EMBO/sd-character-level-ner huggingface dataset:
D Immunoblotting of protein extracts from 1205Lu, SKMEL5 and MM099 cells plated for 48 h on FRC-derived ECM prior a 96 h treatment with vehicle or 5 µM BRAFi in the presence or not of Imatinib (7 µM for 1205Lu, 10 µM for SKMEL5 and MM099) or DDR1-IN-1 (1 µM for 1205Lu, 5 µM for SKMEL5, 3 µM for MM099), using antibodies against the indicated proteins. HSP60, loading control.
E, PI3Kα activation scores from localised PDAC in the TCGA database according to their UICC staging were retrieved, clustered into two groups (low and med) (BH corrected p-values) and their overall survival was plotted, with logrank testing.
(B) MDA-MB-468 cells were treated for 24h with vehicle, AKTi (MK2206 450 nM), gefitinib (3 μM) or cetuximab (100 μg/ml), alone or in the indicated combinations. The cell lysates were probed with the indicated antibodies.
D) ER stress in Tubb1-/- thyroid tissue. Top: Chop and XBPs expression by quantitative PCR in adults, normalized to peptidylprolyl isomerase A. Experiments with at least three tissues per stage for each genotype; wt in black and Tubb1-/- in grey. Bottom: Chop and Actin protein expression by western blotting in three representative wild-type and Tubb1-/- mice. The Chop band quantification normalised for Actin confirms the increased Chop expression demonstrated by quantitative PCR in Tubb1-/- versus wild-type thyroids. All lanes are from the same blot, which was cut where indicated. Student"s test, *p<0.05 and ***p<
B. Flow cytometry histograms of TAMRA-labeled peptide uptake into HEK-293 cells after 1h incubation at 4°C in growth medium. C. Quantification of mean fluorescence intensities in (B). n = 6 independent biological repeats; means ± SEM; * p< 0.05, *** p< 0.001, **** p< 0.0001, ANOVA with Tukey's post-test.
B. T6SS secretion assay of A. tumefaciens 12D1 wild type, ΔtssL, and various toxin-immunity deletion strains harboring the indicated plasmids.
Evaluation of neuronal toxicity following glufosinate treatment. grip strength for all paws (rectangle grid) (G), of the latency to fall off an accelerating rotarod (H), and of the mean paw withdrawal force that caused animals' response in the von Frey test (left hindpaw, I; right hindpaw, J) as an indicator of the development of tactile allodynia in vehicle and glufosinate-treated mice (n=4), before the treatment (baseline), after 1 day (acute Toxicity) and after 15 days (chronic toxicity) (pool of 2 independent experiments; 10 mice per condition in total).
C, Immunofluorescent analysis of the apoptotic marker cleaved caspase 3 in xenografts derived from T387 GSCs expressing shUSP33 or shNT. Disruption of USP33 in GSCs dramatically elevated apoptosis in GBM tumors. Scale bar, 80 μm.
(G) Maximum projection of 2-z slices of Hela-Cdk1as cells stained with anti-RACGAP1 antibody when treated with DMSO and 2µM ZM447439 (ZM) at metaphase and early anaphase, showing the localization of RACGAP1 at spindle midzone even upon Aurora B inhibition at early anaphase. Scale bar - 10 µm
A, Migration inhibition capacities of PI3K inhibitors at 1 µM were tested on pancreatic tumour cells (R211, PDAC8661, PANC-1, 10593, 10158, R6344, R6430, R6065, R6141). The mean of these values was plotted against the in vitro IC50 for each class I PI3K and each inhibitor. IC50 is determined on recombinant proteins. Pearson correlation tests were performed and its p-values were presented separately for each class I PI3K isoform.
(D) Analysis using ICY software of the percentage of cells containing red fibrils among the population of cells containing green aggregates. The graph shows the mean percentages with SEM, respectively 66.3% and 36.9% for donor and acceptor cells, statistical analysis was performed by two-tailed unpaired t-test (**** p =3.65E-05).
(M-O") Tuj1 (green, RGC axons) and S100β (red, astrocytes) IF on P7 WT, HET and KO ONs. Arrowheads point to S100β+ astrocyte groups (N',O') and absence of Tuj1+ fibers (N'',O'') in HET and KO ONs.
The macrophages from Atx∆ΜΕ/∆ΜΕ and Atx+/+ mice were stimulated by LPS [20 ng/mL, 20 min The cell lysates were subjected to immunoblotting analysis with antibodies as indicated. regular Akt were used for a loading control. Presented are the representative image from at least three independent experiments.
Densities (cells/mm2) of DCX+ neuroblasts in V-SVZ whole-mounts of aged mice 3 days after TMZ treatment. n=3, n.s. not significant. Scale bar: 500 μm.
(C) Predicted plasma serine during two weeks of simulated twice-daily supplementation: 24-hour moving average value indicated in red and continuous/momentaneous indicated in gray.
B, Quantification of CD206 expression on macrophages (CD11b+ F480+) from MC38 and KPC tumours, with representative histograms. Data are presented as mean ± SEM and analysed by Mann-Witney (n=6 mice/group).
F MDBs in dorso-lateral tracts of 6-7 week old WT (n = 3), NOKO (n = 3), and NYOKO (n = 3) mice. Data were analyzed using one-way ANOVA. ***P ≤ 0.001, ****P ≤ 0.0001, ns = not significant. Data are means ± SEM.
C) Mean diffusion coefficients D calculated from all individual trajectories. Mann-Whitney test. ***, p<0.001; **, p<0.01; *, p<0.5. Cells analyzed >5 per condition; number of trajectories: 4011 (Glc), 10333 (Gal); Q1: 0.00387 (Glc), 0.0031 (Gal); median DGlc: 0.0142 µm2/s, DGal: 0.00898 µm2/s; Q3: 0.0504 (Glc); 0.02969 Gal; p<10-31.
(D) HEK293 cells that transiently expressed wildtype or mutant COA7HIS were solubilized, and the affinity purification of COA7HIS was performed. The samples were analyzed by reducing and non-reducing SDS-PAGE and Western blot. Load: 3 %. Eluate: 100 %.
(C) Quantification of the number of mitochondria in the perinuclear region (mean ± SEM; n≥5 cells; *p<0.05).
(m,n) hlh-30 is required for starvation-induced lifespan extension. One representative experiment of 2 independent trials; error bars represent mean±s.e.m. Median survival (MS) (wild-type fed) = 10 d; MS (wild-type starved) = 17 d, P0.0001 versus fed using the Log-rank test; MS (hlh-30 fed) = 7 d; MS (hlh-30 starved) = 9 d, P0.0001 versus fed.
E cGAMP production assays. Recombinant cGAS (10 μM) and G3BP1 (10 μM) were incubated, in the presence or absence of dsDNA (200 nM), with or without EGCG (20 μM). The produced cGAMP was quantitatively analyzed by LC-MS/MRM. n = 3 technical replicates. Data information: Error bars, mean with s.d. , *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, two-tailed t-test. NS, non-significant.
A model illustrating the mechanism by which proteasome inhibitors (PIs) selectively kill GSCs. A key factor in low-dosage proteasome inhibition and its selective efficacy against GSCs lies in the sustained accumulation of ubiquitinated conjugates due to the failure of the proteasome (red cross). The resulting proteotoxicity then can activate the apoptotic cascade, among which genes such as ATF3, CHOP and JNK are upregulated and translated into their respective protein counterparts. ATF3 and CHOP also form a heterodimer which serves to maintain the apoptotic cascade. The ATF3-CHOP axis-induced cell death is independent of classical ER stress-associated apoptosis, and may instead directly play a role via NOXA to induce mitochondrial dysfunction (yellow lightning) and eventually cell death.
(A) A significant delay in RPA foci formation in the absence of Snf1. The percentage of cells with RPA foci was calculated and plotted against the incubation time in 200 mM HU. Error bars represent SD from three biological repeats. At least 200 cells were analyzed for each experiment of three independent experiments. Statistical significance was evaluated based on Student's t-test (*0.01 < P-values < 0.05; **0.001 < P-values < 0.01).
I-L. Ci-M1 drives proliferation of CD8+ or CD4+ T cells. BMDMs treated as indicated were transfected with 10 μg/mL of OVA257-264 peptide or OVA323-339 peptide for 1 hours. BMDMs were then washed and co-incubated with CFSE-labeled OT-I or OT-II cells respectively. After 72 hours, OT-I (I) or OT-II (K) cells were stained with anti-CD8a or anti-CD4 fluorochrome-conjugated antibodies and CFSE was detected through flow cytometry to evaluate the dilution of CFSE in T cells. Statistics represent the percentage of divided T cells. (J, L) are statistics analysis of Figure 2I and 2K. The data are means ± SD of three independent experiments. *p < 0.05 (student's t-test).
E EMSA following incubation of GlmY* with 1200 nM RapZ in presence of various GlcN6P concentrations ranging from 0 (lane 2) to 8 mM (lane 10). The fraction of GlmY* remaining in the gel pocket is marked with an asterisk. The RapZ/GlmY* complex is indicated by an arrow.
(C, D, E, G, H) 293T cells were transfected with the indicated constructs, lysed and subjected to GST immunoprecipitation with agarose beads coupled to glutathione. Shown are WBs against the indicated molecules. (C) The N‐terminal CARD of NOD2 (NOD2-CARD1-HA), but not the CARD of NOD1 (NOD1-CARD-HA), co‐precipitates with GST-ATG16L1. (D) The ID of TLR2 (HA-TLR2-ID) co‐precipitates with GST-ATG16L1. (E) Mutated versions (MUT) of NOD2-CARD1-HA and HA-TLR2-ID (as shown) do not co‐precipitate with GST-ATG16L1. (F) Amino‐acid sequences of T3JAM and DEDD2 including the motif. Residues identified by the Prosite algorithm are highlighted. (G) Wild‐type (WT) versions of HA-T3JAM and HA-DEDD2 (as indicated) co‐precipitate with GST-ATG16L1. (H) Mutated versions (MUT) of HA-T3JAM and HA-DEDD2 do not co‐precipitate with GST-ATG16L1. Asterisks indicate irrelevant bands in C, D and G.Source data for this figure is available on the online supplementary information page.
(B) Untransfected (UN) or FLAG-Atg16L1 full-length (FL), 79-623, or 1-265 constructs were expressed in HEK293A cells stably expressing GFP-WIPI2b and immunoprecipitated using GFP-TRAP. Tags were visualized by immunoblotting. I, input; UB, unbound.
C) Overlap between misregulated genes in Id1 KO ESCs, genes significantly affected by Zrf1 depletion in Id1KO ESCs (identified by gene expression analysis), and Polycomb bound-genes in ESC (identified by ChIP-sequencing analysis).
(G) IVIS images showing representative tumors generated by injecting luciferase-expressing MCF7 cells (NTC, shA DVL3) in the mammary fat pad of SCID mice. Color scale (luminescent signal intensity): blue, least intense signal; red, most intense signal. (H) Quantification of luminescence changes in tumors generated by injecting luciferase-expressing MCF7 cells (NTC, shA DVL3) in the mammary fat pad of SCID mice. Average luminescence was used to measure volume of tumor. n=7.
L - Relative mRNA expression of Chat in BMDMs treated for 2 h with veh or 100 μM NE (n = 6). mRNA expression was measured by qPCR and normalized to levels of Tbp using the 2-ΔΔCt method.
I, J The single mutant which can abolish the ULK1 and FUNDC1 interaction was identified. HeLa cells were co‐transfected with Flag‐ULK1 and the indicated constructs. 24 h after transfection, cells were lysed for immunoprecipitation by anti‐Flag antibody.
O, Schematic summary to show how SGK1 inhibition mediates the N+F-induced anti-inflammatory action in glia.
(b) Spinning disk confocal image series of a region live FLCN-GFP/HA-FNIP2 transfected HeLa cell highlighting dynamic FLCN-GFP tubules (Movie EV2). First merge panel shows FLCN-GFP and lysotracker-Red at T=0 Subsequent panels show only FLCN-GFP at 30 second intervals.
D Tumour size in the DMBA-treated Hgf-Cdk4R24CXiapfl/fl and Hgf-Cdk4R24CXiapKO mice at 8 weeks of age (n=3). Dots represent an individual tumour.
, 3D reconstruction of confocal microscopy images of whole-mounted retinas from Nrl-/- (B) recipients 21 days after transplantation with Nrl::GFP donor photoreceptors (top layer) shows that donor and GFP+ acceptor photoreceptors appear to be attached via protrusions.
Detection of Xbp1 mRNA splicing in primary hepatocytes isolated from WT and KI mice treated with 0.2 μM Tg for 2 h (D)
(E) Co-labeling of vGlut2 and PSVue in the dLGN at P6. Circles indicate colocalized vGlut2 and PSVue.
D) mRNA expression of PGC-1β CXCL-1 and p16 in proliferating and senescent (10 days after 10Gy X-ray) wild type and PGC-1β-/- MEFs. Data are mean±S.E.M. of n=3 independent experiments; Asterisks denote statistical significant P<0.05 One-way ANOVA.
(e) The experimental structure of TREM2-TMH was docked to a previously determined structure of DAP12 in complex with NKG2C (Call et al., 2010). The positive charge in K186 is engaged in a salt bridge with D50 of DAP12. This charge complementarity together with hydrophobic interactions stabilize the complex and lead to a straight α-helical conformation in TREM2-TMH. D50 of the second DAP12 monomer is not in direct contact with TREM2, similar to the DAP12-NKG2C complex
Protein lysates from 10-13-week old CTRL and FAKO (Mllt4-/-) mice following retro-orbital injection of insulin (1U) were immunoblotted and quantified. BAT; Immunoblotting of Afadin S1795 phosphorylation (n=4-5).
(b) RNAscope analysis of Lgr5 mRNA in DSS colitis demonstrating loss of Lgr5 transcript (N=3 per condition). Data information: Nuclei are counterstained with Dapi (blue); white dashed lines indicate basement membrane. Scale bars =50µm
c, Representative images of EYFP-Rosa26/D6-cre+/- reporter mice and EYFP-Rosa26 (controls). Co-localization of Defa6 Cre-driven EYFP expression (yellow) with lysozyme-expressing Paneth cells (red; n = 3). DAPI, blue; scale bars, 50 µm.
G. Representative images of sagittal paraffin sections of cortices from P18 FBXO7+/+ and FBXO7-/- mice that were subjected to TUNEL staining. Three independent litter pairs were analyzed (paired t-test, * p<0.05, mean +s.e.m.). Arrows indicate TUNEL+ cells. Scale bar = 40 µm.
(B) The inherent elastic response of a lipid membrane (POPC) was studied by enforcing indentations via the isolated SNARE C-termini in the presence or absence of a short linker peptide, or the linker plus a fluorescent protein tag (FP). We define "relative indentation" as the change in C-terminus (Nyv1) - C-terminus (Vam3) distance that occurs when the SNARE complex performs mechanical work. It reflects the depth of the formed well upon squeezing. The slope of the obtained work profile estimates the required force (thin black line). Perforation (red arrow) requires a force of 80 pN for the wild-type C-termini. The plateau within the work profile indicates that the membrane gives up its elastic response (perforation transition). C-terminal tags oppose such a perforation transition but do not significantly affect the forces observed within the indentation regime. Furthermore, if the unstructured peptide-spacer would be alpha-helical - and thus much shorter - indentation forces would still be only slightly affected.
(a,b) Dual positive cells are more prevalent in epithelial organs and cells. (a) Proportion of ACE2+TMPRSS2+ cells (y axis) per dataset (dots) from 21 tissues and organs (rows).
A) Growth sensitivity to MMS and phleomycin of a Cdk phospho-deficient mutant of Spc110. Ten-fold serial dilutions from overnight cultures of wild-type, spc110S36-91A and a cdc14-1 cells grown on solid rich media containing mock DMSO, MMS or Phleomycin at 30ºC.
Representative in vitro phase-contrast (A), TH/DAPI or TH (insets) (B), and TH/SYNAPSIN-stained (C) images in the cultures terminally differentiated from mutant (c13, c19) and corrected hiPSCs (c22, c59).
E) Quantification graph of the percentage of anterograde and retrograde movements of EB1-GFP comets in the primary protrusion of qNSCs at 0 h ALH and 6 h ALH. n=28 at 0 h ALH; n=64 at 6 h ALH. 3 biological replicates per time point. p=0.9096 (ns)
H: PDX tumors were measured using a slide caliper and tumor volumes were calculated. n=5 animal per group and tumor volume presented as the mean ± SD
Top, flow cytometry density plots of Ki67 expression in CD4 T cells from representative G1 or G2 patients after three cycles of therapy, activated by incubation with A549-SC3 cells. Below, same as above but as a dot-plot graph. A comparison between proliferating CD4 T cells before and after therapy is shown in unpaired patient samples.
(C) Violin plot showing the expression of selected genes. EGFR+ Cluster 14 is circled with a red dotted line.
Citrate synthase staining in the arcuate nucleus of mice in (E) 4 h after treatment with vehicle or 120 mg/kg SH-BC-893 by gavage at ZT8.5; n=3.
Quantification of leaf starch. Data shown are means ± SEM; n = 8 per genotype and time point.
In normal cells (left panel), the newly synthesized histone variant H2AX is predominantly incorporated into the chromatin, where it acts as a major component of DNA repair pathway. Following DNA damage, H2AX is rapidly phosphorylated (hereafter referred to as γ-H2AX), γ-H2AX foci forms at the damaged sites and participate in DNA repair, which allows cell survival. In situations of chronic oxidative stress (middle panel), such as genetic inactivation of the redox sensors JUND or NRF2, aging, aggressive BC or following chemotherapy, H2AX degradation is increased in the nucleoplasm resulting in reduced H2AX content at chromatin. Indeed, ROS induce an enhanced interaction with the E3 ubiquitin ligase RNF168 and poly-ubiquitination on K119, followed by H2AX degradation by the proteasome. As a consequence, γ-H2AX levels are also reduced, cells become more sensitive to DNA damaging agents and are prompted to die. Consistently, in TN BC (right panel), successive cycles of chemotherapy cause a persistent oxidative stress, which modulate NRF2 response and decrease H2AX and consequently γ-H2AX levels. This response varies from one patient to another: some patients show a defective NRF2 activity with an efficient down-regulation of H2AX following chemotherapy (Major H2AX decrease) while some others show a mild or absent reduction of H2AX protein levels (Minor H2AX decrease). Tumours with major H2AX decrease are significantly enriched in oxidative stress signatures, demonstrating the role of redox imbalance in that process. In this group of patients, the efficient down-regulation of the H2AX protein following chemotherapy prevents DNA repair and enhances tumour cell death. Consistently, these patients survive better than the ones with minor H2AX decrease; the latter exhibiting resistance to treatment.
H. Hydroxyproline (HOP) concentration in mdx-Control and mdx-CriptoMy-LOF diaphragm muscle sections. Data are expressed as HOP levels (μg) per muscle section volume (mm3) and as box plots displaying minimum, first quartile, median, third quartile and maximum (n=5 biological replicates; **P<0.01, Student's t-test).
Genes significantly enriched or dropped out after a 14-day treatment with Doxorubicin were identified by plotting as a Log2 fold change compared to untreated. Ranking was determined based on the Log2 fold score (Left). The top ten Doxorubicin sensitizers are indicated on the right with their respective fold change (Fc) in Log2.
(g) Fraction of cellular cytosol occupied by LDs quantified in lymphoblasts from three UC and four HD subjects. Numbers of polyglutamine repeats are shown below. Mean + s.d. of >100 cell profiles. Dotted red line, mean value of the respective samples. *P 0.05.
e, dPVL cells associated with CTL exclusion. Repeated analysis in the same manner as in (d), instead with myCAF, iCAF, dPVL and imPVL clusters divided over all stromal cells independently, highlighting that CTL exclusion is mainly driven by dPVL cells. Representative cohort GSE58812 is shown.
(C) α-KG restores the levels of Rfa1-GFP foci in snf1Δ. Rfa1-GFP foci were measured as in Fig 3. At least 200 cells were analyzed for each experiment. Error bars represent SD from three biological repeats. Statistical significance was evaluated based on Student's t-test (*0.01 < P-values < 0.05).
(A-C) RAB21 is not required for CI-MPR or GLUT1 trafficking. (A) Immunofluorescence of endogenous CI-MPR and TGN46 or GLUT1 with LAMP1 in RAB21-knockout cells. Boxed region is magnified. (B) Per cell Pearson Correlation between CI-MPR and TGN46 or (C) GLUT1 and LAMP1; SEM, n=3 independent experiments. Data information: In (A), scale bars represent 20µm or 5µm in enlarged views for CI-MPR, while they represent 10µm in enlarged views for GLUT1. Statistical tests used: (B) - Unpaired t-tests (C Mann-Whitney tests. All error bars are SEM. Number of cells presented on each graph represents the total number of cells analyzed for all repeats
(a) vBcl-2 binding proteins. After transfection, 293T cells were used for GST-pulldown and the purified proteins were detected by silver staining.
(I) Distribution of number of nascent RNAs at the transcription site determined by smFISH. The distribution of UASwt does not fit a Poisson distribution (grey line), supporting that GAL3 is not constitutively transcribed, but is transcribed in bursts. Example image in shown, yellow arrows indicate TSs. Scale bars: 5 μm. n = 11,839 cells. (J) for cells with UASmut. The distribution of UASmut fits a Poisson distribution, indicating that GAL3-UASmut is transcribed with random initiation of individual polymerases, similar to constitutive genes. n = 10,616 cells.
Same as in (E) but using concanamycin B (50 nM) instead of NH4Cl. Uukuniemi virus (UUKV) was used at a MOI of 150 to control the efficiency of concanamycin B to neutralize endosomal pH in Caco-2 cells. n = 2.
A) NADPH levels are reduced in IDHm compared to wildtype tumors, resulting in a reduced NADPH/NAD+ ratio (n=3/ sample). p-value from T test: *<0.05. NADPH, NADP: reduced, oxydized nicotinamide adenine dinucleotide phosphate, NADH, NAD: reduced, oxydized nicotinamide adenine dinucleotide.
(C-G) (C-D, F) Western-Blot of WT and EMC6KO (6KO) U2OS cell lines transiently transfected with the opsin-tagged constructs probed for HA. When indicated, denatured samples were treated with PNGase to confirm glycosylation. Glycosylated proteins shift upwards in the gel and are indicated by arrows (). (E, G) Western-Blot of WT and EMC6KO (6KO) U2OS cell lines transiently transfected with the opsin-tagged constructs probed for Actin and EMC6.
(A) Isoform-specific subcellular localization shown in cultured hippocampal neurons (DIV14) co-expressing DsRed-CA7 (left) and EGFP-CA2 (middle).
Figure 2Sedimentation velocity analysis of the salt-dependent assembly of nucleosomal array oligomers.A Representative experiment showing the second moment sedimentation coefficients of the oligomeric nucleosomal arrays as a function of MgCl2. The second moment sedimentation coefficient is equivalent to the mass average sedimentation coefficient for the entire sample (see Materials and Methods). The inset shows the mean second moment sedimentation coefficient the standard error for three replicated experiments.B Analysis of the same raw data as in panel (A) by the time derivative method to yield the sedimentation coefficient distribution, g(s*).
(B) Primary root length of the plants tested Data are means ± SE (n = 25, individual plants). Student's t-test (**P < 0.01) was used to analyze statistical significance, and "#" represents the control.
The overall survival of gastric cancer patients (all stages) was analyzed depending on TRF2 and its targets genes expression level (HS3ST4, GPC6 and VCAN collectively named the HSPG genes) Data information: For all panels, the optimal cut-off is determined on KMplot. The p value (log Rank test), the Hazard Ratio and number of patients are indicated.
(C) THP-1 and BMDMs were stimulated with rRv2626c (2.5 μg/ml) for the indicated times, followed by IP with αHis (up) or αTRAF6 (down) and IB with αTRAF6, αHis, and αActin.
E Representative images of the DNA fibers used for the analysis explained in (C, D). CldU (red) and IdU (green) channels are shown.
(D) Immunohistochemical quantifications of fibrinogen deposition in no tumour-bearing- and tumour-bearing- mouse lungs. Shown are averages (N = 7/ group, 14 random fields) with SEM. Welch"s t-test