EMBO/sd-character-level-ner huggingface dataset:
(a) Z-projection (a) and 3D cell reconstruction (a') of stills from two-photon live imaging of an E7.25 embryo mosaically labelled for epiblast cells showing a division giving rise to an epiblast and a mesoderm cell that will exit from the epiblast layer. White dotted lines outline basal (top) and apical (bottom) borders of the epiblast at 0min, 25 min, 50min, 1h15min and 1h40min. (b) (c) Z projection of stills from two-photon live imaging of an E7.25 embryo mosaically labelled for epiblast cells. Non-apical division can be observed in the posterior epiblast only, without (b) or with (c) attachment to the apical side. Stills were taken at 0min, 25 min, 50min, 1h15min and 1h40min for (b) and 50min, 1h15min, 1h40min, 2h05min and 2h30min for (c). White dotted lines outline basal (top) and apical (bottom) borders of the epiblast.
B The expression of the predicted Tetrahymena genes showing more than 19 expressed sequence tags (ESTs) from conjugating cells but not vegetative cells was analyzed by RT-PCR using total RNAs from exponentially growing vegetative cells ("E"); 16‐h starved cells ("S"); or conjugating cells at 2, 4, 6, 8, 10, and 12 hpm. Twenty‐two genes that were exclusively expressed during conjugation are marked with a yellow background. Eleven genes that were analyzed by gene knockout (KO) are indicated in the "KO" column. The phenotypes are described in the "KO phenotype" column. The predicted TTHERM_00526270 contains two genes, which were analyzed separately in this study.
U2OS-LacO cells transiently expressing Myc-LacI-Bub1 and EGFP-TOP2A (970-1531) were subjected to immunofluorescence staining with DAPI and antibodies for the Myc-tag and GFP. Cell lysates were immunoblotted (K).
A. Graph showing effect of ruxolitinib on megakaryocyte differentiation at 50 and 100 nM in healthy CD34+ cells (n= 4 different cords collected with 3 technical replicates). Data information: Error bars indicate standard error of mean. All P values are unpaired Student's unpaired t-test.
"Volcano plots" of statistical significance against Log2 fold-change, depicting the PRGs (Tyssowski et al., 2018) that were differentially expressed in Bic-treated siLemd2- vs scrambled siRNA-transfected cultures (left panel) and Bic-treated Satb2CamkCre vs Satb2 floxed primary cortical cultures (right panel). The down regulated PRGs are indicated in blue (adjusted p-value < 0.05, Log2fold-change < -0.3) and the up-regulated (adjusted p-value < 0.05, Log2fold-change > 0.3) are shown in red.
CY preferentially killed CLL cells over healthy B cells. Data represent mean ± SD
A. Experimental setup to identify transcriptional variability between seedlings during the day and night. RNA-seq was performed on individual seedlings, for a total of 14 seedlings at each time-point. Seedlings were harvested at 12 time-points, every 2 hours across a 24 hour period. Seedlings of different colors represent different transcriptional states, and thus inter-individual expression variability we aim to identify.
(A) Torin 1 induces S142 dephosphorylation. HeLa cells were treated as indicated and total and nuclear extracts were probed with a TFEB p‐S142 phosphoantibody and with anti‐FLAG antibody. Disappearance of TFEB S142 phosphorylation upon starvation or Torin 1 treatment correlates with accumulation of TFEB in the nuclear fraction.
Schematic presentation of the disease associated / homeostatic phenotypes observed in Grn-/- mice versus Trem2-/- and the potential consequences for a therapeutic window of microglial modulation.
A. Overview of holoElongator and individual domains important for the interaction of Elp123 with Elp456. Elp1 (orange), Elp2 (yellow), Elp3 (pink), Elp4 (green), Elp5 (blue) and Elp6 (sand) are shown in surface representation to indicate the topological nature of our model. Individual domains are labeled.
(B) Cyclin-Citrine degradation relative to the nuclear import of 50% Whi5-mCherry was followed in single cells. Plot shows the time from nuclear import of 50% Whi5-mCherry to the degradation of 50% of the indicated cyclin in individual cells. The error bars show 95% CI of the mean.
A: Wild type and mps1 mutant cells were synchronised in G1 with α-factor at 25°C and then released at 34°C in the presence of nocodazole (t=0). Cells were collected at the indicated time points for FACS analysis of DNA contents.
(A) Detection of protein-protein interactions using the two‐hybrid system. Intense staining indicates an interaction between Aut2p and Aut7p, Aut2p and Tub1p, and Aut2p and Tub2p. AUT7, TUB1 and TUB2 are cloned in‐frame with the GAL4‐activator domain. AUT2 and AUT7 were fused to the GAL4‐binding domain (see Materials and methods).
(b) Southern blot analysis of the BSF conditional KOs. Genomic DNA from the T. brucei SM parental strain (+/+), single- (+/−) or double-allele (−/−) KO cells.
Schematic summary: wild-type (H) and OtofPga/Pga ribbon synapse (I) upon stimulation. Not drawn to scale; color coded similar to the legend in B, frequently observed events are highlighted with a black asterisk, no changes are indicated by green (=). The arrows show the sequence of events taking place in wild-type and OtofPga/Pga when stimulated.
E qRT-PCR analysis of levels of inflammatory factors in duodenum tissues of mice treated with Control-Fc or Spike RBD-Fc. Control-Fc, n = 5; Spike RBD-Fc, n = 6. n, biologically independent samples (mice). Data information: All data are shown as mean ± SD. ; for (E), P values are determined by Mann-Whitney test.
G) Total lysate and surface biotinylation western blot analysis of HEL cells overexpressing either GRASP55-V5 or HA-STX5.
i, Pairwise correlation between phase durations for cells incubated at 34°C. Number of cells: 34°C, n = 122
(F) Expressing Tau-k18(-) abolished Tau-induced upregulation of mRNA levels of survival genes (bcl2 and survivin) and dkk1 (downstream of Wnt signaling) in N2a cells measured by Q-PCR (n=6~9 biological replicates each group). Data information: Data are expressed as mean ± SEM, *, P<0.05; **, P<0.01, ***, P<0.001 vs Tau (F Data were analyzed by one-way ANOVA
B The S1P deficiency-induced abnormalities in mitochondrial respiration can be significantly reversed by riboflavin supplementation and ETFA/B overexpression in HaCaT cells. Left panel: Mitochondrial respiration (OCR) was quantified in real time using a Seahorse extracellular flux analyser.
G Co-immunoprecipitation to detect the interaction between HIF2α and the wild-type (WT) or the catalytically dead (CD) USP33. Ectopic HA-tagged HIF2α were expressed in 293T cells with GFP-tagged wild-type or catalytically dead USP33. Cell lysates were subjected to immunoprecipitation with anti-HA antibodies. Co-immunoprecipitated products immunoblotted with the indicated antibodies. The catalytically dead USP33 relative to the wild type USP33 showed a stronger affinity to HIF2α.
Representative images of CYP46A1 IHC staining in GBM and adjacent brain tissues from one specific case. Scale bar = 30 μm.
Representative IF images showing the expression of secretory cell marker CC10, mTORC1 activity p-S6, and DATP marker CLDN4 in Scgb1a1 lineage-labeled toTomato+ cells from serial sections of control and Lats1/2 dKO lung tissues. Tomato (for Scgb1a1 lineage, red), CC10 (green), p-S6 (white), CLDN4 (magenta), and DAPI (blue). Scale bars, 100μm.
A-C) Analysis of RNA Pol II binding (RPB-1/AMA-1 ChIP-seq) at upregulated genes in rpb-9 (mj261) mutants, as defined in Figure 3C. Class I: upregulated genes with increased RNA Pol II binding (A); Class II: upregulated genes with invariant RNA Pol II binding (B); Class III: upregulated genes with reduced RNA Pol II binding (C). n=3 biological replicates are shown per each genotype. (PolyA-selected RNA-seq libraries). Central bands represent the median, boxes represent the 25th and 75th percentiles and whiskers represent the lowest and highest values, excluding outliers.
RAW264.7 macrophages were infected with Mtb WT or Mtb ΔRD1 for 24 h, Ca WT or Ca YL, and Lm WT or Lm Δhly for 60 min. (A) Levels of Rab8A and Rab8A pT72 phosphorylation were analysed by Western blot and quantified by densitometry. Data represent the mean ± SEM of three independent biological experiments. One-way ANOVA followed by Dunnett's test compared to WT strains. ns= non-significant; *p ≤0.05; **p ≤0.01.
(G) Wild-type primary B cells were labelled with Atto633-conjugated Fab fragments against CD22, settled onto nonstimulatory coverslips and treated with vehicle control (DMSO) or 1µM LatA. Single particle trajectories were then analysed. Bars and numbers indicate the median. Data are pooled from two experiments.*P < 0.0001 (Student's t-test).
(A) Representative electron microscopy images of liver samples harvested from wild-type (WT) and AslNeo/Neo mice treated with TB-1 or vehicle. False color on the images indicates glycogen within the nuclei. Scale bar: 1 μm. (B) Quantification of nuclei containing glycogen (approx. 180 nuclei were analyzed in total per condition, n=3 mice/group).
Examples of simulations of IAHC distributions for the IgG (left) or αDll4 (right) treated samples. Simulations were performed with the most likely parameter values described in b and c. Note that only clusters that have at least one colored cell are shown (i.e clusters with non-colored cells are not represented).
Cumulative probability plots of mEPSCs amplitude (500 events per cell) and representative examples of mEPSCs (left panel) recorded from cultured cortical neurons after 48 hours of 1 µM TTX or Veh exposure (E) Fxr1overexpressing neurons (Fxr1/Veh n=10 and Fxr1/TTX n=8)
H1299 cells were transfected with Flag-USP36 or the indicated deletion mutants and assayed by IB. FL, full length.
C and D. Time course analyses of mutant SOD1 accumulation at the MAM in SOD1G85R (C) and SOD1G37R (D) mousespinal cords. Quantitative data from three independent experiments were plotted (bottom). The arrows in the bottom panel are the same as in A and B.
D. Increased G1 phase in Rb∆K7 MEFs. Mean ±SD of propidium Iodide flow cytometry analysis showing a significant increase in G1 and decrease in S phase in synchronized Rb∆K7 MEFs relative to control (n=3 independent MEFs).
B. Time course of ear swelling elicited by topical application of the indicated concentrations of iodine in 0.15% Oxa-challenged mice, and a bar graph highlighting the response at 24 h.
(H) Co-immunoprecipitation showed endogenous proteins of IDH1 and SIRT2 interacted with each other.
(a) DNA-labelling scheme of NSP2 for DNA-PAINT imaging. Low levels of SNAP-tagged NSP2 (a doughnut-shaped NSP2 octamer) are produced in a stable MA104 cell line. A SNAP-tag reactive benzylguanine (BG) DNA derivative (P1 ssDNA docking strand) can form a stable thioether bond with NSP2-SNAP.
(A) Differentiation status (poor, moderate or well-differentiated), circumscription (not infiltrative, focally infiltrative or infiltrative), log10 total number of mutations and Gata6 mutations in 32 human sebaceous carcinomas (SebC) separated in 3 subgroups: pauci-mutational, MSI-related and UV-related For Gata6 mutations, the most deleterious mutation is displayed. n.a.: not assessed.
(D and E) The binding modes of the human cGAS-DNA 2:2 complex in the resting and palmitoylation states. Monomer A, monomer B and DNA-1 in the human cGAS-DNA 2:2 complex in the resting state are shown with pale cyan, light pink and cyan cartoons, respectively, while these components in the human cGAS-DNA 2:2 complex in the palmitoylation state are exhibited with light blue, yellow and slate cartoons, respectively. The C474 and S-palmitoylated C474 residues are highlighted by ruby sticks, while the dominant residues in the human cGAS-DNA 2:2 complex in both the resting and palmitoylation states are shown in sticks.
Collision-induced dissociation spectra of AAUGp, m6AAUGp and m6Am6AUGp. The product ions are assigned as indicated.
H. Representative flow cytometry plots showing gating strategy (left panel) to identify germinal center B cells (PNAhigh, CD95+) from the spleen of unchallenged WT and KO mice and statistical analysis of their absolute number (right panel). Results represent the data pooled from two independent experiments and numbers represent biological replicates for each group (WT; n = 4, KO; n = 6).
Direct comparisons of CNA profiles. Percentages of gene copy number gains and losses across the chromosomes for different sample types. Copy number gains are displayed in green, losses in red. B CNA comparison between early (p04) and late (p30) CTC-ITB-01 passages (upper and medium panel). Significant distinctions between both samples were calculated using Fisher's exact test (Joosse et al, 2018) and are indicated in lowest panel (in blue). Increased blue color intensity represents lower p-value and therefore higher statistical significance.
(A) Quantification of the fraction of cells with ANKRD26 localized at the mature mother centriole. Experiments were performed in PLK4Dox monoclonal knockout cells. Data acquired across n = 3 biological replicates. Mean ± s.e.m.
C. Quantification of U2OS-ACE2 fusion and death by time-lapse microscopy. Results are mean±sd from 3 fields per condition.
IFstaining for DEUP1 reveals a further size increase of deuterosomes of Ccno‐deficient MCCs at later stages of centriole biogenesis (ALI day 7). Deuterosome number and size were quantified in (C). IF using a Centrin antibody shows globally reduced presence of centrioles at ALI day 7, which stay localized below the level of deuterosomes and fail to dock to the apical cellmembrane in Ccno‐deficient MCCs as seen in z‐projection.
B Left panel: qPCR analysis of lnc-SMaRT enrichment in the RNA pull-down performed in C2C12 cells at day 2 of differentiation (DM2); Set#1 and Set#2 probes were used against lnc-SMaRT together with a control set of probes against LacZ mRNA (LacZ). Data are expressed in percentage of input and presented as the mean ± s.e.m. of three biological replicates (dots). Right panel: Western blot analysis showing the specific enrichment of the DHX36 helicase in lnc-SMaRT pull-down; GAPDH was used as the negative control. Representative results from three independent experiments are shown.
B, C Glucose (B) and glutamine (Gln, C) levels in the medium after treatment of melanoma cell lines with LDHAi for 72 hr. Data information: Statistical analysis was performed by ordinary one-way Anova for the comparison of more than two groups. Unpaired t-test was used for the comparison of two groups, N.D., not determined. Data are shown as the mean ± SD, n = 3. ns: not significant, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001.
Predicted kinases are indicated on top of each panel for which one of their marker substrate phosphorylations was assayed. UACC257 cells were serum starved and stimulated with PBS or EDN at 100 nM for 60 min (5 min for CaMKII). Ten μg protein from RIPA lysates were analysed by Western blot. Kinase marker substrate phosphorylations and corresponding loading controls are shown. For each kinase, two independent replicates were performed and are shown. Each gel also had control lanes with increasing concentration of kinase inhibitors to support phospho band identity
C-D) Expression of loricrin is determined by immunoblots and quantified by densitometry. The relative expression level of loricrin upon calcium shift in different cell types was calculated and presented as bar graphs. Statistical analysis is conducted using unpaired Student's t-test. Error bar represents S.D. (standard deviation). N=3 (biological replicates). ***, p<0.001; **, p<0.01; *, p<0.05
(G) Effects of RNF26 knockdown on virus-triggered phosphorylation of TBK1, IRF3 and IκBα. The THP-1-RNF26-RNAi or control cells (1×106) were infected with SeV or HSV-1 for the indicated time points or left uninfected, whole cell lysates were analyzed by immunoblots with anti-p-TBK1, anti-TBK1, anti-p-IRF3, anti-IRF3, anti-p-IκBα, anti-IκBα, anti-RNF26 or anti-β-actin as indicated. All experiments were repeated for at least three times with similar results. The bar graphs show mean ± S.D. (n = 3) of a representative experiment performed in triplicate.
E. Quantifications of SCRN1 recruitment to VAPB-positive structures in COS7 cells (%). Left graph: co-expression of GFP-SCRN1 with HA-VAPB or HA-VAPB-K87D/M89D ( N=2-3, n= 44-46). Right graph: co-expression of HA-VAPB with GFP or GFP-SCRN1, GFP-SCRN1-N, GFP-SCRN1-C, GFP-SCRN1-Y40A, GFP-SCRN1-F144A, GFP-SCRN1-F153A or GFP-SCRN1-F402A (N=2-3, n=41-64). Data information: Data represent Mean ± SEM; NS: not significant; *P < 0.05; **P < 0.01; ***P < 0.001, by Chi-square test with post-hoc analysis including Bonferroni correction.
A Control or UBE2QL1-depleted (for 60 h) HeLa cells were stained with DAPI and an antibody against TFEB and automatically analyzed by confocal microscopy. Note nuclear translocation of TFEB upon loss of UBE2QL1. Scale bar: 20µm.
With LPS stimulation (20 ng/mL, 8 h), iNOS protein production was examined by immunoblotting analysis (E).
A) Immunoblot analysis. Primary hepatocytes were isolated from Nbr1f/f mice and then infected with adenovirus GFP or Cre for 48 hrs. Thereafter, the hepatocytes were divided into 3 groups: 1. Cultured in regular medium (-), 2. Treated with 10 μM As (III) for 12 hr [As (III)] and 3. After treated with 10 μM As (III) for 12 hr, cultured in regular medium for another 12 hr (Wash). Cell lysates were prepared and subjected to immunoblot analysis with indicated antibodies. Data shown are representative of three separate experiments. Bar graphs indicate the quantitative densitometric analysis of the indicated proteins relative to actin. Data are shown as means ± s.e. *P < 0.05, **P < 0.01, and ***P < 0.001 as determined by Welch's t-test.
Mitochondrial stress induces the formation of single membrane TOM20 mitochondrial-derived vesicles (MDVs) through a currently undefined mechanism. Following budding, Tollip is essential for MDV transition into an early endosomal compartment followed by the concomitant recruitment of Parkin. Tollip and Parkin work in close association to transfer MDV cargo through the endosomal system, thus requiring both of their function for trafficking onwards to the lysosome. Fusion with endosomal intermediates to facilitate maturation and subsequently fusion with lysosomal compartments is required to mediate turnover of MDV cargo. Constituents such as Tollip and Rab7 are 'recycled' from the lysosome back to endosomal bodies via a retromer-dependent pathway.
(D) Catalytically active HOIP decreases the number of cells with Htt-Q97 aggregates independently of autophagy. WT and ATG5 KO MEFs were transiently transfected with Htt-Q97-GFP and either control vector (CO), HOIP or HOIP C885A. Cells were treated 24 h after transfection with the proteasomal inhibitor MG132 (1 µM, 16 h). Data are displayed as mean ± SD and were analyzed by one-way ANOVA followed by Tukey's Multiple Comparison Test, n = 7. Data information: *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001.
H Representative images (selected cases obtained from Fig EV6M) and histological score of AHR, DDA1 and UBE4B in human brain metastases (n=16) according to the signal intensity of the corresponding protein in cancer cells.
(A) HeLa cells were infected with Listeria wild‐type (WT) or the LLO/PlcA/PlcB triple knockout (TKO) mutant strain for 0.5-4 h, and lysates were analysed by blotting using indicated antibodies.
B. same as A, but using only GST-tagged Elp3 SAM domain with combinations and variants of Elp1, Elp2, and Elp456.
As expected, the levels of TET1 are decreased in Ts65Dn mouse, however Ts65Dn/DSCR1+/- mouse restores the TET1 mRNA expression. Values are shown as mean ± SEM and tested for statistical significance by one-way ANOVA followed by Bonferroni post hoc test. ß-actin was used for normalization. N = 3 (Diploid), 3 (Ts65Dn), 4 (Ts65Dn/DSCR1+/-) mice, *P< 0.05, **P< 0.01.
(A) Gene Set Enrichment Analysis (GSEA) of Hnf4g KO organoids compared to WT organoids. Significant changing intestinal cell type gene sets from Haber et al (2017) are shown (FDR < 0.05)
Western blots of the proteins in mascRNA S and AS pulldown samples (top 4 panels), and mascRNA and menRNA pulldown samples (Bottom 2 panels). β-tubulin was used as a loading control.
(I) Single-cell Ca2+ traces upon FcγR activation by opsonized 3-μm beads in -Ca2+o expressed as a percentage of Fmax. (I, J) Pre-emptying the ER stores with CPA or thapsigargin (Tg) abolished the global cytosolic Ca2+ response evoked by beads, but a TPC2-G‑GECO1.2 component remained, n = 17 - 121 cells.
G. RHOB immunostaining score evolution in EGFR-mutated lung tumors before treatment and after EGFR-TKI relapse.
Kaplan-Meier analysis showing that fibrillar collagen is significantly associated with reduced survival in human PDAC (20 months vs. 28.3 months, P = 0.033).
Representative images of single plane phase-contrast and Z-stacked immunofluorescence of empty vector (EV) and CEP55-overexpressing MCF10A cells grown on Matrigel for 14 days. Red: Cytokeratin-19; Green: F-actin stained by Phallodin and Blue: DAPI. Z-stack images were acquired through Zeiss LSM 780 confocal microscope-ZMBH.
Asynchronously proliferating HeLa cells were treated with indicated siRNAs, incubated with EdU during 30min and analysed by immunofluorescence microscopy. The percentage of p-Rb and/or EdU positive cells was quantified in (E), 2100 cells were analysed (mean ±SD, *P < 0.05; **P < 0.01; N = 3)
D Fluorescence images of cells expressing Hmg2-GFP and either additionally expressing Sec63-mCherry or stained with CMAC. The upper and lower panel show cytosolic and vacuolar Hmg2-GFP rings, respectively. Scale bars: 2 µm.
BiFC assay showing that UVR8 interacts with MYB73/MYB77 in white light condition. N. benthamiana was co-transformed with MYB73-nYFP/MYB77-nYFP and cCFP, nYFP, and UVR8-cCFP, or MYB73-nYFP/MYB77-nYFP and UVR8-cCFP. BF, bright field. Merge, overlay of the YFP and bright field images. Scale bar = 20 μm.
(G) BNGE, Western blot and immunodetection, with an anti-HA tag antibody, of samples from the cell lines solubilized either with digitonin.
(g) The forced expression of SLC7A11 rescued cell death induced by ATF4 ablation. HLE cells were transfected with a construct coding for SLC7A11 (SLC7A11 OE) or empty vector (EV) and with siCtrl or siATF4 every other day. Cells were then treated with either DMSO or 6μM Sorafenib for 2 weeks. Colony formation was visualized by crystal violet staining. Results represent three independent experiments.
6-week-old male CD36 knockout mice were administered with AAV-TBG-wildtype-CD36, wildtype-CD36 plus KLF10, palmitoylation site mutant CD36, mutant-CD36 plus KLF10 through tail vein injection, and then kept on WD/CCl4 for 12 weeks. n=5 per group. (I) CD36 protein expression in the plasma membrane fractions, and its normalization to ATP1a1. Data information: * P <0.05, ** P <0.01, *** P <0.001. Results are shown as mean ± SD. 1-way ANOVA
D. Average ± SD of minimum Feret's diameter in quadriceps (p = 0.26) and tibialis anterior (p = 0.33) muscles is not significantly different between summer and hibernation.
(o-r) Monodansilcadaverine (MDC) labelling performed on cells unexposed (o) or exposed to 1 (p) or 10 ng ml−1 (q) IL-17A for 4 h. Cells were magnified in the inset (r). Representative results from three independent experiments. The mean values (% hyphal cells with MDC-stained organelles (merge); mean±s.d.) were as follows: none, 9.5±3.2; 1 ng ml−1 IL-17A, 14.0±4.7; 10 ng ml−1 IL-17A, 56.2±18.71 (P=0.004, IL-17A 10 ng ml−1 versus none). Scale bars, 10 μm.
I Western blots show depletion of ATRX protein expression in hTERT-transduced and ATRX-deleted A-1 and A-2 U87 cells.
(F) Magnification of the electron micrograph of the Brucella-infected control cell in (A), showing large vacuoles studded locally with ribosomes (arrows).
Retromer is required for endosomal localization of RAB21. Immunofluorescence of transiently expressed GFP:RAB21 with endogenous (E) EEA1 in parental or VARP- and VPS29-deleted cells. Boxed region is magnified underneath. Data information scale bars represent 10µm or 2.5µm in enlarged views.
Simultaneous expression of Y701F-STAT1 rescued the hTau-induced suppression of NMDARs protein expression measured by Western blotting in hippocampal CA3 of C57 mice (n=4).