EMBO/sd-character-level-ner huggingface dataset:
(b) Schematic illustration of the structure of c-Cbl and alignment of the potential LIR motif with those in known LC3B-interacting proteins.
(D) Adenoviral reintroduction of human PS1 suppresses TLN accumulations. 30-35% of PS1−/− neurons display TLN accumulations, in contrast to <5% in PS1+/+ and +/− cultures as well as in cultures expressing human PS1 in a PS1−/− background. However, suppression of TLN accumulations was obtained by adenoviral introduction of human PS1. A clear dose-dependent inhibition was seen with increasing MOI of adenoviral (AV) human PS1, but also the familial Alzheimer's disease-linked PS1G384A and dominant-negative PS1D257A mutants. Control adenoviral infections with eGFP did not have a significant effect. After 9-11 d post-infection (15 d post-plating), neurons displayed significant PS1 protein expression as demonstrated by double staining for TLN and human PS1(mAb 5.2). Bars, 20 μm.
Snapshot of the SPL6 miR156 translatome in WT and hyl1 backgrounds. Removal of the stele (blue box) reveals subtleties of miR156-mediated gene regulation in the other layers, resulting in a near-mirror image of (A).
(b) Flow cytometry of splenocytes from recipient mice (n = 6) given adoptive transfer of P14 cells transduced with retrovirus as in a, assessed on days 5 and 8 after infection of recipients with LCMV (left), and quantification of P14 cells per spleen (right). Numbers adjacent to outlined areas (left) indicate percent P14 (CD45.1+) cells. *P ≤ 0.0005 (unpaired t-test).
(A) A schematic representation of targeted deletion of mouse Brd4. The exon-intron organization of the Brd4 locus (top). Targeting vector contained exon 3 flanked by LoxP sites (green) and a neomycin resistance gene flanked by FRT (white). Cre mediated recombination should cause deletion of exon 3 resulting in loss of BRD4 expression (bottom).
Violin plots of Notch family elements expression in IgG and αDll4 treated cells (adj p val: *<0.1 and *** p<0.00001).
(A) Decrease of mRNA levels in TubG4, UAS‐CG11347‐RNAi animals compared with TubG4 controls. All measurements were normalized to rp49. *Significant change, P0.05.
(D) Formaldehyde fixed GFP+ S. flexneri supplemented with varying LPS-O55:B5 concentrations were mixed with 5 µM hGBP1F and 2 mM GTP. After 60 min hGBP1F-enclosed S. flexneri were quantified. Combined data from three independent experiments are shown as mean ± SEM. Significance was determined by one-way ANOVA with Tukey's multiple comparison test. ****, P ≤ 0.0001.
(B) Bacterial viability of convertase-labeled bacterial strains exposed to buffer (Conv) or C5-C9 (Conv-MAC). Data information: (B-E) Data represent mean ± SD of 3 independent experiments. (B, D, E) Statistical analysis was done using a ratio paired two-tailed t-test and displayed only when significant as * p≤0.05, ** p≤0.01, *** p≤0.001 or **** p≤0.0001.
Contribution of Nanogtg transplanted cells to LSK, CMP, GMP and MEP populations purified from bone marrow. Percentage of host derived cells (CD45.1+) are show in black, and of donor derived cells (CD45.1/CD45.2 double +) in blue. Individual mice are indicated on the x-axis (n=7).
(D) The cumulated period of calcium signals was recorded for individual unconjugated or conjugated target cells and expressed as percentage of total time. Each dot represents one tumor cell. Bars represent mean values.
Study 1, tumor-bearing male mice receiving GTx-024 (15 mg/kg; n=5), AR-42 (10 mg/kg; n=5 ), Combination (15 mg/kg GTx-024 and 10 mg/kg AR-42; n=5 ) or Vehicle (n=5) and tumor-free mice receiving GTx-024 (15mg/kg; n=6) or Vehicle (n=6) were treated daily by oral gavage for 13 days starting 6 days post-injection of C-26 cells. E) Terminal gastrocnemius (mean±SD) and F) quadriceps muscle mass (mean±SD) compared to tumor-free controls.
Region details and sequence selection. Common residues to TrkB-FL and TrkB-T1 are in light blue and include a KFG sequence completely conserved in Trk proteins (filled black box). In the heatmap representation, dark red, white and green represent respectively strong, weak or no effect of point mutations while black corresponds to wild type residues. Black arrows denote theoretical calpain cleavage sites while the red arrow points an experimentally established site. Sequences included in CPPs are emphasized by black rectangles. TM, transmembrane; TK, tyrosine kinase.
I, J Log2 fold changes in cell viability in presence of IMT1 and rapamycin (I) or FG4592 (J) of a panel of seven cell lines. Data are expressed as ratio of viable cell counts in presence of IMT1 alone and represent the mean ± SD of n=6 (RKO, MiaPaCa-2 and Hela) and n=3 (DLD-1, HCT-15, NCIH460 and A549) individual experiments.
A, Schematic representation of PLT3 protein domains. The areas in red are predicted prion-like domains (PrDs) and were deleted in PLT3ΔPrD-mV. The areas highlighted in yellow contain polyQ-stretches and were deleted in PLT3ΔQ-mV.
(C) Left Panel: Quantification of variant S protein mediated fusion in Vero-GFP split cells by video microscopy. Results are mean ± SD from three fields per condition from one representative experiment. Right Panel: Fusion quantification of at least 3 independent video microscopy experiments, 20h post transfection, normalized to D614G.
(D) T47D-MTVL cells transfected with control or FOXA1 siRNAs were induced or not with hormone, and subjected to ChIP assays with a-BRG1 and IgG as control. Precipitated DNA was analyzed by PCR for the presence of sequences corresponding to the BCAS1, KRT23 and IGFBP5 genes. The histograms show the mean ± SD of 3 experiments performed in duplicate. * P-value < 0.05.
B-D. 3T3-L1 stable cells described in (A) were adipogenically induced. Their adipogenic potential was assessed by triglyceride quantitation (C)
D Developmental trajectories inferred from RNA metabolic labelling. Bold and thin arrows indicate high versus low directionality of RNA velocity. Colors below RNA velocity show latent time (yellow: early latent time; blue: late latent time).
(E) The rectal temperature of Ftoflox/flox and FtoAKO mice fed a HFD during acute cold exposure (4°C) and fasting for 6 h.
A. Immunohistochemistry analysis of FATE1 expression in normal adrenal cortex and adrenal hyperplasia, adenoma and carcinoma (ACC). Testis tissue was used as positive control. Scale bars, 200 µm (low magnification); 50 μ m (high magnification).B. Table summarizing the relative intensity of FATE1IHC staining (H-score) in groups of normal, benign and malignant tissues. The highest FATE1 expression levels were found in ACC. n, number of samples studied for each category of tissues. NBST, normal and benign steroidogenic tissues.
(A-B) Relative frequencies of tumour-infiltrating M1 macrophages and M2 macrophages analyzed by flow cytometry at 21 days (A) and 38 days (B) after grafting.
(C) A scatter diagram shows the change trend of mH2A1.2 and different neurogenesis markers. n = 5 mice, independent replicates.
(A) ARPE-19 cells coexpressing active RagB/D heterodimer and the indicated TFEB plasmids were fixed, permeabilized with 0.2% saponin, and stained with antibodies against GST (used to detect Rag proteins). Regions within the dotted boxes are magnified in the insets. Bars, 10 µm.
(c) Lysates from cells were immunoblotted with anti-FAK, anti-Src, anti-Yes, anti-Fyn, anti-pTyr-416-Src and anti-actin antibodies. Uncropped images of blots are shown in Supplementary Fig. S9.
Representative FACS plots showing gating strategy for the analysis of cell types in the adult V-SVZ.
Model of R0RBR:pUb in complex with UbcH7-Ub derived from NMR chemical shift data and HADDOCK docking (Dominguez et al, 2003). The lowest energy structure is shown and the top 20 structures all showed excellent agreement (RMSD 0.71 ± 0.1Å) although some minor differences were noted for the orientation of the Ub molecule. The structure shows that UbcH7-Ub binds in an open conformation. UbcH7 uses canonical E2-RING E3 interactions that include residues from two loops in the RING1 domain (L1, L2) and two loops in the E2 enzyme (L4, L7) to stabilize the interaction. Ub binds to a RING1/IBR pocket. In this model no attempt was made to move or re-orient any of the domains in parkin
LCI assays showing that BIC1 interacts with PIF4. Leaf epidermal cells of Nicotiana benthamiana were co-transformed with nLUC-BIC1 or nLUC and cLUC-PIF4 or cLUC as indicated.
(G-J) Contribution of PPM1D/Ulk1-dependent autophagy to irradiation-induced apoptosis. (J) Indicated thymocytes were X-ray irradiated (5 Gy), and 3 hr later, caspase3/7 activity was examined using the Caspase-Glo 3/7 assay (Promega) according to the manufacturer's protocol. Data are shown as the mean  ± SD (n = 3 experiments). *p < 0.05, **p < 0.01.
(E) GSEA was performed comparing the IκBα IEC‐KO gene list (n = 4 villin-Cre x floxed IκBα mice and n = 4 littermate controls (GSE 139251) Mikuda et al, 2020(), with a gene signature based on a list of SASP factors Coppe et al, 2010(). NES: normalized enrichment score. FDR: false discovery rate.
C. Growth rate of single cofilin domains, normalized by the cofilin concentration. N = 20 domains for WT mCherry-cofilin-1 (1 experiment) and eGFP-S3D-cofilin-1 (2 experiments). The growth rate was measured at 10 nM WT cofilin-1, and 500 nM and 1 µM S3D-cofilin-1 (Appendix Fig S4C). Bars: mean and S.D. P-value = 8.10-9 (t-test).
(E) Representative NHEJ junctions obtained from siControl- and siPhf5a-treated samples.
Confocal images of macrophages from control embryos and those expressing a dominant negative c-ring of ATP synthase (CV-DN) in macrophages. from Stage 12 embryos and germband edge shown with dotted white line. Data information: show Stage 12 embryos. Scale bars: 50µm
Aberrant accumulation of mitophagosomes co-labeled by antibodies against LC3 and cytochrome c (Cyto c) in the hippocampal mossy fibers of mutant hAPP Tg mouse brains. Note that mitophagosomes indicated by white arrows are not readily observed in WT mouse brains
Human peripheral blood mononuclear cells (PBMCs) were cultivated for 48h in RPMI containing 80mg/dl glucose (NC) and supplemented with 10mM beta-hydroxybutyrate (BHB). T cell stimulation was performed through CD3/CD28 Dynabeads at a bead:cell ratio of 1:8. For JC1 analysis, magnetic CD4+/CD8+ T cell separation was performed prior to staining. G Evaluation of mitochondrial membrane potential of human pan/CD4+/CD8+ T cells using quantification of JC1 fluorescence (MFI PE/ FITC), FCCP served as the negative control, n=8/7/7/7(FCCP) biological replicates. Data information: Data depicted as box plots with median, twenty-fifth and seventy-fifth percentiles and range. Dots indicating individual values. *p<0.05, **p<0.01, paired t-test/ Wilcoxon matched-pairs signed rank test, as appropriate.
Accumulation of intracellular Aβ1−42 in neurons overexpressing the AP2-α-Mut comparing to neurons expressing the AP2-α−WT (WT: 1.14±0.18, Mut: 2.06±0.29, p=0.011, WT=28 and Mut=33 neurons, N=4 biological replicates). Scale bars: 20µm, 2µm (inserts). Data information: All graphs show mean ± SEM, statistical analysis was performed by unpaired two-tailed Student's t‐test n.s.-non-significant. * indicates p≤0.05, ** indicates p≤0.01, *** indicates p≤0.001.
(B) Quantitation of the DRP1 localisation by immunofluorescence microscopy analysis. Upper panel: co-localization of TOMM20 and DRP1 in control and subject fibroblasts was calculated by Mander's and Pearson's coefficients. Bottom panel: quantification of DRP1 localisation in the cytosol and the mitochondria. At least 15 cells per condition were analyzed in 3 independent experiments. Errors bars represent mean +/- SD and p-values were calculated using a student t-test.
A The immunoblot analyses of MCF-7 ENTREP-KO and parent MCF-7 cells. Note that the amount of CXCR4 protein was not changed. The immunoblot analyses were carried out using six independent samples, and their blot bands were semi-quantified using ImageJ software. CXCR4/GAPDH ratio was caluculated as a ratio of GAPDH-adjusted CXCR4 expression. CXCR4/GAPDH ratios shown as mean ± SD from at least four biological replicates. P-values were obtained by Student's t-tests and P < 0.005 was considered as statistically significant. No significant difference was observed.
Double-immunofluorescence labeling is depicted for pDyn and NeuN (A-C) or GFAP (D-F) in the ipsilateral dentate gyrus of KA-treated and AAV-pDyn-injected mice. Enlarged view in (F) represents 15 x 30 µm.
Model for the acquisition of a new 3′ end for tap-1 and an effector-encoding gene as a result of the recombination site within tap-1, and an additional downstream recombination event (not shown).
(B) Immunoblot of netrin-1, DCC, UNC5B, active caspase-3, alpha synuclein FL, alpha synuclein pS129, and Tyrosine Hydroxylase (TH) levels in age-matched controls (n=3) vs Parkinson's disease patients brain samples (n=3) (left panel). Band quantification bar graph (right panel). Bars and error bars represent the mean ± SEM. Statistical significance was determined using a one-way ANOVA followed by post hoc Tukey test for multiple group comparison. P**< 0.01. N=3 replicates
Scatter plot and correlation coefficient (r) of ASK1 mRNA expression and ATG7 Data were collected in lean subjects (n=14), obese subjects (n=23) and obese subjects with type 2 diabetes (n=19). Values are expressed as mean ± SEM (D).
(a) HeLa cells stably expressing GFP-VPS35 WT and D620N were transfected with mRFP-LC3 for 24 h, immunostained for endogenous ATG9A, and imaged by confocal microscopy.
(E). Immunoblots and quantification of OXGR1 protein expression in adrenal chromaffin cells treated with negative control (NC) siRNA or siOXGR1 (n = 3 per group).
Studies show that Opa1 interacts with MICOS complex, promoting closure of CJs. Thus, we tested whether Opa1 was required to maintain the difference in ΔΨm between cristae and IBM. Live-cell Airyscan images of MEF control (top row) vs. Opa1 KO (bottom row), co-stained with NAO and TMRE. Arrowheads indicate decreased intensity of TMRE FI at cristae compared to IBM. Note the more even distribution of TMRE staining, indicating the cristae and IBM are relatively equipotential. Scale bar = 500 nm. Quantification of G, showing Opa1-KO MEFs have significantly decreased ΔΨCr-IBM. N = 3 independent experiments.
Immunofluorescence staining of endothelium (CD31, in red), nuclei (DAPI, in blue), and phosphorylated SMAD2/3 (in cyan) on cryosections of similarly injected muscles confirmed that endothelial SMAD2/3 activation was inhibited by increasing VEGF doses. Scale bar = 10 μm; n = 3.
Body composition of male OXGR1KO mice after 14-days resistance exercise (n = 8 per group).
(A) Design of a functional dynamin mutant to probe PHD stalk interactions. Minimal structure of the PHD and the PHD-Stalk interface showing the location of important residues discussed in this study. The unresolved loop L1NS in the stalk hosts the IAEDANS label and is sensitive to the two tryptophans (W525 and W542) in the PHD. The distance between two introduced cysteines (S357C and native C602) used to construct a double cysteine Dyn1 is also shown.
(C) Glycine/proline-induced currents for mouse SLC6A20A do not show reversal potentials, as shown by the lack of reverse currents induced by increasing holding potentials in HEK293T cells. These experiments were performed using single HEK293T cells in a conventional patch-clamp (not auto-patch) setup. (glycine, n = 3, 7, 3, 3, 3, 3 cells for untransfected HEK293T cells, 10, 11, 5, 6, 6, 5 cells for mouse SLC6A20A, at -90, -60, -30, 0, 30, 60 mV of holding potentials, respectively; proline, n = 4, 7, 4, 5, 3, 4 cells for untransfected HEK293T cells, 3, 6, 3, 3, 3, 3 cells for mouse SLC6A20A, at -90, -60, -30, 0, 30, 60 mV of holding potentials, respectively). The error bars represent SEM.
(I) Experimental layout of the 'acute stress-washout' assay in the presence or absence of the ribosome inhibitor cycloheximide (CHX) as performed in (J). Wild-type cells expressing a mitochondrial matrix-localized Grx1-roGFP2 probe were grown to early exponential phase in SGal (-Leu). Cells were pre-treated either with water or 50 mM H2O2 for 10 mins and afterwards washed and resuspended in fresh medium. During the next 2 hour recovery, cells were either treated with the translation inhibitor cycloheximide (CHX) or with DMSO as a vehicle control. The response of a mitochondrial matrix-localized Grx1-roGFP2 probe to the subsequent addition of 1 mM H2O2 was then measured.
(E) Representative image of cleared brains and immunolabeling for GnRH at the level of the organum vasculosum of the lamina terminalis (OVLT) in the median preoptic area, from a control (left) and a mutant (right) female postnatal brain. Scale bar: 500μm. Oc, optic chiasma.
CryoEM image of an isolated ex vivo S-Ena making a U-turn comprising 19 helical turns (shown schematically in orange), i.e. corresponding to a ~10° axial tilt between consecutive helical turns.
(D, E) HTM-mediated quantification of MPM-2 (D) and H3S10P (E) levels per individual nucleus in U2OS cells treated with DMSO as a control or 50 μM P22077 (USP7i) for 4 hrs. Nuclei were stained with DAPI (blue). Scale bar, 30 μm. The quantification is shown to the right of representative images for each analysis. (*** p<0.05; t-test). Grey lines indicate mean values.
MEF cells were infected for 3 h and transfected with empty plasmid (CTRL), hNDP52, hLC3‐C or hNDP52 and hLC3‐C. Viral production (E) and cell mortality (F) were assessed 24 h post transfection. Isogenic wt or Atg5−/− MEFs were infected for 24 h and cell mortality (that is, fold change relative to mock‐infected cells) (G) and viral production (H) were assessed. MEF cells were infected and immunoprecipitation experiments were performed 24 h p.i. using antibodies to p62 or nonspecific IgG controls. Immunoprecipitated proteins were revealed with anti‐capsid antibody (I).
Pretreatment with 50 μg DEX protects B mice against lethal SIRS induced by 30 μg TNF (−30 min, grey) compared to PBS pretreatment (250 μl, −30 min, black) (both groups n = 13) (left panel). Relative mRNA expression in the liver of B mice 6 h after i.p. injection of PBS (black, n = 10) or DEX (grey, n = 10) (right panel). Significant up-regulation of Tsc22d3, Sgk, Tat and Mrc1. Induction of miR-511 by DEX compared to PBS.
(J) NO inhibits autophagy by S-nitrosylating and inhibiting JNK1 phosphorylation, thereby reducing phospho-Bcl-2 and increasing Bcl-2-Beclin 1 interaction, which disrupts hVps34-Beclin 1 association. NO also S-nitrosylates and inhibits IKKβ phosphorylation, leading to reduced phospho-AMPK and TSC2 activity, which alleviates the inhibitory effect of TSC1/2 on Rheb (denoted by "×"), thereby allowing Rheb to activate mTORC1 and inhibit autophagy. Overexpression of NOS isoforms impairs autophagy by inhibiting the JNK1 pathway, whereas NOS inhibition by L-NAME induces autophagy by mechanism distinct from the NO pathways. Graphical data denote mean ± SEM, except in (E) and (F).
C) Schematic presentation of experimental design. Mice received IP injections of CrossMAb anti-VEGF-A/ANG-2 (species crossreactive, B20.4.1 and LC10), anti ANG-2 (LC10), an anti-VEGF-AIgG1 (B20.4.1) or IgG control at postnatal D14 and D19 followed by fluorescence angiography at D26 (early intervention), results demonstrated in D-K. Alternatively, mice received antibody at postnatal D47 and D55 followed by fluorescence angiography at D60 (late intervention), results demonstrated in L and M.
H Heatmaps show Scl binding to majority of activated hematopoietic and repressed cardiac transcription factors and other proteins. See also Supplementary Fig S1 and Supplementary Table S1A-E.
Relative stability analysis of GAPDH C-terminally tagged with the last 12 residues of indicated proteins with or without DNKLHDC2 treatment by GPS assays. The -3, -4 or -5 residue of SARS-CoV NSP proteins was mutated to Ala (A) as indicated. The experiment was done in triplicate using three independently prepared viruses to express DNKLHDC2. Data are presented as the mean value of GFP/RFP +/- standard deviation from triplicate experiments.
Generation of three lines of Tex11 knockin mice. Each harbors a single amino acid substitution in TEX11 (indicated by asterisks) analogous to a missense mutation identified in a human patient. Nucleotide and respective amino acid changes are indicated. Exons 1, 2, and 3′UTR are from the mouse Tex19.1 gene.
In utero fetal death in wild-type CD-1mice due to infection with GBS WT, hyperhemolytic ΔcovR, and non-hemolytic ΔcovRΔcylE. Fetal death is represented by the number of dead fetuses/total number of fetuses obtained from six pregnant mice per group. 'n' indicates total number of pups (both live and dead); ****P < 0.0001, Fisher's exact test.
Percent of FOXA1- and FOXA2-positive nuclei in PDAC cells from areas of different grade. Tissue microarrays were automatically acquired and quantified using QuPath. The number (n) of analyzed areas of each grade is indicated.
A Young mdx mice and treatment with an CD38 inhibitor. 6-week-old mdx mice were treated for 5 weeks with K-rhein at 2.5 mg/kg/d by intraperitoneal injection. Dot plots showing measurement of the grip duration (A1) and the force (A2) of WT (n=9), mdx (n=7) and K-rhein-treated mdx (n=10) mice. Data information: Each dot of the graphs represents a mouse. A1 one value/mouse; A2, in triplicate. After normality and variance comparison tests, significance was assessed using: A1: Welch's ANOVA followed by Welch's t-tests; A2 ANOVA followed by Fisher's LSD test; Values are expressed as means ± SEM. Significance: *p<0.05, **p<0.01, ***p<0.001
(D) Cytokine analysis (IL-6, IL-1β and TNF) of supernatant of mixed cortical cultures (left; in vitro) incubated with EVs isolated from untreated (black; n=3) or LPS treated (grey; n=3) mice and of CSF (right; in vivo) from untreated (black; n=3) and LPS treated mice (grey; n=6).
D Close-up view of H2A.B-H2B dimer in the structural comparison. The secondary structure of H2A.B-H2B dimer are indicated. The dashed lines highlight the tilt of H2A.B α2-helix.
A: Cal27 and JHU022 cell lysates were immunoprecipitated with control or ILF3 antibodies and RNA was isolated from the precipitates. Relative mRNA expression of EGFR was analyzed by qRT-PCR. n = 3 biological replicates and 3 technical replicates. Data are represented as the mean ± SD,
(C) and (D) MCF-7 cells were co-transfected with the indicated plasmids. Forty-eight hours after transfection, cells were treated with MG132 for 10 h before cellular extracts were harvested for Ni-NTA bead precipitation followed by IB with anti-HDAC1.
(A) Luciferase activity driven by the ISRE promoter in HEK293T cells transfected with Myc-RNF34 and Flag-V, Flag-N-RIG-I, Flag-MAVS, Flag-STING or Flag-TBK1. Luciferase assays were performed 24 hrs after transfection. The luciferase reporter data are presented as means ± SEM. Two-tailed Student's t-tests were used for statistical analyses: *, P < 0.05; **, P < 0.01; and ***, P < 0.001.
(L) Telogen duration in Sirt7-TG and WT mice. n = 6 mice per genotype. Box-and-whisker plots: mid-line, median; box, 25th and 75th percentiles; whiskers, minimum and maximum.
L, Left: Quantification of transcript abundance (mean +/- s.e.m.) by qRT-PCR in AGO1x (black, n=6 for putative targets, n=3 for negative controls) or IgG (orange, n=2) IP from control cells. n.d., not detected. Multiple test corrected P-values for an unpaired two-tailed t-test are depicted above each comparison (* P < 0.05, ** P < 0.01, *** P < 0.001). Right: Concentration of RNA (mean +/- s.d.) obtained with each type of antibody, with P-value from an unpaired two-tailed Student's t-test.
Jurkat cells (a) were infected with EBV-WT or EBV-ΔBRLF1 virus (MOI=500) for 36 h. Then, the cells were collected, and the total RNAs were extracted, reverse-transcribed and analyzed by real-time PCR. Color gradient depicts the mean mRNA expression normalized to the housekeeping gene GAPDH and compared to the mock group.