EMBO/sd-character-level-ner huggingface dataset:
Selected abscission-related gene expression levels in (C) WT and proIDA::CDF4RNAi lines by using qPCR analysis. The expression of these selected genes in the wild-type plant is given as 1. The relative expression level represents only the level of expression of the gene relative to the wild type. ACTIN2 was used as the internal control. Three independent experiments were conducted. Values are given as mean ± SD, n=3. *p<0.05 by Student's t test.
F Representative images of ALP, ARS and Van Gieson's staining of MSCs obtained from Prx1-Cre;Usp34f/f and littermate control mice
C. Averaged percentage of HeLa cells (determined from 100 cells in each experiment) with different types of mitochondria determined by MitoTracker (Red) staining when transfected with GASZ, its SAM/ZIP deletion mutant, or GASZ with MLS mutation.
H. SDS-PAGE analysis of PICUP cross-linked Aβaggregates visualized by silver staining.
F FUNDC1‐knockdown MEFs were transfected with FUNDC1‐Myc or FUNDC1-Myc (S17A) for the indicated times. Cell lysates were used for immunoblotting.
Model depicting how physiological signals such as growth and fasting-feeding are integrated at the ER membrane via the Sel1L-Hrd1 ERAD complex in liver to regulate CREBH protein turnover at the ER membrane, and Fgf21 transcription and metabolic states in the body. New findings elucidated by this study are highlighted in red arrows.
(b) Electron micrographs of striatal cells from mutant huntingtin knock-in (111Q-htt) and wild-type (7Q-htt) mice.
N Morphology of the human PC at weeks 18-19 (H&E staining); (N') is magnification of the boxed region in (N). DC, deciduous canine; PC, permanent canine; IEE, inner enamel epithelium; OEE, outer enamel epithelium. Mesenchyme between DC and PC is indicated with a green arrow.
B Rescue of WNV-poly(A) virus. A pool of in vitro transcribed recombinant RNAs with different lengths of internal poly(A) tract were electroporated into BHK-21 cells, and the supernatants were blind passaged in BHK-21 cells for three rounds (P1-P3) followed by propagating in Vero cells. IFA detection of E protein using 4G2 antibody at different passages was shown.
(E) Lysates from HeLa cells stably expressing GFP-WIPI2B were incubated with agarose beads coated with PI, PI(5) P, and PI(3) P, eluted with SDS-PAGE sample buffer, and recovered proteins were assessed by western blotting using antibodies against GFP. Uncoated beads and lysates from HeLa cells stably expressing GFP alone were used as internal controls.
Quantification was performed to determine average size of positive vesicles per cell (ImageJ software). Nuclei are shown in blue (DAPI). Data represent mean ± SEM of cell fields randomly selected (n=13-20 for (C) and n=11-20 for (D)). Data are collected from at least 3-4 independent experiments. For violin plots (D), thick lines represent median and thin lines interquartile; ***p<0.001; **p<0.01; *p<0.05, unpaired t-test or Mann-Whitney, as accordance.
Tg[fli1:eGFP; vhl-/-] & Tg[fli1:eGFP] zebrafish embryos (5 days post-fertilisation) demonstrate excessive angiogenesis & increased expression of HIF target genes (scale bars: 100um).
(K-R) C2C12 cells were transfected for 24 h with GFP‐Jumpy C330S (Jumpy CS) and tdTomato‐LC3 (LC3), fixed and immunostained with anti‐Atg12(M) antibody. Jumpy CS (green), LC3 (red) and Atg12 (white in L, P or blue in N, R). Boxed areas (K-N) are shown at higher magnification in the corresponding panel below (O-R). White arrows indicate colocalization among Jumpy CS, LC3 and Atg12, yellow arrow indicates colocalization between Jumpy CS and LC3 but not Atg12, blue arrow indicates colocalization between Jumpy CS and Atg12 but not LC3.
A. HeLa cells stably expressing CHMP4B-eGFP were transfected with the mCherry-Galectin3 plasmid. 24 h later, cells were infected with WT Coxiella burnetti. Live-cell imaging started 24 h post-infection and several time points are indicated during the next 24 h of observatio Arrows indicate Coxiella-containing vacuole (DRAQ5 labeling) becoming positive for CHMP4B-eGFP and mCherry-Galectin3. Data information: Scale bars: 50 μm
Upper panel: In a wild type situation, Mif2 does not bind to the Mtw1 complex in the nucleoplasm as a consequence of adopting an auto-inhibitory conformation. Binding of Mif2 to the Cse4 nucleosome allows a conformational change that promotes its interaction with the Mtw1c and thus triggers full kinetochore assembly. Lower panel: Exchanging the N-terminus of Mif2 with the N-terminus of Ame1 prevents the adoption of an auto-inhibitory conformation. As a consequence, Mif2 forms interactions with the Mtw1c already in the nucleoplasm. These interactions might promote the assembly of soluble kinetochores that are able to bind to microtubules or chromatin away from centromeres and are therefore not available for proper kinetochore assembly on Cse4 nucleosomes.
(E). Primary chromaffin cells were transduced with lentivirus containing the gene encoding wild-type MUNC18-1 or different mutants. These cells were stimulated with 100 nM AngII. The amperometric spikes were detected with electrochemical experiments. Typical amperometric traces are shown.
(B) Liver lobes or gallbladders harvested from 7-day or 1-year old mice were minced and cultured in Matrigel in the presence of R-spondin 1 and noggin. Phase contrast microscopy images were acquired one week later. Scale bar: 200 m.
MT polymerization out of Tau:PEG and Tau:PEG:RNA condensates. Addition of tubulin-Alexa647 (5 μM, 10:1 unlabeled:labeled tubulin) and GTP to Tau-Dy488 (25 μM) diluted in BRB80 polymerization buffer induces MT polymerization. Images taken 30 min after addition of tubulin show thin partially curved MT bundles in Tau:PEG system, and thick bundles attached to persisting Tau:RNA condensates in the Tau:PEG:RNA system. Scale bar=5 μm. Cross-sectional intensity plots (line plots) of MT bundles differ between Tau:PEG (yellow/red line plots) and Tau:PEG:RNA (blue/green line plots) systems. Four line plots at random positions are shown per condition.
D. Quantification of the number of secondary tumours (diameter >300 µm) in the murine brain for the indicated treatments and tumour models. BT12 (parental (wt, Ve n = 9, Cle n = 12) and control shRNA infected (Ve n = 5, Cle n = 5), and BT13 (Ve n = 10, Cle n = 9). Data are represented as mean ± SEM. ****P < 0.0001, two-tailed, nonparametric Mann-Whitney's U-test.
AAV-Cre (5×1012 v.g./ml) mixed with AAV-hTau or AAV-eGFP (1.13×1013 v.g./ml) were stereotaxically injected into the hippocampal CA3 of 3-month-old STAT1flox/flox mice. One month later, downregulation of STAT1 was confirmed by Western blotting
J Relative intensity of PI(3) P in neuronal somata (MAP2+) or synapses (Syp+) from the images in I. N ≥ 4 independent experiments (≥ 60 images per condition); Student's t-test. Data information: Data presented as mean ± SEM n.s. not significant; *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001
A Biosynthesis pathway of Moco with all stable intermediates. Gephyrin G- and E-domain catalyze the last two steps as depicted.B In vitro Moco-synthesis assay using 150 pmol purified 6His-tagged gephyrins. D580A is an activity-deficient gephyrin mutation previously identified in Moco-deficient patients (Reiss et al., 2011). Assays without the addition of gephyrin (-gephyrin) or molybdenum (-Mo) served as internal controls of the assay (see also (Belaidi Schwarz, 2013)).C Experiment as in B but with pre-incubation of 6His-gephyrin/G375D in a 1:1 ratio to simulate the heterozygous mutation. n = at least 3 with two independently purified protein batches. Results are expressed as mean ± SEM.
(C) Western blot showing the levels of PP2A-A, PP2A-B, PP2A-C and H2A in the nuclear fraction of RPE cells treated with DMSO (Control), 0.5 μM Okadaic acid for 2 hrs, 25 μM P22077 for 4 hrs and 25 μM BAY 11-7082 for 2 hrs.
HGSOC organoids show differential response to carboplatin treatment, confirming patient-specific sensitivity of the cultures. Cell viability assay was performed after 5 days of treatment with different concentrations of carboplatin on mature organoids from three different donors. Data represent mean ±SD of technical triplicates.
(F) PC3 cells which stably express HA-mChd1-ERT2, were transfected with either mock or siCHD1. After 24 h of transfection cells were treated with 4-OHT for 24 h to induce HA-mChd1-ERT2 nuclear translocation. Western blot analysis of chromatin fractions for CHD1, ERT2 (mChd1), CtIP and RAD51 shown in Figure EV4O were analyzed by densitometry using ImageJ. The relative quantification for the indicated proteins is shown in the graph. See also Figure EV4A-EV4P.
Liver triglyceride (TG) content (ASK1F/F n=7 mice; ASK1Δhep n=7 mice) and quantification of Sirius Red positive area in livers (ASK1F/F n=7 mice; ASK1Δhep n=7 mice) of 15 months old chow-fed mice. Values are expressed as mean ± SEM. #
The relative expression of type I interferon-stimulated genes (ISGs) in sorted DN, DP, 4SP and 8SP thymocytes isolated from WT mice. Values represent the relative gene expression normalized to GAPDH mRNA and are displayed as the mean ± SEM (n = 3; Mann-Whitney U-test, *p < 0.05). The relative expression of ISGs was normalized against the level of expression in DN thymocytes (DN values set to 1).
B. Vs-treated U1 cells were exposed to PMA and viral activation was measured as a function of time, by gag RT-PCR. U1 cells were also treated with Vs or PMA alone.
Relative mRNA expression of Rev-erba (D) and Gdf15 (E) in quadriceps, liver and eWAT (WT day n=9, WT night n=5, TG day n=20, TG night n=12). Data shown are from male wild type (WT) vs. Ucp1-TG (TG) mice sacrificed at day (10am) or night (10pm).
(I, J) Interferon signalling increases in δWD MEFs. MEFs from δWD or littermate control mice were infected with IAV. At the indicated time points, mRNA transcripts were evaluated by qPCR for IFIT1 (I) and ISG15 (J).
(F) 293T cells were first transfected with shRNAs targeting CARS or NTC, then transfected with HA-AMPKα1 or HA-AMPKα1 and Flag-CaMKK2 for 48 h, and then, they were cultured with cystine-deficient medium for 8 h. Cell lysates were immunoprecipitated with anti-Flag and subjected to Western blot analysis.
D, E Neddylated cullin inhibitor: MLN4924-treated HeLa cells were infected with WT GAS, and fixed at 4 h. Cells were immunostained for ubiquitin (FK2: magenta) or LC3 (magenta); scale bar, 10 μm. Representative images and quantification of cells with ubiquitin-positive GAS (D) and LC3-positive GAS (E).
(B) Tumor burden and tumor incidence in DMBA-treated K14ΔNLef1 (n=11) and K14ΔNLef1:cKO (n=8) mice. (***) p-value < 0.001; Wilcoxon matched-pairs signed rank test. Data information: Data are means ± SEM.
(A) Quantification of spheroids' area in MDA-MB-468 cell line (NTC vs. shDVL3). The data are presented as the mean ± SD, n = 3 showing statistical difference after 32h *p < 0.05.
C) Sorted mouse thyroid cells, Tubb1 expression in endothelial cells (Pecam-positive cells), epithelial cells (Epcam), fibroblasts (Pdgfra), and leucocytes (CD45) at E17.5 and adulthood: quantitative PCR results (normalized to Epcam-positive cells at adult stage and peptidylprolyl isomerase A). Mean±SEM of three independent cell-sorting experiments. Statistical comparisons versus epithelial cells (in black) at each stage, *p<0.05 using ANOVA test
Representative Southern blots showing DSB repair products of indicated mutants in regular mating type switching (H-1400 assay).
(O) Schematic representation of the proposed mechanism. In gas-1 mutants, aberrant complex I impairs the proper ETC function, resulting in diminished mitochondrial respiration. Overexpression of CEST-2.2 stimulates fatty acid beta-oxidation, which promotes TCA cycle and the transferring of electrons to ubiquinone/coenzyme Q through complex II and LET-721/ETFDH. This ultimately contributes to electron transport maintenance and ATP production.
C. Immunohistochemistry with antibodies against human Tau (TauY9 antibodies; middle panel) and dendritic marker MAP2 (left panel) in slice cultures at DIV 10. Stratum radiatum of area CA3 is shown. Although MAP2 staining is apparent, no signal is detected by the TauY9 antibody in control slices. In contrast, in hTauAT slices human Tau is detected in both dendrites and axons (see asterisk in merged image).
Ubiquitin and p62 positive structures accumulate in cells expressing CHMP2 mutants. HeLa cells transfected with myc-tagged wild-type CHMP2B (A), CHMP2BIntron5 (B), or CHMP2BΔ10 (C) were labeled with antibodies against c-Myc (red), ubiquitin (green), and p62 (blue) and analyzed by confocal microscopy. Single channel images in black and white are shown. Bars,10 μm.
Similarly, neuronal activity was also reduced to levels comparable to WT-Stat3WT mice in APP/PS1-Stat3KO mice, but significantly increased in APP/PS1-Stat3WT mice (One-Way ANOVA followed by Bonferroni's multiple comparison test; same mice as in B). The cumulative distributions of neuronal calcium transients in APP/PS1-Stat3KO mice were not different from those of WT-Stat3WT mice (p = 0.31, Kolmogorov-Smirnov test), but significantly different from those of APP/PS1-Stat3WT mice (p = 0.001, Kolmogorov-Smirnov test).
(E) 293T cells were co-transfected with expression plasmids for Cherry-STING and either CD4, m152, m152-Δstalk or m152-GSstalk. An anti-V5 IP was performed and samples were analyzed by IB with indicated antibodies. Immunoblot shown is representative of three independent experiments.
Confocal analysis of Lysotracker (green) or FLAG (red) in GSC#9 overexpressing either empty vector (mock) or FLAG-QKI. Scale bars: 10 μm. Nuclei (DAPI) are shown in blue.
Transwell assays (D, with quantitations at the right) indicated that treatment with Tipifarnib (farnesyltransferase inhibitor) can partly reverse oecircFNTA-increased invasion in J82 and UMUC3 cells. Scale bar, 100 μm.
B A549 cells were pre-treated with RK-33 and radiated with 2 Gy, and 53BP1 and γH2AX foci were counted as a measure of DNA damage. Cells with more than 10 foci 53BP1 or γH2AX were counted. More than 400 cells per sample were evaluated.
Expression of MYBL2 is regulated by β-catenin. Expression of MYBL2 (i) protein levels as measured by immunoblotting and (ii) transcripts as measured by qRT-PCR in HPAF-II tumors with or without stabilized β-catenin treated with vehicle or 100 nM ETC-159 for 56 hours. Stabilized β-catenin prevents the ETC-159 induced decrease in both MYBL2 transcripts and protein levels. The horizontal lines represent mean of replicates.
A. A pcDNA3.1 plasmid containing PTENα or canonical PTEN with a C-terminal FLAG tag was used for the detection of PTENα, PTENβ, canonical PTEN, and other unknown PTEN isoforms (upper panel); Indicated plasmids in the upper panel were transfected into HEK293 cells followed by western blotting analysis using FLAG antibody. GAPDH was used as a control (lower panel).
Quantitation of the experiment shown in (C). At least 100 cells were assessed per condition. The horizontal line represents a median, the box spans from 25th to 75th percentile and the whiskers from 10th to 90th percentile.
E. Fixed HEK 293T cells expressing mNG-tagged MKI67 show a clear nucleoli rim localization. Data information: Protein of interest is shown in green, nuclear marker DAPI/Hoechst in blue and microtubules reference marker in red. Scale bar 10 µm.
(B) Representation of the BLI of the four groups of mice. Left panel: CD8+ T cell depleted mice treated with BoxA (n=9) or PBS (n=7). Right panel: non-depleted mice treated with BoxA (n=11) or PBS (n=7).
D Levels of plasma VEGF in COVID-19 patients with (n=8) or without (n=10) disease progression by cytokine assay. Data information: All data are shown as mean ± SD. P values are determined by Student's t-test.
Longitudinal tumor growth follow-up in mice injected with h676 GSCs and treated with the indicated compounds in single agents or combination. n represents number of tumors, in D: Vehicle n=16, PI3K n=16, Gemcitabine n=4, Combination n=4. Pvalues represent the mean of all the time points
Representative IF images showing γH2AX-positive micronuclei (white arrows) under physiological conditions with indicated siRNA mediated depletion. (Scale bar represents 10 µm)   Graph represents quantification of (G), showing percentage of cells with γH2AX-positive micronuclei in U2OS cells. (* P<0.05, **P<0.01, ***P<0.001; unpaired t-test, n=3, mean +SEM, at least 200 randomly selected nuclei were counted per condition per experiment).
(D, E) Representative examples of dose-response curves and time courses. Lines through the dose-response curves are fits to the Michaelis-Menten equation; time courses are fitted to linear equations. Shown are means and standard errors over at least three independent repeats.
C, D Whole blood was either treated with 24F4A for 1 h at 37°C (pre-incubation) or left untreated. PBMC were isolated from each condition. PBMC from the untreated whole blood were subsequently treated with 10 μg/ml 24F4A, and cells from all conditions were stimulated with CpG-A for 16 h. Plot represents mean of duplicate wells. Flow cytometry was used to measure BDCA2 levels (MFI). Shown is a representative donor of eight donors tested.
Schematic of ctDNA detection in matched CSF, plasma and urine samples from HGG and LGG patients using INVAR and/or sWGS. HGG - high grade glioma, LGG - Low grade glioma, CNS - central nervous system, CSF - cerebrospinal fluid, sWGS - shallow whole genome sequencing.
(A, C) Serum anti-C-peptide-immunoglobulins titers of mice immunized with CP (0:1 n=10; 20:1 n=5) (coating: C-peptide) and (D) anti-insulin-IgM titers of mice immunized with complex insulin (cInsulin, n=5) (coating: Insulin) and control-immunization (CI: CpG only, n=3) measured by ELISA at indicated days. Dots represent individual mice. Mean ± SD, statistical significance was calculated by using Kruskal-Wallis test. (B) ELISpot assay showing CP-specific immunoglobulin producing splenocytes at day 7 (left panel) and day 14 (right panel). Top lane showing representative images of wells. Dots represent individual mice (n=4/group) Mean ± SD, statistical significance was calculated by using Kruskal-Wallis test, *P < 0.05, **P < 0.01, ***P < 0.001.
(c,d) Mitochondrial particle size (c) and membrane potential (d) were determined using flow cytometry for TMRE in cardiac mitochondria preparations. Results are shown from 4-8 hearts analysed in duplicate.
Schematic representation of the sequences of the DNA target and sgRNAs. The PAM is shown in yellow. The nontarget DNA strand was labeled with Cy5. The matched and mismatched sequences in sgRNAs are shown in purple and blue, respectively. Representative gel shows DNA cleavage by SaCas9 guided by partially matched sgRNAs.
(B) Time course of Smad4 phosphorylation at Thr277 induced by FGF2 in control and Wip1-depleted HEK293T cells, showing that knockdown of Wip1 up-regulates Smad4 phosphorylation at the MAPK site. A bracket denotes phospho-Smad4.
Double staining of Ang-2 (brown) and CD206 (red) of a S / RTx / CTx / Bev patient, arrowheads indicating perivascular CD206+ cells around Ang-2+ vessels (I). Arrows pointing on parenchymal CD206+ cells (I).
E) Average tumor volume ± SEM of 4T1 Adam17-/- cells expressing the ADAM17 variants injected into the mammary fat pad of Balb/c mice (n=10 for each group). Indicated significances are between the I762A and LEE tumors. Two sided, unpaired Students t-test test was applied to test for significant differences *p<0.05. Mean and standard error of the mean indicated.
F) U2OS cells were synchronized with a single thymidine block, released into G2 and damaged with 0.5 μM Adriamycin for one hour. After a 16 hour G2 arrest cells were harvested for western blot analysis and analyzed for the indicated protein levels. Lanes were all present on the same blot but pasted together for comparison as indicated by the lines.
(E) Data are shown as blood glucose measurement in islet transplant mice treated with IL-33/DT, IL-33/PC61, or IL-33/DT/PC61. The horizontal black line indicates a BGL of 16 mmol/liter, the threshold for rejection. Each line represents one mouse.
Rescue of angiogenic sprouting by Myc overexpression in E11.5 C57Bl/6 Vegfr2Y1212F /Y1212F explant tissue. Representative images of E11.5 explants from C57Bl/6 embryos taken from wildtype (WT) and Vegfr2Y1212F /Y1212F littermates with (MycOE/Cre +) and without (MycOE/Cre-) endothelial-specific overexpression of Myc. Endothelial cell marker (CD31) immunostaining highlights the vasculature in white. Embryonic tissue blacked out to highlight sprouting area.
Immunisation with cGAMP-VLPs enhances VLP-specific CD4 T cell responses. BMMCs from C57BL/6 mice were pulsed overnight with cGAMP-VLPs and used to stimulate cells from spleens of immunised mice. Cells were co-cultured for six hours prior to evaluation of CD4 T cell responses by ICS. the percentage of CD4 T cells co-producing 1, 2 or 3 cytokines is shown in (C).
(B) Percentage of EPG-7 aggregates colocalized with SQST-1 in indicated autophagy mutants.
(D) Schematic overview of the multi-omics approach we took to get a system-wide profile of cell type enriched organoid cultures
D. RT-qPCR using a stem-loop primer to quantify the tRFs levels in shSCR, sh-1, and sh-2. Data information: Statistical analysis was performed using t-tests, and error bars represent mean ± SD for three independent experiments.
d) Quantification of cells staining for phosphoH3. The indicated number of cells were counted and the data are given as percentage of phosphoH3-positive cells of this total number.
It further inhibits oscillations in acetyl-CoA m+2 (d) from isotopic glutamine (representing oxidative versus reductive TCA cycle flux).
E Confocal images of liver cryosections derived from Li-CluhWT and Li-CluhKO-LC3-GFP mice and stained with anti-TOM20 antibody. On the right side, indicated boxes were 3.5x magnified. Arrows point to colocalizing spots. Scale bar, 25 μm. F Manders' colocalization coefficient between TOM20 and LC3 from experiments shown in (E). 5 images were analyzed per animal to get an averaged value (n=5 mice per genotype). Data information , data are presented as histograms showing the mean ± SEM. ***, P≤0.001; *, P≤0.05 (Student's t-test).
E-G METAVIR score of 2-, 4-, and 6-week CCl4-treated mice (F-G) Col1a and F4/80 immunofluorescence of 6-week CCl4-treated and vehicle control WT (F) and ENKO (G) mice.H Mean Col1a+ area per high power field (HPF) shown as percentage of the total area (n = 5-8).
c. To visualize DEGs between subsets of fibroblasts sorted from homeostatic (WT), inflamed (InvEE) or tumour-associated (Pap) skin, each gene was plotted in a hexagonal triwise diagram in which the position of a point represents the relative increased expression in one or two populations, whereas the distance from the origin represents the magnitude of expression. Genes that are 32-fold or more upregulated are plotted on the outer grid line. Grey dots in the centre of the triwise plot represent genes that are not differentially expressed. Genes associated with a fibrotic response are depicted in red.
Co-immunoprecipitation assays showed that the interaction between CIP2A and B56γ in TNBC cells was affected by CIP2A-BP expression.
(D) Elimination of HIV-1-infected cells (strain NLAD8 WT or ΔVpu) over culture with the indicated antibody (E430G), and NHS or HIHS. The frequency of % infected (Gag+) cells is determinined by flow cytometry. The mean relative percentage of infected cells compared to the HIHS condition is depicted. n=6-8 donors of CD4 T cells.
(B) Ectopic PBX3 is detected in all rostro-caudal levels of the VM in Pbx1-/- mice at E12.5, indicating a repressive function of PBX1 on Pbx3 expression.
B. Tumor volume quantification measured by MRI analysis of Tie2-GFP (n=6) or Tie2-IFNα mice (n=9) at the indicated time points post-transplant, one additional Tie2-IFNα mouse showed a tumor volume at day 21 of more than 820 mm3 and was statistically rejected by the Grubbs' test and not further analyzed; mean values are shown; error bars=S.E.M.; p=0.051, by Mann-Whitney test.
(F) PTEN immunohistochemistry analysis of MCF-7-miR-10b-OE or control MCF-7-miR-Scr-OE tumorxenografts.