (Day 3) and luminescence is measured.
H (Left) Heat Map of up and down-regulated genes in the p38 MAPK pathway (WP400) in Myf6-KO and WT satellite cells. (Right) Gene set enrichment analysis of p38 MAPK pathway genes. In each plot, the blue curve represents the gene set enrichment score profile (Subramanian et al., 2005) across p38 MAPK pathway genes that are ranked by their differential expression. The grey curve represents the null expectation. P-values are based on permutation test (10,000 permutations).
E. SHARPIN protein level after silencing with negative control siRNA or SHARPIN siRNA in wt MSFs. Tubulin was used as loading control.
G Intestinal worm burden 13 days post infection in Dusp5+/+ Rag2-/- (open circles) and Dusp5+/+ Rag2-/- (grey squares) mice. Data shown in (G) are cumulative of three independent experiments.
E. Accumulation of COPI-positive vesicles. 10 nm gold particles mark COPI. PM: plasma membrane, nuc: nucleus. Scale bar 100 nm.
D. Filament severing at single cofilin domains. Time t=0 is defined for every domain as the frame on which they nucleate. N = 60 (1 experiment) and 75 (2 experiments) domains of WT and S3D-cofilin-1,respectively. The severing dynamic was measured at 10 nM WT eGFP-cofilin-1 and 1 µM eGFP-S3D-cofilin-1. P-value = 0.98 (log-rank test). Data information: All lines are survival fractions calculated from the experimental data 95% confidence intervals are shown as shaded surfaces.
(C) Live imaging of C. elegans body wall muscle cells expressing TOM70::GFP. Depletion of DRP-1 or UNC-61 caused an increase in mitochondrial elongation and network connectivity, which did not increase upon combination of DRP-1 and UNC-61. Insets represent a twofold magnification. Scale bar: 10 µm.
E. Population frequency of the variant over time in two different alternating environments. Black line, profile of population frequency of the variant, where, at the moment in which the first mutant cell appears, the environment positively selects it; however, in the subsequent environment the selection is negative. Grey line, profile of population frequency of the variant, where, at the moment in which the first mutant cell appears, the environment negatively selects it; however, in the subsequent environment the selection is positive. The area of the plot is divided in grey (E1) and white (E2) sections to indicate the fluctuating environment with positive and negative S.
(B) Immunofluorescence confocal microscopy analysis of LSD1 (green) in LSD1 KO MGC-803 cells (left panel) and LSD1 KO MKN-45 cells (right panel) incubated with 20 μg/mL Con sEVs and KO sEVs for 12 h. The cell membrane was stained with PKH26, while the nuclei were stained with DAPI. Scale bar = 100 µm.
(C) Quantification of total lung hydroxyproline in mice treated with vehicle and barasertib. *P< 0.05, ***P < 0.0005, 1-way ANOVA, (n=7-8 mice/group).
NFAT protein expression in nucleus and cytoplasm of gastrocnemius 0.5 h or 3 h after i. p. injection of 15 mg/kg succinate in C57BL/6J mice (n=4).
(E) T47D-MTVL cells were untreated (0) or treated for 5 min with 10 nM R5020 and subjected to ChIP assays with a-PR, a-LSD1, a-HP1y and H3K9me3 specific antibodies. The precipitated DNA fragments were subjected to PCR analysis to test for the presence of sequences corresponding to the BCAS1, KRT23 and IGFBP5. The values represent the mean and standard deviation from 3 experiments performed in duplicate. * P-value < 0.05.
F-I Delivery of anti-miR-210 (N = 5/group) decreased endothelin-1 in hypoxic mouse lung tissue, *P = 0.0198 (F). As a result, in contrast to anti-miR-Control (N = 8), endothelial-specific anti-miR-210 ameliorated the elevation of RVSP (N = 6), **P = 0.0024 (G), and pulmonary vascular remodeling (N = 6/group), **P = 0.0021, *P = 0.0117 (H-I).
A. Domain structure of human WDTC1 with locations of the H-box and WDXR motifs indicated. Alignment of WDTC1 H-box motifs in different species (boxed in grey) and bolded orange represents key residues contacting DDB1 [13]. Alignment of DWD boxes in different DWD proteins (bottom right) with WDXR submotif indicated; tandem DWD boxes are shown for WDTC1 only.
cortex glial overexpression of htlACT but not InRwt or EgfrACT causes an increase in glial cell (Repo+) numbers quantified in (K) (n=10, 10, 10; 7, 12 brain lobes)
Aliquots from agonist-treated samples shown in Figure 2 were deglycosylated with PNGaseF, run on SDS-PAGE and immunoblotted with antibodies detecting arrestin (upper panels, α-HA) and the GPCRs (as indicated, CRF1R is equipped with a N-terminal FLAG, V2R carries a C-terminal 1D4 epitope).
Schematic strategy for generating PAX6 knockout in hESCs. The exon 8 is shared by all the isoforms and was replaced by the PGK-Puromycin element. The primers indicated in the panel are used to detect the gene knockout.
C Phalloidin staining depicting F-actin organization. Images are maximum intensity projections of 3D stacks. Scale bar: 3 µm. D In vivo actin network deviation indexes. Data are presented as mean +/- SD (n = 30 for all conditions). *P<0.05, ***P<0.001 (Brown-Forsythe and Welch ANOVA tests, with Dunnett's T3 multiple comparisons tests). E Polarity Indexes. Data are presented as mean +/- SD (n = 30 for all conditions). ***P<0.001 (Kruskal-Wallis test, with multiple comparisons).
(D) Growth curves of Nlrp3NeoR-A350V/WT (n=8) and Nlrp3Mac-A350V/WT littermates (n=10). Data information: Statistics were analyzed by (D) student t-test Error bars represent means ± SD. * p<0.05; ** p<0.01; *** p<0.001.
(G) Model. Levels of the cytosolic catalase Ctt1 increase when activity of mitochondrial redox enzymes is impaired, leading to an increased cytosolic capacity for H2O2 removal.
DICER-KO B cells were co-cultured for 24 hours with OTII-derived T cells in the presence or absence of OVA. the distance from the CD4+ T cell MTOC to the contact site with the B cell MTOC-B-cell distance was measured with Imaris analysis software.
Kinetics of β-cat acetylation by Tau. Tau acetylates β-cat in concentration- (F) and its acetyltransferase activity domain-dependent manner. Michaelis-Menten parameters were determined using Graphpad Prism 6 (n = 3 from three independent experiments).
(G) RT-qPCR of ZIKV RNA in hNSCs incubated with vehicle or 100 nM rapamycin, 20 μM chloroquine, 10 nM bafilomycin A1, or 5 mM 3-methyladenine for 24 h. Mean ± SEM of 3 biological replicates. *p < 0.05, ***p < 0.001 by Student's t test.
MCF10A WT or two independent clones for MAVS, RIG-I KO cells were pretreated with DMSO or AZD6738 (250 nM) for 2 hours, and then irradiated with 20 Gy, 3 days later, (B cells were harvested for real-time quantitative PCR instead of immunoblotting. IFNB1 mRNA level was measured by real-time quantitative PCR. Data are presented as mean + standard error of the mean of three biological replicates.
F, qPCR of RAD51 expression measured in NS, BT308 diff, and astrocytes at the indicated time-points after IR (5 Gy, fold vs. non-irradiated cells, ctrl). Data are represented as mean ± SEM.
I Cytoplasmic and nuclear proteins were extracted from WT and SNX10 KO Caco-2 cells treated with or without Tolimidone (10 μM), and the indicated proteins were analyzed by immunoblots.
A. Heatmap profiles of BAZ2A bound regions in PC3 cells and the corresponding signals of input, BAZ2A-BRD mutant (Y1775F), H3K14ac and H3K27ac. Data were ranked to BAZ2A-binding in PC3 cells.
B. qPCR analysis of Cyp1a1 expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 24h as indicated. Cyp1a1 expression was normalized to Hprt1. Cyp1a1 expression among groups was normalized to Medium DMSO. n = 2 independent experiments; mean ± range.
K. Nitrite concentration in heart tissue (n=4/group) Bar graph represent mean±SD
Phase contrast images of embryoid body outgrowths of indicated genotypes after 12 days in differentiation conditions (N2B27 + 10% serum). Scale bars represent 100µm.
Graphical representation of the results of the optokinetic tracking assays reported as fold change of cycles/degree. Visual acuity is preserved in miR-181a/b-1-/- rotenone-injected mice with respect to controls at both one and two weeks after injection. N=10.