EMBO/sd-character-level-ner huggingface dataset:
Growth curves for LN229 cells treated with DMSO, 0.5 μg/mL cholesterol or 10 μM 24OHC in the presence or absence of 0.5 μg/mL cholesterol using trypan blue staining.
E. Lysates of HEK293T cells, transfected with the indicated HA-ubiquitin, GFP-PSMA2 or myc-FBXO7 plasmids, were subjected to boiling, followed by IP with the GFP antibody (PSMA2), followed by IB with the HA antibody (upper panel). Inputs were immunoblotted with the GFP, myc or HA antibody (lower panels). Three independent blots were quantified and band intensity normalized to control (lane 2) average. (ANOVA, Dunnett's multiple comparison ***p<0.001, mean + s.e.m).
Gene expression profiles of PBMCs from P. falciparum symptomatic and healthy immune controls were compared. Hierarchical clustering heatmap (G) displaying DEGs in symptomatic P. falciparum malaria and healthy immune controls predicted to be controlled by IFN-γ and IL-13 upstream regulators.
pΦ from B6 were infected with indicated strains and intracellular bacterial viability was monitored 96 h p.i (mean ± SEM; n=3).
A) Fluorescence emission spectrum of mt-sEcGFP in HeLa cells in situ at different pH values (λex.=405 nm, λem.=415-705 nm; λ-emission scan of transfected cells with 10 nm steps using a cLSM microscope). Before and after the isosbestic point (indicated), the pH dependence of the emission is reversed, allowing for a readout of pH-dependent fluorescence emission in the two indicated channels and ratiometric imaging (λ511/λ464). The λ range for the first channel is larger than the λ range for the second channel, allowing a better match of the signal intensities of the two different channels.
(C) Western blot of WT and iKO cultured keratinocytes after 0 or 6 hours of tamoxifen induction, blotted with actin and Gata6 antibodies, show a decrease in Gata6 protein levels after 6 hours.
The release of mature IL-1β (e) from Ramos cells were measured by enzyme-linked immunosorbent assay (ELISA).
Scatter plots as in (A) highlighting in black subsets of known genes associated with the GO terms extracellular matrix
U2OS WT, PHF6 knockout and PHF6 knock out cells that were reconstituted with GFP-PHF6 were synchronized in G2 and recovery was determined after 2 Gy of IR using flow cytometry with pHH3 staining
C Comparison of precursor organization of AITDs with different origins. NCSS, nonclassical signal sequence; SP, signal peptide; PP, propeptide; MP, mature peptide.
Histograms represent the mean fluorescence intensity for Jup (H) and Emilin1 (I) in LYVE1+ cells in the vicinity of HF in P55 and P70 mouse back skin. n= 3 - 4 skin samples per mouse, n= 3 - 4 mice.
Immortalized Brca1F/− MEFs were infected with retroviruses expressing the indicated shRNAs and/or Cre recombinase. Mitotic chromosomes isolated 48 h later were fixed and stained with a Cy3‐conjugated (CCCTAA)3‐PNA probe. The frequency of end‐to‐end chromosome‐type fusions is represented as a percentage of fusions observed after TRF2 depletion. A minimum of 2,000 chromosomes were scored for each sample. Error bars represent SD of three independent experiments. P‐values were calculated using an unpaired two‐tailed t‐test. NS, P > 0.05.
(D) The total radioactivity associated with Cer, SM and GSLs (GluCer, LacCer, Gb and GM) or GM and Gb was quantified and presented as percentages relative to total. Data represented as means ± SD of 3 independent experiments.
A, Representative photomicrographs taken from the dorsal striatum 13 weeks after AAV-injection. In the GFP control condition, virtually all GFP positive cells depict an astrocytic morphology, many GFP positive cells in ALNe-218 and ALN-treated animals show a neuron-like morphology. Data information: Scale bars indicate 20 µm.
Fig. 3. Multilevel profiling approach of spironolactone treatment assessing target specificities and adapter recruitment.(A) Spironolactone, molecular structure shown left, inhibits ERBB4/PIK3R1 split TEV assay activity (black line), with an IC 50 value of 2.76 µM.
(A). NSF was phosphorylated after stimulation with AngII or KCl. Adrenal medulla cells were stimulated with 100 nM AngII or 70 mM KCl for 5 min and lysed. NSF was immunoprecipitated with a specific NSF antibody coated with Protein A/G beads. A pan-phospho-tyrosine antibody pY20 was used in Western blot to detect the tyrosine-phosphorylated NSF in the adrenal medulla under different conditions.
I. PTI marker gene expression in PBL34 complementation lines. The PTI marker genes FRK1 and NHL10 expression was examined by RT-qPCR in Col-0, pbl34/35/36, and CM-PBL34-2A lines after 3-OH-C10:0 treatments for 4 hrs. Values are means ± SD (n=6; ANOVA; p < 0.01).
Lentiviral vectors with GFP reporter that are controlled by the promoters used in miR-AB lentiviral vectors were constructed for easy assessment of the promoters activity on microscope or flow cytometer.
B An FXR peptide modified by acetylation at Lys 217 (NVKQHADQTVNEDSEGR) was identified in an MS2 spectrum and manually confirmed by a subsequent MS3 scan. Emp: control empty Ad‐Track vector.
A Z score for AUC and IC50 of 37 different drugs (shown along the horizontal axis) identified as hits in 13 of 17 samples screened. A drug hit is defined as z score of less than -2 for both AUC and IC50. Each dot in a column represents a sample screened for that drug. The size of the dot corresponds to the IC50 z score for that sample (the larger the dot, the smaller the IC50). Dots below the black horizontal line represent sample with AUC z score of less than -2. Dots are color coded for drug hit types. All color dots below the black line represent a hit for the corresponding drug.
The apical α-βHSpectrincytoskeleton may be mechanosensory in the wing imaginal discA Schematic diagram of central compression and circumferencial stretching in the third instarwing pouch.B-D Third instarwing imaginal disc stained for beta-galactosidase expressed from the expanded.lacZ reporter gene (B), Crb (C) and Kst-YFP (D). Quantification of line intensity shown below. Note inverse correlation of Crb and Kst-YFP with ex.lacZ. Scale bars, 50 μm.E, F Zoom of Kst-YFP cells under compression (E) and under stretch (F). Scale bars, 10 μm.G Schematic diagram of the effect of force on the apical spectrin cytoskeleton leading to declustering of Crumbs complexes and reduced Hippo signalling.
A diagram of luciferase reporter constructs with wildtype and mutant 4E-BP1 promoter.
Pairwise correlation plots of rpb-9 (mj261) and prg-1 (n4357) (E), hrde-1 (tm1200) transcriptomes. Differentially expressed genes in rpb-9 (mj261) are shown in black, shared upregulated genes in red, shared downregulated genes in blue. The piRNA sensor transcript is highlighted in green. (Total RNA "Ribo-Zero" RNA-seq libraries).
A. Schematic of the full-length Srs2 protein shown as a bar. I - VI indicate Srs2 helicase motifs, K41 - a lysine residue required for ATP binding and hydrolysis, BRCv - BRC repeat variant motif, Rad51-BD - Rad51-binding domain, asterisks - sumoylation sites, PIM - PCNA-interacting motif, SIM - SUMO-interacting motif. Numbers below the protein indicate positions of amino acid residues within the Srs2 protein.
D. The patterns of the Q97-GFP distribution were quantified after different time of expression, n=100. Cell boundaries are indicated by dashed lines.
(B) Activation of Cre recombinase by tamoxifen (TAM) results in COUP-TFII deletion and the expression of LacZ reporter (detected by immunostaining of β-galactosidase (β-Gal, red) in the UUO mice model (n=2). Quantification by confocal micrographs in 200x hpf. **p<0.01; ***p<0.001 by paired t test; mean ± SD.
C, D. U6A cells expressing wild-type or T387A STAT2 were treated with IFN-β for 0, 4, 8, or 24 h. Total RNAs were analyzed by using an Illumina HumanHT-12 v4 Expression BeadChip array. The average signal for each probe was used to determine expression levels. Genes with average signals below 25 and detection P values greater than 0.01 in the untreated or treated cells were excluded from the analysis. Inductions of less than 2-fold were not scored. The Venn diagram shows the numbers of genes induced by 1.2 fold or more in U6A cells expressing T387A STAT2, relative to untreated control cells. The numbers in the table are fold changes calculated from the ratios T387A STAT2 treated / untreated and wild-type STAT2 treated / untreated.
Real-time RT-PCR analysis of mRNA levels of ER-GATA-1 target genes in untreated or b-estradiol-treated (48 hours) WT and mutant clones. ***, P < 0.001 with respect to all values of WT1-3 (n = 4, mean +/- SE).
A Schematic diagram describing organoid culture derivation (AP, Anterior Prostate; DLP, Dorso-Lateral Prostate; VP, Ventral Prostate; SV, Seminal Vesicle; DHT, dihydrotestosterone).
D. Prediction of breast cancer overall survival in two independent published breast datasets (upper panel) Pawitan et al, 2005 and (lower panel) Chin et al, 2006, based on Rab25-associated gene signature. Breast patient classification was determined by BRB tool class prediction function to identify patient with Rab25-associated gene expression signature (Rab25-signature) or without (non-Rab25 signature). All patients from the datasets were included in class prediction.
(B) Quantification of infected macrophages containing ubiquitinated aggregates 10 h after bacterial uptake. Cells were processed as in (A) and analysed by fluorescence microscopy. A minimum of 50 cells were counted for each bacterial infection per experiment and values are the mean ± SEM of at least 3 independent experiments. * p<0.05; *** p<0.001. Uninfected cells (uninf) were from the same wells as infected and therefore were exposed to extracellular bacteria. (C) Immunoelectron microscopy of RAW264.7macrophages infected with the ΔsseL mutant bacteria for 12 h. Arrows and arrowheads indicate ubiquitin (15 nm gold particles) and p62 (10 nm gold particles), respectively (scale bar, 0.5 µm).
B Reduced SG association of TDP-43 by 12D mutations or in vitro phosphorylation. Bar, 20 µm.
(c) Lifespan analysis of WT and transgenic animals overexpressing HLH-30::GFP, and raised and maintained on OP50 was carried out at 20 °C. See Supplementary Table S7 for details of lifespan analyses and replicate experiments.
(D) A rotated view shows that ZW10 forms a highly bent, U-shaped complex with a relatively small inter-protomer interface.
A. Coverage profile for H3K4me3, ATAC, P300, and TRIM28 ChIP at a target locus for the QTL on Chr 4 for both chromatin accessibility (black boxes) and gene expression (Riok3 and Rmc1). LOD scores are listed under each target locus.
E. Averaged Cm traces recorded from Control (Ctrl), Sc, KD (from all three shRNAs, n = 39 for shSyt11-2, n = 7 for shSyt11-1, n = 14 for shSyt11-3), and rescued (with the shSyt11-2-resistant form of Syt11) DRG neurons.
(F) 293T cells were transfected with HA-AMPKγ2 alone or with Flag-CARS for 48 h and then cultured with cystine-deficient medium or complete medium for 8 h. Cell lysates were immunoprecipitated with anti-Flag, and a WB analysis was performed.
F PKG-3Ty parasites were solubilised in either PBS or 1% Triton X-100 (TX100) and split into soluble (S) and pellet (P) fractions. Total lysate is also shown.
Detection of Pbs2 phosphorylation at T518. The yeast strains KT003 (pbs2Δ), KT005 (ste11Δ pbs2Δ), TM280 (ssk2/22Δ pbs2Δ) and KT043 (ste11Δ ssk2/22Δ pbs2Δ) were transformed with YCplac22I'-Pbs2-HA, and were treated with the indicated concentrations of NaCl for 5 min. Pbs2-HA was immunoprecipitated from cell extract, and phosphorylated Pbs2 was analyzed by (B) anti-phospho-T518 immunoblotting.
qRT-PCR analysis of ISGs induction in mock- or BTV-8-infected Vero cells after type II IFN treatment for 8 hr. Mean mRNA fold inductions for 3 experiments are presented.
(A) Western blot analysis of endogenous Sept2 immunoprecipitation from HeLa cells showing that endogenous Drp1 specifically co-immunoprecipitates with Sept2. The asterisks mark the IgG heavy chains.
L. Immunoblot analysis of purified recombinant FLAG-FAM111B proteins and their auto-cleavage products.
D Synergy between mycolactone and BZ in the MM.1S BzR lines, when treated as in (C). Data are Mean Loewe scores ± SD, shown as heatmaps. Differences between treated cells and controls by Student's t-test: *p<0.05; N = 6 (cumulative data of 3 independent experiments with technical duplicates).
(D) HeLa mitochondrial lysates were fractionated on 10-30% sucrose gradients and the distribution of LETM1 and ribosomal proteins was determined by immunoblotting. 55S corresponds to the assembled mitoribosome and 28S and 39S to its small and large subunits, respectively. Mitochondria were lysed in 100 mM or 50 mM NaCl (top and bottom panels, respectively)
C. Confocal images of mitochondrial morphology in Drp1/OPA1DKO 293T cells treated with the indicated siRNAs, combinations of siRNAs or with Myc-hFis1 plasmid (lower three panels) compared to mitochondrial morphology in Drp1-/- 293T cells overexpressing Myc-hFis1 or not (upper panel).
(c) TUNEL staining of apoptotic cells in cultured neurons when H3R was inhibited with thioperamide (scale bar, 50 μm) after OGD/R. TUNEL-positive cells are green, and all cells are stained with 4',6-diamidino-2-phenylindole (blue).
pan-glial (repo-GAL4) htlACT overexpression lengthens NB cell cycle, quantified in (F) The cell cycle length is measured as the length between consecutive divisions.
(B-I) Confocal laser scanning microscopy analyses (as in Fig. 2) in WT MEF treated with BafA1. (J, K) (J) Quantification of ATZxxx-positive endolysosomes and (K) of ATZxxx polymers-positive endolysosomes (mean, n= 18, 30, 24, 14, 27, 22, 27, 18 cells for HA stain and n= 12, 14, 14, 11, 14, 14, 17, 11 cells for 2C1 stain of panels B-I, respectively). One-way ANOVA and Dunnett's multiple comparison test, ns P>0.05, **** P<0.0001.
Aligned pulse profiles averaged for each reporter strain (color-coded as in A). Error bars are SD (4 < n < 37). The data shown are from 2 independent experiments. Pulses are abrogated in the strain devoid of negative regulation.
(O) Two color super-resolution image showing co-clustering of flag-TRIM16 (red) and GFP-Sec22b (green); Scale bar, 200 nm. (P) Cross-correlation analysis of flag-TRIM16 and GFP-Sec22b super-resolution data showing a characteristic separation of ~ 70 nm.
In vivo ubiquitination assays performed in MCF-7 cells. (B) Stable shCTR- or shTRIM46-expressing MCF7 cells were transfected with His-Ub for 40 h. Cells were then treated with MG132 (10 μM) for 12 h before Ni-NTA bead precipitation followed by IB with anti-HDAC1.
F. Diagram of IFT-B. The core 1, core 2, and peripheral subcomplexes (Nakayama & Katoh, 2018) are depicted in different colors.
qPCR results of Rankl in BMAT and peripheral adipose tissues, including epididymal (eWAT), inguinal (iWAT), and interscapular (iBAT) (n=3 independent biological replicates). Data were compared using one-way ANOVA (** indicates P < 0.01), error bars are standard deviations.
C) Average DHS signal at 2882 pDHSs and 2882 invariant DHSs in CD4 TN, TB and TM. The locations of the 2882 pDHSs are indicated in (A) and (B).
(C) MALT1 deficiency inhibits CARD14-induced gene expression in HaCaT keratinocytes. HaCaT cells were transfected with scrambled (scr) or MALT1-targeting siRNA prior to doxycycline-induced CARD14 expression as described in materials and methods. IL-8 and MCP-1 concentration in the cell supernatants was measured 8 h (IL-8) or 24 h (MCP-1) later by ELISA. Values are the mean of triplicates ± s.e. Doxycycline-induced CARD14 expression and MALT1 knock-down were verified by immunoblotting (right panel). Data are representative of two independent experiments.
K Western blotting analysis of ATG5 wild-type or knockout HEK293T cells co-transfected with Flag-NLRP3 and HA-CCDC50 or empty control vector for 24 h. Data information: actin was used as a loading control. All the experiments were repeated at least once.
(J) Increased protein expression of FAM210A and ND1 in miR-574 KO hearts compared to WT hearts upon TAC surgery. N=5 hearts (~110-150 CM cells) were measured per group. The dashed line in the violin plot shows medium value for the group and the dotted lines represent two quartile lines in each group.
C. Immunofluorescence microscopy showing endogenous FATE1 protein (red) induction of expression by Dox-treatment of H295R/TRSF-1 cells. SF-1 (green), DAPI (blue). Scale bars, 10 μm.
(E) Effects of arid2/3/4 epcr1/2 on the transcript levels of ROS1 and IBM1-L as determined by qPCR. The expression of ROS1 and the longer version of IBM1 (IBM1-L) was evaluated by qPCR. ACT7 was amplified as an internal control. Bars represent SD from two independent experiments, each with three technical replications.
(G) Relative mRNA level of sinhcaf in 10hpf or 24hpf WT and Tg(CMV:EGFP;CMV:sinhcaf) embryos as measured by RT-qPCR. Data shown are mean ± SEM (n = 3, biological replicates). Statistical analysis was performed using 2-way ANOVA followed by Holm-Sidak post-hoc test.
Immunhistological staining of α-SMA and its histomorphometric quantification (D) reveals expansion of activated mesangial cells in the glomerular tuft of in the transgenic mice in the time course.
A. Schematic representation of domain organization of Mis18 proteins from S. pombe and human (as suggested by the Conserved Domain Database (CDD) and secondary structure predictions).
(b) As in a, an accumulation of LC3-II was observed in the mitochondrial fraction of healthy control fibroblasts following 1 and 5 h CCCP treatment, but this was reduced in fibroblasts from a patient carrying the R378G mutation. Western blots were performed a minimum of three times.
B. Overall structure of MvcA(green)-ubiquitin(magenta) from the complex in comparison with Apo MvcA(marine). The conformational changes are indicated by two arrows, the black one indicates the shift of the tail domain and the red one indicates the rotation of the insertion domain. The potential clash areas between Apo MvcA and ubiquitin are indicated by a dashed circles.
Kaplan Meier plots representing the survival difference between SKCM patients stratified according to the 40% highest or lowest BNIP3 expression.
(A) Primary hippocampal neurons (DIV6+4) were transfected with myc-tagged TDP-43 wild-type or a mutant lacking the nuclear localization signal (ΔNLS) or an empty vector control. Immunostaining with the indicated antibodies and DAPI to label nuclei. Scale bar represents 50 µm.
The phosphatase PP2ACdc55 lies at the center of a hyperosmotic stress signaling cascade. Under non-stress conditions (left) the balanced activities of PP2ACdc55 and counteracting kinase(s) result in a steady state of low phosphorylation of shared substrates. Hyperosmotic stress signaling transmitted through the Greatwall Kinase/Endosulfin module activates the PP2ACdc55 inhibitors Igo1 and Igo2 via phosphorylation at key regulatory sites (right). The resulting inhibition of the phosphatase is essential to tip the balance towards increased net phosphorylation.
Collagen I staining and its histomorphometric quantification (D) show the progression of interstitial fibrosis in the time course.
(A) Fluidigm analysis of expression of genes involved in sphingolipid metabolism in human dermal fibroblasts (HDFs) upon indicated stimulations for 4 h. Heatmap shows means of 4 independent experiments. The color scale represents the relative gene expression compared to control from lower (blue) to higher levels (red).
Figure 1. DENND2B binds ITSN  Purified GST-SH3-containing proteins were incubated with lysates of HEK-293T cells expressing Flag-DENND2B. Total proteins and bound proteins were detected by Ponceau S staining and Western blot, respectively.
Abundance comparison of GFP N- or C-terminal tagged with the wild-type or mutant N-terminal (aa. 1-24) or C-terminal (a.a. 218-227) motif of MIC19 in cells with indicated treatments. Data from sh#1 is shown here.
LV associated with individual HF further organize associating HF triads, which connect with other HF triads across the skin. P70, 70 d old mice. n= 3 - 4 mice. White arrowheads denote capillaries stemming from HF triads. Scale bar, 100 μm.
a, MRE11::MYC cells were treated as in Fig. 1a. Cell samples were processed for ChIP analysis and the fold enrichment of the 0.2-kb fragment after ChIP of Mre11-Myc without (-VPA) or with (+VPA) VPA was calculated.
H) Freshly isolated PBMC were placed in Boyden chambers towards decreased doses of recombinant AGR2 and incubated for 24 h. CCL2 cytokine was used as positive control for monocyte migration. ns: non-statistically significant, (*): p=0.0171, (**): p=0.0084, (***): p=0.0003.
(D) Immunoprecipitation/mmunoblot of E3 ubiquitin ligases by PERK-ΔN in the presence of LRRK2(S1292A) or LRRK2(S1292D). HEK293 cells were transfected with MARCH5, MULAN, Parkin, and PERK-ΔN LRRK2(S1292A) or LRRK2(S1292D). Cell lysates were immunoprecipitated with antibody against Myc, and precipitates were immunoblotted with antibody indicated the right.
G Left panel, graphic depiction of the ELISA-based DNA binding assay. HSE: heat shock element. Right panel: Immediately following heat shock at 43°C for 30 min, nuclear proteins of the reporter cells treated with and without 10 mM metformin were extracted for assay (mean ± SD, n = 3, Student's t-test, **P < 0.01, ***P < 0.001). Experimental details are described in Materials and Methods.
E. Quantitative flow cytometry-based analysis of the experiment reported in D; n is indicated in the graph (left). Percentage of cells with plasma membrane staining (surface) is reported for each chimera (right).
B. Relative outgrowth of WT, TP53KO and onco-RNF43/TP53KO organoid lines treated with the PORCN inhibitor C59 (1 μM) for 7 days. Graph shows the number of organoids at 5 days after splitting (day 14) relative to the number of organoids at day 2. Error bars represent ±s.d. of the mean of n = 3 experiments.
Bar graph represents that recycling of CD1d between various endomembrane compartments and the cell surface is required for optimal IL-2 secretion by NKT cells. In total, n=2 biological replicates were performed (three technical replicates per biological replicate). Graphs show mean ± SEM of each biological replicate.
3 x 105 mouse fibrosarcoma WEHI 164 cells were injected subcutaneously (s.c) into the flank of immunocompetent syngeneic Balb/c mice When tumors became palpable, the mice were injected intraperitoneally (i.p.) with injectable solution (Ctr) or with 0.5 mg/kg dactinomycin (DACT). A second injection of chemotherapy was performed four days later. Tumor size was assessed regularly and individual tumor growth curves of DACT versus Ctr
(d) Viability assays. Jurkat T cells either overexpressing ATG5 following lentiviral gene transfer or treated with etoposide were cultured in the presence and absence of the indicated pharmacological inhibitors for the indicated times to block autophagy and caspase activity. All values are means±s.d. (n=3).
(e) Percent survival of Col-0 plants with and without ACC under HS, HS+ACC, LAT and LAT+ACC conditions. Data information: All plots represent the means of 3 biological replicates (n=36, 12 plants per biological repeat). Error bars represent SD of three biological repeats. Asterisks indicate a statistical difference based on the Student's t-test (* P≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001).
A, B. The impact of HUWE1 on H2AX phosphorylation and ubiquitination, under normal conditions (A) or upon induction of replication stress (2mM HU for 18h, or 2h after exposure to 40J/m2 UV). Control or HUWE1-knockout HeLa cells were analyzed.
Dose-dependent viability assays of BRCA1-proficient (+BRCA1) or -deficient (-BRCA1) human RPE1-hTERT cells treated with drugs at the indicated concentrations for six days.